@article {pmid39243547,
year = {2024},
author = {Hu, RG and Yang, L and Wang, LY and Yang, YL and Li, HJ and Yang, BT and Kang, YH and Liang, ZL and Cong, W},
title = {Unveiling the pathogenic and multidrug-resistant profiles of Vibrio alfacsensis: A potential identified threat in turbot (Scophthalmus maximus) aquaculture.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135729},
doi = {10.1016/j.jhazmat.2024.135729},
pmid = {39243547},
issn = {1873-3336},
abstract = {Vibrio alfacsensis is traditionally seen as an environmental symbiont within its genus, with no detailedly documented pathogenicity in marine aquaculture to date. This study delves into the largely unexplored pathogenic potential and emerging antibiotic resistance of V. alfacsensis. The VA-1 strain, isolated from recirculating aquaculture system (RAS) effluent of cultured turbot (Scophthalmus maximus), underwent comprehensive analysis including biochemical identification, antibiotic susceptibility testing and reinfection trials. The results confirmed VA-1's pathogenicity and significant multiple antibiotic resistance. VA-1 could induce systemic infection in turbot, with symptoms like kidney enlargement, exhibiting virulence comparable to known Vibrio pathogens, with an LD50 around 2.36 × 10[6] CFU/fish. VA-1's remarkable resistance phenotype (14/22) suggested potential for genetic exchange and resistance factor acquisition in aquaculture environments. Phylogenetic analysis based on 16S rDNA sequences and whole-genome sequencing has firmly placed VA-1 within the V. alfacsensis clade, while genome-wide analysis highlights its similarity and diversity in relation to strains from across the globe. VA-1 contained numerous replicons, indicating the possibility for the spread of resistance and virulence genes. This study suggests V. alfacsensis may acquire and transfer pathogenic and resistant traits through horizontal gene transfer, a likelihood intensified by changing environmental and aquaculture conditions, highlighting the need for vigilant pathogen monitoring and new non-antibiotic treatments.},
}
@article {pmid39243538,
year = {2024},
author = {Lin, L and Li, L and Yang, X and Hou, L and Wu, D and Wang, B and Ma, B and Liao, X and Yan, X and Gad, M and Su, J and Liu, Y and Liu, K and Hu, A},
title = {Unnoticed antimicrobial resistance risk in Tibetan cities unveiled by sewage metagenomic surveillance: Compared to the eastern Chinese cities.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135730},
doi = {10.1016/j.jhazmat.2024.135730},
pmid = {39243538},
issn = {1873-3336},
abstract = {Sewage surveillance is a cost-effective tool for assessing antimicrobial resistance (AMR) in urban populations. However, research on sewage AMR in remote areas is still limited. Here, we used shotgun metagenomic sequencing to profile antibiotic resistance genes (ARGs) and ARG-carrying pathogens (APs) across 15 cities in Tibetan Plateau (TP) and the major cities in eastern China. Notable regional disparities in sewage ARG composition were found, with a significantly higher ARG abundance in TP (2.97 copies/cell). A total of 542 and 545 APs were identified in sewage from TP and the East, respectively, while more than 40 % carried mobile genetic elements (MGEs). Moreover, 65 MGEs-carrying APs were identified as World Health Organization (WHO) priority-like bacterial and fungal pathogens. Notably, a fungal zoonotic pathogen, Enterocytozoon bieneusi, was found for the first time to carry a nitroimidazole resistance gene (nimJ). Although distinct in AP compositions, the relative abundances of APs were comparable in these two regions. Furthermore, sewage in TP was found to be comparable to the cities in eastern China in terms of ARG mobility and AMR risks. These findings provide insights into ARGs and APs distribution in Chinese sewage and stress the importance of AMR surveillance and management strategies in remote regions.},
}
@article {pmid39208359,
year = {2024},
author = {Ares-Arroyo, M and Coluzzi, C and Moura de Sousa, JA and Rocha, EPC},
title = {Hijackers, hitchhikers, or co-drivers? The mysteries of mobilizable genetic elements.},
journal = {PLoS biology},
volume = {22},
number = {8},
pages = {e3002796},
doi = {10.1371/journal.pbio.3002796},
pmid = {39208359},
issn = {1545-7885},
mesh = {*Gene Transfer, Horizontal ; Interspersed Repetitive Sequences/genetics ; Bacteria/genetics ; Evolution, Molecular ; Genomic Islands ; Symbiosis/genetics ; Genome, Bacterial ; },
abstract = {Mobile genetic elements shape microbial gene repertoires and populations. Recent results reveal that many, possibly most, microbial mobile genetic elements require helpers to transfer between genomes, which we refer to as Hitcher Genetic Elements (hitchers or HGEs). They may be a large fraction of pathogenicity and resistance genomic islands, whose mechanisms of transfer have remained enigmatic for decades. Together with their helper elements and their bacterial hosts, hitchers form tripartite networks of interactions that evolve rapidly within a parasitism-mutualism continuum. In this emerging view of microbial genomes as communities of mobile genetic elements many questions arise. Which elements are being moved, by whom, and how? How often are hitchers costly hyper-parasites or beneficial mutualists? What is the evolutionary origin of hitchers? Are there key advantages associated with hitchers' lifestyle that justify their unexpected abundance? And why are hitchers systematically smaller than their helpers? In this essay, we start answering these questions and point ways ahead for understanding the principles, origin, mechanisms, and impact of hitchers in bacterial ecology and evolution.},
}
@article {pmid39242818,
year = {2024},
author = {Porras, MÁG and Assié, A and Tietjen, M and Violette, M and Kleiner, M and Gruber-Vodicka, H and Dubilier, N and Leisch, N},
title = {An intranuclear bacterial parasite of deep-sea mussels expresses apoptosis inhibitors acquired from its host.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39242818},
issn = {2058-5276},
support = {340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; 340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; 340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; 340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; Gottfried Wilhelm Leibniz Prize//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Heisenberggrant GR 5028/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; OIA 1934844//National Science Foundation (NSF)/ ; IOS 2003107//National Science Foundation (NSF)/ ; },
abstract = {A limited number of bacteria are able to colonize the nuclei of eukaryotes. 'Candidatus Endonucleobacter' infects the nuclei of deep-sea mussels, where it replicates to ≥80,000 bacteria per nucleus and causes nuclei to swell to 50 times their original size. How these parasites are able to replicate and avoid apoptosis is not known. Dual RNA-sequencing transcriptomes of infected nuclei isolated using laser-capture microdissection revealed that 'Candidatus Endonucleobacter' does not obtain most of its nutrition from nuclear DNA or RNA. Instead, 'Candidatus Endonucleobacter' upregulates genes for importing and digesting sugars, lipids, amino acids and possibly mucin from its host. It likely prevents apoptosis of host cells by upregulating 7-13 inhibitors of apoptosis, proteins not previously seen in bacteria. Comparative phylogenetic analyses revealed that 'Ca. Endonucleobacter' acquired inhibitors of apoptosis through horizontal gene transfer from their hosts. Horizontal gene transfer from eukaryotes to bacteria is assumed to be rare, but may be more common than currently recognized.},
}
@article {pmid39236533,
year = {2024},
author = {Yuan, Q and Li, W and Goh, SG and Chen, SL and Ng, OT and He, Y and Gin, KY},
title = {Genetic traits and transmission of antimicrobial resistance characteristics of cephalosporin resistant Escherichia coli in tropical aquatic environments.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135707},
doi = {10.1016/j.jhazmat.2024.135707},
pmid = {39236533},
issn = {1873-3336},
abstract = {This study investigates the genetic traits and transmission mechanisms of cephalosporin-resistant Escherichia coli in tropical aquatic environments in Singapore. From 2016 to 2020, monthly samples were collected from wastewater treatment plants, marine niches, community sewage, beaches, reservoirs, aquaculture farms, and hospitals, yielding 557 isolates that were analyzed for antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) using genomic methods. Findings reveal significant genotypic similarities between environmental and hospital-derived strains, particularly the pandemic E. coli ST131. Environmental strains exhibited high levels of intrinsic resistance mechanisms, including mutations in porins and efflux pumps, with key ARGs such as CMY-2 and NDM-9 predominantly carried by MGEs, which facilitate horizontal gene transfer. Notably, pathogenic EPEC and EHEC strains were detected in community sewage and aquaculture farms, posing substantial public health risks. This underscores the critical role of these environments as reservoirs for multidrug-resistant pathogens and emphasizes the interconnectedness of human activities and environmental health.},
}
@article {pmid39236354,
year = {2024},
author = {Brdová, D and Ruml, T and Viktorová, J},
title = {Mechanism of staphylococcal resistance to clinically relevant antibiotics.},
journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy},
volume = {77},
number = {},
pages = {101147},
doi = {10.1016/j.drup.2024.101147},
pmid = {39236354},
issn = {1532-2084},
abstract = {Staphylococcus aureus, a notorious pathogen with versatile virulence, poses a significant challenge to current antibiotic treatments due to its ability to develop resistance mechanisms against a variety of clinically relevant antibiotics. In this comprehensive review, we carefully dissect the resistance mechanisms employed by S. aureus against various antibiotics commonly used in clinical settings. The article navigates through intricate molecular pathways, elucidating the mechanisms by which S. aureus evades the therapeutic efficacy of antibiotics, such as β-lactams, vancomycin, daptomycin, linezolid, etc. Each antibiotic is scrutinised for its mechanism of action, impact on bacterial physiology, and the corresponding resistance strategies adopted by S. aureus. By synthesising the knowledge surrounding these resistance mechanisms, this review aims to serve as a comprehensive resource that provides a foundation for the development of innovative therapeutic strategies and alternative treatments for S. aureus infections. Understanding the evolving landscape of antibiotic resistance is imperative for devising effective countermeasures in the battle against this formidable pathogen.},
}
@article {pmid39235659,
year = {2024},
author = {Fu, Y and Fu, Z and Yu, J and Wang, H and Zhang, Y and Liu, M and Wang, X and Yu, W and Han, F},
title = {Biochemical Characterization of Hyaluronate Lyase CpHly8 from an Intestinal Microorganism Clostridium perfringens G1121.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39235659},
issn = {1559-0291},
support = {2022QNLM030003-1//Qingdao Marine Science and Technology Center/ ; ZR2019ZD18//Natural Science Foundation of Shandong Province/ ; 2018YFC0311105//Shandong Province Technology Innovation Guidance Program/ ; 22-3-6-gjxm-5-gx//Science & Technology Development Project of Qingdao/ ; 21-1-6-gjxm-27-gx//Science & Technology Development Project of Qingdao/ ; 20-11-6-64-gx//Science & Technology Development Project of Qingdao/ ; },
abstract = {Hyaluronic acid (HA) is an important component of extracellular matrices (ECM) and a linear polysaccharide involved in various physiological and pathological processes within the biological system. Several pathogens exploit HA degradation within the extracellular matrix to facilitate infection. While many intestinal microorganisms play significant roles in HA utilization in the human body, there remains a scarcity of related studies. This paper addressed this gap by screening intestinal microorganisms capable of degrading HA, resulting in the isolation of Clostridium perfringens G1121, which had been demonstrated the ability to degrade HA. Subsequent genome sequencing and analysis of C. perfringens G1121 revealed its utilization of the polysaccharide utilization loci of HA (PULHA), which was obtained by horizontal gene transfer. The PULHA contains a sequence encoding a hyaluronic acid-specific degradation enzyme designated CpHly8, belonging to polysaccharide lyase family 8. The specific activity of CpHly8 towards HA was 142.98 U/mg, with the optimum reaction temperature and pH observed at 50℃ and 6.0, respectively. The final product of HA degradation by CpHly8 was unsaturated hyaluronic acid disaccharide. Moreover, subcutaneous diffusion experiments with trypan blue in mice revealed that CpHly8 effectively promoted subcutaneous diffusion and sustained its effects long-term, suggesting its potential application as an adjunct in drug delivery. Overall, our study enriches our understanding of intestinal microbial degradation of HA, provides new evidence for horizontal gene transfer among intestinal microorganisms, and confirms that CpHly8 is a promising candidate for intestinal microbial hyaluronidase.},
}
@article {pmid39235644,
year = {2024},
author = {Jaswal, R and Dubey, H and Kiran, K and Rawal, H and Kumar, G and Rajarammohan, S and Deshmukh, R and Sonah, H and Prasad, P and Bhardwaj, SC and Gupta, N and Sharma, TR},
title = {Identification and functional characterization of the npc-2-like domain containing rust effector protein that suppresses cell death in plants.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {962},
pmid = {39235644},
issn = {1573-4978},
mesh = {*Plant Diseases/microbiology ; *Phylogeny ; *Cell Death ; *Fungal Proteins/metabolism/genetics ; Nicotiana/microbiology/metabolism/genetics ; Basidiomycota/pathogenicity/metabolism/genetics ; Puccinia/pathogenicity/metabolism ; Protein Domains ; Molecular Docking Simulation ; Onions/microbiology/metabolism/genetics ; },
abstract = {The MD-2-related lipid-recognition (ML/Md-2) domain is a lipid/sterol-binding domain that are involved in sterol transfer and innate immunity in eukaryotes. Here we report a genome-wide survey of this family, identifying 84 genes in 30 fungi including plant pathogens. All the studied species were found to have varied ML numbers, and expansion of the family was observed in Rhizophagus irregularis (RI) with 33 genes. The molecular docking studies of these proteins with cholesterol derivatives indicate lipid-binding functional conservation across the animal and fungi kingdom. The phylogenetic studies among eukaryotic ML proteins showed that Puccinia ML members are more closely associated with animal (insect) npc2 proteins than other fungal ML members. One of the candidates from leaf rust fungus Puccinia triticina, Pt5643 was PCR amplified and further characterized using various studies such as qRT-PCR, subcellular localization studies, yeast functional complementation, signal peptide validation, and expression studies. The Pt5643 exhibits the highest expression on the 5th day post-infection (dpi). The confocal microscopy of Pt5643 in onion epidermal cells and N. benthamiana shows its location in the cytoplasm and nucleus. The functional complementation studies of Pt5643 in npc2 mutant yeast showed its functional similarity to the eukaryotic/yeast npc2 gene. Furthermore, the overexpression of Pt5643 also suppressed the BAX, NEP1, and H2O2-induced program cell death in Nicotiana species and yeast. Altogether the present study reports the novel function of ML domain proteins in plant fungal pathogens and their possible role as effector molecules in host defense manipulation.},
}
@article {pmid39235595,
year = {2024},
author = {Xu, R and Huang, C and Yang, B and Wang, S and Zhong, T and Ma, L and Shang, Q and Zhang, M and Chu, Z and Liu, X},
title = {Influence of Two-Dimensional Black Phosphorus on the Horizontal Transfer of Plasmid-Mediated Antibiotic Resistance Genes: Promotion or Inhibition?.},
journal = {Current microbiology},
volume = {81},
number = {10},
pages = {344},
pmid = {39235595},
issn = {1432-0991},
support = {52070063//National Natural Science Foundation of China/ ; 2308085Y38//Science Fund for Distinguished Young Scholars of Anhui Province/ ; 21-22RC30//Hefei University/ ; },
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Phosphorus/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Conjugation, Genetic ; Escherichia coli/genetics/drug effects ; Nanostructures ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial/drug effects ; Bacteria/genetics/drug effects ; },
abstract = {The problem of bacterial resistance caused by antibiotic abuse is seriously detrimental to global human health and ecosystem security. The two-dimensional nanomaterial (2D) such as black phosphorus (BP) is recently expected to become a new bacterial inhibitor and has been widely used in the antibacterial field due to its specific physicochemical properties. Nevertheless, the effects of 2D-BP on the propagation of antibiotic resistance genes (ARGs) in environments and the relevant mechanisms are not clear. Herein, we observed that the sub-inhibitory concentrations of 2D-BP dramatically increased the conjugative transfer of ARGs mediated by the RP4 plasmid up to 2.6-fold at the 125 mg/L exposure level compared with the untreated bacterial cells. Nevertheless, 2D-BP with the inhibitory concentration caused a dramatic decrease in the conjugative frequency. The phenotypic changes revealed that the increase of the conjugative transfer caused by 2D-BP exposure were attributed to the excessive reactive oxygen species and oxidative stress, and increased bacterial cell membrane permeability. The genotypic evidence demonstrated that 2D-BP affecting the horizontal gene transfer of ARGs was probably through the upregulation of mating pair formation genes (trbBp and traF) and DNA transfer and replication genes (trfAp and traJ), as well as the downregulation of global regulatory gene expression (korA, korB, and trbA). In summary, the changes in the functional and regulatory genes in the conjugative transfer contributed to the stimulation of conjugative transfer. This research aims to broaden our comprehension of how nanomaterials influence the dissemination of ARGs by elucidating their effects and mechanisms.},
}
@article {pmid39233522,
year = {2024},
author = {Lee, JH and Tareen, AR and Kim, NH and Jeong, C and Kang, B and Lee, G and Kim, DW and Zahra, R and Lee, SH},
title = {Comparative Genomic Analyses of E. coli ST2178 Strains Originated from Wild Birds in Pakistan.},
journal = {Journal of microbiology and biotechnology},
volume = {34},
number = {10},
pages = {1-8},
doi = {10.4014/jmb.2407.07026},
pmid = {39233522},
issn = {1738-8872},
abstract = {The emergence and spread of multidrug-resistance (MDR) pathogenic Escherichia coli due to horizontal gene transfer of antibiotic resistance genes (ARGs) and virulence factors (VFs) is a global health concern, particularly in developing countries. While numerous studies have focused on major sequence types (STs), the implication of minor STs in ARG dissemination and their pathogenicity remains crucial. In this study, two E. coli strains (PEC1011 and PEC1012) were isolated from wild bird feces in Pakistan and identified as ST2178 based on their complete genome sequences. To understand this minor ST, 204 genome assemblies of ST2178 were comparatively analyzed with the isolates' genomes. The phylogenetic analyses revealed five subclades of ST2178. Subclade E strains were predominantly isolated from human specimens, whereas subclades A and B strains including strains PEC1011 and PEC1012, respectively, were frequently isolated from animal. Mobile genetic elements (MGEs) exhibited the positive correlation with ARGs but not with VFs in this ST. Plasmid-borne ARGs exhibited higher correlation with plasmid-borne MGEs, indicating the role of diverse mobile plasmid structures in ARG transmission. Subclade E exhibited diverse plasmid-borne ARG repertoires correlated with MGEs, marking it as a critical surveillance target. In the case of VFs, they exhibited phylogeny-dependent profiles. Strain PEC1012 harbored various plasmid-borne ARGs, which are similar with conserved ARG repertoires in subclade A. The presence of unique ARG insertion in pPEC1012 highlights the importance of subclade A in ARG dissemination. This study comprehensively elucidates the landscape of ST2178, identifying critical phylogenetic subclades and their characteristics in ARG and VF occurrence.},
}
@article {pmid39233087,
year = {2024},
author = {Kong, F and Qi, Z and Tong, H and Ren, N and You, S},
title = {Case study on the relationship between transmission of antibiotic resistance genes and microbial community under freeze-thaw cycle on cold-region dairy farm.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {175989},
doi = {10.1016/j.scitotenv.2024.175989},
pmid = {39233087},
issn = {1879-1026},
abstract = {Freeze-thaw cycle (FTC) is a naturally occurring phenomenon in high-latitude terrestrial ecosystems, which may exert influence on distribution and evolution of microbial community in the soil. The relationship between transmission of antibiotic resistance genes (ARGs) and microbial community was investigated upon the case study on the soil of cold-region dairy farm under seasonal FTC. The results demonstrated that 37 ARGs underwent decrease in the abundance of blaTEM from 80.4 % for frozen soil to 71.7 % for thawed soil, and that sul2 from 8.8 % for frozen soil to 6.5 % for thawed soil, respectively. Antibiotic deactivation was identified to be closely related to the highest relative abundance of blaTEM, and the spread of sulfonamide resistance genes (SRGs) occurred mainly via target modification. Firmicutes in frozen soil were responsible for dominating the abundance of ARGs by suppressing the native bacteria under starvation effect in cold regions, and then underwent horizontal gene transfer (HGT) among native bacteria through mobile genetic elements (MGEs). The TRB-C (32.6-49.1 %) and tnpA-06 (0.27-7.5 %) were significantly increased in frozen soil, while Int3 (0.67-10.6 %) and tnpA-04 (11.1-19.4 %) were up-regulated in thawed soil. Moreover, the ARGs in frozen soil primarily underwent HGT through MGEs, i.e. TRB-C and tnpA-06, with increased number of Firmicutes serving as carrier. The case study not only demonstrated relationship between transmission of ARGs and microbial community in the soil under practically relevant FTC condition, but also emphasized the importance for formulating better strategies for preventing FTC-induced ARGs in dairy farm in cold regions.},
}
@article {pmid39226958,
year = {2024},
author = {Muñoz, JSC and Aransiola, SA and Reddy, KV and Ranjit, P and Victor-Ekwebelem, MO and Oyedele, OJ and Pérez-Almeida, IB and Maddela, NR and Díaz, JMR},
title = {Antibiotic resistant bacteria and antibiotic resistance genes as contaminants of emerging concern: Occurrences, impacts, mitigations and future guidelines.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {175906},
doi = {10.1016/j.scitotenv.2024.175906},
pmid = {39226958},
issn = {1879-1026},
abstract = {Antibiotic resistance, driven by the proliferation of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARBs), has emerged as a pressing global health concern. Antimicrobial resistance is exacerbated by the widespread use of antibiotics in agriculture, aquaculture, and human medicine, leading to their accumulation in various environmental compartments such as soil, water, and sediments. The presence of ARGs in the environment, particularly in municipal water, animal husbandry, and hospital environments, poses significant risks to human health, as they can be transferred to potential human pathogens. Current remediation strategies, including the use of pyroligneous acid, coagulants, advanced oxidation, and bioelectrochemical systems, have shown promising results in reducing ARGs and ARBs from soil and water. However, these methods come with their own set of challenges, such as the need for elevated base levels in UV-activated persulfate and the long residence period required for photocatalysts. The future of combating antibiotic resistance lies in the development of standardized monitoring techniques, global collaboration, and the exploration of innovative remediation methods. Emphasis on combination therapies, advanced oxidation processes, and monitoring horizontal gene transfer can pave the way for a comprehensive approach to mitigate the spread of antibiotic resistance in the environment.},
}
@article {pmid39224035,
year = {2024},
author = {Chopra, A and Bhuvanagiri, G and Natu, K and Chopra, A},
title = {Role of CRISPR-Cas systems in periodontal disease pathogenesis and potential for periodontal therapy: A review.},
journal = {Molecular oral microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/omi.12483},
pmid = {39224035},
issn = {2041-1014},
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPRs) are DNA sequences capable of editing a host genome sequence. CRISPR and its specific CRISPR-associated (Cas) protein complexes have been adapted for various applications. These include activating or inhibiting specific genetic sequences or acting as molecular scissors to cut and modify the host DNA precisely. CRISPR-Cas systems are also naturally present in many oral bacteria, where they aid in nutrition, biofilm formation, inter- and intraspecies communication (quorum sensing), horizontal gene transfer, virulence, inflammation modulation, coinfection, and immune response evasion. It even functions as an adaptive immune system, defending microbes against invading viruses and foreign genetic elements from other bacteria by targeting and degrading their DNA. Recently, CRISPR-Cas systems have been tested as molecular editing tools to manipulate specific genes linked with periodontal disease (such as periodontitis) and as novel methods of delivering antimicrobial agents to overcome antimicrobial resistance. With the rapidly increasing role of CRISPR in treating inflammatory diseases, its application in periodontal disease is also becoming popular. Therefore, this review aims to discuss the different types of CRISPR-Cas in oral microbes and their role in periodontal disease pathogenesis and precision periodontal therapy.},
}
@article {pmid39223450,
year = {2024},
author = {Valerio, F and Martel, C and Stefanescu, C and van Nouhuys, S and Kankare, M and Duplouy, A},
title = {Wolbachia strain diversity in a complex group of sympatric cryptic parasitoid wasp species.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {319},
pmid = {39223450},
issn = {1471-2180},
mesh = {Animals ; *Wolbachia/genetics/classification/isolation & purification ; *Wasps/microbiology ; *Symbiosis ; *Phylogeny ; Sympatry ; Gene Transfer, Horizontal ; Genetic Variation ; Lepidoptera/microbiology/parasitology ; },
abstract = {BACKGROUND: Maternally-inherited symbionts can induce pre-mating and/or post-mating reproductive isolation between sympatric host lineages, and speciation, by modifying host reproductive phenotypes. The large parasitoid wasp genus Cotesia (Braconidae) includes a diversity of cryptic species, each specialized in parasitizing one to few related Lepidoptera host species. Here, we characterized the infection status of an assemblage of 21 Cotesia species from 15 countries by several microbial symbionts, as a first step toward investigating whether symbionts may provide a barrier to gene flow between these parasitoid host lineages.<br><br>RESULTS: The symbiotic microbes Arsenophonus, Cardinium, Microsporidium and Spiroplasma were not detected in the Cotesia wasps. However, the endosymbiotic bacterium Wolbachia was present in at least eight Cotesia species, and hence we concentrated on it upon screening additional DNA extracts and SRAs from NCBI. Some of the closely related Cotesia species carry similar Wolbachia strains, but most Wolbachia strains showed patterns of horizontal transfer between phylogenetically distant host lineages.<br><br>CONCLUSIONS: The lack of co-phylogenetic signal between Wolbachia and Cotesia suggests that the symbiont and hosts have not coevolved to an extent that would drive species divergence between the Cotesia host lineages. However, as the most common facultative symbiont of Cotesia species, Wolbachia may still function as a key-player in the biology of the parasitoid wasps. Its precise role in the evolution of this complex clade of cryptic species remains to be experimentally investigated.},
}
@article {pmid39222343,
year = {2024},
author = {Lyulina, AS and Liu, Z and Good, BH},
title = {Linkage equilibrium between rare mutations.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyae145},
pmid = {39222343},
issn = {1943-2631},
abstract = {Recombination breaks down genetic linkage by reshuffling existing variants onto new genetic backgrounds. These dynamics are traditionally quantified by examining the correlations between alleles, and how they decay as a function of the recombination rate. However, the magnitudes of these correlations are strongly influenced by other evolutionary forces like natural selection and genetic drift, making it difficult to tease out the effects of recombination. Here we introduce a theoretical framework for analyzing an alternative family of statistics that measure the homoplasy produced by recombination. We derive analytical expressions that predict how these statistics depend on the rates of recombination and recurrent mutation, the strength of negative selection and genetic drift, and the present-day frequencies of the mutant alleles. We find that the degree of homoplasy can strongly depend on this frequency scale, which reflects the underlying timescales over which these mutations occurred. We show how these scaling properties can be used to isolate the effects of recombination, and discuss their implications for the rates of horizontal gene transfer in bacteria.},
}
@article {pmid39221153,
year = {2024},
author = {Belay, WY and Getachew, M and Tegegne, BA and Teffera, ZH and Dagne, A and Zeleke, TK and Abebe, RB and Gedif, AA and Fenta, A and Yirdaw, G and Tilahun, A and Aschale, Y},
title = {Mechanism of antibacterial resistance, strategies and next-generation antimicrobials to contain antimicrobial resistance: a review.},
journal = {Frontiers in pharmacology},
volume = {15},
number = {},
pages = {1444781},
pmid = {39221153},
issn = {1663-9812},
abstract = {Antibacterial drug resistance poses a significant challenge to modern healthcare systems, threatening our ability to effectively treat bacterial infections. This review aims to provide a comprehensive overview of the types and mechanisms of antibacterial drug resistance. To achieve this aim, a thorough literature search was conducted to identify key studies and reviews on antibacterial resistance mechanisms, strategies and next-generation antimicrobials to contain antimicrobial resistance. In this review, types of resistance and major mechanisms of antibacterial resistance with examples including target site modifications, decreased influx, increased efflux pumps, and enzymatic inactivation of antibacterials has been discussed. Moreover, biofilm formation, and horizontal gene transfer methods has also been included. Furthermore, measures (interventions) taken to control antimicrobial resistance and next-generation antimicrobials have been discussed in detail. Overall, this review provides valuable insights into the diverse mechanisms employed by bacteria to resist the effects of antibacterial drugs, with the aim of informing future research and guiding antimicrobial stewardship efforts.},
}
@article {pmid39221073,
year = {2024},
author = {Xie, X and Deng, X and Chen, L and Yuan, J and Chen, H and Wei, C and Liu, X and Wuertz, S and Qiu, G},
title = {Integrated genomics provides insights into the evolution of the polyphosphate accumulation trait of Ca. Accumulibacter.},
journal = {Environmental science and ecotechnology},
volume = {20},
number = {},
pages = {100353},
pmid = {39221073},
issn = {2666-4984},
abstract = {Candidatus Accumulibacter, a prominent polyphosphate-accumulating organism (PAO) in wastewater treatment, plays a crucial role in enhanced biological phosphorus removal (EBPR). The genetic underpinnings of its polyphosphate accumulation capabilities, however, remain largely unknown. Here, we conducted a comprehensive genomic analysis of Ca. Accumulibacter-PAOs and their relatives within the Rhodocyclaceae family, identifying 124 core genes acquired via horizontal gene transfer (HGT) at its least common ancestor. Metatranscriptomic analysis of an enrichment culture of Ca. Accumulibacter revealed active transcription of 44 of these genes during an EBPR cycle, notably including the polyphosphate kinase 2 (PPK2) gene instead of the commonly recognized polyphosphate kinase 1 (PPK1) gene. Intriguingly, the phosphate regulon (Pho) genes showed minimal transcriptions, pointing to a distinctive fact of Pho dysregulation, where PhoU, the phosphate signaling complex protein, was not regulating the high-affinity phosphate transport (Pst) system, resulting in continuous phosphate uptake. To prevent phosphate toxicity, Ca. Accumulibacter utilized the laterally acquired PPK2 to condense phosphate into polyphosphate, resulting in the polyphosphate-accumulating feature. This study provides novel insights into the evolutionary emergence of the polyphosphate-accumulating trait in Ca. Accumulibacter, offering potential advancements in understanding the PAO phenotype in the EBPR process.},
}
@article {pmid39219575,
year = {2024},
author = {He, XY and Chen, JM and Li, ZZ},
title = {Complete organelle genomes of the threatened aquatic species Scheuchzeria palustris (Scheuchzeriaceae): Insights into adaptation and phylogenomic placement.},
journal = {Ecology and evolution},
volume = {14},
number = {9},
pages = {e70248},
pmid = {39219575},
issn = {2045-7758},
abstract = {Scheuchzeria palustris, the only species in the Scheuchzeriaceae family, plays a crucial role in methane production and transportation, influencing the global carbon cycle and maintaining ecosystem stability. However, it is now threatened by human activities and global warming. In this study, we generated new organelle genomes for S. palustris, with the plastome (pt) measuring 158,573 bp and the mitogenome (mt) measuring 420,724 bp. We predicted 296 RNA editing sites in mt protein-coding genes (PCGs) and 142 in pt-PCGs. Notably, abundant RNA editing sites in pt-PCGs likely originated from horizontal gene transfer between the plastome and mitogenome. Additionally, we identified positive selection signals in four mt-PCGs (atp4, ccmB, nad3, and sdh4) and one pt-PCG (rps7), which may contribute to the adaptation of S. palustris to low-temperature and high-altitude environments. Furthermore, we identified 35 mitochondrial plastid DNA (MTPT) segments totaling 58,479 bp, attributed to dispersed repeats near most MTPT. Phylogenetic trees reconstructed from mt- and pt-PCGs showed topologies consistent with the APG IV system. However, the conflicting position of S. palustris can be explained by significant differences in the substitution rates of its mt- and pt-PCGs (p < .001). In conclusion, our study provides vital genomic resources to support future conservation efforts and explores the adaptation mechanisms of S. palustris.},
}
@article {pmid39216666,
year = {2024},
author = {Qiu, T and Shen, L and Guo, Y and Gao, M and Gao, H and Li, Y and Zhao, G and Wang, X},
title = {Impact of aeration rate on the transfer range of antibiotic-resistant plasmids during manure composting.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {124851},
doi = {10.1016/j.envpol.2024.124851},
pmid = {39216666},
issn = {1873-6424},
abstract = {Conjugative plasmids are important vectors of mobile antibiotic resvistance genes (ARGs), facilitating their horizontal transfer within the environment. While composting is recognized as an effective method to reduce antibiotics and ARGs in animal manure, its impact on the bacterial host communities containing antibiotic-resistant plasmids remains unclear. In this study, we investigated the permissiveness of bacterial community during composting when challenged with multidrug-resistant conjugative RP4 plasmids, employing Pseudomonas putida as the donor strain. Ultimately, this represents the first exploration of the effects of aeration rates on the range of RP4 plasmid transfer hosts. Transconjugants were analyzed through fluorescent reporter gene-based fluorescence-activated cell sorting and Illumina sequencing. Overall, aeration rates were found to influence various physicochemical parameters of compost, including temperature, pH, total organic matter, total nitrogen, and potassium. Regarding RP4 plasmid host bacteria, the dominant phylum was determined to shift from Bacteroidetes in the raw material to Proteobacteria in the compost. Notably, a moderate-intensity aeration rate (0.05 L/min/L) was found to be more effective in reducing the diversity and richness of the RP4 plasmid host bacterial community. Following composting, the total percentage of dominant transconjugant-related genera decreased by 66.15-76.62%. Ultimately, this study determined that the aeration rate negatively impacts RP4 plasmid host abundance primarily through alterations to the environmental factors during composting. In summary, these findings enhance our understanding of plasmid host bacterial communities under varying composting aeration rates and offer novel insights into preventing the dissemination of ARGs from animal manure to farmland.},
}
@article {pmid39216410,
year = {2024},
author = {Vissapragada, M and Addala, S and Aggunna, M and Sodasani, M and Grandhi, AVKS and Yedidi, RS},
title = {Leveraging the potential of bacterial lateral gene transfer in boosting the efficacy of an edible probiotic prototype yogurt vaccine for COVID-19.},
journal = {Biochemical and biophysical research communications},
volume = {734},
number = {},
pages = {150622},
doi = {10.1016/j.bbrc.2024.150622},
pmid = {39216410},
issn = {1090-2104},
abstract = {Administration of coronavirus disease-2019 (COVID-19) vaccines with appropriate booster doses through painful injections under clinical supervision was challenging during the recent COVID-19 pandemic. As an alternative solution, we designed a safer, edible probiotic yogurt vaccine prototype (YoVac) that can be orally consumed by circumventing painful injections and clinical supervision. We hypothesized that YoVac prepared using Lactobacillus carrying an antigen coding gene (donor) can transfer the same to other bacteria (recipients) in the human gut microbiome (hgMb) through lateral gene transfer (LGT) for boosted antigen levels potentially triggering a robust immune response. In this study we confirmed the in vitro LGT efficiency of a plasmid (pRBD-Amp[r]) containing severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) spike protein-receptor binding domain (RBD) coding gene along with an ampicillin-resistance gene (selection marker) from the probiotic Lactobacillus (donor) cultured from homemade yogurt to E. coli and Helicobacter pylori (recipients). Both the donor and recipient bacteria not only exhibited ampicillin-resistance from pRBD-Amp[r] but also expressed RBD protein. Furthermore, Lactobacillus isolated from YoVac consistently showed the expression of RBD protein over a period of one month confirming the shelf life of our prototype stored at 4 °C. Taken together, our in vitro results provide a preliminary basis for the potential in vivo transfer of RBD coding gene from YoVac to other bacterial species in the hgMb through LGT and may potentially boost the vaccine dosage by delegating them.},
}
@article {pmid39216330,
year = {2024},
author = {Fernández-Arévalo, U and Fuchs, J and Boll, M and Díaz, E},
title = {Transcriptional regulation of the anaerobic 3-hydroxybenzoate degradation pathway in Aromatoleum sp. CIB.},
journal = {Microbiological research},
volume = {288},
number = {},
pages = {127882},
doi = {10.1016/j.micres.2024.127882},
pmid = {39216330},
issn = {1618-0623},
abstract = {Phenolic compounds are commonly found in anoxic environments, where they serve as both carbon and energy sources for certain anaerobic bacteria. The anaerobic breakdown of m-cresol, catechol, and certain lignin-derived compounds yields the central intermediate 3-hydroxybenzoate/3-hydroxybenzoyl-CoA. In this study, we have characterized the transcription and regulation of the hbd genes responsible for the anaerobic degradation of 3-hydroxybenzoate in the β-proteobacterium Aromatoleum sp. CIB. The hbd cluster is organized in three catabolic operons and a regulatory hbdR gene that encodes a dimeric transcriptional regulator belonging to the TetR family. HbdR suppresses the activity of the three catabolic promoters (PhbdN, PhbdE and PhbdH) by binding to a conserved palindromic operator box (ATGAATGAN4TCATTCAT). 3-Hydroxybenzoyl-CoA, the initial intermediate of the 3-hydroxybenzoate degradation pathway, along with benzoyl-CoA, serve as effector molecules that bind to HbdR inducing the expression of the hbd genes. Moreover, the hbd genes are subject to additional regulation influenced by the presence of non-aromatic carbon sources (carbon catabolite repression), and their expression is induced in oxygen-deprived conditions by the AcpR transcriptional activator. The prevalence of the hbd cluster among members of the Aromatoleum/Thauera bacterial group, coupled with its association with mobile genetic elements, suggests acquisition through horizontal gene transfer. These findings significantly enhance our understanding of the regulatory mechanisms governing the hbd gene cluster in bacteria, paving the way for further exploration into the anaerobic utilization/valorization of phenolic compounds derived from lignin.},
}
@article {pmid39214976,
year = {2024},
author = {Yi, X and Liang, JL and Wen, P and Jia, P and Feng, SW and Liu, SY and Zhuang, YY and Guo, YQ and Lu, JL and Zhong, SJ and Liao, B and Wang, Z and Shu, WS and Li, JT},
title = {Giant viruses as reservoirs of antibiotic resistance genes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7536},
pmid = {39214976},
issn = {2041-1723},
mesh = {*Phylogeny ; *Giant Viruses/genetics ; *Genome, Viral/genetics ; Drug Resistance, Microbial/genetics ; Bacteriophages/genetics/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; Metagenome/genetics ; Gene Transfer, Horizontal ; Trimethoprim/pharmacology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs; also called giant viruses), constituting the phylum Nucleocytoviricota, can infect a wide range of eukaryotes and exchange genetic material with not only their hosts but also prokaryotes and phages. A few NCLDVs were reported to encode genes conferring resistance to beta‑lactam, trimethoprim, or pyrimethamine, suggesting that they are potential vehicles for the transmission of antibiotic resistance genes (ARGs) in the biome. However, the incidence of ARGs across the phylum Nucleocytoviricota, their evolutionary characteristics, their dissemination potential, and their association with virulence factors remain unexplored. Here, we systematically investigated ARGs of 1416 NCLDV genomes including those of almost all currently available cultured isolates and high-quality metagenome-assembled genomes from diverse habitats across the globe. We reveal that 39.5% of them carry ARGs, which is approximately 37 times higher than that for phage genomes. A total of 12 ARG types are encoded by NCLDVs. Phylogenies of the three most abundant NCLDV-encoded ARGs hint that NCLDVs acquire ARGs from not only eukaryotes but also prokaryotes and phages. Two NCLDV-encoded trimethoprim resistance genes are demonstrated to confer trimethoprim resistance in Escherichia coli. The presence of ARGs in NCLDV genomes is significantly correlated with mobile genetic elements and virulence factors.},
}
@article {pmid39047887,
year = {2024},
author = {Wu, X and Jia, W and Fang, Z and Sun, H and Wang, G and Liu, L and Zheng, M and Chen, G},
title = {Cyanobacteria mediate the dissemination of bacterial antibiotic resistance through conjugal transfer.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {359},
number = {},
pages = {124592},
doi = {10.1016/j.envpol.2024.124592},
pmid = {39047887},
issn = {1873-6424},
mesh = {*Drug Resistance, Bacterial/genetics ; *Microcystis/genetics ; *Gene Transfer, Horizontal ; *Cyanobacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Genes, Bacterial ; Bacteria/genetics/drug effects ; },
abstract = {Cyanobacterial blooms are expanding world-wide in freshwater and marine environments, and can cause serious ecological and environmental issues, which also contribute to the spread of antibiotic resistance genes (ARGs). However, the mechanistic understanding of cyanobacteria-mediated resistance dynamics is not fully elucidated yet. We selected Microcystis aeruginosa as a model cyanobacteria to illustrate how cyanobacteria mediate the evolution and transfer processes of bacterial antibiotic resistance. The results show that the presence of cyanobacteria significantly decreased the abundance of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) by 3%-99% and 2%-18%, respectively. In addition, it clearly altered bacterial community structure, with the dominant genera evolving from Acinetobacter (27%) and Enterobacter (42%) to Porphyrobacter (59%). The abundance of ARGs positively correlated with Proteobacteria and Firmicutes, rather than Cyanobacteria, and Bacteroidetes. In the presence of cyanobacteria, the transfer events of bacterial resistance genes via conjugation were found to decrease by 10%-89% (p < 0.05). Surprisingly, we found an extradentary high transfer frequency (about 0.1) for the ARGs via plasmid conjugation from the bacteria into M. aeruginosa population. It confirmed the role of cyanobacterial population as the competent hosts to facilitate ARGs spreading. Our findings provide valuable information on the risk evaluation of ARGs caused by cyanobacterial blooms in aquatic environments, key for the protection and assessment of aquatic environmental quality.},
}
@article {pmid39214865,
year = {2024},
author = {Fonseca, DR and Day, LA and Crone, KK and Costa, KC},
title = {An Extracellular, Ca[2+]-Activated Nuclease (EcnA) Mediates Transformation in a Naturally Competent Archaeon.},
journal = {Molecular microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mmi.15311},
pmid = {39214865},
issn = {1365-2958},
support = {MCB-2148165//National Science Foundation/ ; },
abstract = {Transformation, the uptake of DNA directly from the environment, is a major driver of gene flow in microbial populations. In bacteria, DNA uptake requires a nuclease that processes dsDNA to ssDNA, which is subsequently transferred into the cell and incorporated into the genome. However, the process of DNA uptake in archaea is still unknown. Previously, we cataloged genes essential to natural transformation in Methanococcus maripaludis, but few homologs of bacterial transformation-associated genes were identified. Here, we characterize one gene, MMJJ_16440 (named here as ecnA), to be an extracellular nuclease. We show that EcnA is Ca[2+]-activated, present on the cell surface, and essential for transformation. While EcnA can degrade several forms of DNA, the highest activity was observed with ssDNA as a substrate. Activity was also observed with circular dsDNA, suggesting that EcnA is an endonuclease. This is the first biochemical characterization of a transformation-associated protein in a member of the archaeal domain and suggests that both archaeal and bacterial transformation initiate in an analogous fashion.},
}
@article {pmid39214042,
year = {2024},
author = {Li, G and Long, TF and Zhou, SY and Xia, LJ and Gao, A and Wan, L and Diao, XY and He, YZ and Sun, RY and Yang, JT and Tang, SQ and Ren, H and Fang, LX and Liao, XP and Liu, YH and Chen, L and Sun, J},
title = {CRISPR-AMRtracker: A novel toolkit to monitor the antimicrobial resistance gene transfer in fecal microbiota.},
journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy},
volume = {77},
number = {},
pages = {101142},
doi = {10.1016/j.drup.2024.101142},
pmid = {39214042},
issn = {1532-2084},
abstract = {The spread of antibiotic resistance genes (ARGs), particularly those carried on plasmids, poses a major risk to global health. However, the extent and frequency of ARGs transfer in microbial communities among human, animal, and environmental sectors is not well understood due to a lack of effective tracking tools. We have developed a novel fluorescent tracing tool, CRISPR-AMRtracker, to study ARG transfer. It combines CRISPR/Cas9 fluorescence tagging, fluorescence-activated cell sorting, 16S rRNA gene sequencing, and microbial community analysis. CRISPR-AMRtracker integrates a fluorescent tag immediately downstream of ARGs, enabling the tracking of ARG transfer without compromising the host cell's antibiotic susceptibility, fitness, conjugation, and transposition. Notably, our experiments demonstrate that sfGFP-tagged plasmid-borne mcr-1 can transfer across diverse bacterial species within fecal samples. This innovative approach holds the potential to illuminate the dynamics of ARG dissemination and provide valuable insights to shape effective strategies in mitigating the escalating threat of antibiotic resistance.},
}
@article {pmid39213533,
year = {2024},
author = {Zeng, Q and Wu, X and Song, M and Jiang, L and Zeng, Q and Qiu, R and Luo, C},
title = {Opposite Effects of Planting on Antibiotic Resistomes in Rhizosphere Soil with Different Sulfamethoxazole Levels.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c04258},
pmid = {39213533},
issn = {1520-5118},
abstract = {Achieving consensus about the rhizosphere effect on soil antibiotic resistomes is challenging due to the variability in antibiotic concentrations, sources, and the elusory underlying mechanisms. Here, we characterized the antibiotic resistomes in both the rhizosphere and bulk soils of soybean plants grown in environments with varying levels of antibiotic contamination, using sulfamethoxazole (SMX) as a model compound. We also investigated the factors influencing resistome profiles. Soybean cultivation altered the structure of antibiotic-resistant genes (ARGs) and increased their absolute abundance. However, the rhizosphere effect on the relative abundance of ARGs was dependent on SMX concentrations. At low SMX levels, the rhizosphere effect was characterized by the inhibition of antibiotic-resistant bacteria (ARBs) and the promotion of sensitive bacteria. In contrast, at high SMX levels, the rhizosphere promoted the growth of ARBs and facilitated horizontal gene transfer of ARGs. This novel mechanism provides new insights into accurately assessing the rhizosphere effect on soil antibiotic resistomes.},
}
@article {pmid39213158,
year = {2024},
author = {Ma, Y and Kan, A and Johnson, DR},
title = {Metabolic interactions control the transfer and spread of plasmid-encoded antibiotic resistance during surface-associated microbial growth.},
journal = {Cell reports},
volume = {43},
number = {9},
pages = {114653},
doi = {10.1016/j.celrep.2024.114653},
pmid = {39213158},
issn = {2211-1247},
abstract = {Surface-associated microbial systems are hotspots for the spread of plasmid-encoded antibiotic resistance, but how surface association affects plasmid transfer and proliferation remains unclear. Surface association enables prolonged spatial proximities between different populations, which promotes plasmid transfer between them. However, surface association also fosters strong metabolic interactions between different populations, which can direct their spatial self-organization with consequences for plasmid transfer and proliferation. Here, we hypothesize that metabolic interactions direct the spatial self-organization of different populations and, in turn, regulate the spread of plasmid-encoded antibiotic resistance. We show that resource competition causes populations to spatially segregate, which represses plasmid transfer. In contrast, resource cross-feeding causes populations to spatially intermix, which promotes plasmid transfer. We further show that the spatial positionings that emerge from metabolic interactions determine the proliferation of plasmid recipients. Our results demonstrate that metabolic interactions are important regulators of both the transfer and proliferation of plasmid-encoded antibiotic resistance.},
}
@article {pmid39211246,
year = {2024},
author = {Hughes Lago, C and Blackburn, D and Kinder Pavlicek, M and Threadgill, DS},
title = {Comparative Genomic Analysis of Campylobacter rectus and Closely Related Species.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.07.26.605372},
pmid = {39211246},
issn = {2692-8205},
abstract = {Campylobacter rectus is a gram-negative, anaerobic bacterium strongly associated with periodontitis. It also causes various extraoral infections and is linked to adverse pregnancy outcomes in humans and murine models. C. rectus and related oral Campylobacters have been termed "emerging Campylobacter species" because infections by these organisms are likely underreported. Previously, no comparative methods have been used to analyze more than single C. rectus strains and until recently, very few C. rectus genomes have been publicly available. More sequenced genomes and comparative analyses are needed to study the genomic features and pathogenicity of this species. We sequenced eight new C. rectus strains and used comparative methods to identify regions of interest. An emphasis was put on the type III flagellar secretion system (T3SS), type IV secretion system (T4SS), and type VI secretion system (T6SS) because these protein complexes are important for pathogenesis in other Campylobacter species. RAST, BV-BRC, and other bioinformatics tools were used to assemble, annotate, and compare these regions in the genomes. The pan-genome of C. rectus consists of 2670 genes with core and accessory genomes of 1429 and 1241 genes, respectively. All isolates analyzed in this study have T3SS and T6SS hallmark proteins, while five of the isolates are missing a T4SS system. Twenty-one prophage clusters were identified across the panel of isolates, including four that appear intact. Overall, significant genomic islands were found, suggesting regions in the genomes that underwent horizontal gene transfer. Additionally, the high frequency of CRISPR arrays and other repetitive elements has led to genome rearrangements across the strains, including in areas adjacent to secretion system gene clusters. This study describes the substantial diversity present among C. rectus isolates and highlights tools/assays that have been developed to permit functional genomic studies. Additionally, we have expanded the studies on C. showae T4SS since we have two new C. showae genomes to report. We also demonstrate that unlike C. rectus , C showae does not demonstrate evidence of intact T6SS except for the strain CAM. The only strain of sequenced C. massilensis has neither T4SS or T6SS.},
}
@article {pmid39211212,
year = {2024},
author = {Marcarian, HQ and Sivakoses, A and Arias, AM and Ihedioha, OC and Lee, BR and Bishop, MC and Bothwell, ALM},
title = {Renal cancer cells acquire immune surface protein through trogocytosis and horizontal gene transfer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.08.07.607036},
pmid = {39211212},
issn = {2692-8205},
abstract = {UNLABELLED: Trogocytosis is an underappreciated phenomenon that shapes the immune microenvironment surrounding many types of solid tumors. The consequences of membrane-bound proteins being deposited from a donor immune cell to a recipient cancer cell via trogocytosis are still unclear. Here, we report that human clear cell renal carcinoma tumors stably express the lymphoid markers CD45, CD56, CD14, and CD16. Flow cytometry performed on fresh kidney tumors revealed consistent CD45 expression on tumor cells, as well as varying levels of the other markers mentioned previously. These results were consistent with our immunofluorescent analysis, which also revealed colocalization of lymphoid markers with carbonic anhydrase 9 (CAIX), a standard kidney tumor marker. RNA analysis showed a significant upregulation of genes typically associated with immune cells in tumor cells following trogocytosis. Finally, we show evidence of chromosomal DNA being transferred from immune cells to tumor cells during trogocytosis. This horizontal gene transfer has transcriptional consequences in the recipient tumor cell, resulting in a fusion phenotype that expressed both immune and cancer specific proteins. This work demonstrates a novel mechanism by which tumor cell protein expression is altered through the acquisition of surface membrane fragments and genomic DNA from infiltrating lymphocytes. These results alter the way in which we understand tumor-immune cell interactions and may reveal new insights into the mechanisms by which tumors develop. Additionally, further studies into trogocytosis will help push the field towards the next generation of immunotherapies and biomarkers for treating renal cell carcinoma and other types of cancers.<br><br>SIGNIFICANCE STATEMENT: We have identified trogocytosis as a mechanism by which human clear cell renal carcinoma tumors acquire lymphocyte surface protein expression from tumor infiltrating immune cells. In addition to the transfer of membrane fragments, we have provided evidence to show that genomic DNA is transferred from a normal immune cell to a tumor cell during trogocytosis. This process alters the transcriptome of cancer cells such that they express significantly more mRNA for immune proteins such as the lymphocyte marker CD45 compared to tumor cells that have not undergone trogocytosis. This study provides an in-depth analysis of the interactions between cancer cells and tumor infiltrating lymphocytes, and how these interactions alter the development of human tumors.},
}
@article {pmid39210455,
year = {2024},
author = {Abdellati, S and Gestels, Z and Laumen, JGE and Van Dijck, C and De Baetselier, I and de Block, T and Van den Bossche, D and Vanbaelen, T and Kanesaka, I and Manoharan-Basil, SS and Kenyon, C},
title = {Antimicrobial susceptibility of commensal Neisseria spp. In parents and their children in Belgium: a cross-sectional survey.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnae069},
pmid = {39210455},
issn = {1574-6968},
abstract = {BACKGROUND: Commensal Neisseria species are part of the oropharyngeal microbiome and play an important role in nitrate reduction and protecting against colonization by pathogenic bacteria. They do, however, also serve as a reservoir of antimicrobial resistance. Little is known about the prevalence of these species in the general population, how this varies by age and how antimicrobial susceptibility varies between species.<br><br>METHODS: We assessed the prevalence and antimicrobial susceptibility of commensal Neisseria species in the parents (n&#xa0;=&#xa0;38) and children (n&#xa0;=&#xa0;50) of 35 families in Belgium.<br><br>RESULTS: Various commensal Neisseria (n&#xa0;=&#xa0;5) could be isolated from the participants. Most abundant were N. subflava and N. mucosa. N. subflava was detected in 77 of 88 (87.5%) individuals and N. mucosa in 64 of 88 (72.7%). N. mucosa was more prevalent in children (41/50 [82%]) than parents (23/38 [60.5%]; P&#xa0;<&#xa0;0.05), while N. bacilliformis was more prevalent in parents (7/36 [19.4%]) than children (2/50 [4%]; P&#xa0;<&#xa0;0.05). N. bacilliformis had high ceftriaxone minimum inhibitory concentrations (MICs; median MIC 0.5&#xa0;mg/L; IQR 0.38-0.75). The ceftriaxone MICs of all Neisseria isolates were higher in the parents than in the children. This could be explained by a higher prevalence of N. bacilliformis in the parents.<br><br>INTERPRETATION: The N. bacilliformis isolates had uniformly high ceftriaxone MICs which warrant further investigation.},
}
@article {pmid39207571,
year = {2024},
author = {Smiatek, J},
title = {Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning.},
journal = {Journal of molecular evolution},
volume = {},
number = {},
pages = {},
pmid = {39207571},
issn = {1432-1432},
abstract = {We present a non-equilibrium thermodynamics approach to the multilevel theory of learning for the study of molecular evolution. This approach allows us to study the explicit time dependence of molecular evolutionary processes and their impact on entropy production. Interpreting the mathematical expressions, we can show that two main contributions affect entropy production of molecular evolution processes which can be identified as mutation and gene transfer effects. Accordingly, our results show that the optimal adaptation of organisms to external conditions in the context of evolutionary processes is driven by principles of minimum entropy production. Such results can also be interpreted as the basis of some previous postulates of the theory of learning. Although our macroscopic approach requires certain simplifications, it allows us to interpret molecular evolutionary processes using thermodynamic descriptions with reference to well-known biological processes.},
}
@article {pmid39207102,
year = {2024},
author = {Zhang, W and Fan, Y and Deng, W and Chen, Y and Wang, S and Kang, S and Steenwyk, JL and Xiang, M and Liu, X},
title = {Characterization of genome-wide phylogenetic conflict uncovers evolutionary modes of carnivorous fungi.},
journal = {mBio},
volume = {},
number = {},
pages = {e0213324},
doi = {10.1128/mbio.02133-24},
pmid = {39207102},
issn = {2150-7511},
abstract = {Mass extinction has often paved the way for rapid evolutionary radiation, resulting in the emergence of diverse taxa within specific lineages. The emergence and diversification of carnivorous nematode-trapping fungi (NTF) in Ascomycota have been linked to the Permian-Triassic (PT) extinction, but the processes underlying NTF radiation remain unclear. We conducted phylogenomic analyses using 23 genomes that represent three NTF lineages, each employing distinct nematode traps-mechanical traps (Drechslerella spp.), three-dimensional (3D) adhesive traps (Arthrobotrys spp.), and two-dimensional (2D) adhesive traps (Dactylellina spp.), and the genome of one non-NTF species as the outgroup. These analyses revealed multiple mechanisms that likely contributed to the tempo of the NTF evolution and rapid radiation. The species tree of NTFs based on 2,944 single-copy orthologous genes suggested that Drechslerella emerged earlier than Arthrobotrys and Dactylellina. Extensive genome-wide phylogenetic discordance was observed, mainly due to incomplete lineage sorting (ILS) between lineages. Two modes of non-vertical evolution (introgression and horizontal gene transfer) also contributed to phylogenetic discordance. The ILS genes that are associated with hyphal growth and trap morphogenesis (e.g., those associated with the cell membrane system and polarized cell division) exhibited signs of positive selection.IMPORTANCEBy conducting a comprehensive phylogenomic analysis of 23 genomes across three NTF lineages, the research reveals how diverse evolutionary mechanisms, including ILS and non-vertical evolution (introgression and horizontal gene transfer), contribute to the swift diversification of NTFs. These findings highlight the complex evolutionary dynamics that drive the rapid radiation of NTFs, providing valuable insights into the processes underlying their diversity and adaptation.},
}
@article {pmid39206372,
year = {2024},
author = {Kirk, A and Stavrinides, J},
title = {Distribution and comparative genomic analysis of antimicrobial gene clusters found in Pantoea.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1416674},
doi = {10.3389/fmicb.2024.1416674},
pmid = {39206372},
issn = {1664-302X},
abstract = {Members of the bacterial genus Pantoea produce a variety of antimicrobial products that are effective against plant, animal, and human pathogens. To date, little is known about the distribution and evolutionary history of these clusters. We surveyed the public databases for the 12 currently known antibiotic biosynthetic gene clusters found across Pantoea strains to determine their distribution. We show that some clusters, namely pantocin B, PNP-3, and PNP-4 are found strictly in Pantoea, while agglomerin, andrimid, AGA, dapdiamide, herbicolin, PNP-1, PNP-2, PNP-5, and pantocin A, are more broadly distributed in distantly related genera within Vibrionaceae, Pectobacteriaceae, Yersiniaceae, Morganellaceae, and Hafniaceae. We evaluated the evolutionary history of these gene clusters relative to a cpn60-based species tree, considering the flanking regions of each cluster, %GC, and presence of mobile genetic elements, and identified potential occurrences of horizontal gene transfer. Lastly, we also describe the biosynthetic gene cluster of pantocin B in the strain Pantoea agglomerans Eh318 more than 20 years after this antibiotic was first described.},
}
@article {pmid39203510,
year = {2024},
author = {Lv, N and Ni, J and Fang, S and Liu, Y and Wan, S and Sun, C and Li, J and Zhou, A},
title = {Potential Convergence to Accommodate Pathogenicity Determinants and Antibiotic Resistance Revealed in Salmonella Mbandaka.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
doi = {10.3390/microorganisms12081667},
pmid = {39203510},
issn = {2076-2607},
support = {32260032//National Natural Science Foundation of China/ ; 32370143//National Natural Science Foundation of China/ ; 31800118//National Natural Science Foundation of China/ ; jxsq2019101054//Double Thousand Talents Plan of Jiangxi/ ; },
abstract = {Salmonella species are causal pathogens instrumental in human food-borne diseases. The pandemic survey related to multidrug resistant (MDR) Salmonella genomics enables the prevention and control of their dissemination. Currently, serotype Mbandaka is notorious as a multiple host-adapted non-typhoid Salmonella. However, its epidemic and MDR properties are still obscure, especially its genetic determinants accounting for virulence and MD resistance. Here, we aim to characterize the genetic features of a strain SMEH pertaining to Salmonella Mbandaka (S. Mbandaka), isolated from the patient's hydropericardium, using cell infections, a mouse model, antibiotic susceptibility test and comparative genomics. The antibiotic susceptibility testing showed that it could tolerate four antibiotics, including chloramphenicol, tetracycline, fisiopen and doxycycline by Kirby-Bauer (K-B) testing interpreted according to the Clinical and Laboratory Standards Institute (CLSI). Both the reproducibility in RAW 264.7 macrophages and invasion ability to infect HeLa cells with strain SMEH were higher than those of S. Typhimurium strain 14028S. In contrast, its attenuated virulence was determined in the survival assay using a mouse model. As a result, the candidate genetic determinants responsible for antimicrobial resistance, colonization/adaptability and their transferability were comparatively investigated, such as bacterial secretion systems and pathogenicity islands (SPI-1, SPI-2 and SPI-6). Moreover, collective efforts were made to reveal a potential role of the plasmid architectures in S. Mbandaka as the genetic reservoir to transfer or accommodate drug-resistance genes. Our findings highlight the essentiality of antibiotic resistance and risk assessment in S. Mbandaka. In addition, genomic surveillance is an efficient method to detect pathogens and monitor drug resistance. The genetic determinants accounting for virulence and antimicrobial resistance underscore the increasing clinical challenge of emerging MDR Mbandaka isolates, and provide insights into their prevention and treatment.},
}
@article {pmid39201699,
year = {2024},
author = {Li, H and Liang, T and Liu, Y and Wang, P and Wang, S and Zhao, M and Zhang, Y},
title = {Exploring Mitochondrial Heterogeneity and Evolutionary Dynamics in Thelephora ganbajun through Population Genomics.},
journal = {International journal of molecular sciences},
volume = {25},
number = {16},
pages = {},
doi = {10.3390/ijms25169013},
pmid = {39201699},
issn = {1422-0067},
support = {31870009//National Natural Science Foundation of China/ ; YNWR-QNBJ-2018-355//Top Young Talents Program of the Ten Thousand Talents Plan in Yunnan Province/ ; 2021KF009//YNCUB/ ; },
mesh = {*Genome, Mitochondrial ; *Evolution, Molecular ; Phylogeny ; Introns/genetics ; Mitochondria/genetics ; Basidiomycota/genetics ; DNA, Mitochondrial/genetics ; Genomics/methods ; Gene Transfer, Horizontal ; },
abstract = {Limited exploration in fungal mitochondrial genetics has uncovered diverse inheritance modes. The mitochondrial genomes are inherited uniparentally in the majority of sexual eukaryotes, our discovery of persistent mitochondrial heterogeneity within the natural population of the basidiomycete fungus Thelephora ganbajun represents a significant advance in understanding mitochondrial inheritance and evolution in eukaryotes. Here, we present a comprehensive analysis by sequencing and assembling the complete mitogenomes of 40 samples exhibiting diverse cox1 heterogeneity patterns from various geographical origins. Additionally, we identified heterogeneous variants in the nad5 gene, which, similar to cox1, displayed variability across multiple copies. Notably, our study reveals a distinct prevalence of introns and homing endonucleases in these heterogeneous genes. Furthermore, we detected potential instances of horizontal gene transfer involving homing endonucleases. Population genomic analyses underscore regional variations in mitochondrial genome composition among natural samples exhibiting heterogeneity. Thus, polymorphisms in heterogeneous genes, introns, and homing endonucleases significantly influence mitochondrial structure, structural variation, and evolutionary dynamics in this species. This study contributes valuable insights into mitochondrial genome architecture, population dynamics, and the evolutionary implications of mitochondrial heterogeneity in sexual eukaryotes.},
}
@article {pmid39200594,
year = {2024},
author = {Habibi, N and Uddin, S and Behbehani, M and Mustafa, AS and Al-Fouzan, W and Al-Sarawi, HA and Safar, H and Alatar, F and Al Sawan, RMZ},
title = {Aerosol-Mediated Spread of Antibiotic Resistance Genes: Biomonitoring Indoor and Outdoor Environments.},
journal = {International journal of environmental research and public health},
volume = {21},
number = {8},
pages = {},
doi = {10.3390/ijerph21080983},
pmid = {39200594},
issn = {1660-4601},
mesh = {*Aerosols/analysis ; *Gene Transfer, Horizontal ; Humans ; Biological Monitoring ; Drug Resistance, Microbial/genetics ; Air Microbiology ; Air Pollution, Indoor/analysis ; Environmental Monitoring ; Anti-Bacterial Agents/analysis ; Drug Resistance, Bacterial/genetics ; },
abstract = {Antimicrobial resistance (AMR) has emerged as a conspicuous global public health threat. The World Health Organization (WHO) has launched the "One-Health" approach, which encourages the assessment of antibiotic resistance genes (ARGs) within an environment to constrain and alleviate the development of AMR. The prolonged use and overuse of antibiotics in treating human and veterinary illnesses, and the inability of wastewater treatment plants to remove them have resulted in elevated concentrations of these metabolites in the surroundings. Microbes residing within these settings acquire resistance under selective pressure and circulate between the air-land interface. Initial evidence on the indoor environments of wastewater treatment plants, hospitals, and livestock-rearing facilities as channels of AMR has been documented. Long- and short-range transport in a downwind direction disseminate aerosols within urban communities. Inhalation of such aerosols poses a considerable occupational and public health risk. The horizontal gene transfer (HGT) is another plausible route of AMR spread. The characterization of ARGs in the atmosphere therefore calls for cutting-edge research. In the present review, we provide a succinct summary of the studies that demonstrated aerosols as a media of AMR transport in the atmosphere, strengthening the need to biomonitor these pernicious pollutants. This review will be a useful resource for environmental researchers, healthcare practitioners, and policymakers to issue related health advisories.},
}
@article {pmid39200027,
year = {2024},
author = {Milani, G and Cortimiglia, C and Belloso Daza, MV and Greco, E and Bassi, D and Cocconcelli, PS},
title = {Microplastic-Mediated Transfer of Tetracycline Resistance: Unveiling the Role of Mussels in Marine Ecosystems.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/antibiotics13080727},
pmid = {39200027},
issn = {2079-6382},
support = {PE00000003//Italian Ministry of University and Research funded by the European Union - NextGenerationEU/ ; },
abstract = {The global threat of antimicrobial resistance (AMR) is exacerbated by the mobilization of antimicrobial resistance genes (ARGs) occurring in different environmental niches, including seawater. Marine environments serve as reservoirs for resistant bacteria and ARGs, further complicated by the ubiquity of microplastics (MPs). MPs can adsorb pollutants and promote bacterial biofilm formation, creating conditions favorable to the dissemination of ARGs. This study explores the dynamics of ARG transfer in the marine bivalve Mytilus galloprovincialis within a seawater model, focusing on the influence of polyethylene MPs on the mobilization of the Tn916-carrying tetM gene and plasmid-encoded ermB. Experiments revealed that biofilm formation on MPs by Enterococcus faecium and Listeria monocytogenes facilitated the transfer of the tetM resistance gene, but not the ermB gene. Furthermore, the presence of MPs significantly increased the conjugation frequency of tetM within mussels, indicating that MPs enhance the potential for ARG mobilization in marine environments. These findings highlight the role of MPs and marine organisms in ARG spread, underscoring the ecological and public health implications.},
}
@article {pmid39199982,
year = {2024},
author = {Yao, Y and Imirzalioglu, C and Falgenhauer, L and Falgenhauer, J and Heinmüller, P and , and Domann, E and Chakraborty, T},
title = {Plasmid-Mediated Spread of Carbapenem Resistance in Enterobacterales: A Three-Year Genome-Based Survey.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/antibiotics13080682},
pmid = {39199982},
issn = {2079-6382},
abstract = {The worldwide emergence and dissemination of carbapenem-resistant Gram-negative bacteria (CRGNB) is a challenging problem of antimicrobial resistance today. Outbreaks with CRGNB have severe consequences for both the affected healthcare settings as well as the patients with infection. Thus, bloodstream infections caused by metallo-ß-lactamase-producing Enterobacterales can often have clinical implications, resulting in high mortality rates due to delays in administering effective treatment and the limited availability of treatment options. The overall threat of CRGNB is substantial because carbapenems are used to treat infections caused by ESBL-producing Enterobacterales which also exist with high frequency within the same geographical regions. A genome-based surveillance of 589 CRGNB from 61 hospitals across the federal state Hesse in Germany was implemented using next-generation sequencing (NGS) technology to obtain a high-resolution landscape of carbapenem-resistant isolates over a three-year period (2017-2019). The study examined all reportable CRGNB isolates submitted by participating hospitals. This included isolates carrying known carbapenemases (435) together with carbapenem-resistant non-carbapenemase producers (154). Predominant carbapenemase producers included Klebsiella pneumoniae, Escherichia coli, Citrobacter freundii and Acinetobacter baumannii. Over 80% of 375 carbapenem-resistant determinants including KPC-, NDM-, VIM- and OXA-48-like ones detected in 520 Enterobacterales were plasmid-encoded, and half of these were dominated by a few incompatibility (Inc) types, viz., IncN, IncL/M, IncFII and IncF(K). Our results revealed that plasmids play an extraordinary role in the dissemination of carbapenem resistance in the heterogeneous CRGNB population. The plasmids were also associated with several multispecies dissemination events and local outbreaks throughout the study period, indicating the substantial role of horizontal gene transfer in carbapenemase spread. Furthermore, due to vertical and horizontal plasmid transfer, this can have an impact on implant-associated infections and is therefore important for antibiotic-loaded bone cement and drug-containing devices in orthopedic surgery. Future genomic surveillance projects should increase their focus on plasmid characterization.},
}
@article {pmid39198891,
year = {2024},
author = {Tian, F and Wainaina, JM and Howard-Varona, C and Domínguez-Huerta, G and Bolduc, B and Gazitúa, MC and Smith, G and Gittrich, MR and Zablocki, O and Cronin, DR and Eveillard, D and Hallam, SJ and Sullivan, MB},
title = {Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {159},
pmid = {39198891},
issn = {2049-2618},
support = {ABI#1759874, ABI#2149505, OCE#1536989, OCE#1829831, and OCE#2019589//National Science Foundation/ ; #3790//Gordon and Betty Moore Foundation Investigator Award/ ; },
mesh = {*Oceans and Seas ; *Seawater/virology/microbiology ; Metagenomics ; Bacteria/genetics/classification/metabolism ; Viruses/genetics/classification/isolation &amp; purification ; Prokaryotic Cells/metabolism/virology ; Metagenome ; Metabolic Networks and Pathways/genetics ; Gene Transfer, Horizontal ; Phosphatidylethanolamines/metabolism ; },
abstract = {BACKGROUND: Prokaryotic microbes have impacted marine biogeochemical cycles for billions of years. Viruses also impact these cycles, through lysis, horizontal gene transfer, and encoding and expressing genes that contribute to metabolic reprogramming of prokaryotic cells. While this impact is difficult to quantify in nature, we hypothesized that it can be examined by surveying virus-encoded auxiliary metabolic genes (AMGs) and assessing their ecological context.<br><br>RESULTS: We systematically developed a global ocean AMG catalog by integrating previously described and newly identified AMGs and then placed this catalog into ecological and metabolic contexts relevant to ocean biogeochemistry. From 7.6 terabases of Tara Oceans paired prokaryote- and virus-enriched metagenomic sequence data, we increased known ocean virus populations to 579,904 (up 16%). From these virus populations, we then conservatively identified 86,913 AMGs that grouped into 22,779 sequence-based gene clusters, 7248 (~&#x2009;32%) of which were not previously reported. Using our catalog and modeled data from mock communities, we estimate that&#x2009;~&#x2009;19% of ocean virus populations carry at least one AMG. To understand AMGs in their metabolic context, we identified 340 metabolic pathways encoded by ocean microbes and showed that AMGs map to 128 of them. Furthermore, we identified metabolic "hot spots" targeted by virus AMGs, including nine pathways where most steps (&#x2265;&#x2009;0.75) were AMG-targeted (involved in carbohydrate, amino acid, fatty acid, and nucleotide metabolism), as well as other pathways where virus-encoded AMGs outnumbered cellular homologs (involved in lipid A phosphates, phosphatidylethanolamine, creatine biosynthesis, phosphoribosylamine-glycine ligase, and carbamoyl-phosphate synthase pathways).<br><br>CONCLUSIONS: Together, this systematically curated, global ocean AMG catalog and analyses provide a valuable resource and foundational observations to understand the role of viruses in modulating global ocean metabolisms and their biogeochemical implications. Video Abstract.},
}
@article {pmid39198572,
year = {2024},
author = {Sastre-Dominguez, J and DelaFuente, J and Toribio-Celestino, L and Herencias, C and Herrador-Gómez, P and Costas, C and Hernández-García, M and Cantón, R and Rodríguez-Beltrán, J and Santos-Lopez, A and San Millan, A},
title = {Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria.},
journal = {Nature ecology &amp; evolution},
volume = {},
number = {},
pages = {},
pmid = {39198572},
issn = {2397-334X},
support = {757440-PLASREVOLUTION//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 895671-REPLAY//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101077809-HorizonGT//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PI19/00749//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; CD21/00115//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PI23/01945//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; CP20/00154//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PI21/01363//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; LCF/BQ/PR22/11920001//"la Caixa" Foundation (Caixa Foundation)/ ; Research Grant 2022//European Society of Clinical Microbiology and Infectious Diseases (ESCMID)/ ; },
abstract = {Plasmids are extrachromosomal genetic elements commonly found in bacteria. They are known to fuel bacterial evolution through horizontal gene transfer, and recent analyses indicate that they can also promote intragenomic adaptations. However, the role of plasmids as catalysts of bacterial evolution beyond horizontal gene transfer is poorly explored. In this study, we investigated the impact of a widespread conjugative plasmid, pOXA-48, on the evolution of several multidrug-resistant clinical enterobacteria. Combining experimental and within-patient evolution analyses, we unveiled that plasmid pOXA-48 promotes bacterial evolution through the transposition of plasmid-encoded insertion sequence 1 (IS1) elements. Specifically, IS1-mediated gene inactivation expedites the adaptation rate of clinical strains in vitro and fosters within-patient adaptation in the gut microbiota. We deciphered the mechanism underlying the plasmid-mediated surge in IS1 transposition, revealing a negative feedback loop regulated by the genomic copy number of IS1. Given the overrepresentation of IS elements in bacterial plasmids, our findings suggest that plasmid-mediated IS1 transposition represents a crucial mechanism for swift bacterial adaptation.},
}
@article {pmid39198281,
year = {2024},
author = {He, Z and Smets, BF and Dechesne, A},
title = {Mating Assay: Plating Below a Cell Density Threshold is Required for Unbiased Estimation of Plasmid Conjugation Frequency of RP4 Transfer Between E. coli Strains.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {109},
pmid = {39198281},
issn = {1432-184X},
support = {0236-00022B//Innovationsfonden/ ; 0236-00022B//Innovationsfonden/ ; 0236-00022B//Innovationsfonden/ ; PhD Scholarship//Sino-Danish Center/ ; PhD Scholarship//Sino-Danish Center/ ; },
mesh = {*Escherichia coli/genetics ; *Conjugation, Genetic ; *Plasmids/genetics ; Gene Transfer, Horizontal ; },
abstract = {Mating assays are common laboratory experiments for measuring the conjugation frequency, i.e. efficiency at which a plasmid transfers from a population of donor cells to a population of recipient cells. Selective plating remains a widely used quantification method to enumerate transconjugants at the end of such assays. However, conjugation frequencies may be inaccurately estimated because plasmid transfer can occur on transconjugant-selective plates rather than only during the intended mating duration. We investigated the influence of cell density on this phenomenon. We conducted mating experiments with IncPα plasmid RP4 harbored in Escherichia coli at a fixed cell density and mating conditions, inoculated a serial dilution of the mating mixture on transconjugant-selective plates or in transconjugant-selective broth, and compared the results to a model of cell-to-cell distance distribution. Our findings suggest that irrespective of the mating mode (liquid vs solid), the enumeration of transconjugants becomes significantly biased if the plated cell density exceeds 28 Colony Forming Unit (CFU)/mm[2] (or 1.68•10[5] CFU/standard 9 cm Petri dish). This threshold is determined with a 95% confidence interval of ± 4 CFU/mm[2] (± 2.46•10[4] CFU/standard 9 cm Petri dish). Liquid mating assays were more sensitive to this bias because the conjugation frequency of RP4 is several orders of magnitude lower in suspension compared to surface mating. Therefore, if selective plating is used, we recommend to plate at this density threshold and that negative controls are performed where donors and recipients are briefly mixed before plating at the same dilutions as for the actual mating assay. As an alternative, a liquid enumeration method can be utilized to increase the signal-to-noise ratio and allow for more accurate enumeration of transconjugants.},
}
@article {pmid39194517,
year = {2024},
author = {Yang, X and Liu, Z and Zhang, Y and Shi, X and Wu, Z},
title = {Dinoflagellate-Bacteria Interactions: Physiology, Ecology, and Evolution.},
journal = {Biology},
volume = {13},
number = {8},
pages = {},
pmid = {39194517},
issn = {2079-7737},
support = {42106093 and 41976130//National Natural Science Foundation of China/ ; 2022T150706//China Postdoctoral Science Foundation/ ; GPCGD223103FG015F//Comprehensive Protection and Utilization Program for the Coastal Zone of Guangdong 534 Province (Revision)/ ; DD20230460, DD20230107, and DD20242792//Marine Geological Survey 535 Program of China Geological Survey/ ; },
abstract = {Dinoflagellates and heterotrophic bacteria are two major micro-organism groups within marine ecosystems. Their coexistence has led to a co-evolutionary relationship characterized by intricate interactions that not only alter their individual behaviors but also exert a significant influence on the broader biogeochemical cycles. Our review commenced with an analysis of bacterial populations, both free-living and adherent to dinoflagellate surfaces. Members of Alphaproteobacteria, Gammaproteobacteria, and the Cytophaga-Flavobacterium-Bacteroides group are repeatedly found to be associated with dinoflagellates, with representation by relatively few genera, such as Methylophaga, Marinobacter, and Alteromonas. These bacterial taxa engage with dinoflagellates in a limited capacity, involving nutrient exchange, the secretion of pathogenic substances, or participation in chemical production. Furthermore, the genomic evolution of dinoflagellates has been profoundly impacted by the horizontal gene transfer from bacteria. The integration of bacterial genes into dinoflagellates has been instrumental in defining their biological characteristics and nutritional strategies. This review aims to elucidate the nuanced interactions between dinoflagellates and their associated bacteria, offering a detailed perspective on their complex relationship.},
}
@article {pmid39193949,
year = {2024},
author = {Kim, HJ and Koo, SH and Choi, Q},
title = {Horizontal Gene Transfer of blaNDM-5 Among Three Different Enterobacteriaceae Species Isolated from a Single Patient.},
journal = {Clinical laboratory},
volume = {70},
number = {8},
pages = {},
doi = {10.7754/Clin.Lab.2024.240309},
pmid = {39193949},
issn = {1433-6510},
mesh = {Humans ; *Gene Transfer, Horizontal ; *Microbial Sensitivity Tests ; *beta-Lactamases/genetics ; *Enterobacteriaceae/genetics/drug effects/isolation &amp; purification ; *Anti-Bacterial Agents/pharmacology ; *Plasmids/genetics ; Enterobacteriaceae Infections/microbiology/diagnosis/drug therapy ; Whole Genome Sequencing ; Escherichia coli/genetics/drug effects/isolation &amp; purification ; Klebsiella oxytoca/genetics/isolation &amp; purification/drug effects ; Citrobacter/genetics/isolation &amp; purification/drug effects ; },
abstract = {BACKGROUND: In this study, Escherichia coli, Klebsiella oxytoca, and Citrobacter amalonaticus carrying blaNDM-5 were isolated from a single patient.<br><br>METHODS: The antibiotic susceptibility of the isolates was evaluated by using E-test and agar dilution methods, and blaNDM-5 was identified in genomic and plasmid DNA by using polymerase chain reaction and sequencing. Whole genome sequencing and de novo assembly were used for species characterization, resistance gene identification, and plasmid analysis.<br><br>RESULTS: All three species had identical plasmids, which were similar to pEC463-NDM5, a plasmid harboring blaNDM-5. Transconjugation experiments confirmed the horizontal gene transfer of blaNDM-5, highlighting the need for a close monitoring of Enterobacteriaceae species harboring this gene.<br><br>CONCLUSIONS: This study conclusively demonstrates the propensity for horizontal gene transfer of blaNDM-5 among Enterobacteriaceae species, underlining the importance of vigilant monitoring to combat antibiotic resistance.},
}
@article {pmid39191402,
year = {2024},
author = {Aoun, N and Georgoulis, SJ and Avalos, JK and Grulla, KJ and Miqueo, K and Tom, C and Lowe-Power, TM},
title = {A pangenomic atlas reveals eco-evolutionary dynamics that shape type VI secretion systems in plant-pathogenic Ralstonia.},
journal = {mBio},
volume = {},
number = {},
pages = {e0032324},
doi = {10.1128/mbio.00323-24},
pmid = {39191402},
issn = {2150-7511},
abstract = {Soilborne Ralstonia solanacearum species complex (RSSC) pathogens disrupt microbial communities as they invade roots and fatally wilt plants. RSSC pathogens secrete antimicrobial toxins using a type VI secretion system (T6SS). To investigate how evolution and ecology have shaped the T6SS of these bacterial pathogens, we analyzed the T6SS gene content and architecture across the RSSC and their evolutionary relatives. Our analysis reveals that two ecologically similar Burkholderiaceae taxa, xylem-pathogenic RSSC and Paracidovorax, have convergently evolved to wield large arsenals of T6SS toxins. To understand the mechanisms underlying genomic enrichment of T6SS toxins, we compiled an atlas of 1,066 auxiliary T6SS toxin clusters ("aux" clusters) across 99 high-quality RSSC genomes. We classified 25 types of aux clusters with toxins that predominantly target lipids, nucleic acids, or unknown cellular substrates. The aux clusters were located in diverse genetic neighborhoods and had complex phylogenetic distributions, suggesting frequent horizontal gene flow. Phages and other mobile genetic elements account for most of the aux cluster acquisition on the chromosome but very little on the megaplasmid. Nevertheless, RSSC genomes were more enriched in aux clusters on the megaplasmid. Although the single, ancestral T6SS was broadly conserved in the RSSC, the T6SS has been convergently lost in atypical, non-soilborne lineages. Overall, our data suggest dynamic interplay between the lifestyle of RSSC lineages and the evolution of T6SSes with robust arsenals of toxins. This pangenomic atlas poises the RSSC as an emerging, tractable model to understand the role of the T6SS in shaping pathogen populations.IMPORTANCEWe explored the eco-evolutionary dynamics that shape the inter-microbial warfare mechanisms of a globally significant plant pathogen, the Ralstonia solanacearum species complex. We discovered that most Ralstonia wilt pathogens have evolved extensive and diverse repertoires of type VI secretion system-associated antimicrobial toxins. These expansive toxin arsenals potentially enhance the ability of Ralstonia pathogens to invade plant microbiomes, enabling them to rapidly colonize and kill their host plants. We devised a classification system to categorize the Ralstonia toxins. Interestingly, many of the toxin gene clusters are encoded on mobile genetic elements, including prophages, which may be mutualistic symbionts that enhance the inter-microbial competitiveness of Ralstonia wilt pathogens. Moreover, our findings suggest that the convergent loss of this multi-gene trait contributes to genome reduction in two vector-transmitted lineages of Ralstonia pathogens. Our findings demonstrate that the interplay between microbial ecology and pathogen lifestyle shapes the evolution of a genetically complex antimicrobial weapon.},
}
@article {pmid39191296,
year = {2024},
author = {Xiao, Y and Qin, Y and Jiang, X and Gao, P},
title = {Effects of polypropylene microplastics on digestion performance, microbial community, and antibiotic resistance during microbial anaerobic digestion.},
journal = {Bioresource technology},
volume = {411},
number = {},
pages = {131358},
doi = {10.1016/j.biortech.2024.131358},
pmid = {39191296},
issn = {1873-2976},
abstract = {As an emerging pollutant, microplastics (MPs) have attracted increasing attention worldwide. The effects of polypropylene (PP) MPs on digestion performance, behaviors of dominant microbial communities, antibiotic resistance genes (ARGs) and mobile genetic elements in microbial anaerobic digesters were investigated. The results showed that the addition of PP-MPs to digesters led to an increase in methane production of 10.8% when 300 particles/g TSS of PP-MPs was introduced compared with that in digester not treated with PP-MPs. This increase was attributed to the enrichment of acetogens such as Syntrophobacter (42.0%), Syntrophorhabdus (27.0%), and Syntrophomonas (10.6%), and methanogens including Methanobacterium and Methanosaeta. tetX was highly enriched due to PP-MP exposure, whereas parC exhibited the greatest increase (35.5% - 222.7%). Horizontal gene transfer via ISCR1 and intI1 genes might play an important role in the spread of ARGs. Overall, these findings provide comprehensive insight into the ecological dynamics of PP-MPs during microbial anaerobic digestion.},
}
@article {pmid39191191,
year = {2024},
author = {Middendorf, PS and Zomer, AL and Bergval, IL and Jacobs-Reitsma, WF and den Besten, HMW and Abee, T},
title = {Host associations of Campylobacter jejuni and Campylobacter coli isolates carrying the L-fucose or d-glucose utilization cluster.},
journal = {International journal of food microbiology},
volume = {425},
number = {},
pages = {110855},
doi = {10.1016/j.ijfoodmicro.2024.110855},
pmid = {39191191},
issn = {1879-3460},
abstract = {Campylobacter was considered asaccharolytic, but is now known to carry saccharide metabolization pathways for L-fucose and d-glucose. We hypothesized that these clusters are beneficial for Campylobacter niche adaptation and may help establish human infection. We investigated the distribution of d-glucose and L-fucose clusters among ∼9600 C. jejuni and C. coli genomes of different isolation sources in the Netherlands, the United Kingdom, the United States of America and Finland. The L-fucose utilization cluster was integrated at the same location in all C. jejuni and C. coli genomes, and was flanked by the genes rpoB, rpoC, rspL, repsG and fusA, which are associated with functions in transcription as well as translation and in acquired drug resistance. In contrast, the flanking regions of the d-glucose utilization cluster were variable among the isolates, and integration sites were located within one of the three different 16S23S ribosomal RNA areas of the C. jejuni and C. coli genomes. In addition, we investigated whether acquisition of the L-fucose utilization cluster could be due to horizontal gene transfer between the two species and found three isolates for which this was the case: one C. jejuni isolate carrying a C. coli L-fucose cluster, and two C. coli isolates which carried a C. jejuni L-fucose cluster. Furthermore, L-fucose utilization cluster alignments revealed multiple frameshift mutations, most of which were commonly found in the non-essential genes for L-fucose metabolism, namely, Cj0484 and Cj0489. These findings support our hypothesis that the L-fucose cluster was integrated multiple times across the C. coli/C. jejuni phylogeny. Notably, association analysis using the C. jejuni isolates from the Netherlands showed a significant correlation between human C. jejuni isolates and C. jejuni isolates carrying the L-fucose utilization cluster. This correlation was even stronger when the Dutch isolates were combined with the isolates from the UK, the USA and Finland. No such correlations were observed for C. coli or for the d-glucose cluster for both species. This research provides insight into the spread and host associations of the L-fucose and d-glucose utilization clusters in C. jejuni and C. coli, and the potential benefits in human infection and/or proliferation in humans, conceivably after transmission from any reservoir.},
}
@article {pmid39190937,
year = {2024},
author = {Wen, AX and Herman, C},
title = {Horizontal gene transfer and beyond: the delivery of biological matter by bacterial membrane vesicles to host and bacterial cells.},
journal = {Current opinion in microbiology},
volume = {81},
number = {},
pages = {102525},
doi = {10.1016/j.mib.2024.102525},
pmid = {39190937},
issn = {1879-0364},
abstract = {Membrane vesicles (MVs) are produced in all domains of life. In eukaryotes, extracellular vesicles have been shown to mediate the horizontal transfer of biological material between cells [1]. Therefore, bacterial MVs are also thought to mediate horizontal material transfer to host cells and other bacteria, especially in the context of cell stress. In this review, we discuss the mechanisms of bacterial MV production, evidence that their contents can be trafficked to host cells and other bacteria, and the biological relevance of horizontal material transfer by bacterial MVs.},
}
@article {pmid39190025,
year = {2024},
author = {Alav, I and Pordelkhaki, P and Rodriguez-Navarro, J and Neo, O and Kessler, C and Awodipe, RJ and Cliffe, P and Pulavan, N and Marton, HL and Gibbons, S and Buckner, MMC},
title = {Natural products from food sources can alter the spread of antimicrobial resistance plasmids in Enterobacterales.},
journal = {Microbiology (Reading, England)},
volume = {170},
number = {8},
pages = {},
doi = {10.1099/mic.0.001496},
pmid = {39190025},
issn = {1465-2080},
mesh = {*Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; *Klebsiella pneumoniae/drug effects/genetics ; *Escherichia coli/genetics/drug effects ; *beta-Lactamases/genetics/metabolism ; *Biological Products/pharmacology ; Drug Resistance, Bacterial/genetics ; Conjugation, Genetic ; Bacterial Proteins/genetics/metabolism ; Enterobacteriaceae/drug effects/genetics ; Microbial Sensitivity Tests ; Food Microbiology ; Gene Transfer, Horizontal ; },
abstract = {Antimicrobial resistance (AMR) poses a significant threat to global public health. Notably, resistance to carbapenem and extended-spectrum β-lactam antibiotics in Gram-negative bacteria is a major impediment to treating infections. Genes responsible for antibiotic resistance are frequently carried on plasmids, which can transfer between bacteria. Therefore, exploring strategies to prevent this transfer and the prevalence of AMR plasmids is timely and pertinent. Here, we show that certain natural product extracts and associated pure compounds can reduce the conjugation of AMR plasmids into new bacterial hosts. Using our established high-throughput fluorescence-based flow cytometry assay, we found that the natural products were more active in reducing transmission of the IncK extended-spectrum β-lactamase-encoding plasmid pCT in Escherichia coli EC958c, compared to Klebsiella pneumoniae Ecl8 carrying the IncFII carbapenemase-encoding plasmid pKpQIL. The exception was the natural product rottlerin, also active in K. pneumoniae. In classical conjugation assays, rottlerin also reduced the conjugation frequency of the IncFII bla NDM-1 carrying plasmid pCPE16_3 from a clinical K. pneumoniae isolate. Our data indicate that the natural products tested here, in their current molecular structure, reduced conjugation by a small amount, which is unlikely to achieve a large-scale reduction in AMR in bacterial populations. However, certain natural products like rottlerin could provide a foundation for further research into compounds with effective anti-plasmid activity.},
}
@article {pmid39189989,
year = {2024},
author = {Brewer, TE and Wagner, A},
title = {Horizontal gene transfer of a key translation factor and its role in polyproline proteome evolution.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msae180},
pmid = {39189989},
issn = {1537-1719},
abstract = {Prolines cause ribosomes to stall during translation due to their rigid structure. This phenomenon occurs in all domains of life and is exacerbated at polyproline motifs. Such stalling can be eased by the elongation factor P (EF-P) in bacteria. We discovered a potential connection between the loss of ancestral EF-P, the appearance of horizontally transferred EF-P variants, and genomic signs of EF-P dysfunction. Horizontal transfer of the efp gene has occurred several times among bacteria and is associated with the loss of highly conserved polyproline motifs. In this study, we pinpoint cases of horizontal EF-P transfer among a diverse set of bacteria and examine genomic features associated with these events in the phyla Thermotogota and Planctomycetes. In these phyla, horizontal EF-P transfer is also associated with the loss of entire polyproline motif containing proteins, whose expression is likely dependent on EF-P. In particular, three proteases (Lon, ClpC, and FtsH) and three tRNA synthetases (ValS, IleS1, IleS2) appear highly sensitive to EF-P transfer. The conserved polyproline motifs within these proteins all reside within close proximity to ATP-binding-regions, some of which are crucial for their function. Our work shows that an ancient EF-P dysfunction has left genomic traces that persist to this day, although it remains unclear whether this dysfunction was strictly due to loss of ancestral EF-P or was related to the appearance of an exogenous variant. The latter possibility would imply that the process of 'domesticating' a horizontally transferred efp gene can perturb the overall function of EF-P.},
}
@article {pmid39189956,
year = {2024},
author = {Zheng, X and Huang, L},
title = {Diverse non-canonical electron bifurcating [FeFe]-hydrogenases of separate evolutionary origins in Hydrogenedentota.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0099924},
doi = {10.1128/msystems.00999-24},
pmid = {39189956},
issn = {2379-5077},
abstract = {UNLABELLED: Hydrogenedentota, a globally distributed bacterial phylum-level lineage, is poorly understood. Here, we established a comprehensive genomic catalog of Hydrogenedentota, including a total of seven clades (or families) with 179 genomes, and explored the metabolic potential and evolutionary history of these organisms. We show that a single genome, especially those belonging to Clade 6, often encodes multiple hydrogenases with genomes in Clade 2, which rarely encode hydrogenases being the exception. Notably, most members of Hydrogenedentota contain a group A3 [FeFe]-hydrogenase (BfuABC) with a non-canonical electron bifurcation mechanism, in addition to substrate-level phosphorylation and electron transport-linked phosphorylation pathways, in energy conservation. Furthermore, we show that BfuABC from Hydrogenedentota fall into five sub-types. Phylogenetic analysis reveals five independent routes for the evolution of BfuABC homologs in Hydrogenedentota. We speculate that the five sub-types of BfuABC might be acquired from Bacillota (synonym Firmicutes) through separate horizontal gene transfer events. These data shed light on the diversity and evolution of bifurcating [FeFe]-hydrogenases and provide insight into the strategy of Hydrogenedentota to adapt to survival in various habitats.<br><br>IMPORTANCE: The phylum Hydrogenedentota is widely distributed in various environments. However, their physiology, ecology, and evolutionary history remain unknown, primarily due to the limited availability of the genomes and the lack of cultured representatives of the phylum. Our results have increased the knowledge of the genetic and metabolic diversity of these organisms and shed light on their diverse energy conservation strategies, especially those involving electron bifurcation with a non-canonical mechanism, which are likely responsible for their wide distribution. Besides, the organization and phylogenetic relationships of gene clusters coding for BfuABC in Hydrogenedentota provide valuable clues to the evolutionary history of group A3 electron bifurcating [FeFe]-hydrogenases.},
}
@article {pmid39189770,
year = {2024},
author = {Kopejtka, K and Tomasch, J and Shivaramu, S and Saini, MK and Kaftan, D and Koblížek, M},
title = {Minimal transcriptional regulation of horizontally transferred photosynthesis genes in phototrophic bacterium Gemmatimonas phototrophica.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0070624},
doi = {10.1128/msystems.00706-24},
pmid = {39189770},
issn = {2379-5077},
abstract = {UNLABELLED: The first phototrophic member of the bacterial phylum Gemmatimonadota, Gemmatimonas phototrophica AP64[T], received all its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Here, we investigated how these acquired genes, which are tightly controlled by oxygen and light in the ancestor, are integrated into the regulatory system of its new host. G. phototrophica grew well under aerobic and semiaerobic conditions, with almost no difference in gene expression. Under aerobic conditions, the growth of G. phototrophica was optimal at 80 µmol photon m[-2] s[-1], while higher light intensities had an inhibitory effect. The transcriptome showed only a minimal response to the dark-light shift at optimal light intensity, while the exposure to a higher light intensity (200 µmol photon m[-2] s[-1]) induced already stronger but still transient changes in gene expression. Interestingly, a singlet oxygen defense was not activated under any conditions tested. Our results indicate that G. phototrophica possesses neither the oxygen-dependent repression of photosynthesis genes known from purple bacteria nor the light-dependent repression described in aerobic anoxygenic phototrophs. Instead, G. phototrophica has evolved as a low-light species preferring reduced oxygen concentrations. Under these conditions, the bacterium can safely employ its photoheterotrophic metabolism without the need for complex regulatory mechanisms.<br><br>IMPORTANCE: Horizontal gene transfer is one of the main mechanisms by which bacteria acquire new genes. However, it represents only the first step as the transferred genes have also to be functionally and regulatory integrated into the recipient's cellular machinery. Gemmatimonas phototrophica, a member of bacterial phylum Gemmatimonadota, acquired its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Thus, it represents a unique natural experiment, in which the entire package of photosynthesis genes was transplanted into a distant host. We show that G. phototrophica lacks the regulation of photosynthesis gene expressions in response to oxygen concentration and light intensity that are common in purple bacteria. This restricts its growth to low-light habitats with reduced oxygen. Understanding the regulation of horizontally transferred genes is important not only for microbial evolution but also for synthetic biology and the engineering of novel organisms, as these rely on the successful integration of foreign genes.},
}
@article {pmid39189747,
year = {2024},
author = {Duchin Rapp, Y and Lipsman, V and Yuda, L and Kublanov, IV and Matsliyah, D and Segev, E},
title = {Algal exudates promote conjugation in marine Roseobacters.},
journal = {mBio},
volume = {},
number = {},
pages = {e0106224},
doi = {10.1128/mbio.01062-24},
pmid = {39189747},
issn = {2150-7511},
abstract = {UNLABELLED: Horizontal gene transfer (HGT) is a pivotal mechanism driving bacterial evolution, conferring adaptability within dynamic marine ecosystems. Among HGT mechanisms, conjugation mediated by type IV secretion systems (T4SSs) plays a central role in the ecological success of marine bacteria. However, the conditions promoting conjugation events in the marine environment are not well-understood. Roseobacters, abundant marine bacteria commonly associated with algae, possess a multitude of T4SSs. Many Roseobacters are heterotrophic bacteria that rely on algal secreted compounds to support their growth. These compounds attract bacteria, facilitating colonization and attachment to algal cells. Algae and their metabolites bring bacteria into close proximity, potentially promoting bacterial HGT. Investigation across various Roseobacters revealed that algal exudates indeed enhance plasmid transfer through conjugation. While algal exudates do not influence the transcription of bacterial conjugative machinery genes, they promote bacterial attachment, potentially stabilizing proximity and facilitating HGT. Notably, under conditions where attachment is less advantageous, the impact of algal exudates on conjugation is reduced. These findings suggest that algae enhance bacterial conjugation primarily by fostering attachment and highlight the importance of studying bacterial HGT within the context of algal-bacterial interactions.<br><br>IMPORTANCE: This study explores how algal-bacterial interactions influence horizontal gene transfer (HGT) among marine bacteria. HGT, a key driver of bacterial evolution, is facilitated by conjugation mediated by type IV secretion systems (T4SSs). Through investigating Roseobacters, abundant marine bacteria often found to be associated with algae, the study reveals that algal exudates enhance plasmid transfer via conjugation. This enhancement is attributed to the promotion of bacterial attachment by algal compounds, emphasizing the role of algal-bacterial interactions in shaping genetic exchange within dynamic marine ecosystems. Understanding these mechanisms is crucial for elucidating bacterial adaptability and evolution in the marine environment.},
}
@article {pmid39187833,
year = {2024},
author = {Yutin, N and Tolstoy, I and Mutz, P and Wolf, YI and Krupovic, M and Koonin, EV},
title = {DNA polymerase swapping in Caudoviricetes bacteriophages.},
journal = {Virology journal},
volume = {21},
number = {1},
pages = {200},
pmid = {39187833},
issn = {1743-422X},
mesh = {*DNA-Directed DNA Polymerase/genetics ; *Phylogeny ; *Viral Proteins/genetics/metabolism ; Evolution, Molecular ; Genome, Viral ; Caudovirales/genetics/classification ; DNA, Viral/genetics ; Bacteriophages/genetics/enzymology/classification ; DNA Replication ; },
abstract = {BACKGROUND: Viruses with double-stranded (ds) DNA genomes in the realm Duplodnaviria share a conserved structural gene module but show a broad range of variation in their repertoires of DNA replication proteins. Some of the duplodnaviruses encode (nearly) complete replication systems whereas others lack (almost) all genes required for replication, relying on the host replication machinery. DNA polymerases (DNAPs) comprise the centerpiece of the DNA replication apparatus. The replicative DNAPs are classified into 4 unrelated or distantly related families (A-D), with the protein structures and sequences within each family being, generally, highly conserved. More than half of the duplodnaviruses encode a DNAP of family A, B or C. We showed previously that multiple pairs of closely related viruses in the order Crassvirales encode DNAPs of different families.<br><br>METHODS: Groups of phages in which DNAP swapping likely occurred were identified as subtrees of a defined depth in a comprehensive evolutionary tree of tailed bacteriophages that included phages with DNAPs of different families. The DNAP swaps were validated by constrained tree analysis that was performed on phylogenetic tree of large terminase subunits, and the phage genomes encoding swapped DNAPs were aligned using Mauve. The structures of the discovered unusual DNAPs were predicted using AlphaFold2.<br><br>RESULTS: We identified four additional groups of tailed phages in the class Caudoviricetes in which the DNAPs apparently were swapped on multiple occasions, with replacements occurring both between families A and B, or A and C, or between distinct subfamilies within the same family. The DNAP swapping always occurs "in situ", without changes in the organization of the surrounding genes. In several cases, the DNAP gene is the only region of substantial divergence between closely related phage genomes, whereas in others, the swap apparently involved neighboring genes encoding other proteins involved in phage genome replication. In addition, we identified two previously undetected, highly divergent groups of family A DNAPs that are encoded in some phage genomes along with the main DNAP implicated in genome replication.<br><br>CONCLUSIONS: Replacement of the DNAP gene by one encoding a DNAP of a different family occurred on many independent occasions during the evolution of different families of tailed phages, in some cases, resulting in very closely related phages encoding unrelated DNAPs. DNAP swapping was likely driven by selection for avoidance of host antiphage mechanisms targeting the phage DNAP that remain to be identified, and/or by selection against replicon incompatibility.},
}
@article {pmid39186748,
year = {2024},
author = {Pradel, N and Bartoli, M and Koenen, M and Bale, N and Neumann-Schaal, M and Spröer, C and Bunk, B and Rohde, M and Pester, M and Spring, S},
title = {Description and genome analysis of a novel archaeon isolated from a syntrophic pyrite-forming enrichment culture and reclassification of Methanospirillum hungatei strains GP1 and SK as Methanospirillum purgamenti sp. nov.},
journal = {PloS one},
volume = {19},
number = {8},
pages = {e0308405},
pmid = {39186748},
issn = {1932-6203},
mesh = {*Methanospirillum/genetics/metabolism ; *Phylogeny ; *Genome, Archaeal ; Sulfides/metabolism ; Iron/metabolism ; RNA, Ribosomal, 16S/genetics ; Methane/metabolism ; },
abstract = {The archaeal isolate J.3.6.1-F.2.7.3T was obtained from an anaerobic enrichment culture, where it may play an important role in methane production during pyrite formation. The new isolate formed a species-level clade with Methanospirillum hungatei strains GP1 and SK, which is separate from the type strain JF-1T. Cultivation-independent surveys indicate the occurrence of this phylogenetic group in sediments and anaerobic digesters. The abundance of this clade appears to be negatively affected by high nitrogen loads, indicating a sensitivity to certain nitrogen compounds that is not known in M. hungatei JF-1T. The relatively large core genome of this Methanospirillum clade is indicative of niche specialization and efficient control of horizontal gene transfer. Genes for nitrogenase and F420-dependent secondary alcohol dehydrogenase contribute to the metabolic versatility of this lineage. Characteristics of the new isolate such as the ability to utilize 2-propanol as an electron donor or the requirement for acetate as a carbon source are found also in the strains GP1 and SK, but not in the type strain M. hungatei JF-1T. Based on the genomic differences to related species, a new species within the genus Methanospirillum is proposed with the name M. purgamenti sp. nov. The determined phenotypic characteristics support this proposal and indicate a metabolic adaptation to a separate ecological niche.},
}
@article {pmid39184916,
year = {2024},
author = {Han, H and He, T and Wu, Y and He, T and Zhou, W},
title = {Multidimensional analysis of tumor stem cells: from biological properties, metabolic adaptations to immune escape mechanisms.},
journal = {Frontiers in cell and developmental biology},
volume = {12},
number = {},
pages = {1441081},
pmid = {39184916},
issn = {2296-634X},
abstract = {As a key factor in tumorigenesis, progression, recurrence and metastasis, the biological properties, metabolic adaptations and immune escape mechanisms of CSCs are the focus of current oncological research. CSCs possess self-renewal, multidirectional differentiation and tumorigenicity, and their mechanisms of action can be elucidated by the clonal evolution, hierarchical model and the dynamic CSCs model, of which the dynamic model is widely recognized due to its better explanation of the function and origin of CSCs. The origin hypothesis of CSCs involves cell-cell fusion, horizontal gene transfer, genomic instability and microenvironmental regulation, which together shape the diversity of CSCs. In terms of classification, CSCs include primary CSCs (pri-CSCs), precancerous stem cells (pre-CSCs), migratory CSCs (mig-CSCs), and chemo-radiotherapy-resistant CSCs (cr-CSCs and rr-CSCs), with each type playing a specific role in tumor progression. Surface markers of CSCs, such as CD24, CD34, CD44, CD90, CD133, CD166, EpCAM, and LGR5, offer the possibility of identifying, isolating, and targeting CSCs, but the instability and heterogeneity of their expression increase the difficulty of treatment. CSCs have adapted to their survival needs through metabolic reprogramming, showing the ability to flexibly switch between glycolysis and oxidative phosphorylation (OXPHOS), as well as adjustments to amino acid and lipid metabolism. The Warburg effect typifies their metabolic profiles, and altered glutamine and fatty acid metabolism further contributes to the rapid proliferation and survival of CSCs. CSCs are able to maintain their stemness by regulating the metabolic networks to maintain their stemness characteristics, enhance antioxidant defences, and adapt to therapeutic stress. Immune escape is another strategy for CSCs to maintain their survival, and CSCs can effectively evade immune surveillance through mechanisms such as up-regulating PD-L1 expression and promoting the formation of an immunosuppressive microenvironment. Together, these properties reveal the multidimensional complexity of CSCs, underscoring the importance of a deeper understanding of the biology of CSCs for the development of more effective tumor therapeutic strategies. In the future, therapies targeting CSCs will focus on precise identification of surface markers, intervention of metabolic pathways, and overcoming immune escape, with the aim of improving the relevance and efficacy of cancer treatments, and ultimately improving patient prognosis.},
}
@article {pmid39184814,
year = {2024},
author = {Chen, N and Li, Y and Liang, X and Qin, K and Zhang, Y and Wang, J and Wu, Q and Gupta, TB and Ding, Y},
title = {Bacterial extracellular vesicle: A non-negligible component in biofilm life cycle and challenges in biofilm treatments.},
journal = {Biofilm},
volume = {8},
number = {},
pages = {100216},
pmid = {39184814},
issn = {2590-2075},
abstract = {Bacterial biofilms, especially those formed by pathogens, have been increasingly impacting human health. Bacterial extracellular vesicle (bEV), a kind of spherical membranous structure released by bacteria, has not only been reported to be a component of the biofilm matrix but also plays a non-negligible role in the biofilm life cycle. Nevertheless, a comprehensive overview of the bEVs functions in biofilms remains elusive. In this review, we summarize the biogenesis and distinctive features characterizing bEVs, and consolidate the current literature on their functions and proposed mechanisms in the biofilm life cycle. Furthermore, we emphasize the formidable challenges associated with vesicle interference in biofilm treatments. The primary objective of this review is to raise awareness regarding the functions of bEVs in the biofilm life cycle and lay the groundwork for the development of novel therapeutic strategies to control or even eliminate bacterial biofilms.},
}
@article {pmid39182428,
year = {2024},
author = {Ando, S and Tanaka, R and Ito, H},
title = {Activity examination of plant Mg-dechelatase and its bacterial homolog in plants and in vitro.},
journal = {Plant physiology and biochemistry : PPB},
volume = {215},
number = {},
pages = {109073},
doi = {10.1016/j.plaphy.2024.109073},
pmid = {39182428},
issn = {1873-2690},
abstract = {Chlorophyll a serves as a photosynthetic pigment in plants. Its degradation is initiated by the extraction of the central Mg by the Mg-dechelatase enzyme, which is encoded by Stay-Green (SGR). Plant SGR is believed to be derived from bacterial SGR homolog obtained through horizontal gene transfer into photosynthetic eukaryotes. However, it is not known how the bacterial SGR homolog was modified to function in plants. To assess its adaptation mechanism in plants, a bacterial SGR homolog derived from the Anaerolineae bacterium SM23_63 was introduced into plants. It was found that the bacterial SGR homolog metabolized chlorophyll in plants. However, its chlorophyll catabolic activity was lower than that of plant SGR. Recombinant proteins of the bacterial SGR homolog exhibited higher activity than those of the plant SGR. The reduced chlorophyll catabolic activity of bacterial SGR homologs in plants may be associated with low hydrophobicity of the entrance to the catalytic site compared to that of plant SGR. This hinders the enzyme access to chlorophyll, which is localized in hydrophobic environments. This study offers insights into the molecular changes underlying the optimization of enzyme function.},
}
@article {pmid39107250,
year = {2024},
author = {Barragan, AC and Latorre, SM and Malmgren, A and Harant, A and Win, J and Sugihara, Y and Burbano, HA and Kamoun, S and Langner, T},
title = {Multiple Horizontal Mini-chromosome Transfers Drive Genome Evolution of Clonal Blast Fungus Lineages.},
journal = {Molecular biology and evolution},
volume = {41},
number = {8},
pages = {},
pmid = {39107250},
issn = {1537-1719},
support = {//Gatsby Charitable Foundation/ ; UKRI-BBSRC//UK Research and Innovation Biotechnology and Biological Sciences Research Council/ ; /ERC_/European Research Council/International ; 743165//BLASTOFF/ ; 101077853//PANDEMIC/ ; RSWF\R1\191011//Royal Society/ ; },
mesh = {*Gene Transfer, Horizontal ; *Evolution, Molecular ; Chromosomes, Fungal/genetics ; Ascomycota/genetics ; Plant Diseases/microbiology ; Genome, Fungal ; },
abstract = {Crop disease pandemics are often driven by asexually reproducing clonal lineages of plant pathogens that reproduce asexually. How these clonal pathogens continuously adapt to their hosts despite harboring limited genetic variation, and in absence of sexual recombination remains elusive. Here, we reveal multiple instances of horizontal chromosome transfer within pandemic clonal lineages of the blast fungus Magnaporthe (Syn. Pyricularia) oryzae. We identified a horizontally transferred 1.2Mb accessory mini-chromosome which is remarkably conserved between M. oryzae isolates from both the rice blast fungus lineage and the lineage infecting Indian goosegrass (Eleusine indica), a wild grass that often grows in the proximity of cultivated cereal crops. Furthermore, we show that this mini-chromosome was horizontally acquired by clonal rice blast isolates through at least nine distinct transfer events over the past three centuries. These findings establish horizontal mini-chromosome transfer as a mechanism facilitating genetic exchange among different host-associated blast fungus lineages. We propose that blast fungus populations infecting wild grasses act as genetic reservoirs that drive genome evolution of pandemic clonal lineages that afflict cereal crops.},
}
@article {pmid39089095,
year = {2024},
author = {Zhuang, M and Yan, W and Xiong, Y and Wu, Z and Cao, Y and Sanganyado, E and Siame, BA and Chen, L and Kashi, Y and Leung, KY},
title = {Horizontal plasmid transfer promotes antibiotic resistance in selected bacteria in Chinese frog farms.},
journal = {Environment international},
volume = {190},
number = {},
pages = {108905},
doi = {10.1016/j.envint.2024.108905},
pmid = {39089095},
issn = {1873-6750},
mesh = {Animals ; *Plasmids/genetics ; China ; *Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Farms ; Drug Resistance, Bacterial/genetics ; Rana catesbeiana/microbiology/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/genetics ; },
abstract = {The emergence and dissemination of antibiotic resistance genes (ARGs) in the ecosystem are global public health concerns. One Health emphasizes the interconnectivity between different habitats and seeks to optimize animal, human, and environmental health. However, information on the dissemination of antibiotic resistance genes (ARGs) within complex microbiomes in natural habitats is scarce. We investigated the prevalence of antibiotic resistant bacteria (ARB) and the spread of ARGs in intensive bullfrog (Rana catesbeiana) farms in the Shantou area of China. Antibiotic susceptibilities of 361 strains, combined with microbiome analyses, revealed Escherichia coli, Edwardsiella tarda, Citrobacter and Klebsiella sp. as prevalent multidrug resistant bacteria on these farms. Whole genome sequencing of 95 ARB identified 250 large plasmids that harbored a wide range of ARGs. Plasmid sequences and sediment metagenomes revealed an abundance of tetA, sul1, and aph(3″)-Ib ARGs. Notably, antibiotic resistance (against 15 antibiotics) highly correlated with plasmid-borne rather than chromosome-borne ARGs. Based on sequence similarities, most plasmids (62%) fell into 32 distinct groups, indicating a potential for horizontal plasmid transfer (HPT) within the frog farm microbiome. HPT was confirmed in inter- and intra-species conjugation experiments. Furthermore, identical mobile ARGs, flanked by mobile genetic elements (MGEs), were found in different locations on the same plasmid, or on different plasmids residing in the same or different hosts. Our results suggest a synergy between MGEs and HPT to facilitate ARGs dissemination in frog farms. Mining public databases retrieved similar plasmids from different bacterial species found in other environmental niches globally. Our findings underscore the importance of HPT in mediating the spread of ARGs in frog farms and other microbiomes of the ecosystem.},
}
@article {pmid39180708,
year = {2024},
author = {Witt, ASA and Carvalho, JVRP and Serafim, MSM and Arias, NEC and Rodrigues, RAL and Abrahão, JS},
title = {The GC% landscape of the Nucleocytoviricota.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {39180708},
issn = {1678-4405},
support = {88882.348380/2010-1//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 405249/2022-5//Ministry of Science and Technology/ ; 406441/2022-7//Ministry of Science and Technology/ ; },
abstract = {Genomic studies on sequence composition employ various approaches, such as calculating the proportion of guanine and cytosine within a given sequence (GC% content), which can shed light on various aspects of the organism's biology. In this context, GC% can provide insights into virus-host relationships and evolution. Here, we present a comprehensive gene-by-gene analysis of 61 representatives belonging to the phylum Nucleocytoviricota, which comprises viruses with the largest genomes known in the virosphere. Parameters were evaluated not only based on the average GC% of a given viral species compared to the entire phylum but also considering gene position and phylogenetic history. Our results reveal that while some families exhibit similar GC% among their representatives (e.g., Marseilleviridae), others such as Poxviridae, Phycodnaviridae, and Mimiviridae have members with discrepant GC% values, likely reflecting adaptation to specific biological cycles and hosts. Interestingly, certain genes located at terminal regions or within specific genomic clusters show GC% values distinct from the average, suggesting recent acquisition or unique evolutionary pressures. Horizontal gene transfer and the presence of potential paralogs were also assessed in genes with the most discrepant GC% values, indicating multiple evolutionary histories. Taken together, to the best of our knowledge, this study represents the first global and gene-by-gene analysis of GC% distribution and profiles within genomes of Nucleocytoviricota members, highlighting their diversity and identifying potential new targets for future studies.},
}
@article {pmid39179660,
year = {2024},
author = {Wang, S and Sun, S and Wang, Q and Chen, H and Guo, Y and Cai, M and Yin, Y and Ma, S and Wang, H},
title = {PathoTracker: an online analytical metagenomic platform for Klebsiella pneumoniae feature identification and outbreak alerting.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1038},
pmid = {39179660},
issn = {2399-3642},
support = {32141001//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81991533//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Klebsiella pneumoniae/genetics/isolation &amp; purification ; *Metagenomics/methods ; Humans ; *Disease Outbreaks ; *Klebsiella Infections/microbiology/epidemiology/diagnosis ; *Phylogeny ; China/epidemiology ; Nanopore Sequencing/methods ; Databases, Genetic ; Genome, Bacterial ; },
abstract = {Clinical metagenomics (CMg) Nanopore sequencing can facilitate infectious disease diagnosis. In China, sub-lineages ST11-KL64 and ST11-KL47 Carbapenem-resistant Klebsiella pneumoniae (CRKP) are widely prevalent. We propose PathoTracker, a specially compiled database and arranged method for strain feature identification in CMg samples and CRKP traceability. A database targeting high-prevalence horizontal gene transfer in CRKP strains and a ST11-only database for distinguishing two sub-lineages in China were created. To make the database user-friendly, facilitate immediate downstream strain feature identification from raw Nanopore metagenomic data, and avoid the need for phylogenetic analysis from scratch, we developed data analysis methods. The methods included pre-performed phylogenetic analysis, gene-isolate-cluster index and multilevel pan-genome database and reduced storage space by 10-fold and random-access memory by 52-fold compared with normal methods. PathoTracker can provide accurate and fast strain-level analysis for CMg data after 1 h Nanopore sequencing, allowing early warning of outbreaks. A user-friendly page (http://PathoTracker.pku.edu.cn/) was developed to facilitate online analysis, including strain-level feature, species identifications and phylogenetic analyses. PathoTracker proposed in this study will aid in the downstream analysis of CMg.},
}
@article {pmid39176446,
year = {2024},
author = {Ahmed, M and Kayal, E and Lavrov, DV},
title = {Mitochondrial DNA of the demosponge Acanthella acuta: Linear Architecture and Other Unique Features.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae168},
pmid = {39176446},
issn = {1759-6653},
abstract = {While Acanthella acuta (Schmidt 1862), a common demosponge found in the Mediterranean Sea and Atlantic Ocean, is-morphologically-little distinguishable from other sponges, its mitochondrial DNA (mtDNA) is unique within the class. In contrast to all other studied demosponges, mtDNA of A. acuta is inferred to be linear and displays several unusual features: inverted terminal repeats, group II introns in three mt-genes, and two unique ORFs. One of the ORFs (ORF1535) combines a DNA-polymerase domain with a DNA-directed RNA-polymerase domain, while the second bears no discernible similarity to any reported sequences. The group II intron within the cox2 gene is the first such intron reported in an animal. Our phylogenetic analyses indicate that the cox1 intron is related to similar introns found in other demosponges, while the cox2 intron is likely not of animal origin. The two domains found within ORF1535 do not share a common origin and, along with the cox2 intron, were likely acquired by horizontal transfer. The findings of this paper open new avenues of exploration in the understanding of mtDNA linearization within Metazoa.},
}
@article {pmid39174812,
year = {2024},
author = {Döcker, J and Linz, S and Wicke, K},
title = {Bounding the Softwired Parsimony Score of a Phylogenetic Network.},
journal = {Bulletin of mathematical biology},
volume = {86},
number = {10},
pages = {121},
pmid = {39174812},
issn = {1522-9602},
support = {XXXX//Marsden Fund/ ; },
mesh = {*Phylogeny ; *Models, Genetic ; *Mathematical Concepts ; Algorithms ; Evolution, Molecular ; Sequence Alignment/statistics &amp; numerical data ; },
abstract = {In comparison to phylogenetic trees, phylogenetic networks are more suitable to represent complex evolutionary histories of species whose past includes reticulation such as hybridisation or lateral gene transfer. However, the reconstruction of phylogenetic networks remains challenging and computationally expensive due to their intricate structural properties. For example, the small parsimony problem that is solvable in polynomial time for phylogenetic trees, becomes NP-hard on phylogenetic networks under softwired and parental parsimony, even for a single binary character and structurally constrained networks. To calculate the parsimony score of a phylogenetic network N, these two parsimony notions consider different exponential-size sets of phylogenetic trees that can be extracted from N and infer the minimum parsimony score over all trees in the set. In this paper, we ask: What is the maximum difference between the parsimony score of any phylogenetic tree that is contained in the set of considered trees and a phylogenetic tree whose parsimony score equates to the parsimony score of N? Given a gap-free sequence alignment of multi-state characters and a rooted binary level-k phylogenetic network, we use the novel concept of an informative blob to show that this difference is bounded by k + 1 times the softwired parsimony score of N. In particular, the difference is independent of the alignment length and the number of character states. We show that an analogous bound can be obtained for the softwired parsimony score of semi-directed networks, while under parental parsimony on the other hand, such a bound does not hold.},
}
@article {pmid39173632,
year = {2024},
author = {Yang, XY and Shen, Z and Wang, C and Nakanishi, K and Fu, TM},
title = {DdmDE eliminates plasmid invasion by DNA-guided DNA targeting.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.07.028},
pmid = {39173632},
issn = {1097-4172},
abstract = {Horizontal gene transfer is a key driver of bacterial evolution, but it also presents severe risks to bacteria by introducing invasive mobile genetic elements. To counter these threats, bacteria have developed various defense systems, including prokaryotic Argonautes (pAgos) and the DNA defense module DdmDE system. Through biochemical analysis, structural determination, and in vivo plasmid clearance assays, we elucidate the assembly and activation mechanisms of DdmDE, which eliminates small, multicopy plasmids. We demonstrate that DdmE, a pAgo-like protein, acts as a catalytically inactive, DNA-guided, DNA-targeting defense module. In the presence of guide DNA, DdmE targets plasmids and recruits a dimeric DdmD, which contains nuclease and helicase domains. Upon binding to DNA substrates, DdmD transitions from an autoinhibited dimer to an active monomer, which then translocates along and cleaves the plasmids. Together, our findings reveal the intricate mechanisms underlying DdmDE-mediated plasmid clearance, offering fundamental insights into bacterial defense systems against plasmid invasions.},
}
@article {pmid39173362,
year = {2024},
author = {Zhang, Y and Zuo, S and Zheng, Q and Yu, G and Wang, Y},
title = {Removal of antibiotic resistant bacteria and antibiotic resistance genes by an electrochemically driven UV/chlorine process for decentralized water treatment.},
journal = {Water research},
volume = {265},
number = {},
pages = {122298},
doi = {10.1016/j.watres.2024.122298},
pmid = {39173362},
issn = {1879-2448},
abstract = {The UV/chlorine (UV/Cl2) process is a developing advanced oxidation process and can efficiently remove antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). However, the transportation and storage of chlorine solutions limit the application of the UV/Cl2 process, especially for decentralized water treatment. To overcome the limitation, an electrochemically driven UV/Cl2 process (E-UV/Cl2) where Cl2 can be electrochemically produced in situ from anodic oxidation of chloride (Cl[-]) ubiquitously present in various water matrices was evaluated in this study. >5-log inactivation of the ARB (E. coli) was achieved within 5 s of the E-UV/Cl2 process, and no photoreactivation of the ARB was observed after the treatment. In addition to the ARB, intracellular and extracellular ARGs (tetA, sul1, sul2, and ermB) could be effectively degraded (e.g., log(C0/C) > 4 for i-ARGs) within 5 min of the E-UV/Cl2 process. Atomic force microscopy showed that the most of the i-ARGs were interrupted into short fragments (< 30 nm) during the E-UV/Cl2 process, which can thus effectively prevent the self-repair of i-ARGs and the horizontal gene transfer. Modelling results showed that the abatement efficiencies of i-ARG correlated positively with the exposures of •OH, Cl2[-]•, and ClO• during the E-UV/Cl2 process. Due to the short treatment time (5 min) required for ARB and ARG removal, insignificant concentrations of trihalomethanes (THMs) were generated during of the E-UV/Cl2 process, and the energy consumption (EEO) of ARG removal was ∼0.20‒0.27 kWh/m[3]-log, which is generally comparable to that of the UV/Cl2 process (0.18-0.23 kWh/m[3]-log). These results demonstrate that the E-UV/Cl2 process can provide a feasible and attractive alternative to the UV/Cl2 process for ARB and ARG removal in decentralized water treatment system.},
}
@article {pmid39172952,
year = {2024},
author = {Zhou, W and Karan, KR and Gu, W and Klein, HU and Sturm, G and De Jager, PL and Bennett, DA and Hirano, M and Picard, M and Mills, RE},
title = {Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts.},
journal = {PLoS biology},
volume = {22},
number = {8},
pages = {e3002723},
doi = {10.1371/journal.pbio.3002723},
pmid = {39172952},
issn = {1545-7885},
mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Fibroblasts/metabolism ; *Brain/metabolism ; Male ; Female ; Cell Nucleus/metabolism ; Middle Aged ; Adult ; Aged ; Longevity/genetics ; Aging/physiology/genetics ; },
abstract = {The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in nonhuman species and recently demonstrated to occur in rare instances from one human generation to the next. Here, we investigated numtogenesis dynamics in humans in 2 ways. First, we quantified Numts in 1,187 postmortem brain and blood samples from different individuals. Compared to circulating immune cells (n = 389), postmitotic brain tissue (n = 798) contained more Numts, consistent with their potential somatic accumulation. Within brain samples, we observed a 5.5-fold enrichment of somatic Numt insertions in the dorsolateral prefrontal cortex (DLPFC) compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, an increase in the number of brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment (NCI) who died at younger ages carried approximately 2 more Numts per decade of life lost than those who lived longer. Second, we tested the dynamic transfer of Numts using a repeated-measures whole-genome sequencing design in a human fibroblast model that recapitulates several molecular hallmarks of aging. These longitudinal experiments revealed a gradual accumulation of 1 Numt every ~13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven by cell clonality. Targeted pharmacological perturbations including chronic glucocorticoid signaling or impairing mitochondrial oxidative phosphorylation (OxPhos) only modestly increased the rate of numtogenesis, whereas patient-derived SURF1-mutant cells exhibiting mtDNA instability accumulated Numts 4.7-fold faster than healthy donors. Combined, our data document spontaneous numtogenesis in human cells and demonstrate an association between brain cortical somatic Numts and human lifespan. These findings open the possibility that mito-nuclear horizontal gene transfer among human postmitotic tissues produces functionally relevant human Numts over timescales shorter than previously assumed.},
}
@article {pmid39172793,
year = {2024},
author = {Chen, X and Wang, M and Luo, L and Liu, X and An, L and Nie, Y and Wu, XL},
title = {The evolution of autonomy from two cooperative specialists in fluctuating environments.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {35},
pages = {e2317182121},
doi = {10.1073/pnas.2317182121},
pmid = {39172793},
issn = {1091-6490},
support = {2018YFA0902100//MOST | National Key Research and Development Program of China (NKPs)/ ; 91951204//Data Center of Management Science, National Natural Science Foundation of China - Peking University (DCMS, NSFC-PKU)/ ; },
mesh = {*Naphthalenes/metabolism ; Gene Transfer, Horizontal ; Biological Evolution ; Symbiosis ; Microbial Consortia/genetics/physiology ; Genotype ; },
abstract = {From microbes to humans, organisms perform numerous tasks for their survival, including food acquisition, migration, and reproduction. A complex biological task can be performed by either an autonomous organism or by cooperation among several specialized organisms. However, it remains unclear how autonomy and cooperation evolutionarily switch. Specifically, it remains unclear whether and how cooperative specialists can repair deleted genes through direct genetic exchange, thereby regaining metabolic autonomy. Here, we address this question by experimentally evolving a mutualistic microbial consortium composed of two specialists that cooperatively degrade naphthalene. We observed that autonomous genotypes capable of performing the entire naphthalene degradation pathway evolved from two cooperative specialists and dominated the community. This evolutionary transition was driven by the horizontal gene transfer (HGT) between the two specialists. However, this evolution was exclusively observed in the fluctuating environment alternately supplied with naphthalene and pyruvate, where mutualism and competition between the two specialists alternated. The naphthalene-supplied environment exerted selective pressure that favors the expansion of autonomous genotypes. The pyruvate-supplied environment promoted the coexistence and cell density of the cooperative specialists, thereby increasing the likelihood of HGT. Using a mathematical model, we quantitatively demonstrate that environmental fluctuations facilitate the evolution of autonomy through HGT when the relative growth rate and carrying capacity of the cooperative specialists allow enhanced coexistence and higher cell density in the competitive environment. Together, our results demonstrate that cooperative specialists can repair deleted genes through a direct genetic exchange under specific conditions, thereby regaining metabolic autonomy.},
}
@article {pmid39106433,
year = {2024},
author = {Tan, Y and Aravind, L and Zhang, D},
title = {Genomic Underpinnings of Cytoplasmic Incompatibility: CIF Gene-Neighborhood Diversification Through Extensive Lateral Transfers and Recombination in Wolbachia.},
journal = {Genome biology and evolution},
volume = {16},
number = {8},
pages = {},
doi = {10.1093/gbe/evae171},
pmid = {39106433},
issn = {1759-6653},
support = {//Saint Louis University/ ; //Intramural Research Program of the NIH/ ; /LM/NLM NIH HHS/United States ; },
mesh = {*Wolbachia/genetics ; *Gene Transfer, Horizontal ; *Recombination, Genetic ; Evolution, Molecular ; Phylogeny ; Genome, Bacterial ; Cytoplasm/genetics ; Animals ; Bacterial Proteins/genetics ; },
abstract = {Cytoplasmic incompatibility (CI), a non-Mendelian genetic phenomenon, involves the manipulation of host reproduction by Wolbachia, a maternally transmitted alphaproteobacterium. The underlying mechanism is centered around the CI Factor (CIF) system governed by two genes, cifA and cifB, where cifB induces embryonic lethality, and cifA counteracts it. Recent investigations have unveiled intriguing facets of this system, including diverse cifB variants, prophage association in specific strains, copy number variation, and rapid component divergence, hinting at a complex evolutionary history. We utilized comparative genomics to systematically classify CIF systems, analyze their locus structure and domain architectures, and reconstruct their diversification and evolutionary trajectories. Our new classification identifies ten distinct CIF types, featuring not just versions present in Wolbachia, but also other intracellular bacteria, and eukaryotic hosts. Significantly, our analysis of CIF loci reveals remarkable variability in gene composition and organization, encompassing an array of diverse endonucleases, variable toxin domains, deubiquitinating peptidases (DUBs), prophages, and transposons. We present compelling evidence that the components within the loci have been diversifying their sequences and domain architectures through extensive, independent lateral transfers and interlocus recombination involving gene conversion. The association with diverse transposons and prophages, coupled with selective pressures from host immunity, likely underpins the emergence of CIF loci as recombination hotspots. Our investigation also posits the origin of CifB-REase domains from mobile elements akin to CR (Crinkler-RHS-type) effectors and Tribolium Medea1 factor, which is linked to another non-Mendelian genetic phenomenon. This comprehensive genomic analysis offers novel insights into the molecular evolution and genomic foundations of Wolbachia-mediated host reproductive control.},
}
@article {pmid39168346,
year = {2024},
author = {Li, J and Li, C and Han, Y and Yang, J and Hu, Y and Xu, H and Zhou, Y and Zuo, J and Tang, Y and Lei, C and Li, C and Wang, H},
title = {Bacterial membrane vesicles from swine farm microbial communities harboring and safeguarding diverse functional genes promoting horizontal gene transfer.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {175639},
doi = {10.1016/j.scitotenv.2024.175639},
pmid = {39168346},
issn = {1879-1026},
abstract = {Antibiotic resistance (AMR) poses a significant global health challenge, with swine farms recognized as major reservoirs of antibiotic resistance genes (ARGs). Recently, bacterial membrane vesicles (BMVs) have emerged as novel carriers mediating horizontal gene transfer. However, little is known about the ARGs carried by BMVs in swine farm environments and their transfer potential. This study investigated the distribution, sources, and microbiological origins of BMVs in three key microbial habitats of swine farms (feces, soil, and fecal wastewater), along with the ARGs and mobile genetic elements (MGEs) they harbor. Characterization of BMVs revealed particle sizes ranging from 20 to 500 nm and concentrations from 10[8] to 10[12] particles/g, containing DNA and proteins. Metagenomic sequencing identified BMVs predominantly composed of members of the Proteobacteria phyla, including Pseudomonadaceae, Moraxellaceae, and Enterobacteriaceae, carrying diverse functional genes encompassing resistance to 14 common antibiotics and 74,340 virulence genes. Notably, multidrug resistance, tetracycline, and chloramphenicol resistance genes were particularly abundant. Furthermore, BMVs harbored various MGEs, primarily plasmids, and demonstrated the ability to protect their DNA cargo from degradation and facilitate horizontal gene transfer, including the transmission of resistance genes. In conclusion, this study reveals widespread presence of BMVs carrying ARGs and potential virulence genes in swine farm feces, soil, and fecal wastewater. These findings not only provide new insights into the role of extracellular DNA in the environment but also highlight concerns regarding the gene transfer potential mediated by BMVs and associated health risks.},
}
@article {pmid39167960,
year = {2024},
author = {Nasu, T and Maeda, S},
title = {Escherichia coli persisters in biofilm can perform horizontal gene transfer by transformation.},
journal = {Biochemical and biophysical research communications},
volume = {738},
number = {},
pages = {150549},
doi = {10.1016/j.bbrc.2024.150549},
pmid = {39167960},
issn = {1090-2104},
abstract = {Persisters represent a subset of cells that exhibit transient tolerance to antimicrobials. These persisters can withstand sudden exposure to antimicrobials, even as the majority of normal cells perish. In this study, we have demonstrated the capacity of ampicillin-tolerant and alkali-tolerant persisters to execute horizontal gene transfer via in situ transformation within biofilms. Air-solid biofilms, comprising two Escherichia coli populations each with a distinct plasmid, were formed on agar media. They were treated with lethal doses of ampicillin or NaOH for 24 h, followed by a 1-min glass-ball roll. This process led to a high frequency of horizontal plasmid transfer (10[-7]-10[-6] per cell) from dead cells to surviving persisters within the biofilms. Plasmid transfer was DNase-sensitive and also occurred by adding purified plasmid DNA to plasmid-free biofilms, demonstrating a transformation mechanism. This marks the first evidence of persisters' novel ability for horizontal gene transfer, via transformation.},
}
@article {pmid39166873,
year = {2024},
author = {Kwan, S-Y and Sabotta, CM and Cruz, LR and Wong, MC and Ajami, NJ and McCormick, JB and Fisher-Hoch, SP and Beretta, L},
title = {Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0043424},
doi = {10.1128/msystems.00434-24},
pmid = {39166873},
issn = {2379-5077},
abstract = {Mexican Americans are disproportionally affected by metabolic dysfunction-associated steatotic liver disease (MASLD), which often co-occurs with diabetes. Despite extensive evidence on the causative role of the gut microbiome in MASLD, studies determining the involvement of the gut phageome are scarce. In this cross-sectional study, we characterized the gut phageome in Mexican Americans of South Texas by stool shotgun metagenomic sequencing of 340 subjects, concurrently screened for liver steatosis by transient elastography. Inter-individual variations in the phageome were associated with gender, country of birth, diabetes, and liver steatosis. The phage signatures for diabetes and liver steatosis were subsequently determined. Enrichment of Inoviridae was associated with both diabetes and liver steatosis. Diabetes was further associated with the enrichment of predominantly temperate Escherichia phages, some of which possessed virulence factors. Liver steatosis was associated with the depletion of Lactococcus phages r1t and BK5-T, and enrichment of the globally prevalent Crassvirales phages, including members of genus cluster IX (Burzaovirus coli, Burzaovirus faecalis) and VI (Kahnovirus oralis). The Lactococcus phages showed strong correlations and co-occurrence with Lactococcus lactis, while the Crassvirales phages, B. coli, B. faecalis, and UAG-readthrough crAss clade correlated and co-occurred with Prevotella copri. In conclusion, we identified the gut phageome signatures for two closely linked metabolic diseases with significant global burden. These phage signatures may have utility in risk modeling and disease prevention in this high-risk population, and identification of potential bacterial targets for phage therapy.IMPORTANCEPhages influence human health and disease by shaping the gut bacterial community. Using stool samples from a high-risk Mexican American population, we provide insights into the gut phageome changes associated with diabetes and liver steatosis, two closely linked metabolic diseases with significant global burden. Common to both diseases was an enrichment of Inoviridae, a group of phages that infect bacterial hosts chronically without lysis, allowing them to significantly influence bacterial growth, virulence, motility, biofilm formation, and horizontal gene transfer. Diabetes was additionally associated with the enrichment of Escherichia coli-infecting phages, some of which contained virulence factors. Liver steatosis was additionally associated with the depletion of Lactococcus lactis-infecting phages, and enrichment of Crassvirales phages, a group of virulent phages with high global prevalence and persistence across generations. These phageome signatures may have utility in risk modeling, as well as identify potential bacterial targets for phage therapy.},
}
@article {pmid39166856,
year = {2024},
author = {Karpenko, A and Shelenkov, A and Manzeniuk, I and Kulikova, N and Gevorgyan, A and Mikhaylova, Y and Akimkin, V},
title = {Whole genome analysis of multidrug-resistant Escherichia coli isolate collected from drinking water in Armenia revealed the plasmid-borne mcr-1.1-mediated colistin resistance.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0075124},
doi = {10.1128/spectrum.00751-24},
pmid = {39166856},
issn = {2165-0497},
abstract = {UNLABELLED: The rate of polymyxin-resistant Enterobacteriaceae, as well as human and animal infections caused by them, is increasing worldwide, posing a high epidemiological threat since colistin represents a last-resort antibiotic to treat complicated infections. The study of environmental niches, in particular, aquatic ecosystems in terms of genome analysis of inhabiting antimicrobial-resistant (AMR) microorganisms as reservoirs of acquired resistance determinants (AMR genes), represents a specific concern from a One Health approach. Here, we present a phenotypic AMR analysis and molecular characterization of Escherichia coli isolate found in municipal drinking water after an accident in the water supply system of a residential building in Armenia in 2021. CrieF1144 E. coli isolate was resistant to ampicillin, ampicillin/sulbactam, cefuroxime, ciprofloxacin, levofloxacin, trimethoprim/sulfamethoxazole, colistin, and tigecycline, whereas whole genome sequencing (WGS) revealed blaTEM-1B, tet(A), and a combination of dfrA14 with sul1 resistance determinants, which corresponds well with phenotypic resistance above. Moreover, the multidrug-resistant isolate studied harbored mcr-1.1 gene on a conjugative 251 Kb IncHI2 plasmid, whose structure was determined using hybrid short- and long-reads assembly. CrieF1141_p1 plasmid carried all antimicrobial resistance genes revealed in the isolate and did not harbor any virulence determinants, so it could contribute to the spread of AMR genes in the bacterial population. Two copies of ISApl1 transposase-encoding element, which is likely to mediate mcr-1.1 gene mobilization, were revealed surrounding this gene in a plasmid.<br><br>IMPORTANCE: Evolutionary patterns of Escherichia coli show that they usually develop into highly pathogenic forms by acquiring fitness advantages such as antimicrobial resistance (AMR) and various virulence factors through horizontal gene transfer mediated by mobile elements. This has led to high prevalence of multidrug-resistant (MDR) strains, which highlights the relevancy of enhanced surveillance to monitor and prevent transmission of the MDR bacteria to human and animal populations. However, the limited number of reports regarding the whole genome sequencing (WGS) investigation of MDR E. coli strains isolated from drinking water and harboring mcr genes hampers the adoption of a comprehensive approach to address the relationship between environmental E. coli populations and human and veterinary infections. Our results highlight the relevance of analyzing the environment, especially water, as a part of the surveillance programs to understand the origins and dissemination of antimicrobial resistance within the One Health concept.},
}
@article {pmid39166427,
year = {2024},
author = {Wu, JJ and Deng, QW and Qiu, YY and Liu, C and Lin, CF and Ru, YL and Sun, Y and Lai, J and Liu, LX and Shen, XX and Pan, R and Zhao, YP},
title = {Post-transfer adaptation of HGT-acquired genes and contribution to guanine metabolic diversification in land plants.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.20040},
pmid = {39166427},
issn = {1469-8137},
support = {32071484//National Natural Science Foundation of China/ ; 32200231//National Natural Science Foundation of China/ ; 32371691//National Natural Science Foundation of China/ ; LZ21C030003//Natural Science Foundation of Zhejiang Province/ ; LZ23C020002//Natural Science Foundation of Zhejiang Province/ ; LR23C140001//Natural Science Foundation of Zhejiang Province/ ; 2023000CC0010//Beijing Life Science Academy/ ; 226-2023-00021//Fundamental Research Funds for the Central Universities/ ; 2022YFD1401600//National Key Research and Development Program of China/ ; },
abstract = {Horizontal gene transfer (HGT) is a major driving force in the evolution of prokaryotic and eukaryotic genomes. Despite recent advances in distribution and ecological importance, the extensive pattern, especially in seed plants, and post-transfer adaptation of HGT-acquired genes in land plants remain elusive. We systematically identified 1150 foreign genes in 522 land plant genomes that were likely acquired via at least 322 distinct transfers from nonplant donors and confirmed that recent HGT events were unevenly distributed between seedless and seed plants. HGT-acquired genes evolved to be more similar to native genes in terms of average intron length due to intron gains, and HGT-acquired genes containing introns exhibited higher expression levels than those lacking introns, suggesting that intron gains may be involved in the post-transfer adaptation of HGT in land plants. Functional validation of bacteria-derived gene GuaD in mosses and gymnosperms revealed that the invasion of foreign genes introduced a novel bypass of guanine degradation and resulted in the loss of native pathway genes in some gymnosperms, eventually shaping three major types of guanine metabolism in land plants. We conclude that HGT has played a critical role in land plant evolution.},
}
@article {pmid39165128,
year = {2024},
author = {Trost, K and Knopp, MR and Wimmer, JLE and Tria, FDK and Martin, WF},
title = {A universal and constant rate of gene content change traces pangenome flux to LUCA.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnae068},
pmid = {39165128},
issn = {1574-6968},
abstract = {Prokaryotic genomes constantly undergo gene flux via lateral gene transfer, generating a pangenome structure consisting of a conserved core genome surrounded by a more variable accessory genome shell. Over time, flux generates change in genome content. Here we measure and compare the rate of genome flux for 5 655 prokaryotic genomes as a function of amino acid sequence divergence in 36 universally distributed proteins of the informational core (IC). We find a clock of gene content change. The long-term average rate of gene content flux is remarkably constant across all higher prokaryotic taxa sampled, whereby the size of the accessory genome-the proportion of the genome harboring gene content difference for genome pairs-varies across taxa. The proportion of species-level accessory genes per genome, varies from 0% (Chlamydia) to 30-33% (Alphaproteobacteria, Gammaproteobacteria, Clostridia). A clock-like rate of gene content change across all prokaryotic taxa sampled suggest that pangenome structure is a general feature of prokaryotic genomes and that it has been in existence since the divergence of bacteria and archaea.},
}
@article {pmid39163267,
year = {2024},
author = {Kloub, L and Gosselin, S and Graf, J and Gogarten, JP and Bansal, MS},
title = {Investigating Additive and Replacing Horizontal Gene Transfers Using Phylogenies and Whole Genomes.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae180},
pmid = {39163267},
issn = {1759-6653},
abstract = {Horizontal gene transfer (HGT) is fundamental to microbial evolution and adaptation. When a gene is horizontally transferred, it may either add itself as a new gene to the recipient genome (possibly displacing non-homologous genes) or replace an existing homologous gene. Currently, studies do not usually distinguish between "additive" and "replacing" HGTs, and their relative frequencies, integration mechanisms, and specific roles in microbial evolution are poorly understood. In this work, we develop a novel computational framework for large-scale classification of HGTs as either additive or replacing. Our framework leverages recently developed phylogenetic approaches for HGT detection and classifies HGTs inferred between terminal edges based on gene orderings along genomes and phylogenetic relationships between the microbial species under consideration. The resulting 9 method, called DART, is highly customizable and scalable and can classify a large fraction of inferred HGTs with high confidence and statistical support. Our application of DART to a large dataset of thousands of gene families from 103 Aeromonas genomes provides insights into the relative frequencies, functional biases, and integration mechanisms of additive and replacing HGTs. Among other results, we find that (i) the relative frequency of additive HGT increases with increasing phylogenetic distance, (ii) replacing HGT dominates at shorter phylogenetic distances, (iii) additive and replacing HGTs have strikingly different functional profiles, (iv) homologous recombination in flanking regions of a novel gene may be a frequent integration mechanism for additive HGT, and (v) phages and mobile genetic elements likely play an important role in facilitating additive HGT.},
}
@article {pmid39162532,
year = {2024},
author = {Ito, Y and Hashimoto, Y and Suzuki, M and Kaneko, N and Yoshida, M and Nakayama, H and Tomita, H},
title = {The emergence of metronidazole-resistant Prevotella bivia harboring nimK gene in Japan.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0056224},
doi = {10.1128/spectrum.00562-24},
pmid = {39162532},
issn = {2165-0497},
abstract = {UNLABELLED: We present the identification and characterization of the complete genome of metronidazole (MTZ)-resistant Prevotella bivia strain TOH-2715 [minimum inhibitory concentration (MIC): 8 mg/L], isolated from the urine of an elderly Japanese woman, as well as details of its mobile genetic elements (MGEs) containing antimicrobial resistance (AMR) genes and its relationship with other bacterial species determined using whole-genome sequencing (WGS) data. TOH-2715 possessed two chromosomes with putative MGEs containing AMR genes. Two AMR-related MGE regions were present in chromosome 2. MGE-region 1 (7,821 bp) included Tn6456, where nimK was located, and MGE-region 2 (58.8 Kbp) included the integrative and conjugative element (ICE), where tet(Q) and ermF were located. The genetic structure of the ICE of TOH-2715 was similar to that of CTnDOT-family transposons, where ermF and tet(Q) are located. A search of public databases revealed that nimK was present in Prevotella spp., including P. bivia, and was partially composed of a Tn6456-like element lacking the efflux transporter gene qacE and the Crp/Fnr family transcriptional regulator gene in some cases. Core ICE gene analysis showed that ICEs similar to that of TOH-2715 were present in Prevotella spp. and Bacteroides spp., suggesting horizontal gene transfer among anaerobes. This is the report of WGS analysis of an MTZ-resistant clinical strain of P. bivia (TOH-2715) with Tn6456 encoding nimK. Other submitted genomes have described the presence of nimK, but none of them have described MTZ resistance. Additionally, we described putative MGE regions containing the AMR gene within the genus Prevotella and among anaerobes, raising concerns about the future spread of nimK among anaerobes.<br><br>IMPORTANCE: Metronidazole (MTZ) is an important antimicrobial agent in anaerobic infections and is widely used in clinical settings. The rate of MTZ resistance in anaerobic bacteria has been increasing in recent years, and the nim gene (nitro-imidazole reductase) is one of the resistance mechanisms. Prevotella bivia is found in humans in the urinary tract and vagina and is known to cause infections in some cases. One of the nim genes, nimK, has recently been discovered in this species of bacteria, but there are no reports of antimicrobial resistance (AMR)-related regions in its whole genome level. In this study, we analyzed the AMR region of nimK-positive P. bivia derived from clinical specimens based on comparisons with other anaerobic genomes. P. bivia was found to be engaged in horizontal gene transfer with other anaerobic bacteria, and the future spread of the nimK gene is a concern.},
}
@article {pmid39162515,
year = {2024},
author = {Wang, Z and Hülpüsch, C and Foesel, B and Traidl-Hoffmann, C and Reiger, M and Schloter, M},
title = {Genomic and functional divergence of Staphylococcus aureus strains from atopic dermatitis patients and healthy individuals: insights from global and local scales.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0057124},
doi = {10.1128/spectrum.00571-24},
pmid = {39162515},
issn = {2165-0497},
abstract = {Atopic dermatitis (AD) is the most common chronic inflammatory skin disease worldwide and is characterized by a complex interplay with skin microbiota, with Staphylococcus aureus often abnormally more abundant in AD patients than in healthy individuals (HE). S. aureus harbors diverse strains with varied genetic compositions and functionalities, which exhibit differential connections with the severity of AD. However, the differences in S. aureus strains between AD and HE remain unclear, with most variations seen at a specific geographic level, implying spontaneous adaptations rather than systematic distinctions. This study presents genomic and functional differences between these S. aureus strains from AD and HE on both global and local levels. We observed reduced gene content diversity but increased functional variation in the global AD-associated strains. Two additional AD-dominant clusters emerged, with Cluster 1 enriched in transposases and Cluster 2 showcasing genes linked to adaptability and antibiotic resistance. Particularly, robust evidence illustrates that the lantibiotic operon of S. aureus, involved in the biosynthesis of lantibiotics, was acquired via horizontal gene transfer from environmental bacteria. Comparisons of the gene abundance profiles in functional categories also indicate limited zoonotic potential between human and animal isolates. Local analysis mirrored global gene diversity but showed distinct functional variations between AD and HE strains. Overall, this research provides foundational insights into the genomic evolution, adaptability, and antibiotic resistance of S. aureus, with significant implications for clinical microbiology.IMPORTANCEOur study uncovers significant genomic variations in Staphylococcus aureus strains associated with atopic dermatitis. We observed adaptive evolution tailored to the disease microenvironment, characterized by a smaller pan-genome than strains from healthy skin both on the global and local levels. Key functional categories driving strain diversification include "replication and repair" and "transporters," with transposases being pivotal. Interestingly, the local strains predominantly featured metal-related genes, whereas global ones emphasized antimicrobial resistances, signifying scale-dependent diversification nuances. We also pinpointed horizontal gene transfer events, indicating interactions between human-associated and environmental bacteria. These insights expand our comprehension of S. aureus's genetic adaptation in atopic dermatitis, yielding valuable implications for clinical approaches.},
}
@article {pmid39159726,
year = {2024},
author = {Zhang, Y and Wang, N and Wan, J and Jousset, A and Jiang, G and Wang, X and Wei, Z and Xu, Y and Shen, Q},
title = {Exploring the antibiotic resistance genes removal dynamics in chicken manure by composting.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131309},
doi = {10.1016/j.biortech.2024.131309},
pmid = {39159726},
issn = {1873-2976},
abstract = {Prolonged antibiotic usage in livestock farming leads to the accumulation of antibiotic resistance genes in animal manure. Composting has been shown as an effective way of removing antibiotic resistance from manures, but the specific mechanisms remain unclear. This study used time-series sampling and metagenomics to analyse the resistome types and their bacterial host in chicken manures. Composting significantly altered the physicochemical properties and microbiome composition, reduced antibiotic resistance genes by 65.71 %, mobile genetic elements by 68.15 % and horizontal gene transfer frequency. Source tracking revealed that Firmicutes, Actinobacteria, and Proteobacteria are the major bacterial hosts involved in resistome and gene transfer events. Composting reduces the resistome risk by targeting pathogens such as Staphylococcus aureus. Structural equation modelling confirmed that composting reduces resistome risk by changing pH and pathogen abundance. This study demonstrates that composting is an effective strategy for mitigating resistome risk in chicken manure, thereby supporting the "One Health" initiative.},
}
@article {pmid39158272,
year = {2024},
author = {Upreti, C and Kumar, P and Durso, LM and Palmer, KL},
title = {CRISPR-Cas inhibits plasmid transfer and immunizes bacteria against antibiotic resistance acquisition in manure.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0087624},
doi = {10.1128/aem.00876-24},
pmid = {39158272},
issn = {1098-5336},
abstract = {The horizontal transfer of antibiotic resistance genes among bacteria is a pressing global issue. The bacterial defense system clustered regularly interspaced short palindromic repeats (CRISPR)-Cas acts as a barrier to the spread of antibiotic resistance plasmids, and CRISPR-Cas-based antimicrobials can be effective to selectively deplete antibiotic-resistant bacteria. While significant surveillance efforts monitor the spread of antibiotic-resistant bacteria in the clinical context, a major, often overlooked aspect of the issue is resistance emergence in agriculture. Farm animals are commonly treated with antibiotics, and antibiotic resistance in agriculture is on the rise. Yet, CRISPR-Cas efficacy has not been investigated in this setting. Here, we evaluate the prevalence of CRISPR-Cas in agricultural Enterococcus faecalis strains and its antiplasmid efficacy in an agricultural niche: manure. Analyzing 1,986 E. faecalis genomes from human and animal hosts, we show that the prevalence of CRISPR-Cas subtypes is similar between clinical and agricultural E. faecalis strains. Using plasmid conjugation assays, we found that CRISPR-Cas is a significant barrier against resistance plasmid transfer in manure. Finally, we used a CRISPR-based antimicrobial approach to cure resistant E. faecalis of erythromycin resistance, but this was limited by delivery efficiency of the CRISPR antimicrobial in manure. However, immunization of bacteria against resistance gene acquisition in manure was highly effective. Together, our results show that E. faecalis CRISPR-Cas is prevalent and effective in an agricultural setting and has the potential to be utilized for depleting antibiotic-resistant populations. Our work has broad implications for tackling antibiotic resistance in the increasingly relevant agricultural setting, in line with a One Health approach.IMPORTANCEAntibiotic resistance is a growing global health crisis in human and veterinary medicine. Previous work has shown technologies based on CRISPR-Cas-a bacterial defense system-to be effective in tackling antibiotic resistance. Here we test if CRISPR-Cas is present and effective in agricultural niches, specifically in the ubiquitously present bacterium, Enterococcus faecalis. We show that CRISPR-Cas is both prevalent and functional in manure and has the potential to be used to specifically kill bacteria carrying antibiotic resistance genes. This study demonstrates the utility of CRISPR-Cas-based strategies for control of antibiotic resistance in agricultural settings.},
}
@article {pmid39158107,
year = {2024},
author = {Ming, Y and Abdullah Al, M and Zhang, D and Zhu, W and Liu, H and Cai, L and Yu, X and Wu, K and Niu, M and Zeng, Q and He, Z and Yan, Q},
title = {Insights into the evolutionary and ecological adaption strategies of nirS- and nirK-type denitrifying communities.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17507},
doi = {10.1111/mec.17507},
pmid = {39158107},
issn = {1365-294X},
support = {SML2020SP004//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2021SP203//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP205//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 42377111//National Natural Science Foundation of China/ ; //Ocean Negative Carbon Emissions (ONCE) Program/ ; },
abstract = {Denitrification is a crucial process in the global nitrogen cycle, in which two functionally equivalent genes, nirS and nirK, catalyse the critical reaction and are usually used as marker genes. The nirK gene can function independently, whereas nirS requires additional genes to encode nitrite reductase and is more sensitive to environmental factors than nirK. However, the ecological differentiation mechanisms of those denitrifying microbial communities and their adaptation strategies to environmental stresses remain unclear. Here, we conducted metagenomic analysis for sediments and bioreactor samples from Lake Donghu, China. We found that nirS-type denitrifying communities had a significantly lower horizontal gene transfer frequency than that of nirK-type denitrifying communities, and nirS gene phylogeny was more congruent with taxonomy than that of nirK gene. Metabolic reconstruction of metagenome-assembled genomes further revealed that nirS-type denitrifying communities have robust metabolic systems for energy conservation, enabling them to survive under environmental stresses. Nevertheless, nirK-type denitrifying communities seemed to adapt to oxygen-limited environments with the ability to utilize various carbon and nitrogen compounds. Thus, this study provides novel insights into the ecological differentiation mechanism of nirS and nirK-type denitrifying communities, as well as the regulation of the global nitrogen cycle and greenhouse gas emissions.},
}
@article {pmid39153565,
year = {2024},
author = {Yang, C and Yan, S and Zhang, B and Yao, X and Mo, J and Rehman, F and Guo, J},
title = {Spatiotemporal distribution of the planktonic microbiome and antibiotic resistance genes in a typical urban river contaminated by macrolide antibiotics.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119808},
doi = {10.1016/j.envres.2024.119808},
pmid = {39153565},
issn = {1096-0953},
abstract = {The widespread application of macrolide antibiotics has caused antibiotic resistance pollution, threatening the river ecological health. In this study, five macrolide antibiotics (azithromycin, clarithromycin, roxithromycin, erythromycin, and anhydro erythromycin A) were monitored in the Zao River across three hydrological periods (April, July, and December). Simultaneously, the changes in antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and planktonic bacterial communities were determined using metagenomic sequencing. A clear pollution gradient was observed for azithromycin and roxithromycin, with the concentrations in the dry season surpassing those in other seasons. The highest concentration was observed for azithromycin (1.36 μg/L). The abundance of MLS resistance genes increased along the Zao River during the dry season, whereas the opposite trend was obtained during the wet season. A significant correlation between the levels of MLS resistance genes and macrolide antibiotics was identified during the dry season. Notably, compared with the reference site, the abundance of transposase in the effluent from wastewater treatment plants (WWTPs) was significantly elevated in both dry and wet seasons, whereas the abundance of insertion sequences (IS) and plasmids declined during the dry season. The exposure to wastewater containing macrolide antibiotics altered the diversity of planktonic bacterial communities. The bacterial host for ARGs appeared to be Pseudomonas, primarily associated with multidrug subtypes. Moreover, the ARG subtypes were highly correlated with MGEs (transposase and istA). The partial least-squares path model (PLS-PM) demonstrated a positive correlation between the abundance of MGEs and ARGs, indicating the significance of horizontal gene transfer (HGT) in the dissemination of ARGs within the Zao River. Environmental variables, such as TN and NO3[-]-N, were significantly correlated with the abundance of MGEs, ARGs, and bacteria. Collectively, our findings could provide insights into the shift patterns of the microbiome and ARGs across the contamination gradient of AZI and ROX in the river.},
}
@article {pmid39153075,
year = {2024},
author = {Panickar, A and Manoharan, A and Anbarasu, A and Ramaiah, S},
title = {Respiratory tract infections: an update on the complexity of bacterial diversity, therapeutic interventions and breakthroughs.},
journal = {Archives of microbiology},
volume = {206},
number = {9},
pages = {382},
pmid = {39153075},
issn = {1432-072X},
support = {IRIS ID: 2021-11889//Indian Council of Medical Research/ ; },
mesh = {*Respiratory Tract Infections/microbiology/drug therapy ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/genetics/drug effects/classification ; Drug Resistance, Bacterial ; Bacterial Infections/microbiology/drug therapy ; Virulence ; },
abstract = {Respiratory tract infections (RTIs) have a significant impact on global health, especially among children and the elderly. The key bacterial pathogens Streptococcus pneumoniae, Haemophilus influenzae, Klebsiella pneumoniae, Staphylococcus aureus and non-fermenting Gram Negative bacteria such as Acinetobacter baumannii and Pseudomonas aeruginosa are most commonly associated with RTIs. These bacterial pathogens have evolved a diverse array of resistance mechanisms through horizontal gene transfer, often mediated by mobile genetic elements and environmental acquisition. Treatment failures are primarily due to antimicrobial resistance and inadequate bacterial engagement, which necessitates the development of alternative treatment strategies. To overcome this, our review mainly focuses on different virulence mechanisms and their resulting pathogenicity, highlighting different therapeutic interventions to combat resistance. To prevent the antimicrobial resistance crisis, we also focused on leveraging the application of artificial intelligence and machine learning to manage RTIs. Integrative approaches combining mechanistic insights are crucial for addressing the global challenge of antimicrobial resistance in respiratory infections.},
}
@article {pmid39149034,
year = {2024},
author = {Kadkhoda, H and Gholizadeh, P and Samadi Kafil, H and Ghotaslou, R and Pirzadeh, T and Ahangarzadeh Rezaee, M and Nabizadeh, E and Feizi, H and Aghazadeh, M},
title = {Role of CRISPR-Cas systems and anti-CRISPR proteins in bacterial antibiotic resistance.},
journal = {Heliyon},
volume = {10},
number = {14},
pages = {e34692},
pmid = {39149034},
issn = {2405-8440},
abstract = {The emergence and development of antibiotic resistance in bacteria is a serious threat to global public health. Antibiotic resistance genes (ARGs) are often located on mobile genetic elements (MGEs). They can be transferred among bacteria by horizontal gene transfer (HGT), leading to the spread of drug-resistant strains and antibiotic treatment failure. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated genes) is one of the many strategies bacteria have developed under long-term selection pressure to restrict the HGT. CRISPR-Cas systems exist in about half of bacterial genomes and play a significant role in limiting the spread of antibiotic resistance. On the other hand, bacteriophages and other MGEs encode a wide range of anti-CRISPR proteins (Acrs) to counteract the immunity of the CRISPR-Cas system. The Acrs could decrease the CRISPR-Cas system's activity against phages and facilitate the acquisition of ARGs and virulence traits for bacteria. This review aimed to assess the relationship between the CRISPR-Cas systems and Acrs with bacterial antibiotic resistance. We also highlighted the CRISPR technology and Acrs to control and prevent antibacterial resistance. The CRISPR-Cas system can target nucleic acid sequences with high accuracy and reliability; therefore, it has become a novel gene editing and gene therapy tool to prevent the spread of antibiotic resistance. CRISPR-based approaches may pave the way for developing smart antibiotics, which could eliminate multidrug-resistant (MDR) bacteria and distinguish between pathogenic and beneficial microorganisms. Additionally, the engineered anti-CRISPR gene-containing phages in combination with antibiotics could be used as a cutting-edge treatment approach to reduce antibiotic resistance.},
}
@article {pmid39148687,
year = {2024},
author = {Santos, AJDC and Dias, RS and da Silva, CHM and Vidigal, PMP and de Sousa, MP and da Silva, CC and de Paula, SO},
title = {Genomic analysis of Oceanotoga teriensis strain UFV_LIMV02, a multidrug-resistant thermophilic bacterium isolated from an offshore oil reservoir.},
journal = {Access microbiology},
volume = {6},
number = {8},
pages = {},
pmid = {39148687},
issn = {2516-8290},
abstract = {Bacteria of the species Oceanotoga teriensis belong to the family Petrotogaceae, are Gram-negative bacilli, are moderately thermophilic and are included in the group of thiosulfate-reducing bacteria, being capable of significantly accelerating corrosion in metallic structures. However, no in-depth study on the genome, antibiotic resistance and mobile elements has been carried out so far. In this work, the isolation, phenotypic and genotypic characterization of the multi-resistant O. teriensis UFV_LIMV02 strain was carried out, from water samples from an offshore oil extraction platform in Rio de Janeiro (Brazil). We determined that the isolate has a genome of 2 812 778 bp in size, with 26 % GC content, organized into 34 contigs. Genomic annotation using Rapid Annotation using Subsystem Technology revealed the presence of genes related to resistance to antibiotics and heavy metals. By evaluating the antimicrobial resistance of the isolate using the disc diffusion technique, resistance was verified for the classes of antibiotics, beta-lactams, fluoroquinolones, aminoglycosides, sulfonamides, lincosamides and rifamycins, a total of 14 antibiotics. The search for genomic islands, prophages and defence systems against phage infection revealed the presence of five genomic islands in its genome, containing genes related to resistance to heavy metals and antibiotics, most of which are efflux pumps and several transposases. No prophage was found in its genome; however, nine different defence systems against phage infection were detected. When analysing the clustered regularly interspaced short palindromic repeat (CRISPR) systems, four CRISPR arrays, classified as types I-B and III-B, with 272 spacers, can provide the strain with immunity to different mobile genetic elements and bacteriophage infection. The results found in this study show that the isolate UFV_LIVM02 is an environmental bacterium, resistant to different classes of antibiotics, and that the proteins encoded by the predicted genomic islands may be associated with the development of greater resistance to antibiotics and heavy metals. They provide evidence that environmental bacteria found in offshore oil exploration residues may pose a risk for the spread of antibiotic resistance genes. More comprehensive studies on the microbial community present in oil waste are needed to assess the risks of horizontal gene transfer.},
}
@article {pmid39147525,
year = {2024},
author = {Wu, Q and Li, W and Kwok, LY and Lv, H and Sun, J and Sun, Z},
title = {Regional variation and adaptive evolution in Bifidobacterium pseudocatenulatum: Insights into genomic and functional diversity in human gut.},
journal = {Food research international (Ottawa, Ont.)},
volume = {192},
number = {},
pages = {114840},
doi = {10.1016/j.foodres.2024.114840},
pmid = {39147525},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Phylogeny ; *Genome, Bacterial ; *Bifidobacterium pseudocatenulatum/genetics/metabolism ; Genetic Variation ; Genomics ; Diet ; },
abstract = {Bifidobacterium pseudocatenulatum is a prevalent gut microbe in humans of all ages and plays a crucial role in host health. However, its adaptive evolutionary characteristics remain poorly understood. This study analyzed the genome of 247 B. pseudocatenulatum isolates from Chinese, Vietnamese, Japanese and other region populations using population genomics and functional genomics. Our findings revealed high genetic heterogeneity and regional clustering within B. pseudocatenulatum isolates. Significant differences were observed in genome characteristics, phylogeny, and functional genes. Specifically, Chinese and Vietnamese isolates exhibited a higher abundance of genes involved in the metabolism of plant-derived carbohydrates (GH13, GH43, and GH5 enzyme families), aligning with the predominantly vegetable-, wheat- and fruit-based diets of these populations. Additionally, we found widespread transmission of antibiotic resistance genes (tetO and tetW) through mobile genetic elements, such as genomic islands (GIs), resulting in substantial intra-regional differences. Our findings highlight distinct adaptive evolution in B. pseudocatenulatum driven by gene specialization, possibly in response to regional variations in diet and lifestyle. This study sheds light on bifidobacteria colonization mechanisms in the host gut. IMPORTANCE: Gut microbiota, as a key link in the gut-brain axis, helps to maintain the health of the organism, among which, Bifidobacterium pseudocatenulatum (B. pseudocatenulatum) is an important constituent member of the gut microbiota, which plays an important role in maintaining the balance of gut microbiota. The probiotic properties of B. pseudocatenulatum have been widely elaborated, and in order to excavate its evolutionary features at the genomic level, here we focused on the genetic background and evolutionary mechanism of the B. pseudocatenulatum genomes isolated from the intestinal tracts of different populations. Ultimately, based on the phylogenetic tree, we found that B. pseudocatenulatum has high genetic diversity and regional clustering phenomenon, in which plant-derived carbohydrate metabolism genes (GH13, GH43, GH5) showed significant regional differences, and this genetic differentiation drove the adaptive evolution, which likely shaped by diet and lifestyle.},
}
@article {pmid39144201,
year = {2024},
author = {Pramanik, S and Sil, AK},
title = {Anti-foam cell activity of metabolites of a bacterium isolated from yogurt.},
journal = {Food science and biotechnology},
volume = {33},
number = {11},
pages = {2597-2610},
pmid = {39144201},
issn = {2092-6456},
abstract = {UNLABELLED: Existing literature documents the beneficial effects of probiotics against atherosclerosis, a major cause of human death. However, it suffers from a serious limitation due to horizontal gene transfer. Therefore, currently, efforts are targeted to examine the beneficial effects of metabolites obtained from probiotics. In this context, the current study isolated a bacterium from yogurt and investigated the effect of its metabolites on foam cell formation, a key event for developing atherosclerosis. Results showed that the cell-free conditioned medium (CM) of this isolate and di-chloro methane extract of CM (CME) not only prevented the formation but also reduced the level of preformed foam cells. To understand the mechanism, the GC-MS study revealed the presence of compounds known to exert anti-atherogenic activities like anti-oxidant, anti-NF-κB, and lipolytic activities. Consistently, CME exhibited substantial anti-oxidant and anti-NF-κB activity. In conclusion, metabolites of this bacterium have anti-atherogenic activities and thus have therapeutic potential.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-023-01515-7.},
}
@article {pmid39141729,
year = {2024},
author = {Lai, S and Wang, H and Bork, P and Chen, WH and Zhao, XM},
title = {Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts.},
journal = {Science advances},
volume = {10},
number = {33},
pages = {eadn3316},
doi = {10.1126/sciadv.adn3316},
pmid = {39141729},
issn = {2375-2548},
mesh = {*Bacteriophages/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/virology/genetics ; *Gene Transfer, Horizontal ; Metagenomics/methods ; Genetic Variation ; Virome/genetics ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; },
abstract = {Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here, we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By using virome-enriched long-read metagenomic sequencing across 91 individuals, we identified a total of 14,438 nonredundant phage SVs and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Notably, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibit a higher frequency of genetic exchange with bacterial chromosomes and then virulent phages. Collectively, our findings provide insights into the genetic landscape of the human gut phageome.},
}
@article {pmid39141562,
year = {2024},
author = {Karan, J and Mandal, S and Khan, G and Arya, H and Samhita, L},
title = {Enhanced Extraction of Low-Molecular Weight DNA from Wastewater for Comprehensive Assessment of Antimicrobial Resistance.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {209},
pages = {},
doi = {10.3791/66899},
pmid = {39141562},
issn = {1940-087X},
mesh = {*Wastewater/microbiology/chemistry ; Polyethylene Glycols/chemistry ; Molecular Weight ; DNA, Bacterial/genetics/isolation &amp; purification ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; },
abstract = {Environmental surveillance is recognized as an important tool for assessing public health in the post-pandemic era. Water, in particular wastewater, has emerged as the source of choice to sample pathogen burdens in the environment. Wastewater from open drains and community water treatment plants is a reservoir of both pathogens and antimicrobial resistance (AMR) genes, and frequently comes in contact with humans. While there are many methods of tracking AMR from water, isolating good-quality DNA at high yields from heterogeneous samples remains a challenge. To compensate, sample volumes often need to be high, creating practical constraints. Additionally, environmental DNA is frequently fragmented, and the sources of AMR (plasmids, phages, linear DNA) consist of low-molecular-weight DNA. Yet, few extraction processes have focused on methods for high-yield extraction of linear and low-molecular-weight DNA. Here, a simple method for high-yield linear DNA extraction from small volumes of wastewater using the precipitation properties of polyethylene glycol (PEG) is reported. This study makes a case for increasing overall DNA yields from water samples collected for metagenomic analyses by enriching the proportion of linear DNA. In addition, enhancing low-molecular-weight DNA overcomes the current problem of under-sampling environmental AMR due to a focus on high-molecular-weight and intracellular DNA. This method is expected to be particularly useful when extracellular DNA exists but at low concentrations, such as with effluents from treatment plants. It should also enhance the environmental sampling of AMR gene fragments that spread through horizontal gene transfer.},
}
@article {pmid39096644,
year = {2024},
author = {Wu, Q and Wu, GG and Pan, KN and Wang, XP and Li, HY and Tian, Z and Jin, RC and Fan, NS},
title = {Beta-blocker drives the conjugative transfer of multidrug resistance genes in pure and complex biological systems.},
journal = {Journal of hazardous materials},
volume = {477},
number = {},
pages = {135403},
doi = {10.1016/j.jhazmat.2024.135403},
pmid = {39096644},
issn = {1873-3336},
mesh = {*Metoprolol ; *Plasmids/genetics ; *Conjugation, Genetic/drug effects ; Drug Resistance, Multiple, Bacterial/genetics/drug effects ; Adrenergic beta-Antagonists/pharmacology ; Gene Transfer, Horizontal ; Bacteria/genetics/drug effects/metabolism ; Anti-Bacterial Agents/pharmacology ; Genes, MDR/genetics ; Microbiota/drug effects ; },
abstract = {Drug resistance poses a high risk to human health. Extensive use of non-antibiotic drugs contributes to antibiotic resistance genes (ARGs) transfer. However, how they affect the spread of broad-host plasmids in complex biological systems remains unknown. This study investigated the effect of metoprolol on the transfer frequency and host range of ARGs in both intrageneric and intergeneric pure culture systems, as well as in anammox microbiome. The results showed that environmental concentrations of metoprolol significantly promoted the intrageneric and intergeneric conjugative transfer. Initially, metoprolol induced excessive oxidative stress, resulting in high cell membrane permeability and bacterial SOS response. Meanwhile, more pili formation increased the adhesion and contact between bacteria, and the abundance of conjugation-related genes also increased significantly. Activation of the electron transport chain provided more ATP for this energy-consuming process. The underlying mechanism was further verified in the complex anammox conjugative system. Metoprolol induced the enrichment of ARGs and mobile genetic elements. The enhanced bacterial interaction and energy generation facilitated the high conjugative transfer frequency of ARGs. In addition, plasmid-borne ARGs tended to transfer to opportunistic pathogens. This work raises public concerns about the health and ecological risks of non-antibiotic drugs.},
}
@article {pmid39139006,
year = {2024},
author = {Rao, Y and Wang, Y and Zhang, H and Wang, Y and He, Q and Yuan, X and Guo, J and Chen, H},
title = {A Strategy of Killing Two Birds With One Stone for Blocking Drug Resistance Spread With Engineered Bdellovibrio bacteriovorus.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e2406910},
doi = {10.1002/adma.202406910},
pmid = {39139006},
issn = {1521-4095},
support = {21935008//National Natural Science Foundation of China/ ; SKJY2021042//Livelihood Technology Project of Suzhou/ ; 23KJA150008//Jiangsu Province Higher Education Natural Science Research Major Project/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
abstract = {Drug-resistant pathogens significantly threaten human health and life. Simply killing drug-resistant pathogens cannot effectively eliminate their threat since the drug-resistant genes (DRGs) released from dead drug-resistant pathogens are difficult to eliminate and can further spread via horizontal gene transfer, leading to the spread of drug resistance. The development of antibacterial materials with sterilization and DRGs cleavage activities is highly crucial. Herein, a living system, Ce-PEA@Bdello, is fabricated with bacterial killing and DRGs cleavage activities for blocking bacterial drug resistance dissemination by engineered Bdellovibrio bacteriovorus (Bdello). Ce-PEA@Bdello is obtained by engineering Bdello with dopamine and a multinuclear cerium (IV) complex. Ce-PEA@Bdello can penetrate and eliminate kanamycin-resistant P. aeruginosa (Kan[R]) biofilms via the synergistic effect of predatory Bdello and photothermal polydopamine under near-infrared light. Additionally, the DNase-mimicking ability of Ce-PEA@Bdello endows it with genome and plasmid DNA cleavage ability. An in vivo study reveals that Ce-PEA@Bdello can eliminate P. aeruginosa (Kan[R]) and cleave DRGs in scald/burn infected wounds to block the spread of drug resistance and accelerate wound healing. This bioactive system constructed from natural living materials offers a promising means for blocking the spread of drug resistance.},
}
@article {pmid39135654,
year = {2024},
author = {Winter, M and Vos, M and Buckling, A and Johnsen, PJ and Harms, K},
title = {Effect of chemotherapeutic agents on natural transformation frequency in Acinetobacter baylyi.},
journal = {Access microbiology},
volume = {6},
number = {7},
pages = {},
pmid = {39135654},
issn = {2516-8290},
abstract = {Natural transformation is the ability of a bacterial cell to take up extracellular DNA which is subsequently available for recombination into the chromosome (or maintenance as an extrachromosomal element). Like other mechanisms of horizontal gene transfer, natural transformation is a significant driver for the dissemination of antimicrobial resistance. Recent studies have shown that many pharmaceutical compounds such as antidepressants and anti-inflammatory drugs can upregulate transformation frequency in the model species Acinetobacter baylyi. Chemotherapeutic compounds have been shown to increase the abundance of antimicrobial resistance genes and increase colonization rates of potentially pathogenic bacteria in patient gastrointestinal tracts, indicating an increased risk of infection and providing a pool of pathogenicity or resistance genes for transformable commensal bacteria. We here test for the effect of six cancer chemotherapeutic compounds on A. baylyi natural transformation frequency, finding two compounds, docetaxel and daunorubicin, to significantly decrease transformation frequency, and daunorubicin to also decrease growth rate significantly. Enhancing our understanding of the effect of chemotherapeutic compounds on the frequency of natural transformation could aid in preventing the horizontal spread of antimicrobial resistance genes.},
}
@article {pmid39132438,
year = {2024},
author = {Liu, H and Fan, S and Zhang, X and Yuan, Y and Zhong, W and Wang, L and Wang, C and Zhou, Z and Zhang, S and Geng, Y and Peng, G and Wang, Y and Zhang, K and Yan, Q and Luo, Y and Shi, K and Zhong, Z},
title = {Antibiotic-resistant characteristics and horizontal gene transfer ability analysis of extended-spectrum β-lactamase-producing Escherichia coli isolated from giant pandas.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1394814},
pmid = {39132438},
issn = {2297-1769},
abstract = {Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) is regarded as one of the most important priority pathogens within the One Health interface. However, few studies have investigated the occurrence of ESBL-EC in giant pandas, along with their antibiotic-resistant characteristics and horizontal gene transfer abilities. In this study, we successfully identified 12 ESBL-EC strains (8.33%, 12/144) out of 144 E. coli strains which isolated from giant pandas. We further detected antibiotic resistance genes (ARGs), virulence-associated genes (VAGs) and mobile genetic elements (MGEs) among the 12 ESBL-EC strains, and the results showed that 13 ARGs and 11 VAGs were detected, of which bla CTX-M (100.00%, 12/12, with 5 variants observed) and papA (83.33%, 10/12) were the most prevalent, respectively. And ISEcp1 (66.67%, 8/12) and IS26 (66.67%, 8/12) were the predominant MGEs. Furthermore, horizontal gene transfer ability analysis of the 12 ESBL-EC showed that all bla CTX-M genes could be transferred by conjugative plasmids, indicating high horizontal gene transfer ability. In addition, ARGs of rmtB and sul2, VAGs of papA, fimC and ompT, MGEs of ISEcp1 and IS26 were all found to be co-transferred with bla CTX-M. Phylogenetic analysis clustered these ESBL-EC strains into group B2 (75.00%, 9/12), D (16.67%, 2/12), and B1 (8.33%, 1/12), and 10 sequence types (STs) were identified among 12 ESBL-EC (including ST48, ST127, ST206, ST354, ST648, ST1706, and four new STs). Our present study showed that ESBL-EC strains from captive giant pandas are reservoirs of ARGs, VAGs and MGEs that can co-transfer with bla CTX-M via plasmids. Transmissible ESBL-EC strains with high diversity of resistance and virulence elements are a potential threat to humans, animals and surrounding environment.},
}
@article {pmid39128935,
year = {2024},
author = {Wang, W and Ge, Q and Wen, J and Zhang, H and Guo, Y and Li, Z and Xu, Y and Ji, D and Chen, C and Guo, L and Xu, M and Shi, C and Fan, G and Xie, C},
title = {Horizontal gene transfer and symbiotic microorganisms regulate the adaptive evolution of intertidal algae, Porphyra sense lato.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {976},
pmid = {39128935},
issn = {2399-3642},
support = {42176117//National Natural Science Foundation of China (National Science Foundation of China)/ ; U21A20265//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32100514//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Symbiosis/genetics ; *Porphyra/microbiology/genetics ; Adaptation, Physiological/genetics ; Phylogeny ; Biological Evolution ; },
abstract = {Intertidal algae may adapt to environmental challenges by acquiring genes from other organisms and relying on symbiotic microorganisms. Here, we obtained a symbiont-free and chromosome-level genome of Pyropia haitanensis (47.2 Mb), a type of intertidal algae, by using multiple symbiont screening methods. We identified 286 horizontal gene transfer (HGT) genes, 251 of which harbored transposable elements (TEs), reflecting the importance of TEs for facilitating the transfer of genes into P. haitanensis. Notably, the bulked segregant analysis revealed that two HGT genes, sirohydrochlorin ferrochelatase and peptide-methionine (R)-S-oxide reductase, play a significant role in the adaptation of P. haitanensis to heat stress. Besides, we found Pseudomonas, Actinobacteria, and Bacteroidetes are the major taxa among the symbiotic bacteria of P. haitanensis (nearly 50% of the HGT gene donors). Among of them, a heat-tolerant actinobacterial strain (Saccharothrix sp.) was isolated and revealed to be associated with the heat tolerance of P. haitanensis through its regulatory effects on the genes involved in proline synthesis (proC), redox homeostasis (ggt), and protein folding (HSP20). These findings contribute to our understanding of the adaptive evolution of intertidal algae, expanding our knowledge of the HGT genes and symbiotic microorganisms to enhance their resilience and survival in challenging intertidal environments.},
}
@article {pmid39127705,
year = {2024},
author = {Park, H and Bulzu, PA and Shabarova, T and Kavagutti, VS and Ghai, R and Kasalický, V and Jezberová, J},
title = {Uncovering the genomic basis of symbiotic interactions and niche adaptations in freshwater picocyanobacteria.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {150},
pmid = {39127705},
issn = {2049-2618},
support = {20&#x2011;12496X//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; 20&#x2011;12496X//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; 23-05081S//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; 19-23261S//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; 20&#x2011;12496X//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; 19-23261S//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; 19-23261S//Grantov&#xe1; Agentura Cesk&#xe9; Republiky (GA&#x10c;R)/ ; },
mesh = {*Symbiosis ; *Fresh Water/microbiology ; *Genome, Bacterial ; *Phylogeny ; *Cyanobacteria/genetics/classification ; Adaptation, Physiological/genetics ; Europe ; Ecosystem ; Gene Transfer, Horizontal ; Genomics ; },
abstract = {BACKGROUND: Picocyanobacteria from the genera Prochlorococcus, Synechococcus, and Cyanobium are the most widespread photosynthetic organisms in aquatic ecosystems. However, their freshwater populations remain poorly explored, due to uneven and insufficient sampling across diverse inland waterbodies.<br><br>RESULTS: In this study, we present 170 high-quality genomes of freshwater picocyanobacteria from non-axenic cultures collected across Central Europe. In addition, we recovered 33 genomes of their potential symbiotic partners affiliated with four genera, Pseudomonas, Mesorhizobium, Acidovorax, and Hydrogenophaga. The genomic basis of symbiotic interactions involved heterotrophs benefiting from picocyanobacteria-derived nutrients while providing detoxification of ROS. The global abundance patterns of picocyanobacteria revealed ecologically significant ecotypes, associated with trophic status, temperature, and pH as key environmental factors. The adaptation of picocyanobacteria in (hyper-)eutrophic waterbodies could be attributed to their colonial lifestyles and CRISPR-Cas systems. The prevailing CRISPR-Cas subtypes in picocyanobacteria were I-G and I-E, which appear to have been acquired through horizontal gene transfer from other bacterial phyla.<br><br>CONCLUSIONS: Our findings provide novel insights into the population diversity, ecology, and evolutionary strategies of the most widespread photoautotrophs within freshwater ecosystems. Video Abstract.},
}
@article {pmid39125965,
year = {2024},
author = {Sadowska-Bartosz, I and Bartosz, G},
title = {Antioxidant Defense in the Toughest Animals on the Earth: Its Contribution to the Extreme Resistance of Tardigrades.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39125965},
issn = {1422-0067},
mesh = {Animals ; *Tardigrada/metabolism/genetics ; *Antioxidants/metabolism ; Oxidative Stress ; Earth, Planet ; Trehalose/metabolism ; },
abstract = {Tardigrades are unique among animals in their resistance to dehydration, mainly due to anhydrobiosis and tun formation. They are also very resistant to high-energy radiation, low and high temperatures, low and high pressure, and various chemical agents, Interestingly, they are resistant to ionizing radiation both in the hydrated and dehydrated states to a similar extent. They are able to survive in the cosmic space. Apparently, many mechanisms contribute to the resistance of tardigrades to harmful factors, including the presence of trehalose (though not common to all tardigrades), heat shock proteins, late embryogenesis-abundant proteins, tardigrade-unique proteins, DNA repair proteins, proteins directly protecting DNA (Dsup and TDR1), and efficient antioxidant system. Antioxidant enzymes and small-molecular-weight antioxidants are an important element in the tardigrade resistance. The levels and activities of many antioxidant proteins is elevated by anhydrobiosis and UV radiation; one explanation for their induction during dehydration is provided by the theory of "preparation for oxidative stress", which occurs during rehydration. Genes coding for some antioxidant proteins are expanded in tardigrades; some genes (especially those coding for catalases) were hypothesized to be of bacterial origin, acquired by horizontal gene transfer. An interesting antioxidant protein found in tardigrades is the new Mn-dependent peroxidase.},
}
@article {pmid39125866,
year = {2024},
author = {Cheng, X and Liu, X and Jordan, KW and Yu, J and Whitworth, RJ and Park, Y and Chen, MS},
title = {Frequent Acquisition of Glycoside Hydrolase Family 32 (GH32) Genes from Bacteria via Horizontal Gene Transfer Drives Adaptation of Invertebrates to Diverse Sources of Food and Living Habitats.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39125866},
issn = {1422-0067},
mesh = {*Gene Transfer, Horizontal ; *Glycoside Hydrolases/genetics/metabolism ; Animals ; *Bacteria/genetics/enzymology ; *Phylogeny ; Invertebrates/genetics ; Adaptation, Physiological/genetics ; Ecosystem ; Evolution, Molecular ; },
abstract = {Glycoside hydrolases (GHs, also called glycosidases) catalyze the hydrolysis of glycosidic bonds in polysaccharides. Numerous GH genes have been identified from various organisms and are classified into 188 families, abbreviated GH1 to GH188. Enzymes in the GH32 family hydrolyze fructans, which are present in approximately 15% of flowering plants and are widespread across microorganisms. GH32 genes are rarely found in animals, as fructans are not a typical carbohydrate source utilized in animals. Here, we report the discovery of 242 GH32 genes identified in 84 animal species, ranging from nematodes to crabs. Genetic analyses of these genes indicated that the GH32 genes in various animals were derived from different bacteria via multiple, independent horizontal gene transfer events. The GH32 genes in animals appear functional based on the highly conserved catalytic blades and triads in the active center despite the overall low (35-60%) sequence similarities among the predicted proteins. The acquisition of GH32 genes by animals may have a profound impact on sugar metabolism for the recipient organisms. Our results together with previous reports suggest that the acquired GH32 enzymes may not only serve as digestive enzymes, but also may serve as effectors for manipulating host plants, and as metabolic enzymes in the non-digestive tissues of certain animals. Our results provide a foundation for future studies on the significance of horizontally transferred GH32 genes in animals. The information reported here enriches our knowledge of horizontal gene transfer, GH32 functions, and animal-plant interactions, which may result in practical applications. For example, developing crops via targeted engineering that inhibits GH32 enzymes could aid in the plant's resistance to animal pests.},
}
@article {pmid39125715,
year = {2024},
author = {Bucka-Kolendo, J and Kiousi, DE and Dekowska, A and Mikołajczuk-Szczyrba, A and Karadedos, DM and Michael, P and Galanis, A and Sokołowska, B},
title = {Exploration of Alicyclobacillus spp. Genome in Search of Antibiotic Resistance.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39125715},
issn = {1422-0067},
mesh = {*Alicyclobacillus/genetics/drug effects ; *Genome, Bacterial ; *Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Guaiacol/pharmacology/analogs &amp; derivatives ; },
abstract = {The study investigates the antibiotic resistance (AR) profiles and genetic determinants in three strains of guaiacol-producing Alicyclobacillus spp. isolated from orchard soil and pears. Their phenotypic characteristics, such as spore formation; resistance to different factors, including drugs or disinfectants; or production of off-flavor compounds, can affect the taste and aroma of spoiled products. Food and beverages are potential vectors for the transfer of antibiotic resistance genes, which is a growing health concern; thus, microorganisms in food and beverages should not be a potential source of drug resistance to consumers. Whole-genome sequencing (WGS) was utilized to identify antibiotic resistance genes, metabolic pathways, and elements associated with guaiacol and halophenol production. Minimum inhibitory concentration (MIC) testing revealed that all strains were susceptible to eight out of nine tested antibiotics (ampicillin, gentamycin, kanamycin, streptomycin, clindamycin, tetracycline, chloramphenicol, and vancomycin) but exhibited high resistance to erythromycin. Analysis indicated that the erythromycin resistance gene, ribosomal RNA small subunit methyltransferase A (RsmA), was intrinsic and likely acquired through horizontal gene transfer (HGT). The comprehensive genomic analysis provides insights into the molecular mechanisms of antibiotic resistance in Alicyclobacillus spp., highlighting the potential risk of these bacteria as vectors for antibiotic resistance genes in the food chain. This study expands the understanding of the genetic makeup of these spoilage bacteria and their role in antimicrobial resistance dissemination.},
}
@article {pmid39122691,
year = {2024},
author = {Williams, SK and Jerlström Hultqvist, J and Eglit, Y and Salas-Leiva, DE and Curtis, B and Orr, RJS and Stairs, CW and Atalay, TN and MacMillan, N and Simpson, AGB and Roger, AJ},
title = {Extreme mitochondrial reduction in a novel group of free-living metamonads.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6805},
pmid = {39122691},
issn = {2041-1723},
support = {FRN-142349//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; },
mesh = {*Mitochondria/metabolism/genetics ; *Phylogeny ; *Proteome/metabolism/genetics ; Transcriptome ; Eukaryota/genetics/metabolism/classification ; Gene Transfer, Horizontal ; Iron-Sulfur Proteins/metabolism/genetics ; },
abstract = {Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered 'mitochondrion-related organelles' (MROs) with reduced functions, however the degree of reduction varies. Here, we generate high-quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we name the 'BaSk' (Barthelonids+Skoliomonads) clade, a deeply branching sister group to the Fornicata, a phylum that includes parasitic and free-living flagellates. Bioinformatic analyses of gene models shows that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system Fe/S cluster pathway by lateral gene transfer. One of the isolates, Skoliomonas litria, appears to have lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade demonstrates that mitochondrial functions may be completely lost even in free-living organisms.},
}
@article {pmid37754684,
year = {2023},
author = {Zhang, Y and Kitazumi, A and Liao, Y-T and de Los Reyes, BG and Wu, VCH},
title = {Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem.},
journal = {Microbiology spectrum},
volume = {11},
number = {5},
pages = {e0022623},
pmid = {37754684},
issn = {2165-0497},
support = {2030-42000-0055-000-D//USDA | Agricultural Research Service (ARS)/ ; },
mesh = {*Bacteriophages/genetics ; *Gene Transfer, Horizontal ; *Metagenomics ; *Agriculture ; *Bacteria/genetics/virology/drug effects ; *Microbiota/genetics ; Metagenome ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; Drug Resistance, Bacterial/genetics ; Soil Microbiology ; },
abstract = {Antibiotic resistance has become a serious health concern worldwide. The potential impact of viruses, bacteriophages in particular, on spreading antibiotic resistance genes is still controversial due to the complexity of bacteriophage-bacterial interactions within diverse environments. In this study, we determined the microbiome profiles and the potential antibiotic resistance gene (ARG) transfer between bacterial and viral populations in different agricultural samples using a high-resolution analysis of the metagenomes. The results of this study provide compelling genetic evidence for ARG transfer through bacteriophage-bacteria interactions, revealing the inherent risks associated with bacteriophage-mediated ARG transfer across the agricultural microbiome.},
}
@article {pmid39121985,
year = {2024},
author = {Yan, Y and Lu, H and Liang, X and Xu, T and Yan, S and Yu, Y and Wang, Y},
title = {The virulence plasmid associated with AHPND in shrimp appears to have originated from Vibrio owensii through a process of homologous recombination of parental plasmids and the transposable insertion of two large fragments.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108173},
doi = {10.1016/j.jip.2024.108173},
pmid = {39121985},
issn = {1096-0805},
abstract = {Acute hepatopancreatic necrosis disease (AHPND) is a highly contagious and lethal disease of shrimp caused by Vibrio strains carrying the virulence plasmid (pAHPND) containing the pirAB virulence genes. Through analysis of plasmid sequence similarity, clustering, and phylogeny, a horizontal transfer element similar to IS91 was discovered within the pAHPND plasmid. Additionally, two distinct clades of plasmids related to pAHPND (designated as pAHPND-r1 and pAHPND-r2) were identified, which may serve as potential parental plasmids for pAHPND. The available evidence, including the difference in G+C content between the plasmid and its host, codon usage preference, and plasmid recombination event prediction, suggests that the formation of the pAHPND plasmid in the Vibrio owensii strain was likely due to the synergistic effect of the recombinase RecA and the associated proteins RecBCD on the pAHPND-r1 and pAHPND-r2, resulting in the recombination and formation of the precursor plasmid for pAHPND (pre-pAHPND). The emergence of pAHPND was found to be a result of successive insertions of the horizontal transfer elements of pirAB-Tn903 and IS91-like segment, which led to the deletion of one third of the pre-pAHPND. This plasmid was then able to spread horizontally to other Vibrio strains, contributing to the epidemics of AHPND. These findings shed light on previously unknown mechanisms involved in the emergence of pAHPND and improve our understanding of the disease's spread.},
}
@article {pmid39119206,
year = {2024},
author = {Zaer-Anaqz, Z and Khakvar, R and Mohammadi, SA and Bannazadeh Baghi, H and Koolivand, D},
title = {Physicochemical Characterization of Novel Bacteriophages of Pseudomonas syringe from Northwest Iran.},
journal = {PHAGE (New Rochelle, N.Y.)},
volume = {5},
number = {2},
pages = {99-106},
pmid = {39119206},
issn = {2641-6549},
abstract = {Bacterial canker, caused by Pseudomonas syringae, is a devastating disease of stone fruit trees worldwide. The bacterium has a broad host range and a high capacity for adaptation and dissemination, owing to its high mutation rate and horizontal gene transfer. Traditional control methods based on copper compounds and antibiotics have resulted in the development of resistance in the bacterial population. Thus, alternative approaches are needed, such as phage therapy. This study aimed to characterize the physicochemical and biological properties of novel Pseudomonas syringae pv. syringae (Pss)-specific phages isolated from the soils of northwestern Iran. Seventy-five phage isolates were obtained, and their host range was determined against various bacterial pathogens. Five phages exhibiting the highest lytic activity against Pss and a narrow host range were selected for subsequent analysis. The stability of the selected phages was assessed under different conditions such as ultraviolet irradiation, temperature, pH, NaCl concentration, and chloroform exposure. The selected phages demonstrated significant effectiveness in vivo, exerting substantial suppression on the population of Pss. This reduction was observed for both individual phages and when the phages were utilized as a mixture. The findings indicate that phages have the potential to be used as biocontrol agents in agriculture.},
}
@article {pmid39119203,
year = {2024},
author = {Delesalle, VA and Ankeriasniemi, RE and Lewis, CM and Mody, JM and Roy, AM and Sarvis, WA and Vo, DD and Walsh, AE and Zappia, RJ},
title = {Introducing Casbah, Kronus, and MmasiCarm, Members of the Mycobacteriophage Subcluster B3.},
journal = {PHAGE (New Rochelle, N.Y.)},
volume = {5},
number = {2},
pages = {84-90},
pmid = {39119203},
issn = {2641-6549},
abstract = {BACKGROUND: As part of a large science education effort, bacteriophages that lyse Mycobacterium smegmatis mc[2]155 continue to be discovered.<br><br>MATERIALS AND METHODS: Phages were isolated from soil samples from urban sites in the Northeastern United States. Their genomes were sequenced, assembled, and bioinformatically compared.<br><br>RESULTS: Three lytic siphoviruses belonging to subcluster B3 with high similarity to each other and other B3 mycobacteriophages were isolated. These phages contain double-stranded DNA genomes (68,754 to 69,495 bp) with high GC content (67.4-67.5%) and 102-104 putative protein coding genes. Notable features include a HicA-like toxin and 33 genes exclusive to subcluster B3. One phage had an intein in its terminase sequence.<br><br>CONCLUSIONS: Genomic analyses of these phages provide insights into genome evolution and horizontal gene transfer (HGT). The networks for HGT are apparently vast and gene specific. Interestingly, a number of genes are found in both B3 and Gordonia DR phages.},
}
@article {pmid39117207,
year = {2024},
author = {Erler, T and Droop, F and Lübbert, C and Knobloch, JK and Carlsen, L and Papan, C and Schwanz, T and Zweigner, J and Dengler, J and Hoffmann, M and Mutters, NT and Savin, M},
title = {Analysing carbapenemases in hospital wastewater: Insights from intracellular and extracellular DNA using qPCR and digital PCR.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {175344},
doi = {10.1016/j.scitotenv.2024.175344},
pmid = {39117207},
issn = {1879-1026},
abstract = {The widespread dissemination of carbapenem-resistant bacteria in wastewater systems, particularly from clinical sources, poses a significant public health risk. This study assessed the concentrations and distributions of extracellular DNA (exDNA) and intracellular DNA (iDNA) harboring carbapenemase genes in wastewater from six tertiary care hospitals in Germany. We collected a total of 36 samples, comprising six biological replicates from each hospital, and analysed them using quantitative real-time PCR (qPCR) and digital PCR (dPCR). The analysis targeted seven carbapenemase genes: blaNDM, blaKPC, blaIMP, blaVIM, blaOXA-23-like, blaOXA-48-like, and blaOXA-58-like across both DNA fractions. Our results revealed significant variability in the concentrations of exDNA and iDNA across the sampling sites, with iDNA typically present at higher concentrations. Using NanoDrop One spectrophotometry and the Qubit dsDNA kit, exDNA concentrations ranged from 2.7 to 7.7 ng/mL, while Qubit recorded lower values between 1.1 and 4.0 ng/mL. Conversely, iDNA concentrations were markedly higher, spanning from 42.3 to 191.7 ng/mL with NanoDrop and 12.0 to 46.5 ng/mL with Qubit, highlighting the variability between DNA types and quantification methods. Despite its lower concentrations, exDNA comprised up to 18.2 % of total DNA, highlighting its potential role in the horizontal transfer of antimicrobial resistance genes (ARGs). The study detected target ARGs in both DNA fractions at all sites, with notable differences in their concentrations; iDNA consistently exhibited higher levels of ARGs, with the highest concentrations reaching 10.57 ± 0.20 log gene copies per liter (GC/L) for blaVIM in iDNA and 6.96 ± 0.72 log GC/L for blaIMP in exDNA. dPCR demonstrated greater sensitivity than qPCR, especially effective for detecting low-abundance targets like blaOXA-23-like in the exDNA fraction. Additionally, qPCR's susceptibility to inhibition and contamination emphasizes the superior robustness of dPCR. This research highlights the need for improved monitoring and the implementation of advanced treatment technologies to mitigate ARG dissemination in wastewater.},
}
@article {pmid39113256,
year = {2024},
author = {Hossain, AKMZ and Chowdhury, AMMA},
title = {Understanding the Evolution and Transmission Dynamics of Antibiotic Resistance Genes: A Comprehensive Review.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e2400259},
doi = {10.1002/jobm.202400259},
pmid = {39113256},
issn = {1521-4028},
abstract = {Antibiotic resistance poses a formidable challenge to global public health, necessitating comprehensive understanding and strategic interventions. This review explores the evolution and transmission dynamics of antibiotic resistance genes, with a focus on Bangladesh. The indiscriminate use of antibiotics, compounded by substandard formulations and clinical misdiagnosis, fuels the emergence and spread of resistance in the country. Studies reveal high resistance rates among common pathogens, emphasizing the urgent need for targeted interventions and rational antibiotic use. Molecular assessments uncover a diverse array of antibiotic resistance genes in environmental reservoirs, highlighting the complex interplay between human activities and resistance dissemination. Horizontal gene transfer mechanisms, particularly plasmid-mediated conjugation, facilitate the exchange of resistance determinants among bacterial populations, driving the evolution of multidrug-resistant strains. The review discusses clinical implications, emphasizing the interconnectedness of environmental and clinical settings in resistance dynamics. Furthermore, bioinformatic and experimental evidence elucidates novel mechanisms of resistance gene transfer, underscoring the dynamic nature of resistance evolution. In conclusion, combating antibiotic resistance requires a multifaceted approach, integrating surveillance, stewardship, and innovative research to preserve the efficacy of antimicrobial agents and safeguard public health.},
}
@article {pmid39103341,
year = {2024},
author = {Hu, K and Chou, CW and Wilke, CO and Finkelstein, IJ},
title = {Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6653},
pmid = {39103341},
issn = {2041-1723},
support = {R01 GM124141/GM/NIGMS NIH HHS/United States ; R01GM088344//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 GM088344/GM/NIGMS NIH HHS/United States ; F-1808//Welch Foundation/ ; R01GM124141//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*DNA Transposable Elements/genetics ; *Escherichia coli/genetics/metabolism ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *Gene Transfer, Horizontal ; *CRISPR-Associated Proteins/metabolism/genetics ; Escherichia coli Proteins/genetics/metabolism ; },
abstract = {CASTs use both CRISPR-associated proteins and Tn7-family transposons for RNA-guided vertical and horizontal transmission. CASTs encode minimal CRISPR arrays but can't acquire new spacers. Here, we report that CASTs can co-opt defense-associated CRISPR arrays for horizontal transmission. A bioinformatic analysis shows that CASTs co-occur with defense-associated CRISPR systems, with the highest prevalence for type I-B and type V CAST sub-types. Using an E. coli quantitative transposition assay and in vitro reconstitution, we show that CASTs can use CRISPR RNAs from these defense systems. A high-resolution structure of the type I-F CAST-Cascade in complex with a type III-B CRISPR RNA reveals that Cas6 recognizes direct repeats via sequence-independent π - π interactions. In addition to using heterologous CRISPR arrays, type V CASTs can also transpose via an unguided mechanism, even when the S15 co-factor is over-expressed. Over-expressing S15 and the trans-activating CRISPR RNA or a single guide RNA reduces, but does not abrogate, off-target integration for type V CASTs. Our findings suggest that some CASTs may exploit defense-associated CRISPR arrays and that this fact must be considered when porting CASTs to heterologous bacterial hosts. More broadly, this work will guide further efforts to engineer the activity and specificity of CASTs for gene editing applications.},
}
@article {pmid39102038,
year = {2024},
author = {Olanrewaju, OS and Molale-Tom, LG and Bezuidenhout, CC},
title = {Genomic diversity, antibiotic resistance, and virulence in South African Enterococcus faecalis and Enterococcus lactis isolates.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {10},
pages = {289},
pmid = {39102038},
issn = {1573-0972},
mesh = {South Africa ; *Genome, Bacterial ; *Enterococcus faecalis/genetics/drug effects/pathogenicity/isolation &amp; purification ; Virulence/genetics ; *Genetic Variation ; *Anti-Bacterial Agents/pharmacology ; *Virulence Factors/genetics ; Humans ; Drug Resistance, Bacterial/genetics ; Genomic Islands/genetics ; Gram-Positive Bacterial Infections/microbiology ; Enterococcus/genetics/drug effects/pathogenicity/isolation &amp; purification/classification ; Phylogeny ; Gene Transfer, Horizontal ; Genomics ; Microbial Sensitivity Tests ; },
abstract = {This study presents the empirical findings of an in-depth genomic analysis of Enterococcus faecalis and Enterococcus lactis isolates from South Africa. It offers valuable insights into their genetic characteristics and their significant implications for public health. The study uncovers nuanced variations in the gene content of these isolates, despite their similar GC contents, providing a comprehensive view of the evolutionary diversity within the species. Genomic islands are identified, particularly in E. faecalis, emphasizing its propensity for horizontal gene transfer and genetic diversity, especially in terms of antibiotic resistance genes. Pangenome analysis reveals the existence of a core genome, accounting for a modest proportion of the total genes, with 2157 core genes, 1164 shell genes, and 4638 cloud genes out of 7959 genes in 52 South African E. faecalis genomes (2 from this study, 49 south Africa genomes downloaded from NCBI, and E. faecalis reference genome). Detecting large-scale genomic rearrangements, including chromosomal inversions, underscores the dynamic nature of bacterial genomes and their role in generating genetic diversity. The study uncovers an array of antibiotic resistance genes, with trimethoprim, tetracycline, glycopeptide, and multidrug resistance genes prevalent, raising concerns about the effectiveness of antibiotic treatment. Virulence gene profiling unveils a diverse repertoire of factors contributing to pathogenicity, encompassing adhesion, biofilm formation, stress resistance, and tissue damage. These empirical findings provide indispensable insights into these bacteria's genomic dynamics, antibiotic resistance mechanisms, and virulence potential, underlining the pressing need to address antibiotic resistance and implement robust control measures.},
}
@article {pmid39101807,
year = {2024},
author = {Dhurve, G and Behera, SR and Kodetham, G and Siddavattam, D},
title = {Outer membrane vesicles of Acinetobacter baumannii DS002 carry circular DNA similar to bovine meat and milk factors (BMMFs) and SPHINX 2.36 and probably play a role in interdomain lateral gene transfer.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0081724},
doi = {10.1128/spectrum.00817-24},
pmid = {39101807},
issn = {2165-0497},
abstract = {UNLABELLED: The discovery of Replication Competent Circular DNA molecules in mammalian cells and tissues is being linked to debilitating diseases, such as multiple sclerosis (MS), bovine spongiform encephalopathy (BSE), and colorectal cancer (CRC). These circular DNA molecules, otherwise known as bovine meat and milk factors (BMMFs) and Slow Progressive Hidden INfections of variable (X) latency (SPHINX), bear significant (80%) sequence similarity with the plasmids of Acinetobacter baumannii strains. Nanostructures, such as bacterial outer membrane vesicles (OMVs) serve as vehicles for transporting biomolecular cargo and have the potential to facilitate interkingdom lateral mobility of DNA. Strengthening the proposed hypothesis, this study demonstrates that OMVs derived from A. baumannii DS002 carrying four plasmids and genome (pTS236) of phage, AbDs1, successfully reached different parts of the body, including the central nervous system, following the injection of fluorescein isothiocyanate (FITC)-labeled OMVs into experimental mice. Out of the four OMV-associated plasmids, three (pTS4586, pTS9900, and pTS134338) were identified within the lumen, and the fourth one (pTS11291) was found on the surface of OMVs. In addition to the indigenous plasmids, the phage-encoded protein, Orf96, anchored on the surface of the OMVs by establishing a strong interaction with the OMV-associated porin, OmpA. Intriguingly, a subset of labeled OMVs, when incubated with Neuro2A cells, translocated across the membrane and reached to the cytoplasmic space of the cells. Collectively, the experimental evidence presented herein underscores the promising potential of OMVs as vehicles for delivering molecular cargo containing plasmids and phage genomes to diverse mammalian tissues and cells.<br><br>IMPORTANCE: Several independent studies have demonstrated the existence of replication competent circular DNA molecules of bacterial and viral origin in mammalian cells and tissues. However, studies about their origin and lateral mobility to mammalian cells are scarce. Our work describes the existence of circular DNA, similar to that of DNA molecules identified in mammalian cells, OMVs derived from soil isolate of A. baumannii DS002. Furthermore, the work also provides visual evidence that demonstrates the passage of labeled OMVs to different organs of experimental mice within hours after intravenously administering OMVs into experimental mice. Some of the labeled OMVs have even crossed the membrane of Neuro2A, suggesting the existence of interkingdom horizontal mobility between bacteria and mammals.},
}
@article {pmid39101574,
year = {2024},
author = {Rappaport, HB and Oliverio, AM},
title = {Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life.},
journal = {Genome biology and evolution},
volume = {16},
number = {8},
pages = {},
pmid = {39101574},
issn = {1759-6653},
mesh = {*Eukaryota/genetics ; *Extremophiles/genetics ; Adaptation, Physiological/genetics ; Genomics ; Genome ; Evolution, Molecular ; Phylogeny ; },
abstract = {From hydrothermal vents, to glaciers, to deserts, research in extreme environments has reshaped our understanding of how and where life can persist. Contained within the genomes of extremophilic organisms are the blueprints for a toolkit to tackle the multitude of challenges of survival in inhospitable environments. As new sequencing technologies have rapidly developed, so too has our understanding of the molecular and genomic mechanisms that have facilitated the success of extremophiles. Although eukaryotic extremophiles remain relatively understudied compared to bacteria and archaea, an increasing number of studies have begun to leverage 'omics tools to shed light on eukaryotic life in harsh conditions. In this perspective paper, we highlight a diverse breadth of research on extremophilic lineages across the eukaryotic tree of life, from microbes to macrobes, that are collectively reshaping our understanding of molecular innovations at life's extremes. These studies are not only advancing our understanding of evolution and biological processes but are also offering a valuable roadmap on how emerging technologies can be applied to identify cellular mechanisms of adaptation to cope with life in stressful conditions, including high and low temperatures, limited water availability, and heavy metal habitats. We shed light on patterns of molecular and organismal adaptation across the eukaryotic tree of life and discuss a few promising research directions, including investigations into the role of horizontal gene transfer in eukaryotic extremophiles and the importance of increasing phylogenetic diversity of model systems.},
}
@article {pmid39100236,
year = {2024},
author = {Bhattacharya, A and Aluquin, A and Kennedy, DA},
title = {Exceptions to the rule: When does resistance evolution not undermine antibiotic therapy in human bacterial infections?.},
journal = {Evolution letters},
volume = {8},
number = {4},
pages = {478-493},
pmid = {39100236},
issn = {2056-3744},
abstract = {The use of antibiotics to treat bacterial infections often imposes strong selection for antibiotic resistance. However, the prevalence of antibiotic resistance varies greatly across different combinations of pathogens and drugs. What underlies this variation? Systematic reviews, meta-analyses, and literature surveys capable of integrating data across many studies have tried to answer this question, but the vast majority of these studies have focused only on cases where resistance is common or problematic. Yet much could presumably be learned from the cases where resistance is infrequent or absent. Here we conducted a literature survey and a systematic review to study the evolution of antibiotic resistance across a wide range of pathogen-by-drug combinations (57 pathogens and 53 antibiotics from 15 drug classes). Using Akaike information criterion-based model selection and model-averaged parameter estimation we explored 14 different factors posited to be associated with resistance evolution. We find that the most robust predictors of high resistance are nosocomial transmission (i.e., hospital-acquired pathogens) and indirect transmission (e.g., vector-, water-, air-, or vehicle-borne pathogens). While the former was to be expected based on prior studies, the positive correlation between high resistance frequencies and indirect transmission is, to our knowledge, a novel insight. The most robust predictor of low resistance is zoonosis from wild animal reservoirs. We also found partial support that resistance was associated with pathogen type, horizontal gene transfer, commensalism, and human-to-human transmission. We did not find support for correlations between resistance and environmental reservoirs, mechanisms of drug action, and global drug use. This work explores the relative explanatory power of various pathogen and drug factors on resistance evolution, which is necessary to identify priority targets of stewardship efforts to slow the spread of drug-resistant pathogens.},
}
@article {pmid39100235,
year = {2024},
author = {Ciach, MA and Pawłowska, J and Górecki, P and Muszewska, A},
title = {The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities.},
journal = {Evolution letters},
volume = {8},
number = {4},
pages = {526-538},
pmid = {39100235},
issn = {2056-3744},
abstract = {Numerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand the hosts' metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided an extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), a similar characterization is still missing. In order to fill this gap, we have designed a computational pipeline to obtain a statistical sample of reliable HGT events with a low false discovery rate. We have analyzed 44 EDF proteomes and identified 829 xenologs in fungi ranging from Chytridiomycota to Mucoromycota. We have identified several patterns and statistical properties of EDF HGT. We show that HGT is driven by bursts of gene exchange and duplication, resulting in highly divergent numbers and molecular properties of xenologs between fungal lineages. Ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. Endosymbiotic bacteria can be a source of useful xenologs, as exemplified by NOD-like receptors transferred to Mortierellomycota. Closely related fungi have similar rates of intronization of xenologs. Posttransfer gene fusions and losses of protein domains are common and may influence the encoded proteins' functions. We argue that there is no universal approach for HGT identification and inter- and intra-kingdom transfers require tailored identification methods. Our results help to better understand how and to what extent HGT has shaped the metabolic, adaptive, and immune capabilities of fungi.},
}
@article {pmid39098155,
year = {2024},
author = {Wang, H and Gao, J and Ren, H and Zhao, Y and Wang, Y and An, J and Chen, H and Wang, Q},
title = {Whatever does not kill them makes them stronger: Using quaternary ammonia antimicrobials to alleviate the inhibition of ammonia oxidation under perfluorooctanoic acid stress.},
journal = {Water research},
volume = {263},
number = {},
pages = {122171},
doi = {10.1016/j.watres.2024.122171},
pmid = {39098155},
issn = {1879-2448},
abstract = {Perfluorooctanoic acid (PFOA), benzalkyl dimethylammonium compounds (BAC) and antibiotic resistance genes (ARGs) have negative effects on biological sewage treatment. The performance of nitrification systems under stress of PFOA (0.1-5 mg/L) or/and BAC (0.2-10 mg/L) was explored during 84-day experiments using four sequencing batch reactors, in this study. Low (0.1 mg/L) concentration PFOA had a positive influence on ammonia removal, while medium and high (2 and 5 mg/L) concentrations PFOA caused severe inhibition. Meanwhile, PFOA stress resulted in the enrichment of ARGs in water (w-ARGs). BAC (0-10 mg/L) had no obvious influence on ammonia removal. However, BAC promoted the reduction of ARGs and the bacterial community was the main participator (48.07%) for the spread of ARGs. Interestingly, the joint stress of PFOA and BAC increased the ammonia-oxidizing bacteria (AOB) activity from 5.81 ± 0.19 and 6.05 ± 0.79 mg N/(g MLSS·h) to 7.09 ± 0.87 and 7.23 ± 0.29 mg N/(g MLSS·h) in medium and high concentrations, compared to single stress of PFOA, which was observed for the first time. BAC could reduce bioavailability of PFOA through competitive adsorption and decreasing sludge hydrophobicity by the lower β-Sheet and α-Helix in tightly bound protein. Furthermore, the joint stress of PFOA and BAC was able to intensify the proliferation of w-ARGs and extracellular ARGs in sludge, and developed the most active horizontal gene transfer mediated by intl1 compared to single stress of PFOA or BAC. The batch tests verified the detoxification capacity of BAC on nitrification under 2.5 mg/L PFOA (48 h exposing), and the maximum alleviation of AOB activity was achieved at BAC and PFOA mass ratio of 2:1. In summary, BAC could be used to alleviate the inhibition of PFOA on ammonia oxidation, providing an efficient and sustainable approach in wastewater treatment.},
}
@article {pmid39096995,
year = {2024},
author = {Tian, J and Xu, L and Sun, JQ},
title = {Taxonomic characterization and comparative genomic analysis of a novel Devosia species revealed that phenolic acid-degrading traits are ubiquitous in the Devosia genus.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119724},
doi = {10.1016/j.envres.2024.119724},
pmid = {39096995},
issn = {1096-0953},
abstract = {Phenolic acids (PAs) are widely distributed allelochemicals in various environments. To better understand the fate of PAs in environments, a halotolerant PAs-degrading bacterium (named strain RR2S18[T]) isolated from rhizosphere soil was identified as a novel species of Devosia, named Devosia rhizosphaerae sp. nov. The strain initially degraded PAs into central ring-fission intermediates (protocatechuic acid) using the CoA-dependent non-β-oxidation pathway. The produced ring-fission intermediates were then consecutively degraded by an ortho-cleavage reaction and the β-ketoadipic acid pathway. A comparative genomics analysis of 62 Devosia strains revealed that PAs-degrading genes were ubiquitous in their genomes, indicating that PAs degradation is universal among members of this genus. The analysis also suggested that the genes involved in CoA-dependent non-β-oxidation are inherent to Devosia strains, while those involved in ring-fission and β-ketoadipic acid pathways were obtained by horizontal gene transfer.},
}
@article {pmid39095425,
year = {2024},
author = {Landa, CR and Ariza-Mateos, A and Briones, C and Perales, C and Wagner, A and Domingo, E and Gómez, J},
title = {Adapting the rhizome concept to an extended definition of viral quasispecies and the implications for molecular evolution.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {17914},
pmid = {39095425},
issn = {2045-2322},
mesh = {*Rhizome/virology ; *Evolution, Molecular ; *Quasispecies/genetics ; *Phylogeny ; RNA Viruses/genetics/classification ; Gene Transfer, Horizontal ; Mutation ; Genome, Viral ; },
abstract = {The rhizome concept proposed by Gilles Deleuze and Félix Guattari offers a novel perspective on the organization and interdependence of complex constellations of heterogeneous entities, their mapping and their ruptures. The emphasis of the present study is placed on the dynamics of contacts and communication among such entities that arise from experimentation, without any favored hierarchy or origin. When applied to biological evolution, the rhizome concept integrates all types of heterogeneity resulting from "symbiotic" relationships among living beings (or their genomic material), horizontal genetic transfer, recombination and mutation, and breaks away from the approach that gives rise to the phylogenetic tree of life. It has already been applied to describe the dynamics and evolution of RNA viruses. Thus, here we introduce a novel framework for the interpretation the viral quasispecies concept, which explains the evolution of RNA virus populations as the result of dynamic interconnections and multifaceted interdependence between highly heterogeneous viral sequences and its inherently heterogeneous host cells. The rhizome network perspective underlines even further the medical implications of the broad mutant spectra of viruses that are in constant flow, given the multiple pathways they have available for fitness loss and gain.},
}
@article {pmid39095161,
year = {2025},
author = {Guo, Z and Tang, X and Wang, W and Luo, Z and Zeng, Y and Zhou, N and Yu, Z and Wang, D and Song, B and Zhou, C and Xiong, W},
title = {The photo-based treatment technology simultaneously removes resistant bacteria and resistant genes from wastewater.},
journal = {Journal of environmental sciences (China)},
volume = {148},
number = {},
pages = {243-262},
doi = {10.1016/j.jes.2024.01.005},
pmid = {39095161},
issn = {1001-0742},
mesh = {*Wastewater/chemistry ; *Waste Disposal, Fluid/methods ; Bacteria ; Disinfection/methods ; Drug Resistance, Bacterial/genetics ; Ultraviolet Rays ; Water Purification/methods ; },
abstract = {Because of the recent widespread usage of antibiotics, the acquisition and dissemination of antibiotic-resistance genes (ARGs) were prevalent in the majority of habitats. Generally, the biological wastewater treatment processes used in wastewater treatment plants have a limited efficiencies of antibiotics resistant bacteria (ARB) disinfection and ARGs degradation and even promote the proliferation of ARGs. Problematically, ARB and ARGs in effluent pose potential risks if they are not further treated. Photocatalytic oxidation is considered a promising disinfection technology, where the photocatalytic process generates many free radicals that enhance the interaction between light and deoxyribonucleic acid (DNA) for ARB elimination and subsequent degradation of ARGs. This review aims to illustrate the progress of photocatalytic oxidation technology for removing antibiotics resistant (AR) from wastewater in recent years. We discuss the sources and transfer of ARGs in wastewater. The overall removal efficiencies of ultraviolet radiation (UV)/chlorination, UV/ozone, UV/H2O2, and UV/sulfate-radical based system for ARB and ARGs, as well as the experimental parameters and removal mechanisms, are systematically discussed. The contribution of photocatalytic materials based on TiO2 and g-C3N4 to the inactivation of ARB and degradation of ARGs is highlighted, producing many free radicals to attack ARB and ARGs while effectively limiting the horizontal gene transfer (HGT) in wastewater. Finally, based on the reviewed studies, future research directions are proposed to realize specific photocatalytic oxidation technology applications and overcome current challenges.},
}
@article {pmid39093595,
year = {2024},
author = {Wu, J and Meng, L and Gaïa, M and Hikida, H and Okazaki, Y and Endo, H and Ogata, H},
title = {Gene transfer among viruses substantially contributes to gene gain of giant viruses.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msae161},
pmid = {39093595},
issn = {1537-1719},
abstract = {The phylum Nucleocytoviricota comprises a diverse group of double-stranded DNA viruses that display a wide range of gene repertoires. Although these gene repertoires determine the characteristics of individual viruses, the evolutionary processes that have shaped the gene repertoires of extant viruses since their common ancestor are poorly characterized. In this study, we aimed to address this gap in knowledge by using amalgamated likelihood estimation (ALE), a probabilistic tree reconciliation method that infers evolutionary scenarios by distinguishing origination, gene duplications, virus-to-virus horizontal gene transfer (vHGT), and gene losses. We analyzed over 4,700 gene families from 195 genomes spanning all known viral orders. The evolutionary reconstruction suggests a history of extensive gene gains and losses during the evolution of these viruses, notably with vHGT contributing to gene gains at a comparable level to duplications and originations. The vHGT frequently occurred between phylogenetically closely related viruses, as well as between distantly related viruses with an overlapping host range. We observed a pattern of massive gene duplications that followed vHGTs for gene families that was potentially related to host range control and virus-host arms race. These results suggest that vHGT represents a previously overlooked, yet important, evolutionary force that integrates the evolutionary paths of multiple viruses and affects shaping of Nucleocytoviricota virus gene repertoires.},
}
@article {pmid39082809,
year = {2024},
author = {Kanno, K and Kuriki, R and Yasuno, Y and Shinada, T and Ito, T and Hemmi, H},
title = {Archaeal mevalonate pathway in the uncultured bacterium Candidatus Promineifilum breve belonging to the phylum Chloroflexota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0110624},
doi = {10.1128/aem.01106-24},
pmid = {39082809},
issn = {1098-5336},
abstract = {The archaeal mevalonate pathway is a recently discovered modified version of the eukaryotic mevalonate pathway. This pathway is widely conserved in archaea, except for some archaeal lineages possessing the eukaryotic or other modified mevalonate pathways. Although the pathway seems almost exclusive to the domain Archaea, the whole set of homologous genes of the pathway is found in the metagenome-assembled genome sequence of an uncultivated bacterium, Candidatus Promineifilum breve, of the phylum Chloroflexota. To prove the existence of the archaea-specific pathway in the domain Bacteria, we confirmed the activities of the enzymes specific to the pathway, phosphomevalonate dehydratase and anhydromevalonate phosphate decarboxylase, because only these two enzymes are absent in closely related Chloroflexota bacteria that possess a different type of modified mevalonate pathway. The activity of anhydromevalonate phosphate decarboxylase was evaluated by carotenoid production via the archaeal mevalonate pathway reconstituted in Escherichia coli cells, whereas that of phosphomevalonate dehydratase was confirmed by an in vitro assay using the recombinant enzyme after purification and iron-sulfur cluster reconstruction. Phylogenetic analyses of some mevalonate pathway-related enzymes suggest an evolutionary route for the archaeal mevalonate pathway in Candidatus P. breve, which probably involves horizontal gene transfer events.IMPORTANCEThe recent discovery of various modified mevalonate pathways in microorganisms, such as archaea and Chloroflexota bacteria, has shed light on the complexity of the evolution of metabolic pathways, including those involved in primary metabolism. The fact that the archaeal mevalonate pathway, which is almost exclusive to the domain Archaea, exists in a Chloroflexota bacterium provides valuable insights into the molecular evolution of the mevalonate pathways and associated enzymes. Putative genes probably involved in the archaeal mevalonate pathway have also been found in the metagenome-assembled genomes of Chloroflexota bacteria. Such genes can contribute to metabolic engineering for the bioproduction of valuable isoprenoids because the archaeal mevalonate pathway is known to be an energy-saving metabolic pathway that consumes less ATP than other mevalonate pathways do.},
}
@article {pmid38823494,
year = {2024},
author = {Tang, C and Shen, S and Yang, W and Shi, Q and Ding, L and Han, R and Hu, F},
title = {Dynamic evolution of ceftazidime-avibactam resistance from a single patient through the IncX3_NDM-5 plasmid transfer and blaKPC mutation.},
journal = {International journal of antimicrobial agents},
volume = {64},
number = {2},
pages = {107228},
doi = {10.1016/j.ijantimicag.2024.107228},
pmid = {38823494},
issn = {1872-7913},
mesh = {*Ceftazidime/pharmacology ; *Azabicyclo Compounds/pharmacology ; *Drug Combinations ; *Plasmids/genetics ; Humans ; *Klebsiella pneumoniae/genetics/drug effects ; *beta-Lactamases/genetics ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; *Enterobacter cloacae/genetics/drug effects ; *Mutation ; *Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/genetics/drug effects ; Klebsiella Infections/microbiology/drug therapy ; Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects ; },
abstract = {The rapid dissemination of carbapenem-resistant Enterobacterales (CRE) especially carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a great threat to global public health. Ceftazidime-avibactam, a novel β-lactam/β-lactamase inhibitor combination, has been widely used due to its excellent antibacterial activity against KPC-producing K. pneumoniae. However, several resistance mechanisms have been reported since its use. Here, we conducted a series of in vitro experiments to reveal and demonstrate the dynamic evolution of ceftazidime-avibactam resistance including interspecies IncX3_NDM-5 plasmid transfer between Enterobacter cloacae and K. pneumoniae and blaKPC mutation from blaKPC-2 to blaKPC-33. Through the analysis of conjugation frequency and fitness cost, the IncX3_NDM-5 plasmid in this study showed strong transmissibility and stability in E. coli EC600 and clinical strain K. pneumoniae 5298 as recipient strain. With increasing ceftazidime-avibactam concentration, the conjugation frequency remained at 10[-3]-10[-5], while the mutation frequency of K. pneumoniae 5298 was 10[-6]-10[-8] at the same concentration. Further plasmid analysis (the IncX3_NDM plasmid from this study and other 658 plasmids from the NCBI database) revealed the diverse origin and genetic structure of blaNDM-5 carrying plasmids. E. coli (42.9%), China (43.9%), IncX3 (66.6%) are the most common strains, regions, and Inc types respectively. By analysing of genetic environment detected in IncX3 plasmids, the dominant structures (168/258, 65.1%) were identified: ISKox3-IS26-blaNDM-5-IS5-ISAba125-Tn3000-Tn3. In additon, several structural variations were found in the core gene structure. In conclusion, the high fitness and transmissibility of the IncX3_NDM-5 plasmids were noteworthy. More importantly, the diverse ceftazidime-avibactam resistance mechanisms including blaNDM-5 tranfer and blaKPC-2 mutation highlighted the importance of the continuous monitoring of antimicrobial susceptibility and carbapenemases subtype during ceftazidime-avibactam treatment.},
}
@article {pmid39080678,
year = {2024},
author = {Rajput, M and Pandey, M and Dixit, R and Shukla, VK},
title = {Is cross-species horizontal gene transfer responsible for gallbladder carcinogenesis.},
journal = {World journal of surgical oncology},
volume = {22},
number = {1},
pages = {201},
pmid = {39080678},
issn = {1477-7819},
mesh = {Humans ; *Gene Transfer, Horizontal ; *Gallbladder Neoplasms/genetics/pathology/virology ; Carcinogenesis/genetics ; RNA, Antisense/genetics ; Gene Expression Regulation, Neoplastic ; Transcriptome ; },
abstract = {BACKGROUND: Cross-species horizontal gene transfer (HGT) involves the transfer of genetic material between different species of organisms. In recent years, mounting evidence has emerged that cross-species HGT does take place and may play a role in the development and progression of diseases.<br><br>METHODS: Transcriptomic data obtained from patients with gallbladder cancer (GBC)&#xa0;was assessed for the differential expression of antisense RNAs (asRNAs). The Basic Local Alignment Search Tool (BLAST) was used for&#xa0;cross-species analysis with viral, bacterial, fungal, and ancient human genomes to elucidate the evolutionary cross species origins of these differential asRNAs. Functional enrichment analysis and text mining were conducted and a network of asRNAs targeting mRNAs was constructed to understand the function of differential asRNAs better.<br><br>RESULTS: A total of 17 differentially expressed antisense RNAs (asRNAs) were identified in gallbladder cancer tissue&#xa0;compared to that of normal gallbladder. BLAST analysis of 15 of these asRNAs (AFAP1-AS1, HMGA2-AS1, MNX1-AS1, SLC2A1-AS1, BBOX1-AS1, ELFN1-AS1, TRPM2-AS, DNAH17-AS1, DCST1-AS1, VPS9D1-AS1, MIR1-1HG-AS1, HAND2-AS1, PGM5P4-AS1, PGM5P3-AS1, and MAGI2-AS) showed varying degree of similarities with bacterial and viral genomes, except for UNC5B-AS1 and SOX21-AS1, which were conserved during evolution. Two of these 15&#xa0;asRNAs, (VPS9D1-AS1 and SLC2A1-AS1) exhibited a high degree of similarity with viral genomes (Chikungunya virus, Human immunodeficiency virus 1, Stealth virus 1, and Zika virus) and bacterial genomes including (Staphylococcus sp., Bradyrhizobium sp., Pasteurella multocida sp., and, Klebsiella pneumoniae sp.), indicating potential HGT during evolution.<br><br>CONCLUSION: The results provide novel evidence supporting the hypothesis that differentially expressed asRNAs in GBC exhibit varying sequence similarity with bacterial, viral, and ancient human genomes, indicating a potential shared evolutionary origin. These non-coding genes are enriched with methylation and were found to be associated with cancer-related pathways, including the P53 and PI3K-AKT signaling pathways, suggesting their possible involvement in tumor development.},
}
@article {pmid39079455,
year = {2024},
author = {Russell, SL and Penunuri, G and Condon, C},
title = {Diverse genetic conflicts mediated by molecular mimicry and computational approaches to detect them.},
journal = {Seminars in cell &amp; developmental biology},
volume = {165},
number = {},
pages = {1-12},
doi = {10.1016/j.semcdb.2024.07.001},
pmid = {39079455},
issn = {1096-3634},
abstract = {In genetic conflicts between intergenomic and selfish elements, driver and killer elements achieve biased survival, replication, or transmission over sensitive and targeted elements through a wide range of molecular mechanisms, including mimicry. Driving mechanisms manifest at all organismal levels, from the biased propagation of individual genes, as demonstrated by transposable elements, to the biased transmission of genomes, as illustrated by viruses, to the biased transmission of cell lineages, as in cancer. Targeted genomes are vulnerable to molecular mimicry through the conserved motifs they use for their own signaling and regulation. Mimicking these motifs enables an intergenomic or selfish element to control core target processes, and can occur at the sequence, structure, or functional level. Molecular mimicry was first appreciated as an important phenomenon more than twenty years ago. Modern genomics technologies, databases, and machine learning approaches offer tremendous potential to study the distribution of molecular mimicry across genetic conflicts in nature. Here, we explore the theoretical expectations for molecular mimicry between conflicting genomes, the trends in molecular mimicry mechanisms across known genetic conflicts, and outline how new examples can be gleaned from population genomic datasets. We discuss how mimics involving short sequence-based motifs or gene duplications can evolve convergently from new mutations. Whereas, processes that involve divergent domains or fully-folded structures occur among genomes by horizontal gene transfer. These trends are largely based on a small number of organisms and should be reevaluated in a general, phylogenetically independent framework. Currently, publicly available databases can be mined for genotypes driving non-Mendelian inheritance patterns, epistatic interactions, and convergent protein structures. A subset of these conflicting elements may be molecular mimics. We propose approaches for detecting genetic conflict and molecular mimicry from these datasets.},
}
@article {pmid39078126,
year = {2024},
author = {Ai, C and Cui, P and Liu, C and Wu, J and Xu, Y and Liang, X and Yang, Q and Tang, X and Zhou, S and Liao, H and Friman, V-P},
title = {Viral and thermal lysis facilitates transmission of antibiotic resistance genes during composting.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0069524},
doi = {10.1128/aem.00695-24},
pmid = {39078126},
issn = {1098-5336},
abstract = {UNLABELLED: While the distribution of extracellular ARGs (eARGs) in the environment has been widely reported, the factors governing their release remain poorly understood. Here, we combined multi-omics and direct experimentation to test whether the release and transmission of eARGs are associated with viral lysis and heat during cow manure composting. Our results reveal that the proportion of eARGs increased 2.7-fold during composting, despite a significant and concomitant reduction in intracellular ARG abundances. This relative increase of eARGs was driven by composting temperature and viral lysis of ARG-carrying bacteria based on metagenome-assembled genome (MAG) analysis. Notably, thermal lysis of mesophilic bacteria carrying ARGs was a key factor in releasing eARGs at the thermophilic phase, while viral lysis played a relatively stronger role during the non-thermal phase of composting. Furthermore, MAG-based tracking of ARGs in combination with direct transformation experiments demonstrated that eARGs released during composting pose a potential transmission risk. Our study provides bioinformatic and experimental evidence of the undiscovered role of temperature and viral lysis in co-driving the spread of ARGs in compost microbiomes via the horizontal transfer of environmentally released DNA.<br><br>IMPORTANCE: The spread of antibiotic resistance genes (ARGs) is a critical global health concern. Understanding the factors influencing the release of extracellular ARGs (eARGs) is essential for developing effective strategies. In this study, we investigated the association between viral lysis, heat, and eARG release during composting. Our findings revealed a substantial increase in eARGs despite reduced intracellular ARG abundance. Composting temperature and viral lysis were identified as key drivers, with thermal lysis predominant during the thermophilic phase and viral lysis during non-thermal phases. Moreover, eARGs released during composting posed a transmission risk through horizontal gene transfer. This study highlights the significance of temperature and phage lysis in ARG spread, providing valuable insights for mitigating antibiotic resistance threats.},
}
@article {pmid38598855,
year = {2024},
author = {Hsieh, SC and Peters, JE},
title = {Natural and Engineered Guide RNA-Directed Transposition with CRISPR-Associated Tn7-Like Transposons.},
journal = {Annual review of biochemistry},
volume = {93},
number = {1},
pages = {139-161},
doi = {10.1146/annurev-biochem-030122-041908},
pmid = {38598855},
issn = {1545-4509},
mesh = {*DNA Transposable Elements/genetics ; *CRISPR-Cas Systems ; *RNA, Guide, CRISPR-Cas Systems/genetics/metabolism ; *Transposases/metabolism/genetics ; Gene Editing/methods ; Bacteria/genetics ; Plasmids/metabolism/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; },
abstract = {CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated nuclease) defense systems have been naturally coopted for guide RNA-directed transposition on multiple occasions. In all cases, cooption occurred with diverse elements related to the bacterial transposon Tn7. Tn7 tightly controls transposition; the transposase is activated only when special targets are recognized by dedicated target-site selection proteins. Tn7 and the Tn7-like elements that coopted CRISPR-Cas systems evolved complementary targeting pathways: one that recognizes a highly conserved site in the chromosome and a second pathway that targets mobile plasmids capable of cell-to-cell transfer. Tn7 and Tn7-like elements deliver a single integration into the site they recognize and also control the orientation of the integration event, providing future potential for use as programmable gene-integration tools. Early work has shown that guide RNA-directed transposition systems can be adapted to diverse hosts, even within microbial communities, suggesting great potential for engineering these systems as powerful gene-editing tools.},
}
@article {pmid39073917,
year = {2024},
author = {Gao, L and Liu, L and Lv, AP and Fu, L and Lian, ZH and Nunoura, T and Hedlund, BP and Xu, QY and Wu, D and Yang, J and Ali, M and Li, MM and Liu, YH and Antunes, A and Jiang, HC and Cheng, L and Jiao, JY and Li, WJ and Fang, BZ},
title = {Reversed oxidative TCA (roTCA) for carbon fixation by an Acidimicrobiia strain from a saline lake.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae147},
pmid = {39073917},
issn = {1751-7370},
abstract = {Acidimicrobiia are widely distributed in nature and suggested to be autotrophic via the Calvin-Benson-Bassham (CBB) cycle. However, direct evidence of chemolithoautotrophy in Acidimicrobiia is lacking. Here, we report a chemolithoautotrophic enrichment from a saline lake, and the subsequent isolation and characterization of a chemolithoautotroph, Salinilacustristhrix flava EGI L10123T, which belongs to a new Acidimicrobiia family. Although strain EGI L10123T is autotrophic, neither its genome nor Acidimicrobiia metagenome-assembled genomes (MAGs) from the enrichment culture encode genes necessary for the CBB cycle. Instead, genomic, transcriptomic, enzymatic, and stable-isotope probing data hinted at the activity of the reversed oxidative TCA (roTCA) coupled with the oxidation of sulfide as the electron donor. Phylogenetic analysis and ancestral character reconstructions of Acidimicrobiia suggested that the essential CBB gene rbcL was acquired through multiple horizontal gene transfer events from diverse microbial taxa. In contrast, genes responsible for sulfide- or hydrogen-dependent roTCA carbon fixation were already present in the last common ancestor of extant Acidimicrobiia. These findings imply the possibility of roTCA carbon fixation in Acidimicrobiia and the ecological importance of Acidimicrobiia. Further research in the future is necessary to confirm whether these characteristics are truly widespread across the clade.},
}
@article {pmid39071422,
year = {2024},
author = {Robinson, LR and Mcdevitt, CJ and Regan, MR and Quail, SL and Wadsworth, CB},
title = {In vitro evolution of ciprofloxacin resistance in Neisseria commensals and derived mutation population dynamics in natural Neisseria populations.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39071422},
issn = {2692-8205},
support = {R15 AI174182/AI/NIAID NIH HHS/United States ; },
abstract = {Commensal Neisseria are members of a healthy human oropharyngeal microbiome; however, they also serve as a reservoir of antimicrobial resistance for their pathogenic relatives. Despite their known importance as sources of novel genetic variation for pathogens, we still do not understand the full suite of resistance mutations commensal species can harbor. Here, we use in vitro selection to assess the mutations that emerge in response to ciprofloxacin selection in commensal Neisseria by passaging 4 replicates of 4 different species in the presence of a selective antibiotic gradient for 20 days; then categorized derived mutations with whole genome sequencing. 10/16 selected cells lines across the 4 species evolved ciprofloxacin resistance (≥ 1 ug/ml); with resistance-contributing mutations primarily emerging in DNA gyrase subunit A and B (gyrA and gyrB), topoisomerase IV subunits C and E (parC and parE), and the multiple transferable efflux pump repressor (mtrR). Of note, these derived mutations appeared in the same loci responsible for ciprofloxacin reduced susceptibility in the pathogenic Neisseria, suggesting conserved mechanisms of resistance across the genus. Additionally, we tested for zoliflodacin cross-resistance in evolved strain lines and found 6 lineages with elevated zoliflodacin minimum inhibitory concentrations. Finally, to interrogate the likelihood of experimentally derived mutations emerging and contributing to resistance in natural Neisseria, we used a population-based approach and identified GyrA 91I as a substitution circulating within commensal Neisseria populations and ParC 85C in a single gonococcal isolate. Small clusters of gonococcal isolates had commensal-like alleles at parC and parE, indicating recent cross-species recombination events.},
}
@article {pmid39071318,
year = {2024},
author = {Sloan, DB and Broz, AK and Kuster, SA and Muthye, V and Peñafiel-Ayala, A and Marron, JR and Lavrov, DV and Brieba, LG},
title = {Expansion of the MutS Gene Family in Plants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.07.17.603841},
pmid = {39071318},
issn = {2692-8205},
abstract = {UNLABELLED: The MutS gene family is distributed across the tree of life and is involved in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded the set of MutS genes in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes. Land plants, green algae, red algae, and glaucophytes share cyanobacterial-like MutS1 and MutS2 genes that presumably were gained via plastid endosymbiotic gene transfer. MutS1 was subsequently lost in some taxa, including seed plants, whereas MutS2 was duplicated in Viridiplantae (i.e., land plants and green algae) with widespread retention of both resulting paralogs. Viridiplantae also have two anciently duplicated copies of the eukaryotic MSH6 gene (i.e., MSH6 and MSH7) and acquired MSH1 via horizontal gene transfer - potentially from a nucleocytovirus. Despite sharing the same name, "plant MSH1 " is not directly related to the gene known as MSH1 in some fungi and animals, which may be an ancestral eukaryotic gene acquired via mitochondrial endosymbiosis and subsequently lost in most eukaryotic lineages. There has been substantial progress in understanding the functions of MSH1 and MSH6 / MSH7 in plants, but the roles of the cyanobacterial-like MutS1 and MutS2 genes remain uncharacterized. Known functions of bacterial homologs and predicted protein structures, including fusions to diverse nuclease domains, provide hypotheses about potential molecular mechanisms. Because most plant-specific MutS proteins are targeted to the mitochondria and/or plastids, the expansion of this family appears to have played a large role in shaping plant organelle genetics.<br><br>ONE-SENTENCE SUMMARY: Plants are distinguished from other eukaryotes by a functionally diverse complement of MutS proteins gained via a combination of gene duplication, endosymbiotic gene transfer, and horizontal gene transfer.},
}
@article {pmid38964386,
year = {2024},
author = {Shi, J and Sun, C and An, T and Jiang, C and Mei, S and Lv, B},
title = {Unraveling the effect of micro/nanoplastics on the occurrence and horizontal transfer of environmental antibiotic resistance genes: Advances, mechanisms and future prospects.},
journal = {The Science of the total environment},
volume = {947},
number = {},
pages = {174466},
doi = {10.1016/j.scitotenv.2024.174466},
pmid = {38964386},
issn = {1879-1026},
mesh = {*Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Microplastics ; Anti-Bacterial Agents ; Bacteria/drug effects ; Genes, Bacterial ; },
abstract = {Microplastics can not only serve as vectors of antibiotic resistance genes (ARGs), but also they and even nanoplastics potentially affect the occurrence of ARGs in indigenous environmental microorganisms, which have aroused great concern for the development of antibiotic resistance. This article specifically reviews the effects of micro/nanoplastics (concentration, size, exposure time, chemical additives) and their interactions with other pollutants on environmental ARGs dissemination. The changes of horizontal genes transfer (HGT, i.e., conjugation, transformation and transduction) of ARGs caused by micro/nanoplastics were also summarized. Further, this review systematically sums up the mechanisms of micro/nanoplastics regulating HGT process of ARGs, including reactive oxygen species production, cell membrane permeability, transfer-related genes expression, extracellular polymeric substances production, and ARG donor-recipient adsorption/contaminants adsorption/biofilm formation. The underlying mechanisms in changes of bacterial communities induced by micro/nanoplastics were also discussed as it was an important factor for structuring the profile of ARGs in the actual environment, including causing environmental stress, providing carbon sources, forming biofilms, affecting pollutants distribution and environmental factors. This review contributes to a systematical understanding of the potential risks of antibiotic resistance dissemination caused by micro/nanoplastics and provokes thinking about perspectives for future research and the management of micro/nanoplastics and plastics.},
}
@article {pmid39071313,
year = {2024},
author = {Yang, XY and Shen, Z and Wang, C and Nakanishi, K and Fu, TM},
title = {DdmDE eliminates plasmid invasion by DNA-guided DNA targeting.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.07.20.604412},
pmid = {39071313},
issn = {2692-8205},
abstract = {Horizontal gene transfer is a key driver of bacterial evolution, but it also presents severe risks to bacteria by introducing invasive mobile genetic elements. To counter these threats, bacteria have developed various defense systems, including prokaryotic Argonautes (pAgo) and the D NA D efense M odule DdmDE system. Through biochemical analysis, structural determination, and in vivo plasmid clearance assays, we elucidate the assembly and activation mechanisms of DdmDE, which eliminates small, multicopy plasmids. We demonstrate that DdmE, a pAgo-like protein, acts as a catalytically inactive, DNA-guided, DNA-targeting defense module. In the presence of guide DNA, DdmE targets plasmids and recruits a dimeric DdmD, which contains nuclease and helicase domains. Upon binding to DNA substrates, DdmD transitions from an autoinhibited dimer to an active monomer, which then translocates along and cleaves the plasmids. Together, our findings reveal the intricate mechanisms underlying DdmDE-mediated plasmid clearance, offering fundamental insights into bacterial defense systems against plasmid invasions.},
}
@article {pmid39067739,
year = {2024},
author = {Chen, X and Song, X and Liang, Y and Wang, F and Pan, C and Wei, Z},
title = {Evaluation of the potential horizontal gene transfer ability during chicken manure and pig manure composting.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {124621},
doi = {10.1016/j.envpol.2024.124621},
pmid = {39067739},
issn = {1873-6424},
abstract = {Resistance genes have been identified as emerging pollutants due to their ability to rapidly spread in the environment through horizontal gene transfer (HGT). Microbial community serves as the pivotal factor influencing the frequency of HGT during manure composting. However, the characteristics of HGT in microbial community from different types of manure were unclear. Therefore, this study aimed to evaluate the potential risk of HGT in bacterial community through the co-composting of chicken manure and pig manure in different proportions. The experimental results showed that the abundance of sulfonamide antibiotic resistance genes and integrase genes was higher during pig manure composting than those during chicken manure composting. In addition, the addition of pig manure also increased resistance genes abundance during chicken manure composting. These results suggested that the potential HGT risk was greater during pig manure composting. Furthermore, microbial analysis of co-composting suggested bacterial community of pig manure was more competitive and adaptable than that of chicken manure. Ultimately, statistical analysis indicated that compared to chicken manure composting, the potential ability of HGT was greater during pig manure composting. This study provided the vital theoretical support and scientific guidance for mitigating the HGT risk during manure composting.},
}
@article {pmid38920383,
year = {2024},
author = {Rakibova, Y and Dunham, DT and Seed, KD and Freddolino, L},
title = {Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae.},
journal = {mSphere},
volume = {9},
number = {7},
pages = {e0001124},
doi = {10.1128/msphere.00011-24},
pmid = {38920383},
issn = {2379-5042},
support = {R35 GM128637/GM/NIGMS NIH HHS/United States ; R01AI127652//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2018257700//National Science Foundation (NSF)/ ; AI134678//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {*Bacterial Proteins/genetics/metabolism ; *Vibrio cholerae/genetics/pathogenicity/metabolism ; *Gene Expression Regulation, Bacterial ; *Cholera/microbiology ; DNA-Binding Proteins/genetics/metabolism ; Humans ; Transcription, Genetic ; Virulence ; Virulence Factors/genetics ; Gene Transfer, Horizontal ; },
abstract = {UNLABELLED: Vibrio cholerae, the causative agent of the diarrheal disease cholera, poses an ongoing health threat due to its wide repertoire of horizontally acquired elements (HAEs) and virulence factors. New clinical isolates of the bacterium with improved fitness abilities, often associated with HAEs, frequently emerge. The appropriate control and expression of such genetic elements is critical for the bacteria to thrive in the different environmental niches they occupy. H-NS, the histone-like nucleoid structuring protein, is the best-studied xenogeneic silencer of HAEs in gamma-proteobacteria. Although H-NS and other highly abundant nucleoid-associated proteins (NAPs) have been shown to play important roles in regulating HAEs and virulence in model bacteria, we still lack a comprehensive understanding of how different NAPs modulate transcription in V. cholerae. By obtaining genome-wide measurements of protein occupancy and active transcription in a clinical isolate of V. cholerae, harboring recently discovered HAEs encoding for phage defense systems, we show that a lack of H-NS causes a robust increase in the expression of genes found in many HAEs. We further found that TsrA, a protein with partial homology to H-NS, regulates virulence genes primarily through modulation of H-NS activity. We also identified few sites that are affected by TsrA independently of H-NS, suggesting TsrA may act with diverse regulatory mechanisms. Our results demonstrate how the combinatorial activity of NAPs is employed by a clinical isolate of an important pathogen to regulate recently discovered HAEs.<br><br>IMPORTANCE: New strains of the bacterial pathogen Vibrio cholerae, bearing novel horizontally acquired elements (HAEs), frequently emerge. HAEs provide beneficial traits to the bacterium, such as antibiotic resistance and defense against invading bacteriophages. Xenogeneic silencers are proteins that help bacteria harness new HAEs and silence those HAEs until they are needed. H-NS is the best-studied xenogeneic silencer; it is one of the nucleoid-associated proteins (NAPs) in gamma-proteobacteria and is responsible for the proper regulation of HAEs within the bacterial transcriptional network. We studied the effects of H-NS and other NAPs on the HAEs of a clinical isolate of V. cholerae. Importantly, we found that H-NS partners with a small and poorly characterized protein, TsrA, to help domesticate new HAEs involved in bacterial survival and in causing disease. A proper understanding of the regulatory state in emerging isolates of V. cholerae will provide improved therapies against new isolates of the pathogen.},
}
@article {pmid39067603,
year = {2024},
author = {Miaomiao, L and Ikuro, K},
title = {Impact of chlorine disinfection on intracellular and extracellular antimicrobial resistance genes in wastewater treatment and water reclamation.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {175046},
doi = {10.1016/j.scitotenv.2024.175046},
pmid = {39067603},
issn = {1879-1026},
abstract = {Wastewater treatment plants and water reclamation facilities are reservoirs of antimicrobial resistance genes (ARGs). These ARGs are not limited solely to intracellular DNA (inARGs) but include extracellular DNA (exARGs) present in wastewater. The release of exARGs from cells can be exacerbated by treatment processes, including chlorine disinfection, which disrupts bacterial cells. Given the potential for exARGs to drive horizontal gene transfer and contribute to the proliferation of antimicrobial resistance, it is imperative to recognize these fractions as emerging environmental pollutants. In this study, we conducted a comprehensive year-long assessment of both inARGs and exARGs, further differentiating between dissolved exARGs (Dis_exARGs) and exARGs adsorbed onto particulate matter (Ads_exARGs), within a full-scale wastewater treatment and water reclamation facility. The results revealed that Ads_exARGs comprised up to 30 % of the total ARGs in raw sewage with high biomass content. Generally, treatments at low and high doses of chlorine increased the abundance of Dis_exARGs and Ads_exARGs. The fate of ARG levels that varied depending on the type of ARGs suggested variations in the susceptibility of the host bacteria to chlorination. Moreover, co-occurrence of several potential opportunistic pathogenic bacteria and ARGs were observed. Therefore, we propose higher doses of chlorination as a prerequisite for the effective removal of inARGs and exARGs.},
}
@article {pmid39066295,
year = {2024},
author = {Li, W and Tahiri, N},
title = {Host-Virus Cophylogenetic Trajectories: Investigating Molecular Relationships between Coronaviruses and Bat Hosts.},
journal = {Viruses},
volume = {16},
number = {7},
pages = {},
pmid = {39066295},
issn = {1999-4915},
support = {326911//Fonds de recherche du Qu&#xe9;bec/ ; RGPIN-2022-04322//Natural Sciences and Engineering Research Council/ ; },
mesh = {*Chiroptera/virology ; Animals ; *Phylogeny ; *Coronavirus/genetics/classification/physiology ; Evolution, Molecular ; Host-Pathogen Interactions/genetics ; Spike Glycoprotein, Coronavirus/genetics/metabolism ; Host Specificity ; Coronavirus Infections/virology ; },
abstract = {Bats, with their virus tolerance, social behaviors, and mobility, are reservoirs for emerging viruses, including coronaviruses (CoVs) known for genetic flexibility. Studying the cophylogenetic link between bats and CoVs provides vital insights into transmission dynamics and host adaptation. Prior research has yielded valuable insights into phenomena such as host switching, cospeciation, and other dynamics concerning the interaction between CoVs and bats. Nonetheless, a distinct gap exists in the current literature concerning a comparative cophylogenetic analysis focused on elucidating the contributions of sequence fragments to the co-evolution between hosts and viruses. In this study, we analyzed the cophylogenetic patterns of 69 host-virus connections. Among the 69 host-virus links examined, 47 showed significant cophylogeny based on ParaFit and PACo analyses, affirming strong associations. Focusing on two proteins, ORF1ab and spike, we conducted a comparative analysis of host and CoV phylogenies. For ORF1ab, the specific window ranged in multiple sequence alignment (positions 520-680, 770-870, 2930-3070, and 4910-5080) exhibited the lowest Robinson-Foulds (RF) distance (i.e., 84.62%), emphasizing its higher contribution in the cophylogenetic association. Similarly, within the spike region, distinct window ranges (positions 0-140, 60-180, 100-410, 360-550, and 630-730) displayed the lowest RF distance at 88.46%. Our analysis identified six recombination regions within ORF1ab (positions 360-1390, 550-1610, 680-1680, 700-1710, 2060-3090, and 2130-3250), and four within the spike protein (positions 10-510, 50-560, 170-710, and 230-730). The convergence of minimal RF distance regions with combination regions robustly affirms the pivotal role of recombination in viral adaptation to host selection pressures. Furthermore, horizontal gene transfer reveals prominent instances of partial gene transfer events, occurring not only among variants within the same host species but also crossing host species boundaries. This suggests a more intricate pattern of genetic exchange. By employing a multifaceted approach, our comprehensive strategy offers a nuanced understanding of the intricate interactions that govern the co-evolutionary dynamics between bat hosts and CoVs. This deeper insight enhances our comprehension of viral evolution and adaptation mechanisms, shedding light on the broader dynamics that propel viral diversity.},
}
@article {pmid39061350,
year = {2024},
author = {Drane, K and Sheehan, M and Whelan, A and Ariel, E and Kinobe, R},
title = {The Role of Wastewater Treatment Plants in Dissemination of Antibiotic Resistance: Source, Measurement, Removal and Risk Assessment.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {39061350},
issn = {2079-6382},
support = {2256.95982.2331//Townsville City Council, Townsville Australia/ ; },
abstract = {Antibiotic Resistance Genes (ARGs) are contaminants of emerging concern with marked potential to impact public and environmental health. This review focusses on factors that influence the presence, abundance, and dissemination of ARGs within Wastewater Treatment Plants (WWTPs) and associated effluents. Antibiotic-Resistant Bacteria (ARB) and ARGs have been detected in the influent and the effluent of WWTPs worldwide. Different levels of wastewater treatment (primary, secondary, and tertiary) show different degrees of removal efficiency of ARGs, with further differences being observed when ARGs are captured as intracellular or extracellular forms. Furthermore, routinely used molecular methodologies such as quantitative polymerase chain reaction or whole genome sequencing may also vary in resistome identification and in quantifying ARG removal efficiencies from WWTP effluents. Additionally, we provide an overview of the One Health risk assessment framework, as well as future strategies on how WWTPs can be assessed for environmental and public health impact.},
}
@article {pmid39061343,
year = {2024},
author = {Fahy, S and O'Connor, JA and Sleator, RD and Lucey, B},
title = {From Species to Genes: A New Diagnostic Paradigm.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {39061343},
issn = {2079-6382},
abstract = {Molecular diagnostics has the potential to revolutionise the field of clinical microbiology. Microbial identification and nomenclature have, for too long, been restricted to phenotypic characterisation. However, this species-level view fails to wholly account for genetic heterogeneity, a result of lateral gene transfer, mediated primarily by mobile genetic elements. This genetic promiscuity has helped to drive virulence development, stress adaptation, and antimicrobial resistance in several important bacterial pathogens, complicating their detection and frustrating our ability to control them. We argue that, as clinical microbiologists at the front line, we must embrace the molecular technologies that allow us to focus specifically on the genetic elements that cause disease rather than the bacterial species that express them. This review focuses on the evolution of microbial taxonomy since the introduction of molecular sequencing, the role of mobile genetic elements in antimicrobial resistance, the current and emerging assays in clinical laboratories, and the comparison of phenotypic versus genotypic analyses. In essence, it is time now to refocus from species to genes as part of a new diagnostic paradigm.},
}
@article {pmid38032214,
year = {2023},
author = {Kubori, T},
title = {A two-component system serves as a central hub for connecting energy metabolism and plasmid dissemination in bacteria.},
journal = {mBio},
volume = {14},
number = {6},
pages = {e0247423},
pmid = {38032214},
issn = {2150-7511},
support = {//Takeda Science Foundation (TSF)/ ; },
mesh = {*Plasmids/genetics ; *Acinetobacter baumannii/genetics/metabolism ; *Energy Metabolism/genetics ; *Conjugation, Genetic ; Bacterial Proteins/genetics/metabolism ; Type IV Secretion Systems/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Gene Expression Regulation, Bacterial ; },
abstract = {Mobile genetic elements such as conjugative plasmids play a key role in the acquisition of antibiotic resistance by pathogenic bacteria. Resistance genes on plasmids can be transferred between bacteria using specialized conjugation machinery. Acinetobacter baumannii, the most common bacterium associated with nosocomial infections, harbors a large conjugative plasmid that encodes a type IV secretion system (T4SS). Feng et al. recently found that the A. baumannii T4SS is specialized for plasmid transfer, suggesting that it may be involved in multidrug resistance (Z. Feng, L. Wang, Q. Guan, X. Chu, and Z.-Q. Luo, mBio e02276-23, 2023, https://doi.org/10.1128/mbio.02276-23), T4SS-encoding genes are shown to be controlled by a versatile GacA/S two-component regulatory system. GacA/S is also found to regulate genes involved in central metabolism. The coordinated regulation of metabolism and plasmid conjugation may be a bacterial strategy for adapting to selective pressure from antibiotics.},
}
@article {pmid39061274,
year = {2024},
author = {Ghazawi, A and Anes, F and Mouftah, S and Elbediwi, M and Baig, A and Alketbi, M and Almazrouei, F and Alhashmi, M and Alzarooni, N and Manzoor, A and Habib, I and Strepis, N and Nabi, A and Khan, M},
title = {Genomic Study of High-Risk Clones of Enterobacter hormaechei Collected from Tertiary Hospitals in the United Arab Emirates.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/antibiotics13070592},
pmid = {39061274},
issn = {2079-6382},
support = {G00004620 and G00004164//United Arab Emirates University/ ; },
abstract = {Enterobacter hormaechei has emerged as a significant pathogen within healthcare settings due to its ability to develop multidrug resistance (MDR) and survive in hospital environments. This study presents a genome-based analysis of carbapenem-resistant Enterobacter hormaechei isolates from two major hospitals in the United Arab Emirates. Eight isolates were subjected to whole-genome sequencing (WGS), revealing extensive resistance profiles including the blaNDM-1, blaOXA-48, and blaVIM-4 genes. Notably, one isolate belonging to ST171 harbored dual carbapenemase genes, while five isolates exhibited colistin resistance without mcr genes. The presence of the type VI secretion system (T6SS), various adhesins, and virulence genes contributes to the virulence and competitive advantage of the pathogen. Additionally, our isolates (87.5%) possessed ampC β-lactamase genes, predominantly blaACT genes. The genomic context of blaNDM-1, surrounded by other resistance genes and mobile genetic elements, highlights the role of horizontal gene transfer (HGT) in the spread of resistance. Our findings highlight the need for rigorous surveillance, strategic antibiotic stewardship, and hospital-based WGS to manage and mitigate the spread of these highly resistant and virulent pathogens. Accurate identification and monitoring of Enterobacter cloacae complex (ECC) species and their resistance mechanisms are crucial for effective infection control and treatment strategies.},
}
@article {pmid39060998,
year = {2024},
author = {Seth-Smith, H and Bommana, S and Dean, D and Read, TD and Marti, H},
title = {Chlamydia suis undergoes interclade recombination promoting Tet-island exchange.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {724},
pmid = {39060998},
issn = {1471-2164},
support = {323530_177579//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
abstract = {BACKGROUND: The obligate intracellular bacterial family Chlamydiaceae comprises a number of different species that cause disease in various vertebrate hosts including humans. Chlamydia suis, primarily found in the gastrointestinal tract of pigs, is the only species of the Chlamydiaceae family to have naturally gained tetracycline resistance (TetR), through a genomic island (Tet-island), integrated into the middle of chromosomal invasin-like gene inv. Previous studies have hypothesised that the uptake of the Tet-island from a host outside the Chlamydiaceae family was a unique event, followed by spread among C. suis through homologous recombination. In vitro recombination studies have shown that Tet-island exchange between C. suis strains is possible. Our aim in this study was to gain a deeper understanding of the interclade recombination of the Tet-island, among currently circulating C. suis field strains compared to in vitro-generated recombinants, using published whole genome sequences of C. suis field strains (n = 35) and in vitro-generated recombinants (n = 63).<br><br>RESULTS: We found that the phylogeny of inv better reflected the phylogeny of the Tet-island than that of the whole genome, supporting recombination rather than site-specific insertion as the means of transfer. There were considerable differences between the distribution of recombinations within in vitro-generated strains compared to that within the field strains. These differences are likely because in vitro-generated recombinants were selected for a tetracycline and rifamycin/rifampicin resistant background, leading to the largest peak of recombination across the Tet-island. Finally, we found that interclade recombinations across the Tet-island were more variable in length downstream of the Tet-island than upstream.<br><br>CONCLUSIONS: Our study supports the hypothesis that the occurrence of TetR strains in both clades of C. suis came about through interclade recombination after a single ancestral horizontal gene transfer event.},
}
@article {pmid39058093,
year = {2024},
author = {Peñil-Celis, A and Tagg, KA and Webb, HE and Redondo-Salvo, S and Francois Watkins, L and Vielva, L and Griffin, C and Kim, JY and Folster, JP and Garcillan-Barcia, MP and de la Cruz, F},
title = {Mobile genetic elements define the non-random structure of the Salmonella enterica serovar Typhi pangenome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0036524},
doi = {10.1128/msystems.00365-24},
pmid = {39058093},
issn = {2379-5077},
abstract = {Bacterial relatedness measured using select chromosomal loci forms the basis of public health genomic surveillance. While approximating vertical evolution through this approach has proven exceptionally valuable for understanding pathogen dynamics, it excludes a fundamental dimension of bacterial evolution-horizontal gene transfer. Incorporating the accessory genome is the logical remediation and has recently shown promise in expanding epidemiological resolution for enteric pathogens. Employing k-mer-based Jaccard index analysis, and a novel genome length distance metric, we computed pangenome (i.e., core and accessory) relatedness for the globally important pathogen Salmonella enterica serotype Typhi (Typhi), and graphically express both vertical (homology-by-descent) and horizontal (homology-by-admixture) evolutionary relationships in a reticulate network of over 2,200 U.S. Typhi genomes. This analysis revealed non-random structure in the Typhi pangenome that is driven predominantly by the gain and loss of mobile genetic elements, confirming and expanding upon known epidemiological patterns, revealing novel plasmid dynamics, and identifying avenues for further genomic epidemiological exploration. With an eye to public health application, this work adds important biological context to the rapidly improving ways of analyzing bacterial genetic data and demonstrates the value of the accessory genome to infer pathogen epidemiology and evolution.IMPORTANCEGiven bacterial evolution occurs in both vertical and horizontal dimensions, inclusion of both core and accessory genetic material (i.e., the pangenome) is a logical step toward a more thorough understanding of pathogen dynamics. With an eye to public, and indeed, global health relevance, we couple contemporary tools for genomic analysis with decades of research on mobile genetic elements to demonstrate the value of the pangenome, known and unknown, annotated, and hypothetical, for stratification of Salmonella enterica serovar Typhi (Typhi) populations. We confirm and expand upon what is known about Typhi epidemiology, plasmids, and antimicrobial resistance dynamics, and offer new avenues of exploration to further deduce Typhi ecology and evolution, and ultimately to reduce the incidence of human disease.},
}
@article {pmid39056664,
year = {2024},
author = {Aguirre-Carvajal, K and Munteanu, CR and Armijos-Jaramillo, V},
title = {Database Bias in the Detection of Interdomain Horizontal Gene Transfer Events in Pezizomycotina.},
journal = {Biology},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/biology13070469},
pmid = {39056664},
issn = {2079-7737},
support = {PRG.BIO.23.14.01//Universidad de Las Am&#xe9;ricas/ ; },
abstract = {Horizontal gene transfer (HGT) is a widely acknowledged phenomenon in prokaryotes for generating genetic diversity. However, the impact of this process in eukaryotes, particularly interdomain HGT, is a topic of debate. Although there have been observed biases in interdomain HGT detection, little exploration has been conducted on the effects of imbalanced databases. In our study, we conducted experiments to assess how different databases affect the detection of interdomain HGT using proteomes from the Pezizomycotina fungal subphylum as our focus group. Our objective was to simulate the database imbalance commonly found in public biological databases, where bacterial and eukaryotic sequences are unevenly represented, and demonstrate that an increase in uploaded eukaryotic sequences leads to a decrease in predicted HGTs. For our experiments, four databases with varying proportions of eukaryotic sequences but consistent proportions of bacterial sequences were utilized. We observed a significant reduction in detected interdomain HGT candidates as the proportion of eukaryotes increased within the database. Our data suggest that the imbalance in databases bias the interdomain HGT detection and highlights challenges associated with confirming the presence of interdomain HGT among Pezizomycotina fungi and potentially other groups within Eukarya.},
}
@article {pmid39053184,
year = {2024},
author = {Checcucci, A and Buscaroli, E and Modesto, M and Luise, D and Blasioli, S and Scarafile, D and Di Vito, M and Bugli, F and Trevisi, P and Braschi, I and Mattarelli, P},
title = {The swine waste resistome: Spreading and transfer of antibiotic resistance genes in Escherichia coli strains and the associated microbial communities.},
journal = {Ecotoxicology and environmental safety},
volume = {283},
number = {},
pages = {116774},
doi = {10.1016/j.ecoenv.2024.116774},
pmid = {39053184},
issn = {1090-2414},
abstract = {The overuse of antimicrobials in livestock farming has led to the development of resistant bacteria and the spread of antibiotic-resistant genes (ARGs) among animals. When manure containing these antibiotics is applied to agricultural fields, it creates a selective pressure that promotes the acquisition of ARGs by bacteria, primarily through horizontal gene transfer. Most research on ARGs focuses on their role in clinical antibiotic resistance and their transfer from environmental sources to bacteria associated with humans, such as Escherichia coli. The study investigates the spread of antibiotic-resistant genes (ARGs) through class 1 integrons in 27 Escherichia coli strains from pig manure. It focuses on six common ARGs (ermB, cmlA, floR, qnrS, tetA, and TEM) and the class 1 integron gene, assessing their prevalence in manure samples from three pig farms. The study found correlations and anticorrelations among these genes, indicating a predisposition of the integron in spreading certain ARGs. Specifically, cmlA and tetA genes were positively correlated with each other and negatively with int1, suggesting they are not transferred via Int1. Farm B had the highest int1 counts and a higher abundance of the TEM gene, but lower levels of cmlA and tetA genes. The results underscore the complexity of predicting ARG spread in agricultural environments and the associated health risks to humans through the food chain. The study's results offer valuable insights into the antibiotic-resistant genes (ARGs) profile in swine livestock, potentially aiding in the development of methods to trace ARGs in the environment.},
}
@article {pmid39052705,
year = {2024},
author = {Wan, Y and Myall, AC and Boonyasiri, A and Bolt, F and Ledda, A and Mookerjee, S and Weiße, AY and Getino, M and Turton, JF and Abbas, H and Prakapaite, R and Sabnis, A and Abdolrasouli, A and Malpartida-Cardenas, K and Miglietta, L and Donaldson, H and Gilchrist, M and Hopkins, KL and Ellington, MJ and Otter, JA and Larrouy-Maumus, G and Edwards, AM and Rodriguez-Manzano, J and Didelot, X and Barahona, M and Holmes, AH and Jauneikaite, E and Davies, F},
title = {Integrated Analysis of Patient Networks and Plasmid Genomes to Investigate a Regional, Multispecies Outbreak of Carbapenemase-Producing Enterobacterales Carrying Both blaIMP and mcr-9 Genes.},
journal = {The Journal of infectious diseases},
volume = {230},
number = {1},
pages = {e159-e170},
doi = {10.1093/infdis/jiae019},
pmid = {39052705},
issn = {1537-6613},
support = {//Faculty of Medicine, Siriraj Hospital, Mahidol University/ ; MR/T005254/1/MRC_/Medical Research Council/United Kingdom ; MRF-145-0004-TPG-AVISO/MRF/MRF/United Kingdom ; EP/N014529///EPSRC Centre for Mathematics of Precision Healthcare/ ; //National Institute for Health Research/ ; //Imperial Biomedical Research Centre/ ; //Rosetrees Trust/ ; M683//Stoneygate Trust/ ; /WT_/Wellcome Trust/United Kingdom ; PSN109//Imperial College London/ ; //Imperial Health Charity/ ; //NIHR Health Protection Research Unit in Genomics and Enabling Data/ ; //NIHR Health Protection Research Unit/ ; NIHR200915//University of Oxford/ ; //UK Health Security Agency/ ; },
mesh = {Humans ; *Plasmids/genetics ; *beta-Lactamases/genetics ; *Enterobacteriaceae Infections/epidemiology/microbiology/transmission ; *Disease Outbreaks ; *Bacterial Proteins/genetics ; London/epidemiology ; Anti-Bacterial Agents/pharmacology ; Phylogeny ; Genome, Bacterial ; Male ; Female ; Middle Aged ; Microbial Sensitivity Tests ; Adult ; Enterobacteriaceae/genetics/drug effects ; Aged ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation &amp; purification ; Colistin/pharmacology ; },
abstract = {BACKGROUND: Carbapenemase-producing Enterobacterales (CPE) are challenging in healthcare, with resistance to multiple classes of antibiotics. This study describes the emergence of imipenemase (IMP)-encoding CPE among diverse Enterobacterales species between 2016 and 2019 across a London regional network.<br><br>METHODS: We performed a network analysis of patient pathways, using electronic health records, to identify contacts between IMP-encoding CPE-positive patients. Genomes of IMP-encoding CPE isolates were overlaid with patient contacts to imply potential transmission events.<br><br>RESULTS: Genomic analysis of 84 Enterobacterales isolates revealed diverse species (predominantly Klebsiella spp, Enterobacter spp, and Escherichia coli); 86% (72 of 84) harbored an IncHI2 plasmid carrying blaIMP and colistin resistance gene mcr-9 (68 of 72). Phylogenetic analysis of IncHI2 plasmids identified 3 lineages showing significant association with patient contacts and movements between 4 hospital sites and across medical specialties, which was missed in initial investigations.<br><br>CONCLUSIONS: Combined, our patient network and plasmid analyses demonstrate an interspecies, plasmid-mediated outbreak of blaIMPCPE, which remained unidentified during standard investigations. With DNA sequencing and multimodal data incorporation, the outbreak investigation approach proposed here provides a framework for real-time identification of key factors causing pathogen spread. Plasmid-level outbreak analysis reveals that resistance spread may be wider than suspected, allowing more interventions to stop transmission within hospital networks.SummaryThis was an investigation, using integrated pathway networks and genomics methods, of the emergence of imipenemase-encoding carbapenemase-producing Enterobacterales among diverse Enterobacterales species between 2016 and 2019 in patients across a London regional hospital network, which was missed on routine investigations.},
}
@article {pmid39052112,
year = {2024},
author = {Li, H and Liu, B and Li, M and Shen, M},
title = {Livestock and poultry breeding farms as a fixed and underestimated source of antibiotic resistance genes.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {39052112},
issn = {1614-7499},
abstract = {The excessive use of antibiotics, disinfectants, and drugs in livestock and poultry breeding has resulted in a rise in the presence of antibiotic resistance genes (ARGs). Antibiotic-resistant bacteria (ARB) and ARGs have been widely found in animal feces, farm wastewater, and farm air. ARGs can not only spread across media through adsorption and migration, but also transfer resistance across bacterial genera through horizontal gene transfer. Livestock breeding has become a fixed and unavoidable source of ARGs in the environment. Existing technologies for controlling ARGs, such as composting, disinfection, and sewage treatment, are not efficient in removing ARB and ARGs from waste. Furthermore, the remaining ARGs still possess a strong capacity for dissemination. At present, antibiotics used in animal husbandry are difficult to replace in a short period of time. The growth and potential risks of resistance genes in livestock and poultry breeding sources in the receiving environment are not yet clear. In this paper, we summarize the current situation of ARGs in the livestock and poultry breeding environment. We also explain the key environmental processes, main influencing factors, and corresponding ecological risks associated with ARGs in this environment. The advantages and disadvantages of current technologies for the removal of ARGs are primarily discussed. There is a particular emphasis on clarifying the spatiotemporal evolution patterns and environmental process mechanisms of ARGs, as well as highlighting the importance and urgency of developing efficient pollution control technologies.},
}
@article {pmid39052074,
year = {2024},
author = {Allman, ES and Baños, H and Garrote-Lopez, M and Rhodes, JA},
title = {Identifiability of Level-1 Species Networks from Gene Tree Quartets.},
journal = {Bulletin of mathematical biology},
volume = {86},
number = {9},
pages = {110},
pmid = {39052074},
issn = {1522-9602},
support = {DMS-2051760//National Science Foundation/ ; DMS-2331660//National Science Foundation/ ; P20GM103395//Foundation for the National Institutes of Health/ ; },
mesh = {*Phylogeny ; *Mathematical Concepts ; *Models, Genetic ; *Gene Transfer, Horizontal ; Evolution, Molecular ; Genetic Speciation ; Gene Regulatory Networks ; Computer Simulation ; Hybridization, Genetic ; },
abstract = {When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several recently proposed methods are based on quartet concordance factors-the probabilities that a tree relating a gene sampled from the species displays the possible 4-taxon relationships. Building on earlier results, we investigate what level-1 network features are identifiable from concordance factors under the network multispecies coalescent model. We obtain results on both topological features of the network, and numerical parameters, uncovering a number of failures of identifiability related to 3-cycles in the network. Addressing these identifiability issues is essential for designing statistically consistent inference methods.},
}
@article {pmid39044460,
year = {2024},
author = {Roulet, ME and Ceriotti, LF and Gatica-Soria, L and Sanchez-Puerta, MV},
title = {Horizontally transferred mitochondrial DNA tracts become circular by microhomology-mediated repair pathways.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19984},
pmid = {39044460},
issn = {1469-8137},
support = {PICT2020-01018//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; 06/A092-T1//Secretar&#xed;a de Investigaci&#xf3;n, Internacionales y Posgrado, Universidad Nacional de Cuyo/ ; },
abstract = {The holoparasitic plant Lophophytum mirabile exhibits remarkable levels of mitochondrial horizontal gene transfer (HGT). Gathering comparative data from other individuals and host plants can provide insights into the HGT process. We sequenced the mitochondrial genome (mtDNA) from individuals of two species of Lophophytum and from mimosoid hosts. We applied a stringent phylogenomic approach to elucidate the origin of the whole mtDNAs, estimate the timing of the transfers, and understand the molecular mechanisms involved. Ancestral and recent HGT events replaced and enlarged the multichromosomal mtDNA of Lophophytum spp., with the foreign DNA ascending to 74%. A total of 14 foreign mitochondrial chromosomes originated from continuous regions in the host mtDNA flanked by short direct repeats. These foreign tracts are circularized by microhomology-mediated repair pathways and replicate independently until they are lost or they eventually recombine with other chromosomes. The foreign noncoding chromosomes are variably present in the population and likely evolve by genetic drift. We present the 'circle-mediated HGT' model in which foreign mitochondrial DNA tracts become circular and are maintained as plasmid-like molecules. This model challenges the conventional belief that foreign DNA must be integrated into the recipient genome for successful HGT.},
}
@article {pmid39042422,
year = {2024},
author = {Alves, J and Dry, I and White, JH and Dryden, DTF and Lynskey, NN},
title = {Generation of tools for expression and purification of the phage-encoded Type I restriction enzyme inhibitor, Ocr.},
journal = {Microbiology (Reading, England)},
volume = {170},
number = {7},
pages = {},
doi = {10.1099/mic.0.001465},
pmid = {39042422},
issn = {1465-2080},
mesh = {*Recombinant Proteins/genetics/metabolism/isolation &amp; purification ; Viral Proteins/genetics/metabolism ; Bacteriophages/genetics/enzymology ; Streptococcus pyogenes/genetics/enzymology/metabolism ; Transformation, Bacterial ; Deoxyribonucleases, Type I Site-Specific/metabolism/genetics ; Gene Expression ; Escherichia coli/genetics/metabolism ; },
abstract = {DNA manipulation is an essential tool in molecular microbiology research that is dependent on the ability of bacteria to take up and preserve foreign DNA by horizontal gene transfer. This process can be significantly impaired by the activity of bacterial restriction modification systems; bacterial operons comprising paired enzymatic activities that protectively methylate host DNA, while cleaving incoming unmodified foreign DNA. Ocr is a phage-encoded protein that inhibits Type I restriction modification systems, the addition of which significantly improves bacterial transformation efficiency. We recently established an improved and highly efficient transformation protocol for the important human pathogen group A Streptococcus using commercially available recombinant Ocr protein, manufacture of which has since been discontinued. In order to ensure the continued availability of Ocr protein within the research community, we have generated tools and methods for in-house Ocr production and validated the activity of the purified recombinant protein.},
}
@article {pmid39039821,
year = {2024},
author = {Bohl, V and Mogk, A},
title = {When the going gets tough, the tough get going-Novel bacterial AAA+ disaggregases provide extreme heat resistance.},
journal = {Environmental microbiology},
volume = {26},
number = {7},
pages = {e16677},
doi = {10.1111/1462-2920.16677},
pmid = {39039821},
issn = {1462-2920},
support = {MO970/7-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Bacterial Proteins/metabolism/genetics ; HSP70 Heat-Shock Proteins/metabolism/genetics ; Thermotolerance ; Hot Temperature ; Bacteria/genetics/metabolism ; Endopeptidase Clp/metabolism/genetics ; Heat-Shock Proteins/metabolism/genetics ; Heat-Shock Response ; },
abstract = {Heat stress can lead to protein misfolding and aggregation, potentially causing cell death due to the loss of essential proteins. Bacteria, being particularly exposed to environmental stress, are equipped with disaggregases that rescue these aggregated proteins. The bacterial Hsp70 chaperone DnaK and the ATPase associated with diverse cellular activities protein ClpB form the canonical disaggregase in bacteria. While this combination operates effectively during physiological heat stress, it is ineffective against massive aggregation caused by temperature-based sterilization protocols used in the food industry and clinics. This leaves bacteria unprotected against these thermal processes. However, bacteria that can withstand extreme, man-made stress conditions have emerged. These bacteria possess novel ATPase associated with diverse cellular activities disaggregases, ClpG and ClpL, which are key players in extreme heat resistance. These disaggregases, present in selected Gram-negative or Gram-positive bacteria, respectively, function superiorly by exhibiting increased thermal stability and enhanced threading power compared to DnaK/ClpB. This enables ClpG and ClpL to operate at extreme temperatures and process large and tight protein aggregates, thereby contributing to heat resistance. The genes for ClpG and ClpL are often encoded on mobile genomic islands or conjugative plasmids, allowing for their rapid spread among bacteria via horizontal gene transfer. This threatens the efficiency of sterilization protocols. In this review, we describe the various bacterial disaggregases identified to date, characterizing their commonalities and the specific features that enable these novel disaggregases to provide stress protection against extreme stress conditions.},
}
@article {pmid39039101,
year = {2024},
author = {Brown, CL and Maile-Moskowitz, A and Lopatkin, AJ and Xia, K and Logan, LK and Davis, BC and Zhang, L and Vikesland, PJ and Pruden, A},
title = {Author Correction: Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6166},
doi = {10.1038/s41467-024-50577-6},
pmid = {39039101},
issn = {2041-1723},
}
@article {pmid39038713,
year = {2024},
author = {Sun, B and Bai, Z and Li, R and Song, M and Zhang, J and Wang, J and Zhuang, X},
title = {Efficient elimination of antibiotic resistome in livestock manure by semi-permeable membrane covered hyperthermophilic composting.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131134},
doi = {10.1016/j.biortech.2024.131134},
pmid = {39038713},
issn = {1873-2976},
abstract = {Livestock manure is a hotspot for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and an important contributor to antibiotic resistance in non-clinical settings. This study investigated the effectiveness and potential mechanisms of a novel composting technology, semi-permeable membrane covered hyperthermophilic composting (smHTC), in removal of ARGs and MGEs in chicken manure. Results showed that smHTC was more efficient in removal of ARGs and MGEs (92% and 93%) compared to conventional thermophilic composting (cTC) (76% and 92%). The efficient removal in smHTC is attributed to direct or indirect negative effects caused by the high temperature, including reducing the involvement of bio-available heavy metals (HMs) in co-selection processes of antibiotic resistance, decreasing the bacterial abundance and diversity, suppressing the horizontal gene transfer and killing potential ARGs hosts. Overall, smHTC can efficiently remove the resistome in livestock manure, reducing the risk to crops and humans from ARGs residues in compost products.},
}
@article {pmid39038196,
year = {2024},
author = {Mori, BA and Coutu, C and Erlandson, MA and Hegedus, DD},
title = {Exploring the contribution of the salivary gland and midgut to digestion in the swede midge (Contarinia nasturtii) through a genomics-guided approach.},
journal = {Archives of insect biochemistry and physiology},
volume = {116},
number = {3},
pages = {e22135},
doi = {10.1002/arch.22135},
pmid = {39038196},
issn = {1520-6327},
support = {//Alberta Canola Producers Commission/ ; //Alberta Barley Commission/ ; //Alberta Wheat Commission/ ; 545088//NSERC Industrial Research Chair/ ; RGPIN-2021-02479//NSERC/ ; //Agriculture &amp; Agri-Food Canada Genomics Research and Development Initiative/ ; //Alberta Pulse Growers Commission/ ; },
mesh = {Animals ; *Salivary Glands/metabolism/enzymology ; *Larva/genetics/metabolism/growth &amp; development ; *Diptera/genetics/enzymology/metabolism ; Transcriptome ; Digestion ; Genomics ; Gastrointestinal Tract/metabolism ; Insect Proteins/metabolism/genetics ; },
abstract = {The larvae of Contarinia nasturtii (Kieffer) (Diptera: Cecidomyiidae), the swede midge, targets the meristem of brassica crops where they induce the formation of galls and disrupt seed and vegetable production. Previously, we examined the salivary gland transcriptome of newly-hatched first instar larvae as they penetrated the host and initiated gall formation. Here we examine the salivary gland and midgut transcriptome of third instar larvae and provide evidence for cooperative nutrient acquisition beginning with secretion of enzymes and feeding facilitators followed by gastrointestinal digestion. Sucrose, presumably obtained from the phloem, appeared to be a major nutrient source as several α-glucosidases (sucrases, maltases) and β-fructofuranosidases (invertases) were identified. Genes encoding β-fructofuranosidases/invertases were among the most highly expressed in both tissues and represented two distinct gene families that may have originated via horizontal gene transfer from bacteria. The importance of the phloem as a nutrient source is underscored by the expression of genes encoding regucalcin and ARMET (arginine-rich mutated in early stages of tumor) which interfere with calcium signalling and prevent sieve tube occlusion. Lipids, proteins, and starch appear to serve as a secondary nutrient sources. Genes encoding enzymes involved in the detoxification of glucosinolates (myrosinases, arylsulfatases, and glutathione-S-transferases) were expressed indicative of Brassicaceae host specialization. The midgut expressed simple peritrophins and mucins typical of those found in Type II peritrophic matrices, the first such description for a gall midge.},
}
@article {pmid39038013,
year = {2024},
author = {Berg, A and Berntsson, RP and Barandun, J},
title = {Nematocida displodere mechanosensitive ion channel of small conductance 2 assembles into a unique 6-channel super-structure in vitro.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0301951},
doi = {10.1371/journal.pone.0301951},
pmid = {39038013},
issn = {1932-6203},
mesh = {*Ion Channels/metabolism/chemistry/genetics ; *Cryoelectron Microscopy ; Animals ; Caenorhabditis elegans/metabolism/genetics ; Microsporidia/metabolism/genetics ; Mechanotransduction, Cellular ; },
abstract = {Mechanosensitive ion channels play an essential role in reacting to environmental signals and sustaining cell integrity by facilitating ion flux across membranes. For obligate intracellular pathogens like microsporidia, adapting to changes in the host environment is crucial for survival and propagation. Despite representing a eukaryote of extreme genome reduction, microsporidia have expanded the gene family of mechanosensitive ion channels of small conductance (mscS) through repeated gene duplication and horizontal gene transfer. All microsporidian genomes characterized to date contain mscS genes of both eukaryotic and bacterial origin. Here, we investigated the cryo-electron microscopy structure of the bacterially derived mechanosensitive ion channel of small conductance 2 (MscS2) from Nematocida displodere, an intracellular pathogen of Caenorhabditis elegans. MscS2 is the most compact MscS-like channel known and assembles into a unique superstructure in vitro with six heptameric MscS2 channels. Individual MscS2 channels are oriented in a heterogeneous manner to one another, resembling an asymmetric, flexible six-way cross joint. Finally, we show that microsporidian MscS2 still forms a heptameric membrane channel, however the extreme compaction suggests a potential new function of this MscS-like protein.},
}
@article {pmid39037483,
year = {2024},
author = {de Carvalho, A and Giambiagi-deMarval, M and Rossi, CC},
title = {Mammaliicoccus sciuri's Pan-Immune System and the Dynamics of Horizontal Gene Transfer Among Staphylococcaceae: a One-Health CRISPR Tale.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {39037483},
issn = {1976-3794},
support = {408564/2023-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 304839/2022-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; E-26/010.000172/2016; 010.00128/2016; E-26.210.875/2016//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 101056/2018; 001463/2019; 211.554/2019; 201.071/2020//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 200.895/2021//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; E-26/204.925/2022//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; APQ-03498-22//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; 23038.002486/2018-26//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
abstract = {Recently emancipated from the Staphylococcus genus due to genomic differences, Mammaliicoccus sciuri, previously classified as an occasional pathogen, emerges as a significant player in the landscape of resistance gene dissemination among Staphylococcaceae. Despite its classification, its role remained enigmatic. In this study, we delved into the genomic repertoire of M. sciuri to unravel its contribution to resistance and virulence gene transfer in the context of One Health. Through comprehensive analysis of publicly available genomes, we unveiled a diverse pan-immune system adept at defending against exogenous genetic elements, yet concurrently fostering horizontal gene transfer (HGT). Specifically, exploration of CRISPR-Cas systems, with spacer sequences as molecular signatures, elucidated a global dissemination pattern spanning environmental, animal, and human hosts. Notably, we identified the integration of CRISPR-Cas systems within SCCmecs (Staphylococcal Cassette Chromosome mec), harboring key genes associated with pathogenicity and resistance, especially the methicillin resistance gene mecA, suggesting a strategic adaptation to outcompete other mobile genetic elements. Our findings underscored M. sciuri's active engagement in HGT dynamics and evolutionary trajectories within Staphylococcaceae, emphasizing its central role in shaping microbial communities and highlighting the significance of understanding its implications in the One Health framework, an interdisciplinary approach that recognizes the interconnectedness of human, animal, and environmental health to address global health challenges.},
}
@article {pmid39035534,
year = {2024},
author = {Gheorghe-Barbu, I and Surleac, M and Barbu, IC and Paraschiv, S and Bănică, LM and Rotaru, LI and Vrâncianu, CO and Niță Lazăr, M and Oțelea, D and Chifiriuc, MC},
title = {Decoding the resistome, virulome and mobilome of clinical versus aquatic Acinetobacter baumannii in southern Romania.},
journal = {Heliyon},
volume = {10},
number = {13},
pages = {e33372},
pmid = {39035534},
issn = {2405-8440},
abstract = {Acinetobacter baumannii, a notorious opportunistic pathogen, presents a formidable challenge in both clinical and environmental fields due to its resilience and ability to acquire resistance. This study undertook a comprehensive analysis of 183 A. baumannii isolates collected between 2019 and 2022 from intra-hospital infections (IHI), hospital sewages (Hs), wastewater treatment plants (WWTP), and adjacent river waters from two Southern cities, focusing on their resistome, virulome, and mobilome through isolation on chromogenic media, identification by MALDI-TOF-MS and antibiotic susceptibility testing by disk diffusion) followed by genotypic characterization [Whole Genome Sequencing (WGS), 3rd generation sequencing through the MinION (ONT) platform, pangenome description, and respectively horizontal gene transfer through conjugation assays]. Our findings reveal significant genomic plasticity and the prevalence of high-risk international clones, underlining the potential of these isolates to act as reservoirs for antibiotic resistance genes (ARGs) that could be dynamically exchanged between clinical and environmental settings through mobile genetic elements (MGEs) such as the pMAL1 plasmids and the critical role of WWTPs in the persistence and spread of A. baumannii. Moreover, our study presents the first report of the co-occurrence of bla OXA-23 and bla OXA-72 in A. baumannii ST2 clone. Thus, our research underscores the necessity for integrated surveillance and targeted interventions across healthcare and environmental sectors to mitigate the risk posed by this adaptable pathogen.},
}
@article {pmid39030691,
year = {2024},
author = {Gan, D and Lin, Z and Zeng, L and Deng, H and Walsh, TR and Zhou, S and Yang, QE},
title = {Housefly gut microbiomes as a reservoir and facilitator for the spread of antibiotic resistance.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae128},
pmid = {39030691},
issn = {1751-7370},
abstract = {Arthropods, such as houseflies, play a significant role on the dissemination of antimicrobial resistance (AMR); however, their impact has often been overlooked in comparison to other AMR vectors. Understanding the contribution of arthropods to the spread of AMR is critical for implementing robust policies to mitigate the spread of AMR across "One Health" sectors. Herein, we investigated the in-situ transfer of a gfp-labelled AMR plasmid (IncA/C carrying a mcr-8 gene, pA/C_MCR-8) in the gut microbiota of housefly (Musca domestica) by applying single-cell sorting, 16S rRNA gene amplicon sequencing, and whole genome sequencing. Our findings demonstrate that the pA/C_MCR-8 positive E. coli donor strain is capable of colonizing the gut microbiome of houseflies and persists in the housefly intestine for five days, however, no transfer was detectable above the detection threshold of 10-5 per cell. The conjugative plasmid, pA/C_MCR-8 demonstrated a high transfer frequency ranging from 4.1 × 10-3 to 5.0 × 10-3 per cell in vitro, and exhibited transfer across various bacterial phyla, primarily encompassing Pseudomonadota and Bacillota. Phylogenic analysis has revealed that Providencia stuartii, a human opportunistic pathogen, was a notable recipient of pA/C_MCR-8. The conjugation assays further revealed that newly formed P. stuartii transconjugants readily transfer pA/C_MCR-8 to other clinically relevant pathogens (e.g. Klebsiella pneumoniae). Our findings indicate the potential transfer of AMR plasmids from houseflies to human opportunistic pathogens and further advocates the adoption of a One Health approach in developing infection control policies that address AMR across clinical settings.},
}
@article {pmid39030685,
year = {2024},
author = {Echeveste Medrano, MJ and Leu, AO and Pabst, M and Lin, Y and Mcllroy, SJ and Tyson, GW and van Ede, J and Sánchez-Andrea, I and Jetten, MSM and Jansen, R and Welte, CU},
title = {Osmoregulation in freshwater anaerobic methane oxidizing archaea under salt stress.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae137},
pmid = {39030685},
issn = {1751-7370},
abstract = {Climate change-driven sea level rise threatens freshwater ecosystems and elicits salinity stress in microbiomes. Methane emissions in these systems are largely mitigated by methane-oxidizing microorganisms. Here, we characterized the physiological and metabolic response of freshwater methanotrophic archaea to salt stress. In our microcosm experiments, inhibition of methanotrophic archaea started at 1%. However, during gradual increase of salt up to 3% in a reactor over 12 weeks, the culture continued to oxidize methane. Using gene expression profiles and metabolomics, we identified a pathway for salt-stress response that produces the osmolyte of anaerobic methanotrophic archaea: N(ε)-acetyl-β-L-lysine. An extensive phylogenomic analysis on N(ε)-acetyl-β-L-lysine-producing enzymes revealed that they are widespread across both bacteria and archaea, indicating a potential horizontal gene transfer and a link to BORG extrachromosomal elements. Physicochemical analysis of bioreactor biomass further indicated the presence of sialic acids and the consumption of intracellular polyhydroxyalkanoates in anaerobic methanotrophs during salt stress.},
}
@article {pmid39029947,
year = {2024},
author = {Azizpour, A and Balaji, A and Treangen, TJ and Segarra, S},
title = {Graph-based self-supervised learning for repeat detection in metagenomic assembly.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279136.124},
pmid = {39029947},
issn = {1549-5469},
abstract = {Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene duplication, and gene loss/gain complicate accurate genome assembly from metagenomic communities. Detecting repeats is a crucial first step in overcoming these challenges. To address this issue, we propose GraSSRep, a novel approach that leverages the assembly graph's structure through graph neural networks (GNNs) within a self-supervised learning framework to classify DNA sequences into repetitive and non-repetitive categories. Specifically, we frame this problem as a node classification task within a metagenomic assembly graph. In a self-supervised fashion, we rely on a high-precision (but low-recall) heuristic to generate pseudo-labels for a small proportion of the nodes. We then use those pseudo-labels to train a GNN embedding and a random forest classifier to propagate the labels to the remaining nodes. In this way, GraSSRep combines sequencing features with predefined and learned graph features to achieve state-of-the-art performance in repeat detection. We evaluate our method using simulated and synthetic metagenomic datasets. The results on the simulated data highlight our GraSSRep's robustness to repeat attributes, demonstrating its effectiveness in handling the complexity of repeated sequences. Additionally, our experiments with synthetic metagenomic datasets reveal that incorporating the graph structure and the GNN enhances our detection performance. Finally, in comparative analyses, GraSSRep outperforms existing repeat detection tools with respect to precision and recall.},
}
@article {pmid37345922,
year = {2023},
author = {Bosch, DE and Abbasian, R and Parajuli, B and Peterson, SB and Mougous, JD},
title = {Structural disruption of Ntox15 nuclease effector domains by immunity proteins protects against type VI secretion system intoxication in Bacteroidales.},
journal = {mBio},
volume = {14},
number = {4},
pages = {e0103923},
pmid = {37345922},
issn = {2150-7511},
support = {K08 AI159619/AI/NIAID NIH HHS/United States ; P30 GM124169/GM/NIGMS NIH HHS/United States ; R01 AI080609/AI/NIAID NIH HHS/United States ; S10 OD021832/OD/NIH HHS/United States ; },
mesh = {*Type VI Secretion Systems/metabolism/genetics ; *Bacterial Proteins/genetics/metabolism/chemistry/immunology ; Humans ; Gene Transfer, Horizontal ; },
abstract = {Bacteroidales use type VI secretion systems (T6SS) to competitively colonize and persist in the colon. We identify a horizontally transferred T6SS with Ntox15 family nuclease effector (Tde1) that mediates interbacterial antagonism among Bacteroidales, including several derived from a single human donor. Expression of cognate (Tdi1) or orphan immunity proteins in acquired interbacterial defense systems protects against Tde1-dependent attack. We find that immunity protein interaction induces a large effector conformational change in Tde nucleases, disrupting the active site and altering the DNA-binding site. Crystallographic snapshots of isolated Tde1, the Tde1/Tdi1 complex, and homologs from Phocaeicola vulgatus (Tde2/Tdi2) illustrate a conserved mechanism of immunity inserting into the central core of Tde, splitting the nuclease fold into two subdomains. The Tde/Tdi interface and immunity mechanism are distinct from all other polymorphic toxin-immunity interactions of known structure. Bacteroidales abundance has been linked to inflammatory bowel disease activity in prior studies, and we demonstrate that Tde and T6SS structural genes are each enriched in fecal metagenomes from ulcerative colitis subjects. Genetically mobile Tde1-encoding T6SS in Bacteroidales mediate competitive growth and may be involved in inflammatory bowel disease. Broad immunity is conferred by Tdi1 homologs through a fold-disrupting mechanism unique among polymorphic effector-immunity pairs of known structure. IMPORTANCE Bacteroidales are related to inflammatory bowel disease severity and progression. We identify type VI secretion system (T6SS) nuclease effectors (Tde) which are enriched in ulcerative colitis and horizontally transferred on mobile genetic elements. Tde-encoding T6SSs mediate interbacterial competition. Orphan and cognate immunity proteins (Tdi) prevent intoxication by multiple Tde through a new mechanism among polymorphic toxin systems. Tdi inserts into the effector central core, splitting Ntox15 into two subdomains and disrupting the active site. This mechanism may allow for evolutionary diversification of the Tde/Tdi interface as observed in colicin nuclease-immunity interactions, promoting broad neutralization of Tde by orphan Tdi. Tde-dependent T6SS interbacterial antagonism may contribute to Bacteroidales diversity in the context of ulcerative colitis.},
}
@article {pmid39028534,
year = {2024},
author = {da Rosa, EEB and Kremer, FS},
title = {The mobilome landscape of biocide-resistance in Brazilian ESKAPE isolates.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {39028534},
issn = {1678-4405},
support = {Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
abstract = {The increasing frequency of antibiotic-resistant bacteria is a constant threat to global human health. Therefore, the pathogens of the ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Enterobacter spp.) are among the most relevant causes of hospital infections responsible for millions of deaths every year. However, little has been explored about the danger of microorganisms resistant to biocides such as antiseptics and disinfectants. Widely used in domestic, industrial, and hospital environments, these substances reach the environment and can cause selective pressure for resistance genes and induce cross-resistance to antibiotics, further aggravating the problem. Therefore, it is necessary to use innovative and efficient strategies to monitor the spread of genes related to resistance to biocides. Whole genome sequencing and bioinformatics analysis aiming to search for sequences encoding resistance mechanisms are essential to help monitor and combat these pathogens. Thus, this work describes the construction of a bioinformatics tool that integrates different databases to identify gene sequences that may confer some resistance advantage about biocides. Furthermore, the tool analyzed all the genomes of Brazilian ESKAPE isolates deposited at NCBI and found a series of different genes related to resistance to benzalkonium chloride, chlorhexidine, and triclosan, which were the focus of this work. As a result, the presence of resistance genes was identified in different types of biological samples, environments, and hosts. Regarding mobile genetic elements (MGEs), around 52% of isolates containing genes related to resistance to these compounds had their genes identified in plasmids, and 48.7% in prophages. These data show that resistance to biocides can be a silent, underestimated danger spreading across different environments and, therefore, requires greater attention.},
}
@article {pmid39025839,
year = {2024},
author = {Nowell, RW and Rodriguez, F and Hecox-Lea, BJ and Mark Welch, DB and Arkhipova, IR and Barraclough, TG and Wilson, CG},
title = {Bdelloid rotifers deploy horizontally acquired biosynthetic genes against a fungal pathogen.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5787},
pmid = {39025839},
issn = {2041-1723},
support = {NE/J01933X/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/S010866/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/M01651X/1//RCUK | Natural Environment Research Council (NERC)/ ; LTF-733-2010//European Molecular Biology Organization (EMBO)/ ; R01GM111917//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R21AG046899//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
mesh = {*Gene Transfer, Horizontal ; Animals ; *Rotifera/genetics/metabolism ; Biosynthetic Pathways/genetics ; Peptide Synthases/genetics/metabolism ; Polyketides/metabolism ; Phylogeny ; Multigene Family ; },
abstract = {Coevolutionary antagonism generates relentless selection that can favour genetic exchange, including transfer of antibiotic synthesis and resistance genes among bacteria, and sexual recombination of disease resistance alleles in eukaryotes. We report an unusual link between biological conflict and DNA transfer in bdelloid rotifers, microscopic animals whose genomes show elevated levels of horizontal gene transfer from non-metazoan taxa. When rotifers were challenged with a fungal pathogen, horizontally acquired genes were over twice as likely to be upregulated as other genes - a stronger enrichment than observed for abiotic stressors. Among hundreds of upregulated genes, the most markedly overrepresented were clusters resembling bacterial polyketide and nonribosomal peptide synthetases that produce antibiotics. Upregulation of these clusters in a pathogen-resistant rotifer species was nearly ten times stronger than in a susceptible species. By acquiring, domesticating, and expressing non-metazoan biosynthetic pathways, bdelloids may have evolved to resist natural enemies using antimicrobial mechanisms absent from other animals.},
}
@article {pmid39021167,
year = {2024},
author = {Barcan, AS and Barcan, RA and Vamanu, E},
title = {Genomic Insights into Bacterial Antimicrobial Resistance Transmission and Mitigation Strategies.},
journal = {Current pharmaceutical biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113892010304596240629102419},
pmid = {39021167},
issn = {1873-4316},
abstract = {The rapid emergence and global spread of antimicrobial resistance in recent years have raised significant concerns about the future of modern medicine. Superbugs and multidrugresistant bacteria have become endemic in many parts of the world, raising the specter of untreatable infections. The overuse and misuse of antimicrobials over the past 80 years have undoubtedly contributed to the development of antimicrobial resistance, placing immense pressure on healthcare systems worldwide. Nonetheless, the molecular mechanisms underlying antimicrobial resistance in bacteria have existed since ancient times. Some of these mechanisms and processes have served as the precursors of current resistance determinants, highlighting the ongoing arms race between bacteria and their antimicrobial adversaries. Moreover, the environment harbors many putative resistance genes, yet we cannot still predict which of these genes will emerge and manifest as pathogenic resistance phenotypes. The presence of antibiotics in natural habitats, even at sub-inhibitory concentrations, may provide selective pressures that favor the emergence of novel antimicrobial resistance apparatus and, thus, underscores the need for a comprehensive understanding of the factors driving the persistence and spread of antimicrobial resistance. As the development of antimicrobial strategies that evade resistance is urgently needed, a clear perception of these critical factors could ultimately pave the way for the design of innovative therapeutic targets.},
}
@article {pmid39012117,
year = {2024},
author = {Zalewska, M and Błażejewska, A and Gawor, J and Adamska, D and Goryca, K and Szeląg, M and Kalinowski, P and Popowska, M},
title = {A newly identified IncY plasmid from multi-drug-resistant Escherichia coli isolated from dairy cattle feces in Poland.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0087724},
doi = {10.1128/spectrum.00877-24},
pmid = {39012117},
issn = {2165-0497},
abstract = {UNLABELLED: Comprehensive whole-genome sequencing was performed on two multi-drug-resistant Escherichia coli strains isolated from cattle manure from a typical dairy farm in Poland in 2020. The identified strains are resistant to beta-lactams, aminoglycosides, tetracyclines, trimethoprim/sulfamethoxazole, and fluoroquinolones. The complete sequences of the harbored plasmids revealed antibiotic-resistance genes located within many mobile genetic elements (e.g., insertional sequences or transposons) and genes facilitating conjugal transfer or promoting horizontal gene transfer. These plasmids are hitherto undescribed. Similar plasmids have been identified, but not in Poland. The identified plasmids carried resistance genes, including the tetracycline resistance gene tet(A), aph family aminoglycoside resistance genes aph(3″)-lb and aph (6)-ld, beta-lactam resistance genes blaTEM-1 and blaCTX-M-15, sulfonamide resistance gene sul2, fluoroquinolone resistance gene qnrS1, and the trimethoprim resistance gene dfrA14. The characterized resistance plasmids were categorized into the IncY incompatibility group, indicating a high possibility for dissemination among the Enterobacteriaceae. While similar plasmids (99% identity) have been found in environmental and clinical samples, none have been identified in farm animals. These findings are significant within the One Health framework, as they underline the potential for antimicrobial-resistant E. coli from livestock and food sources to be transmitted to humans and vice versa. It highlights the need for careful monitoring and strategies to limit the spread of antibiotic resistance in the One Health approach.<br><br>IMPORTANCE: This study reveals the identification of new strains of antibiotic-resistant Escherichia coli in cattle manure from a dairy farm in Poland, offering critical insights into the spread of drug resistance. Through whole-genome sequencing, researchers discovered novel plasmids within these bacteria, which carry genes resistant to multiple antibiotics. These findings are particularly alarming, as these plasmids can transfer between different bacterial species, potentially escalating the spread of antibiotic resistance. This research underscores the vital connection between the health of humans, animals, and the environment, emphasizing the concept of One Health. It points to the critical need for global vigilance and strategies to curb the proliferation of antibiotic resistance. By showcasing the presence of these strains and their advanced resistance mechanisms, the study calls for enhanced surveillance and preventive actions in both agricultural practices and healthcare settings to address the imminent challenge of antibiotic-resistant bacteria.},
}
@article {pmid39012101,
year = {2024},
author = {Duran-Bedolla, J and Téllez-Sosa, J and Bocanegra-Ibarias, P and Schilmann, A and Bravo-Romero, S and Reyna-Flores, F and Villa-Reyes, T and Barrios-Camacho, H},
title = {Citrobacter spp. and Enterobacter spp. as reservoirs of carbapenemase blaNDM and blaKPC resistance genes in hospital wastewater.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0116524},
doi = {10.1128/aem.01165-24},
pmid = {39012101},
issn = {1098-5336},
abstract = {UNLABELLED: Antibiotic resistance has emerged as a global threat to public health, generating a growing interest in investigating the presence of antibiotic-resistant bacteria in environments influenced by anthropogenic activities. Wastewater treatment plants in hospital serve as significant reservoirs of antimicrobial-resistant bacteria, where a favorable environment is established, promoting the proliferation and transfer of resistance genes among different bacterial species. In our study, we isolated a total of 243 strains from 5 hospital wastewater sites in Mexico, belonging to 21 distinct Gram-negative bacterial species. The presence of β-lactamase was detected in 46.9% (114/243) of the isolates, which belonging to the Enterobacteriaceae family. We identified a total of 169 β-lactamase genes; blaTEM in 33.1%, blaCTX-M in 25.4%, blaKPC in 25.4%, blaNDM 8.8%, blaSHV in 5.3%, and blaOXA-48 in 1.1% distributed in 12 different bacteria species. Among the 114 of the isolates, 50.8% were found to harbor at least one carbapenemase and were discharged into the environment. The carbapenemase blaKPC was found in six Citrobacter spp. and E. coli, while blaNDM was detected in two distinct Enterobacter spp. and E. coli. Notably, blaNDM-1 was identified in a 110 Kb IncFII conjugative plasmid in E. cloacae, E. xiangfangensis, and E. coli within the same hospital wastewater. In conclusion, hospital wastewater showed the presence of Enterobacteriaceae carrying a high frequency of carbapenemase blaKPC and blaNDM. We propose that hospital wastewater serves as reservoirs for resistance mechanism within bacterial communities and creates an optimal environment for the exchange of this resistance mechanism among different bacterial strains.<br><br>IMPORTANCE: The significance of this study lies in its findings regarding the prevalence and diversity of antibiotic-resistant bacteria and genes identified in hospital wastewater in Mexico. The research underscores the urgent need for enhanced surveillance and prevention strategies to tackle the escalating challenge of antibiotic resistance, particularly evident through the elevated frequencies of carbapenemase genes such as blaKPC and blaNDM within the Enterobacteriaceae family. Moreover, the identification of these resistance genes on conjugative plasmids highlights the potential for widespread transmission via horizontal gene transfer. Understanding the mechanisms of antibiotic resistance in hospital wastewater is crucial for developing targeted interventions aimed at reducing transmission, thereby safeguarding public health and preserving the efficacy of antimicrobial therapies.},
}
@article {pmid39011898,
year = {2024},
author = {Yuan, W and Yu, J and Li, Z},
title = {Rapid functional activation of horizontally transferred eukaryotic intron-containing genes in the bacterial recipient.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae628},
pmid = {39011898},
issn = {1362-4962},
support = {2020YFA0908000//National Key Research and Development Program of China/ ; TSBICIP-CXRC-001//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project/ ; 2060302//The ability establishment of sustainable use for valuable Chinese medicine resources/ ; },
abstract = {Horizontal gene transfer has occurred across all domains of life and contributed substantially to the evolution of both prokaryotes and eukaryotes. Previous studies suggest that many horizontally transferred eukaryotic genes conferred selective advantages to bacterial recipients, but how these eukaryotic genes evolved into functional bacterial genes remained unclear, particularly how bacteria overcome the expressional barrier posed by eukaryotic introns. Here, we first confirmed that the presence of intron would inactivate the horizontally transferred gene in Escherichia coli even if this gene could be efficiently transcribed. Subsequent large-scale genetic screens for activation of gene function revealed that activation events could rapidly occur within several days of selective cultivation. Molecular analysis of activation events uncovered two distinct mechanisms how bacteria overcome the intron barrier: (i) intron was partially deleted and the resulting stop codon-removed mutation led to one intact foreign protein or (ii) intron was intactly retained but it mediated the translation initiation and the interaction of two split small proteins (derived from coding sequences up- and downstream of intron, respectively) to restore gene function. Our findings underscore the likelihood that horizontally transferred eukaryotic intron-containing genes could rapidly acquire functionality if they confer a selective advantage to the prokaryotic recipient.},
}
@article {pmid39010965,
year = {2024},
author = {Jinnai, M and Yamaguchi, T and Minh, DTN and Hoang, ON and Le Thi, H and Thanh, PN and Hoai, PH and Do, PN and Van, CD and Kumeda, Y and Hase, A and Nakayama, T},
title = {Edible river fish-derived extended-spectrum β-lactamase (ESBL)-producing Enterobacterales harboring transferable plasmids encoding bla CTX-M-15, bla CTX-M-27, and bla CTX-M-55.},
journal = {One health (Amsterdam, Netherlands)},
volume = {18},
number = {},
pages = {100685},
pmid = {39010965},
issn = {2352-7714},
abstract = {Transmission of extended-spectrum β-lactamase (ESBL) genes has increased the global prevalence of ESBL-producing bacteria, especially in developing countries. Human infection with these bacteria may be food-mediated but has not been fully elucidated. Therefore, we aimed to examine ESBL-producing bacteria in edible river fish and elucidate their potential for horizontal gene transfer. A total of 173 ESBL-producing Enterobacterales were isolated (Escherichia coli [n = 87], Klebsiella pneumoniae [n = 52], Enterobacter cloacae complex [n = 18], Citrobacter freundii complex [n = 14], Atlantibacter hermannii [n = 1] and Serratia fonticola [n = 1]) from 56 of 80 fish intestinal contents sampled. Among the bacterial bla CTX-M genotypes, bla CTX-M-55 was the most predominant, followed by bla CTX-M-15, bla CTX-M-27, and bla CTX-M-65. Furthermore, we found that ESBL-producing Enterobacterales were able to transfer their bla CTX-M genes to E. coli. In summary, our results suggest that ESBL-producing Enterobacterales transfer bla CTX-M to indigenous gut E. coli in humans, following the consumption of contaminated fish.},
}
@article {pmid39007976,
year = {2024},
author = {Zalewska, M and Błażejewska, A and Gawor, J and Adamska, D and Goryca, K and Szeląg, M and Kalinowski, P and Popowska, M},
title = {The IncC and IncX1 resistance plasmids present in multi-drug resistant Escherichia coli strains isolated from poultry manure in Poland.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {39007976},
issn = {1614-7499},
support = {2017/25/Z/NZ7/03026//Narodowym Centrum Nauki/ ; },
abstract = {The study describes the whole-genome sequencing of two antibiotic-resistant representative Escherichia coli strains, isolated from poultry manure in 2020. The samples were obtained from a commercial chicken meat production facility in Poland. The antibiotic resistance profile was characterized by co-resistance to β-lactam antibiotics, aminoglycosides, and fluoroquinolones. The three identified resistance plasmids (R-plasmids), pECmdr13.2, pECmdr13.3, and pECmdr14.1, harbored various genes conferring resistance to tetracyclines (tetR[A]) for, aminoglycoside (aph, aac, and aad families), β-lactam (blaCMY-2, blaTEM-176), sulfonamide (sul1, sul2), fluoroquinolone (qnrS1), and phenicol (floR). These plasmids, which have not been previously reported in Poland, were found to carry IS26 insertion elements, the intI1-integrase gene, and conjugal transfer genes, facilitating horizontal gene transfer. Plasmids pECmdr13.2 and pECmdr14.1 also possessed a mercury resistance gene operon related to transposon Tn6196; this promotes plasmid persistence even without antibiotic selection pressure due to co-selection mechanisms such as co-resistance. The chicken manure-derived plasmids belonged to the IncX1 (narrow host range) and IncC (broad host range) incompatibility groups. Similar plasmids have been identified in various environments, clinical isolates, and farm animals, including cattle, swine, and poultry. This study holds significant importance for the One Health approach, as it highlights the potential for antibiotic-resistant bacteria from livestock and food sources, particularly E. coli, to transfer through the food chain to humans and vice versa.},
}
@article {pmid39001714,
year = {2024},
author = {Williams, TA and Davin, AA and Szánthó, LL and Stamatakis, A and Wahl, NA and Woodcroft, BJ and Soo, RM and Eme, L and Sheridan, PO and Gubry-Rangin, C and Spang, A and Hugenholtz, P and Szöllősi, GJ},
title = {Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae129},
pmid = {39001714},
issn = {1751-7370},
abstract = {In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree, and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution, and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host-microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature and oxygen use, offer enormous potential for understanding the rich tapestry of microbial life.},
}
@article {pmid38992783,
year = {2024},
author = {Klimov, PB and Hubert, J and Erban, T and Alejandra Perotti, M and Braig, HR and Flynt, A and He, Q and Cui, Y},
title = {Genomic and metagenomic analyses of the domestic mite Tyrophagus putrescentiae identify it as a widespread environmental contaminant and a host of a basal, mite-specific Wolbachia lineage (supergroup Q).},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijpara.2024.07.001},
pmid = {38992783},
issn = {1879-0135},
abstract = {Tyrophagus putrescentiae (mould mite) is a global, microscopic trophic generalist that commonly occurs in various human-created habitats, causing allergies and damaging stored food. Its ubiquity and extraordinary ability to penetrate research samples or cultures through air currents or by active walking through tights spaces (such as treads of screw caps) may lead to sample contamination and introduction of its DNA to research materials in the laboratory. This prompts a thorough investigation into potential sequence contamination in public genomic databases. The trophic success of T. putrescentiae is primarily attributed to the symbiotic bacteria housed in specialized internal mite structures, facilitating adaptation to varied nutritional niches. However, recent work suggests that horizontal transfer of bacterial/fungal genes related to nutritional functionality may also contribute to the mite's trophic versatility. This aspect requires independent confirmation. Additionally, T. putrescentiae harbors an uncharacterized and genetically divergent bacterium, Wolbachia, displaying blocking and microbiome-modifying effects. The phylogenomic position and supergroup assignment of this bacterium are unknown. Here, we sequenced and assembled the T. putrescentiae genome, analyzed its microbiome, and performed detailed phylogenomic analyses of the mite-specific Wolbachia. We show that T. putrescentiae DNA is a substantial source of contamination of research samples. Its DNA may inadvertently be co-extracted with the DNA of the target organism, eventually leading to sequence contamination in public databases. We identified a diversity of bacterial species associated with T. putrescentiae, including those capable of rapidly developing antibiotic resistance, such as Escherichia coli. Despite the presence of diverse bacterial communities in T. putrescentiae, we did not detect any recent horizontal gene transfers in this mite species and/or in astigmatid (domestic) mites in general. Our phylogenomic analysis of Wolbachia recovered a basal, mite-specific lineage (supergroup Q) represented by two Wolbachia spp. from the mould mite and a gall-inducing plant mite. Fluorescence in situ hybridization confirmed the presence of Wolbachia inside the mould mite. The discovery of an early derivative Wolbachia lineage (supergroup Q) in two phylogenetically unrelated and ecologically dissimilar mites suggests that this endosymbiotic bacterial lineage formed a long-term association with mites. This finding provides a unique insight into the early evolution and host associations of Wolbachia. Further discoveries of Wolbachia diversity in acariform mites are anticipated.},
}
@article {pmid38992444,
year = {2024},
author = {Soni, K and Jyoti, K and Kumar, A and Chandra, R},
title = {Coexistence of multidrug resistance and ESBL encoding genes - blaTEM, blaSHV, and blaCTX-M; its amplification and dispersion in the environment via municipal wastewater treatment plant.},
journal = {Chemosphere},
volume = {362},
number = {},
pages = {142829},
doi = {10.1016/j.chemosphere.2024.142829},
pmid = {38992444},
issn = {1879-1298},
abstract = {Municipal wastewater treatment plants (MWWTPs) are a global source of antibiotic resistance genes (ARGs), collecting wastewater from a variety of sources, including hospital wastewater, domestic wastewater, runoff from agricultural and livestock farms, etc. These sources are contaminated with organic and inorganic pollutants, ARGs and antibiotic-resistant bacteria (ARB). Such pollutants aided eutrophication and encouraged bacterial growth. During bacterial growth horizontal gene transfer (HGT) and vertical gene transfer (VGT) of ARGs and extended-spectrum β-lactamase (ESBL) encoding genes may facilitate, resulting in the spread of antibiotic resistance exponentially. The current study investigated the prevalence of multidrug resistance (MDR) and ESBL encoding genes in various treatment units of MWWTP and their spread in the environment. A total of three sampling sites (BUT, BRO, and BFB) were chosen, and 33 morphologically distinct bacterial colonies were isolated. 14 of the 33 isolates tested positive for antibiotic resistance and were further tested for the coexistence of MDR and ESBL production. The selected 14 isolates showed the highest resistance to trimethoprim (85.71%), followed by ciprofloxacin, azithromycin, and ampicillin (71.42%), tetracycline (57.14%), and vancomycin, gentamicin, and colistin sulphate (50%). A total of 9 isolates (64.28%) were phenotypically positive for ESBL production (BUT2, BUT3, BUT5, BRO1, BRO2, BRO3, BRO4, BRO5 and BFB1). The molecular detection of ESBL encoding genes, i.e. blaTEM, blaSHV, and blaCTX-M was carried out. The most prevalent gene was blaTEM (69.23%), followed by blaSHV (46.15%), and blaCTX-M (23.07%). In this study, 9 isolates (64.28%) out of 14 showed the coexistence of MDR and ESBL encoding genes, namely BUT3, BUT4, BUT5, BUT6, BUT7, BRO1, BRO2, BRO4, and BFB1. The coexistence of ESBL encoding genes and resistance to other antibiotic classes exacerbates human health and the environment.},
}
@article {pmid38992349,
year = {2024},
author = {Nazir, R and Shua, D and Shen, JP and Hu, HW and Wang, J and He, JZ},
title = {Effect of meddling ARBs on ARGs dynamics in fungal infested soil and their selective dispersal along spatially distant mycelial networks.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {174594},
doi = {10.1016/j.scitotenv.2024.174594},
pmid = {38992349},
issn = {1879-1026},
abstract = {During the recent times, environmental antibiotic resistance genes (ARGs) and their potential transfer to other bacterial hosts of pathogenic importance are of serious concern. However, the dissemination strategies of such ARGs are largely unknown. We tested that saprotrophic soil fungi differentially enriched antibiotic resistant bacteria (ARBs) and subsequently contributed in spatial distribution of selective ARGs. Wafergen qPCR analysis of 295 different ARGs was conducted for manure treated pre-sterilized soil incubated or not with selected bacterial-fungal consortia. The qPCR assay detected unique ARGs specifically found in the mycosphere of ascomycetous and basidiomycetous fungi. Both fungi exerted potentially different selection pressures on ARBs, resulting in different patterns of ARGs dissemination (to distant places) along their respective growing fungal highways. The relative abundance of mobile genetic elements (MGEs) was significantly decreased along fungal highways compared to the respective inoculation points. Moreover, the decrease in MGEs and ARGs (along fungal highways) was more prominent over time which depicts the continuous selection pressure of growing fungi on ARBs for enrichment of particular ARGs in mycosphere. Such data also indicate the potential role of saprotrophic soil fungi to facilitate horizontal gene transfer within mycospheric environmental settings. Our study, therefore, advocates to emphasize the future investigations for such (bacteria-fungal) interactive microbial consortia for potential (spatial) dissemination of resistance determinants which may ultimately increase the exposure risks of ARGs.},
}
@article {pmid38990885,
year = {2024},
author = {Windels, A and Franceus, J and Pleiss, J and Desmet, T},
title = {CANDy: Automated analysis of domain architectures in carbohydrate-active enzymes.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0306410},
doi = {10.1371/journal.pone.0306410},
pmid = {38990885},
issn = {1932-6203},
mesh = {*Protein Domains ; Glycoside Hydrolases/chemistry/metabolism/genetics ; Catalytic Domain ; Software ; Carbohydrate Metabolism ; Carbohydrates/chemistry ; Animals ; },
abstract = {Carbohydrate-active enzymes (CAZymes) can be found in all domains of life and play a crucial role in metabolic and physiological processes. CAZymes often possess a modular structure, comprising not only catalytic domains but also associated domains such as carbohydrate-binding modules (CBMs) and linker domains. By exploring the modular diversity of CAZy families, catalysts with novel properties can be discovered and further insight in their biological functions and evolutionary relationships can be obtained. Here we present the carbohydrate-active enzyme domain analysis tool (CANDy), an assembly of several novel scripts, tools and databases that allows users to analyze the domain architecture of all protein sequences in a given CAZy family. CANDy's usability is shown on glycoside hydrolase family 48, a small yet underexplored family containing multi-domain enzymes. Our analysis reveals the existence of 35 distinct domain assemblies, including eight known architectures, with the remaining assemblies awaiting characterization. Moreover, we substantiate the occurrence of horizontal gene transfer from prokaryotes to insect orthologs and provide evidence for the subsequent removal of auxiliary domains, likely through a gene fission event. CANDy is available at https://github.com/PyEED/CANDy.},
}
@article {pmid38987681,
year = {2024},
author = {Elgayar, FA and Gouda, MK and Badran, AA and El Halfawy, NM},
title = {Pathogenomics analysis of high-risk clone ST147 multidrug-resistant Klebsiella pneumoniae isolated from a patient in Egypt.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {256},
pmid = {38987681},
issn = {1471-2180},
mesh = {*Klebsiella pneumoniae/genetics/drug effects/isolation &amp; purification/classification ; Humans ; Egypt ; *Drug Resistance, Multiple, Bacterial/genetics ; *Klebsiella Infections/microbiology/epidemiology ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; *Virulence Factors/genetics ; *Whole Genome Sequencing ; *Genome, Bacterial/genetics ; beta-Lactamases/genetics ; Bacterial Proteins/genetics ; Plasmids/genetics ; },
abstract = {BACKGROUND: The emergence of multi-drug-resistant Klebsiella pneumoniae (MDR-KP) represents a serious clinical health concern. Antibiotic resistance and virulence interactions play a significant role in the pathogenesis of K. pneumoniae infections. Therefore, tracking the clinical resistome and virulome through monitoring antibiotic resistance genes (ARG) and virulence factors in the bacterial genome using computational analysis tools is critical for predicting the next epidemic.<br><br>METHODS: In the current study, one hundred extended spectrum &#x3b2;-lactamase (ESBL)-producing clinical isolates were collected from Mansoura University Hospital, Egypt, in a six-month period from January to June 2022. One isolate was selected due to the high resistance phenotype, and the genetic features of MDR-KP recovered from hospitalized patient were investigated. Otherwise, the susceptibility to 25 antimicrobials was determined using the DL Antimicrobial Susceptibility Testing (AST) system. Whole genome sequencing (WGS) using Illumina NovaSeq 6000 was employed to provide genomic insights into K. pneumoniae WSF99 clinical isolate.<br><br>RESULTS: The isolate K. pneumoniae WSF99 was phenotypically resistant to the antibiotics under investigation via antibiotic susceptibility testing. WGS analysis revealed that WSF99 total genome length was 5.7&#xa0;Mb with an estimated 5,718 protein-coding genes and a G&#x2009;+&#x2009;C content of 56.98&#xa0;mol%. Additionally, the allelic profile of the WSF99 isolate was allocated to the high-risk clone ST147. Furthermore, diverse antibiotic resistance genes were determined in the genome that explain the high-level resistance phenotypes. Several &#x3b2;-lactamase genes, including blaCTX-M-15, blaTEM-1, blaTEM-12, blaSHV-11, blaSHV-67, and blaOXA-9, were detected in the WSF99 isolate. Moreover, a single carbapenemase gene, blaNDM-5, was predicted in the genome, positioned within a mobile cassette. In addition, other resistance genes were predicted in the genome including, aac(6')-Ib, aph(3')-VI, sul1, sul2, fosA, aadA, arr-2, qnrS1, tetA and tetC. Four plasmid replicons CoIRNAI, IncFIB(K), IncFIB(pQil), and IncR were predicted in the genome. The draft genome analysis revealed the occurrence of genetic mobile elements positioned around the ARGs, suggesting the ease of dissemination via horizontal gene transfer.<br><br>CONCLUSIONS: This study reports a comprehensive pathogenomic analysis of MDR-KP isolated from a hospitalized patient. These findings could be relevant for future studies investigating the diversity of antimicrobial resistance and virulence in Egypt.},
}
@article {pmid38986507,
year = {2024},
author = {Irusan, D and Akshay, SD and Shetty, VP and Karunasagar, I and Deekshit, VK and Rohit, A},
title = {Analysis of mcr family of colistin resistance genes in Gram-negative isolates from a tertiary care hospital in India.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxae172},
pmid = {38986507},
issn = {1365-2672},
abstract = {AIM: Colistin serves as the drug of last resort for combating numerous multidrug-resistant (MDR) Gram-negative infections. Its efficacy is hampered by the prevalent issue of colistin resistance, which severely limits treatment options for critically ill patients. Identifying resistance genes is crucial for controlling resistance spread, with horizontal gene transfer being the primary mechanism among bacteria. This study aimed to assess the prevalence of plasmid-mediated mcr genes associated with colistin resistance in Gram-negative bacteria, utilizing both genotypic and phenotypic tests.<br><br>METHODS AND RESULTS: The clinical isolates (n=913) were obtained from a tertiary care center in Chennai, India. Colistin resistance was seen among Gram-negative isolates. These strains underwent screening for mcr-1, mcr-3, mcr-4, and mcr-5 genes via conventional PCR. Additionally, mcr-positive isolates were confirmed through Sanger sequencing and phenotypic testing. The bacterial isolates predominantly comprised Klebsiella pneumoniae (62.43%), Escherichia coli (19.71%), Pseudomonas aeruginosa (10.73%), Acinetobacter baumannii (4.81%), along with other species. All isolates exhibited multidrug resistance to three or more antibiotic classes. Colistin resistance, determined via broth microdilution (BMD) using CLSI guidelines, was observed in 13.08% of the isolates studied. Notably, mcr-5 was detected in K. pneumoniae in PCR, despite their absence in Sanger sequencing and phenotypic tests (including the combined-disk test, colistin MIC in the presence of EDTA, and Zeta potential assays). This finding underscores the importance of employing multiple diagnostic approaches to accurately identify colistin resistance mechanisms.<br><br>CONCLUSION AND IMPACT: The study highlights a concerning prevalence of colistin resistance among Enterobacterales, especially those producing carbapenemase, thereby impacting mortality rates. Nonetheless, further investigations are warranted to elucidate common mechanisms of colistin resistance and to evaluate the efficacy of screening techniques in detecting isolates carrying mcr genes responsible for enzyme-mediated lipopolysaccharide (LPS) modification.},
}
@article {pmid38986416,
year = {2024},
author = {Chi, W and Zou, Y and Qiu, T and Shi, W and Tang, L and Xu, M and Wu, H and Luan, X},
title = {Horizontal gene transfer plays a crucial role in the development of antibiotic resistance in an antibiotic-free shrimp farming system.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {135150},
doi = {10.1016/j.jhazmat.2024.135150},
pmid = {38986416},
issn = {1873-3336},
abstract = {Antibiotic selective pressure in aquaculture systems often results in the antibiotic resistance genes (ARGs) proliferation. Nonetheless, a paucity of data exists concerning the mechanisms of ARGs development in aquaculture systems without the influences of antibiotics. This study utilized metagenomic approaches to elucidate the dynamics and transfer mechanisms of ARGs throughout the aquaculture of Pacific white shrimp. A marked change in the resistome was observed throughout the aquaculture without antibiotics. The total ARGs relative abundance increased from 0.05 to 0.33 by day 90 of cultivation, with even higher in mixed wastewater (0.44). Both bacterial communities and mobile genetic elements play pivotal roles in the development of ARGs. Metagenome-assembled genomes showed enrichment of environmentally intrinsic ARGs on chromosomes including macB and mdtK. The plasmid-mediated horizontal transfer was recognized as a principal factor contributing to the rise of ARGs, particularly for tetG and floR, and this led to an escalation of resistance risk, peaking at a risks core of 35.43 on day 90. This study demonstrates that horizontal gene transfer plays a crucial role in ARGs development without antibiotic pressure, which can provide a theoretical foundation for controlling ARGs proliferation in aquaculture systems.},
}
@article {pmid38942024,
year = {2024},
author = {Harder, CB and Miyauchi, S and Virágh, M and Kuo, A and Thoen, E and Andreopoulos, B and Lu, D and Skrede, I and Drula, E and Henrissat, B and Morin, E and Kohler, A and Barry, K and LaButti, K and Salamov, A and Lipzen, A and Merényi, Z and Hegedüs, B and Baldrian, P and Stursova, M and Weitz, H and Taylor, A and Koriabine, M and Savage, E and Grigoriev, IV and Nagy, LG and Martin, F and Kauserud, H},
title = {Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations.},
journal = {Cell genomics},
volume = {4},
number = {7},
pages = {100586},
doi = {10.1016/j.xgen.2024.100586},
pmid = {38942024},
issn = {2666-979X},
mesh = {*Genome, Fungal/genetics ; *Agaricales/genetics ; Phylogeny ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Plants/microbiology/genetics ; },
abstract = {Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.},
}
@article {pmid38983623,
year = {2024},
author = {Chin, HS and Ravi Varadharajulu, N and Lin, ZH and Chen, WY and Zhang, ZH and Arumugam, S and Lai, CY and Yu, SS},
title = {Isolation, molecular identification, and genomic analysis of Mangrovibacter phragmitis strain ASIOC01 from activated sludge harboring the bioremediation prowess of glycerol and organic pollutants in high-salinity.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1415723},
pmid = {38983623},
issn = {1664-302X},
abstract = {The physiological and genotypic characteristics of Mangrovibacter (MGB) remain largely unexplored, including their distribution and abundance within ecosystems. M. phragmitis (MPH) ASIOC01 was successfully isolated from activated sludge (AS), which was pre-enriched by adding 1,3-dichloro-2-propanol and 3-chloro-1,2-propanediol as carbon sources. The new isolate, MPH ASIOC01, exhibited resilience in a medium containing sodium chloride concentration up to 11% (with optimal growth observed at 3%) and effectively utilizing glycerol as their sole carbon source. However, species delimitation of MGBs remains challenging due to high 16S rRNA sequence similarity (greater than 99% ANI) among different MGBs. In contrast, among the housekeeping gene discrepancies, the tryptophan synthase beta chain gene can serve as a robust marker for fast species delimitation among MGBs. Furthermore, the complete genome of MPH ASIOC01 was fully sequenced and circlized as a single contig using the PacBio HiFi sequencing method. Comparative genomics revealed genes potentially associated with various phenotypic features of MGBs, such as nitrogen-fixing, phosphate-solubilizing, cellulose-digesting, Cr-reducing, and salt tolerance. Computational analysis suggested that MPH ASIOC01 may have undergone horizontal gene transfer events, possibly contributing unique traits such as antibiotic resistance. Finally, our findings also disclosed that the introduction of MPH ASIOC01 into AS can assist in the remediation of wastewater chemical oxygen demand, which was evaluated using gas chromatograph-mass spectrometry. To the best of our knowledge, this study offers the most comprehensive understanding of the phenotypic and genotypic features of MGBs to date.},
}
@article {pmid38980659,
year = {2024},
author = {Poddar, BJ and Khardenavis, AA},
title = {Genomic Insights into the Landfill Microbial Community: Denitrifying Activity Supporting One-Carbon Utilization.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {38980659},
issn = {1559-0291},
support = {EMR/2016/006589//SERB, New Delhi/ ; },
abstract = {In spite of the developments in understanding of denitrifying methylotrophy in the recent years, challenges still exist in unravelling the overall biochemistry of nitrate-dependent methane oxidation in novel or poorly characterized/not-yet-cultured bacteria. In the present study, landfill site was mined for novel C1-carbon-metabolizing bacteria which can use nitrate/nitrite as an electron acceptor. A high-throughput rapid plate assay identified three bacterial isolates with eminent ability for nitrate-dependent methane metabolism under anaerobic conditions. Taxonomic identification by whole-genome sequence-based overall genome relatedness indices accurately assigned the isolates AAK_M13, AAK_M29, and AAK_M39 at the species level to Enterobacter cloacae, Bacillus subtilis, and Bacillus halotolerans, respectively. Several genes encoding sub-components involved in alcohol utilization and denitrification pathways, such as adh, fdh, fdo, nar, nir, and nor, were identified in all the genomes. Though no gene clusters encoding MMO/AMO were annotated, sequencing of PCR amplicons revealed similarity with pMMO/AMO gene using translated nucleotide sequence of strains AAK_M29 and AAK_M39, while strain AAK_M13 showed similarity with XRE family transcriptional regulator. This suggests the horizontal gene transfer and/or presence of a truncated version of a housekeeping enzyme encoded by genes exhibiting partial sequence similarity with pMMO genes that mimicked its function at greenhouse gas emission sites. Owing to lack of conclusive evidence for presence of methane metabolism genes in the selected isolates, further experiment was performed to validate their nitrate-dependent methane oxidation capacities. Bacillus subtilis AAK_M29, Bacillus halotolerans AAK_M39, and Enterobacter cloacae AAK_M13 could oxidize 60%, 75%, and 85% of the added methane respectively accompanied by high nitrate reduction (56-62%) thus supporting the correlation between these two activities. The remarkable ability of these isolates for nitrate-dependent methane metabolism has highlighted their role in ecological contribution and biotechnological potential to serve as methane and nitrate sinks in the landfill sites.},
}
@article {pmid38977308,
year = {2024},
author = {Vakirlis, N and Kupczok, A},
title = {Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.278977.124},
pmid = {38977308},
issn = {1549-5469},
abstract = {Species-specific genes, also known as orphans, are ubiquitous across life's domains. In prokaryotes, species-specific orphan genes (SSOGs) are mostly thought to originate in external elements such as viruses followed by horizontal gene transfer, whereas the scenario of native origination, through rapid divergence or de novo, is mostly dismissed. However, quantitative evidence supporting either scenario is lacking. Here, we systematically analyzed genomes from 4644 human gut microbiome species and identified more than 600,000 unique SSOGs, representing an average of 2.6% of a given species' pangenome. These sequences are mostly rare within each species yet show signs of purifying selection. Overall, SSOGs use optimal codons less frequently, and their proteins are more disordered than those of conserved genes (i.e., non-SSOGs). Importantly, across species, the GC content of SSOGs closely matches that of conserved ones. In contrast, the ∼5% of SSOGs that share similarity to known viral sequences have distinct characteristics, including lower GC content. Thus, SSOGs with similarity to viruses differ from the remaining SSOGs, contrasting an external origination scenario for most of them. By examining the orthologous genomic region in closely related species, we show that a small subset of SSOGs likely evolved natively de novo and find that these genes also differ in their properties from the remaining SSOGs. Our results challenge the notion that external elements are the dominant source of prokaryotic genetic novelty and will enable future studies into the biological role and relevance of species-specific genes in the human gut.},
}
@article {pmid38975782,
year = {2024},
author = {Price, CTD and Hanford, HE and Al-Quadan, T and Santic, M and Shin, CJ and Da'as, MSJ and Abu Kwaik, Y},
title = {Amoebae as training grounds for microbial pathogens.},
journal = {mBio},
volume = {},
number = {},
pages = {e0082724},
doi = {10.1128/mbio.00827-24},
pmid = {38975782},
issn = {2150-7511},
abstract = {Grazing of amoebae on microorganisms represents one of the oldest predator-prey dynamic relationships in nature. It represents a genetic "melting pot" for an ancient and continuous multi-directional inter- and intra-kingdom horizontal gene transfer between amoebae and its preys, intracellular microbial residents, endosymbionts, and giant viruses, which has shaped the evolution, selection, and adaptation of microbes that evade degradation by predatory amoeba. Unicellular phagocytic amoebae are thought to be the ancient ancestors of macrophages with highly conserved eukaryotic processes. Selection and evolution of microbes within amoeba through their evolution to target highly conserved eukaryotic processes have facilitated the expansion of their host range to mammals, causing various infectious diseases. Legionella and environmental Chlamydia harbor an immense number of eukaryotic-like proteins that are involved in ubiquitin-related processes or are tandem repeats-containing proteins involved in protein-protein and protein-chromatin interactions. Some of these eukaryotic-like proteins exhibit novel domain architecture and novel enzymatic functions absent in mammalian cells, such as ubiquitin ligases, likely acquired from amoebae. Mammalian cells and amoebae may respond similarly to microbial factors that target highly conserved eukaryotic processes, but mammalian cells may undergo an accidental response to amoeba-adapted microbial factors. We discuss specific examples of microbes that have evolved to evade amoeba predation, including the bacterial pathogens- Legionella, Chlamydia, Coxiella, Rickettssia, Francisella, Mycobacteria, Salmonella, Bartonella, Rhodococcus, Pseudomonas, Vibrio, Helicobacter, Campylobacter, and Aliarcobacter. We also discuss the fungi Cryptococcus, and Asperigillus, as well as amoebae mimiviruses/giant viruses. We propose that amoeba-microbe interactions will continue to be a major "training ground" for the evolution, selection, adaptation, and emergence of microbial pathogens equipped with unique pathogenic tools to infect mammalian hosts. However, our progress will continue to be highly dependent on additional genomic, biochemical, and cellular data of unicellular eukaryotes.},
}
@article {pmid38971740,
year = {2024},
author = {Bhat, A and Sharma, R and Desigan, K and Lucas, MM and Mishra, A and Bowers, RM and Woyke, T and Epstein, B and Tiffin, P and Pueyo, JJ and Paape, T},
title = {Horizontal gene transfer of the Mer operon is associated with large effects on the transcriptome and increased tolerance to mercury in nitrogen-fixing bacteria.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {247},
pmid = {38971740},
issn = {1471-2180},
support = {Quantitative Plant Science Initiative (QPSI)//U.S. Department of Energy/ ; Quantitative Plant Science Initiative (QPSI)//U.S. Department of Energy/ ; Quantitative Plant Science Initiative (QPSI)//U.S. Department of Energy/ ; Quantitative Plant Science Initiative (QPSI)//U.S. Department of Energy/ ; 3092-53000-001-00D//U.S. Department of Agriculture/ ; 3092-53000-001-00D//U.S. Department of Agriculture/ ; },
mesh = {*Gene Transfer, Horizontal ; *Mercury/metabolism/toxicity ; *Operon ; *Transcriptome ; *Symbiosis ; Nitrogen-Fixing Bacteria/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Nitrogen Fixation ; Rhizobium leguminosarum/genetics/metabolism ; Soil Microbiology ; },
abstract = {BACKGROUND: Mercury (Hg) is highly toxic and has the potential to cause severe health problems for humans and foraging animals when transported into edible plant parts. Soil rhizobia that form symbiosis with legumes may possess mechanisms to prevent heavy metal translocation from roots to shoots in plants by exporting metals from nodules or compartmentalizing metal ions inside nodules. Horizontal gene transfer has potential to confer immediate de novo adaptations to stress. We used comparative genomics of high quality de novo assemblies to identify structural differences in the genomes of nitrogen-fixing rhizobia that were isolated from a mercury (Hg) mine site that show high variation in their tolerance to Hg.<br><br>RESULTS: Our analyses identified multiple structurally conserved merA homologs in the genomes of Sinorhizobium medicae and Rhizobium leguminosarum but only the strains that possessed a Mer operon exhibited 10-fold increased tolerance to Hg. RNAseq analysis revealed nearly all genes in the Mer operon were significantly up-regulated in response to Hg stress in free-living conditions and in nodules. In both free-living and nodule environments, we found the Hg-tolerant strains with a Mer operon exhibited the fewest number of differentially expressed genes (DEGs) in the genome, indicating a rapid and efficient detoxification of Hg from the cells that reduced general stress responses to the Hg-treatment. Expression changes in S. medicae while in bacteroids showed that both rhizobia strain and host-plant tolerance affected the number of DEGs. Aside from Mer operon genes, nif genes which are involved in nitrogenase activity in S. medicae showed significant up-regulation in the most Hg-tolerant strain while inside the most Hg-accumulating host-plant. Transfer of a plasmid containing the Mer operon from the most tolerant strain to low-tolerant strains resulted in an immediate increase in Hg tolerance, indicating that the Mer operon is able to confer hyper tolerance to Hg.<br><br>CONCLUSIONS: Mer operons have not been previously reported in nitrogen-fixing rhizobia. This study demonstrates a pivotal role of the Mer operon in effective mercury detoxification and hypertolerance in nitrogen-fixing rhizobia. This finding has major implications not only for soil bioremediation, but also host plants growing in mercury contaminated soils.},
}
@article {pmid38971360,
year = {2024},
author = {Zhang, W and Geng, J and Sun, M and Jiang, C and Lin, H and Chen, H and Yang, Y},
title = {Distinct species turnover patterns shaped the richness of antibiotic resistance genes on eight different microplastic polymers.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119562},
doi = {10.1016/j.envres.2024.119562},
pmid = {38971360},
issn = {1096-0953},
abstract = {Elucidating the formation mechanism of plastisphere antibiotic resistance genes (ARGs) on different polymers is necessary to understand the ecological risks of plastisphere ARGs. Here, we explored the turnover and assembly mechanism of plastisphere ARGs on 8 different microplastic polymers (4 biodegradable (bMPs) and 4 non-biodegradable microplastics (nMPs)) by metagenomic sequencing. Our study revealed the presence of 479 ARGs with abundance ranging from 41.37 to 58.17 copies/16S rRNA gene in all plastispheres. These ARGs were predominantly multidrug resistance genes. The richness of plastisphere ARGs on different polymers had a significant correlation with the contribution of species turnover to plastisphere ARGs β diversity. Furthermore, polymer type was the most critical factor affecting the composition of plastisphere ARGs. More opportunistic pathogens carrying diverse ARGs on BMPs (PBAT, PBS, and PHA) with higher horizontal gene transfer potential may further magnify the ecological risks and human health threats. For example, the opportunistic pathogens Riemerella anatipestifer, Vibrio campbellii, and Vibrio cholerae are closely related to human production and life, which were the important potential hosts of many plastisphere ARGs and mobile genetic elements on BMPs. Thus, we emphasize the urgency of developing the formation mechanism of plastisphere ARGs and the necessity of controlling BMPs and ARG pollution, especially BMPs, with ever-increasing usage in daily life.},
}
@article {pmid38969684,
year = {2024},
author = {Salem, S and Abdelsalam, NA and Shata, AH and Mouftah, SF and Cobo-Díaz, JF and Osama, D and Atteya, R and Elhadidy, M},
title = {Unveiling the microevolution of antimicrobial resistance in selected Pseudomonas aeruginosa isolates from Egyptian healthcare settings: A genomic approach.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {15500},
pmid = {38969684},
issn = {2045-2322},
support = {CRP/EGY22-03//CRP-ICGEB grant/ ; },
mesh = {*Pseudomonas aeruginosa/genetics/drug effects/isolation &amp; purification ; Egypt/epidemiology ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; Pseudomonas Infections/microbiology/epidemiology ; Biofilms/drug effects/growth &amp; development ; Whole Genome Sequencing/methods ; Genomics/methods ; Genome, Bacterial ; Evolution, Molecular ; Drug Resistance, Bacterial/genetics ; Multilocus Sequence Typing ; Polymorphism, Single Nucleotide ; Drug Resistance, Multiple, Bacterial/genetics ; Phylogeny ; },
abstract = {The incidence of Pseudomonas aeruginosa infections in healthcare environments, particularly in low-and middle-income countries, is on the rise. The purpose of this study was to provide comprehensive genomic insights into thirteen P. aeruginosa isolates obtained from Egyptian healthcare settings. Phenotypic analysis of the antimicrobial resistance profile and biofilm formation were performed using minimum inhibitory concentration and microtiter plate assay, respectively. Whole genome sequencing was employed to identify sequence typing, resistome, virulome, and mobile genetic elements. Our findings indicate that 92.3% of the isolates were classified as extensively drug-resistant, with 53.85% of these demonstrating strong biofilm production capabilities. The predominant clone observed in the study was ST773, followed by ST235, both of which were associated with the O11 serotype. Core genome multi-locus sequence typing comparison of these clones with global isolates suggested their potential global expansion and adaptation. A significant portion of the isolates harbored Col plasmids and various MGEs, all of which were linked to antimicrobial resistance genes. Single nucleotide polymorphisms in different genes were associated with the development of antimicrobial resistance in these isolates. In conclusion, this pilot study underscores the prevalence of extensively drug-resistant P. aeruginosa isolates and emphasizes the role of horizontal gene transfer facilitated by a diverse array of mobile genetic elements within various clones. Furthermore, specific insertion sequences and mutations were found to be associated with antibiotic resistance.},
}
@article {pmid38968733,
year = {2024},
author = {Li, Y and Zhang, S and Chen, Z and Huang, W and Liu, Q and Fang, H and Chi, B and Yang, N and Zhang, Q},
title = {Deciphering the impact of organic loading rate and digestate recirculation on the occurrence patterns of antibiotics and antibiotic resistance genes in dry anaerobic digestion of kitchen waste.},
journal = {Water research},
volume = {261},
number = {},
pages = {122005},
doi = {10.1016/j.watres.2024.122005},
pmid = {38968733},
issn = {1879-2448},
abstract = {Organic loading rate (OLR) is crucial for determining the stability of dry anaerobic digestion (AD). Digestate recirculation contributes to reactor stability and enhances methane production. Nevertheless, the understanding of how OLR and digestate recirculation affect the abundance and diversity of antibiotics and antibiotic resistance genes (ARGs), as well as the mechanisms involved in the dissemination of ARGs, remains limited. This study thoroughly investigated this critical issue through a long-term pilot-scale experiment. The metabolome analyses revealed the enrichment of various antibiotics, such as aminoglycoside, tetracycline, and macrolide, under low OLR conditions (OLR ≤ 4.0 g·VS/L·d) and the reactor instability. Antibiotics abundance decreased by approximately 19.66-31.69 % during high OLR operation (OLR ≥ 6.0 g·VS/L·d) with digestate recirculation. The metagenome analyses demonstrated that although low OLR promoted reactor stability, it facilitated the proliferation of antibiotic-resistant bacteria, such as Pseudomonas, and triggered functional profiles related to ATP generation, oxidative stress response, EPS secretion, and cell membrane permeability, thereby facilitating horizontal gene transfer (HGT) of ARGs. However, under stable operation at an OLR of 6.0 g·VS/L·d, there was a decrease in ARGs abundance but a notable increase in human pathogenic bacteria (HPB) and mobile genetic elements (MGEs). Subsequently, during reactor instability, the abundance of ARGs and HPB increased. Notably, during digestate recirculation at OLR levels of 6.0 and 7.0 g·VS/L·d, the process attenuated the risk of ARGs spread by reducing the diversity of ARGs hosts, minimizing interactions among ARGs hosts, ARGs, and MGEs, and weakening functional profiles associated with HGT of ARGs. Overall, digestate recirculation aids in reducing the abundance of antibiotics and ARGs under high OLR conditions. These findings provide advanced insights into how OLR and digestate recirculation affect the occurrence patterns of antibiotics and ARGs in dry AD.},
}
@article {pmid38965531,
year = {2024},
author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV},
title = {Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {148},
pmid = {38965531},
issn = {1741-7007},
support = {Intramural Research Program//U.S. National Library of Medicine/ ; },
mesh = {*Gene Transfer, Horizontal ; *Microbiota/genetics ; Biodiversity ; Symbiosis/genetics ; Models, Theoretical ; Models, Biological ; },
abstract = {BACKGROUND: Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically remains stable across a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. Therefore, the long-term persistence of microbiome diversity calls for an explanation.<br><br>RESULTS: To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis were obtained, namely, pure competition, host-parasite relationship, and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environment.<br><br>CONCLUSIONS: The results of this modeling study show that basic phenomena that are universal in microbial communities, namely, environmental variation and HGT, provide for stabilization and persistence of microbial diversity, and emergence of ecological complexity.},
}
@article {pmid38964677,
year = {2024},
author = {Xu, G and Yang, S},
title = {Evolution of orphan and atypical histidine kinases and response regulators for microbial signaling diversity.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {133635},
doi = {10.1016/j.ijbiomac.2024.133635},
pmid = {38964677},
issn = {1879-0003},
abstract = {Two-component signaling systems (TCS) are the predominant means of microbes for sensing and responding to environmental stimuli. Typically, TCS is comprised of a sensor histidine kinase (HK) and a cognate response regulator (RR), which might have coevolved together. They usually involve the phosphoryl transfer signaling mechanism. However, there are also some orphan and atypical HK and RR homologs, and their evolutionary origins are still not very clear. They are not associated with cognate pairs or lack the conserved residues for phosphoryl transfer, but they could receive or respond to signals from other regulators. The objective of this study is to reveal the evolutionary history of these orphan and atypical HK and RR homologs. Structural, domain, sequence, and phylogenetic analyses indicated that their evolution process might undergo gene duplication, divergence, and domain shuffling. Meanwhile, lateral gene transfer might also be involved for their gene distribution. Evolution of orphan and atypical HK and RR homologs have increased their signaling diversity, which could be helpful for microbial adaption in complex environments.},
}
@article {pmid38964571,
year = {2024},
author = {Xu, C and Hu, C and Li, F and Liu, W and Xu, Y and Shi, D},
title = {Antibiotic resistance genes risks in relation to host pathogenicity and mobility in a typical hospital wastewater treatment process.},
journal = {Environmental research},
volume = {259},
number = {},
pages = {119554},
doi = {10.1016/j.envres.2024.119554},
pmid = {38964571},
issn = {1096-0953},
abstract = {Hospital wastewaters (HWWs) serve as critical reservoirs for disseminating antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB). However, the dynamics and noteworthy shifts of ARGs and their associated pathogenicity, mobility, and resistome risks during HWWs treatment processes remain poorly understood. Utilizing metagenomic sequencing and assembly, we identified 817 ARG subtypes conferring resistance to 20 classes of antibiotics across 18 HWW samples from influent to effluent. Genes encoding resistance to multidrug, aminoglycoside and beta_lactam were the most prevalent ARG types, reflecting patterns observed in clinical settings. On-site treatment efforts decreased the relative abundance of ARGs by 77.4% from influent to secondary sedimentation, whereas chlorine disinfection significantly increased their abundance in the final effluent. Deterministic processes primarily drove the taxonomic assembly, with Proteobacteria being the most abundant phylum and serving as the primary host for 15 ARG types. Contig-based analysis further revealed 114 pathogenic ARB, with Escherichia coli, Pseudomonas alcaligenes, and Pseudomonas aeruginosa exhibiting multidrug-resistant. The contributions of host bacteria and pathogenic ARB varied throughout wastewater treatment. In addition, 7.10%-31.0 % ARGs were flanked by mobile genetic elements (MGEs), predominantly mediated by transposase (74.1%). Notably, tnpA exhibited the highest potential for ARG dissemination, frequently co-occurring with beta-lactam resistance genes (35.2%). Considering ARG profiles, pathogenic hosts, and transferability, raw influent exhibited the highest antibiotic resistome risk index (ARRI), followed by the final effluent. Chlorine disinfection exacerbated resistome risks by inducing potential pathogenic ARB and mobile ARGs, posing threats to the receiving environment. This study delineates ARG occurrence patterns, highlights mechanisms of ARG carriage and horizontal gene transfer, and provides insights for assessing resistance risks and prioritizing interventions in clinical settings.},
}
@article {pmid38964320,
year = {2024},
author = {Kadibalban, AS and Landan, G and Dagan, T},
title = {The extent and characteristics of DNA transfer between plasmids and chromosomes.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.06.030},
pmid = {38964320},
issn = {1879-0445},
abstract = {Plasmids are extrachromosomal genetic elements that reside in prokaryotes. The acquisition of plasmids encoding beneficial traits can facilitate short-term survival in harsh environmental conditions or long-term adaptation of new ecological niches. Due to their ability to transfer between cells, plasmids are considered agents of gene transfer. Nonetheless, the frequency of DNA transfer between plasmids and chromosomes remains understudied. Using a novel approach for detection of homologous loci between genome pairs, we uncover gene sharing with the chromosome in 1,974 (66%) plasmids residing in 1,016 (78%) taxonomically diverse isolates. The majority of homologous loci correspond to mobile elements, which may be duplicated in the host chromosomes in tens of copies. Neighboring shared genes often encode similar functional categories, indicating the transfer of multigene functional units. Rare transfer events of antibiotics resistance genes are observed mainly with mobile elements. The frequent erosion of sequence similarity in homologous regions indicates that the transferred DNA is often devoid of function. DNA transfer between plasmids and chromosomes thus generates genetic variation that is akin to workings of endosymbiotic gene transfer in eukaryotic evolution. Our findings imply that plasmid contribution to gene transfer most often corresponds to transfer of the plasmid entity rather than transfer of protein-coding genes between plasmids and chromosomes.},
}
@article {pmid38963857,
year = {2024},
author = {Weimann, A and Dinan, AM and Ruis, C and Bernut, A and Pont, S and Brown, K and Ryan, J and Santos, L and Ellison, L and Ukor, E and Pandurangan, AP and Krokowski, S and Blundell, TL and Welch, M and Blane, B and Judge, K and Bousfield, R and Brown, N and Bryant, JM and Kukavica-Ibrulj, I and Rampioni, G and Leoni, L and Harrison, PT and Peacock, SJ and Thomson, NR and Gauthier, J and Fothergill, JL and Levesque, RC and Parkhill, J and Floto, RA},
title = {Evolution and host-specific adaptation of Pseudomonas aeruginosa.},
journal = {Science (New York, N.Y.)},
volume = {385},
number = {6704},
pages = {eadi0908},
doi = {10.1126/science.adi0908},
pmid = {38963857},
issn = {1095-9203},
mesh = {*Pseudomonas aeruginosa/genetics/physiology/pathogenicity ; *Pseudomonas Infections/microbiology ; Humans ; *Cystic Fibrosis/microbiology ; Evolution, Molecular ; Adaptation, Physiological ; Gene Transfer, Horizontal ; Host Specificity ; Host Adaptation ; Macrophages/microbiology/immunology ; },
abstract = {The major human bacterial pathogen Pseudomonas aeruginosa causes multidrug-resistant infections in people with underlying immunodeficiencies or structural lung diseases such as cystic fibrosis (CF). We show that a few environmental isolates, driven by horizontal gene acquisition, have become dominant epidemic clones that have sequentially emerged and spread through global transmission networks over the past 200 years. These clones demonstrate varying intrinsic propensities for infecting CF or non-CF individuals (linked to specific transcriptional changes enabling survival within macrophages); have undergone multiple rounds of convergent, host-specific adaptation; and have eventually lost their ability to transmit between different patient groups. Our findings thus explain the pathogenic evolution of P. aeruginosa and highlight the importance of global surveillance and cross-infection prevention in averting the emergence of future epidemic clones.},
}
@article {pmid38962965,
year = {2024},
author = {Diamant, I and Adani, B and Sylman, M and Rahav, G and Gal-Mor, O},
title = {The transcriptional regulation of the horizontally acquired iron uptake system, yersiniabactin and its contribution to oxidative stress tolerance and pathogenicity of globally emerging salmonella strains.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2369339},
doi = {10.1080/19490976.2024.2369339},
pmid = {38962965},
issn = {1949-0984},
mesh = {Animals ; *Oxidative Stress ; *Iron/metabolism ; Mice ; *Bacterial Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; *Salmonella enterica/genetics/metabolism/pathogenicity ; Virulence/genetics ; Phenols/metabolism ; Thiazoles/metabolism ; Humans ; Salmonella Infections/microbiology ; Gene Transfer, Horizontal ; Female ; Virulence Factors/genetics/metabolism ; Plasmids/genetics ; },
abstract = {The bacterial species Salmonella enterica (S. enterica) is a highly diverse pathogen containing more than 2600 distinct serovars, which can infect a wide range of animal and human hosts. Recent global emergence of multidrug resistant strains, from serovars Infantis and Muenchen is associated with acquisition of the epidemic megaplasmid, pESI that augments antimicrobial resistance and pathogenicity. One of the main pESI's virulence factors is the potent iron uptake system, yersiniabactin encoded by fyuA, irp2-irp1-ybtUTE, ybtA, and ybtPQXS gene cluster. Here we show that yersiniabactin, has an underappreciated distribution among different S. enterica serovars and subspecies, integrated in their chromosome or carried by different conjugative plasmids, including pESI. While the genetic organization and the coding sequence of the yersiniabactin genes are generally conserved, a 201-bp insertion sequence upstream to ybtA, was identified in pESI. Despite this insertion, pESI-encoded yersiniabactin is regulated by YbtA and the ancestral Ferric Uptake Regulator (Fur), which binds directly to the ybtA and irp2 promoters. Furthermore, we show that yersiniabactin genes are specifically induced during the mid-late logarithmic growth phase and in response to iron-starvation or hydrogen peroxide. Concurring, yersiniabactin was found to play a previously unknown role in oxidative stress tolerance and to enhance intestinal colonization of S. Infantis in mice. These results indicate that yersiniabactin contributes to Salmonella fitness and pathogenicity in vivo and is likely to play a role in the rapid dissemination of pESI among globally emerging Salmonella lineages.},
}
@article {pmid38962322,
year = {2024},
author = {Sobh, G and Araj, GF and Finianos, M and Sourenian, T and Hrabak, J and Pappagianitsis, CC and Chaar, ME and Bitar, I},
title = {Molecular characterization of carbapenem and ceftazidime-avibactam-resistant Enterobacterales and horizontal spread of bla NDM-5 gene at a Lebanese medical center.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1407246},
pmid = {38962322},
issn = {2235-2988},
mesh = {*Ceftazidime/pharmacology ; *Azabicyclo Compounds/pharmacology ; Humans ; Lebanon ; *beta-Lactamases/genetics/metabolism ; *Klebsiella pneumoniae/genetics/drug effects ; *Whole Genome Sequencing ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics/drug effects ; *Carbapenems/pharmacology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Drug Combinations ; Plasmids/genetics ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; Genome, Bacterial ; Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects/isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Tertiary Care Centers ; },
abstract = {INTRODUCTION: In the battle against multidrug-resistant bacterial infections, ceftazidime- avibactam (CZA) stands as a pivotal defense, particularly against carbapenemresistant (CR) Gram-negative pathogens. However, the rise in resistance against this drug poses a significant threat to its effectiveness, highlighting the critical need for in-depth studies about its resistance mechanisms.<br><br>METHODS: This research focuses on the genomic characterization of CR- and CZA-resistant Escherichia coli (n=26) and Klebsiella pneumoniae (n=34) strains, harboring the blaNDM and/or blaOXA-48-like genes, at a major Lebanese tertiary care medical center, using whole genome sequencing (WGS).<br><br>RESULTS: Our findings revealed a notable prevalence of blaNDM in all K. pneumoniae strains isolates, with 27 of these also harboring blaOXA-48. On the other hand, E. coli strains predominantly carried the blaNDM-5 gene. Whole genome sequencing (WGS) identified a predominance of ST383 among K. pneumoniae strains, which possessed a multi-replicon IncFIB-IncHI1B plasmid harboring the blaNDM-5. Additionally, various Inc group plasmids in K. pneumoniae across multiple sequence types were found to carry the blaNDM. Similarly, diverse STs of E. coli were observed to carry blaNDM-5 on different plasmids.<br><br>DISCUSSION: The study underscores NDM carbapenemases as a paramount resistance mechanism in Lebanon,jeopardizing critical last-resort treatments. It also illuminates the role of varied sequence types and mobile genetic elements in the spread of NDM resistance,stressing the urgent need for strategies to mitigate this threat, especially in nosocomial infections.},
}
@article {pmid38961341,
year = {2024},
author = {Yang, Y and Zhou, P and Tian, D and Wang, W and Zhou, Y and Jiang, X},
title = {CRISPR-Cas3 and type I restriction-modification team up against blaKPC-IncF plasmid transfer in Klebsiella pneumoniae.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {240},
pmid = {38961341},
issn = {1471-2180},
support = {82102439//National Natural Science Foundation of China/ ; 82202564//National Natural Science Foundation of China/ ; 82172315//National Natural Science Foundation of China/ ; 22YF1437500//Shanghai Sailing Program/ ; },
mesh = {*Klebsiella pneumoniae/genetics ; *Plasmids/genetics ; *CRISPR-Cas Systems ; *Conjugation, Genetic ; beta-Lactamases/genetics ; DNA Restriction-Modification Enzymes/genetics ; China ; Klebsiella Infections/microbiology ; Gene Transfer, Horizontal ; Humans ; Genome, Bacterial/genetics ; },
abstract = {OBJECTIVE: We explored whether the Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas and restriction-modification (R-M) systems are compatible and act together to resist plasmid attacks.<br><br>METHODS: 932 global whole-genome sequences from GenBank, and 459 K. pneumoniae isolates from six provinces of China, were collected to investigate the co-distribution of CRISPR-Cas, R-M systems, and blaKPC plasmid. Conjugation and transformation assays were applied to explore the anti-plasmid function of CRISPR and R-M systems.<br><br>RESULTS: We found a significant inverse correlation between the presence of CRISPR and R-M systems and blaKPC plasmids in K. pneumoniae, especially when both systems cohabited in one host. The multiple matched recognition sequences of both systems in blaKPC-IncF plasmids (97%) revealed that they were good targets for both systems. Furthermore, the results of conjugation assay demonstrated that CRISPR-Cas and R-M systems in K. pneumoniae could effectively hinder blaKPC plasmid invasion. Notably, CRISPR-Cas and R-M worked together to confer a 4-log reduction in the acquisition of blaKPC plasmid in conjugative events, exhibiting robust synergistic anti-plasmid immunity.<br><br>CONCLUSIONS: Our results indicate the synergistic role of CRISPR and R-M in regulating horizontal gene transfer in K. pneumoniae and rationalize the development of antimicrobial strategies that capitalize on the immunocompromised status of KPC-KP.},
}
@article {pmid38960277,
year = {2024},
author = {Li, W and Wang, Y and Zhao, K and Xu, L and Shi, T and Ma, B and Lv, X},
title = {Host-virus coevolution drives soil microbial function succession along a millennium land reclamation chronosequence.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2024.06.022},
pmid = {38960277},
issn = {2090-1224},
abstract = {INTRODUCTION: Gene exchange between viruses and hosts plays an important role in driving virus-host coevolution, enabling adaptation of both viruses and hosts to environmental changes. However, the mechanisms and functional significance of virus-host gene exchanges over long-term scales remain largely unexplored.<br><br>OBJECTIVE: The present study aimed to gain insights into the role of viruses in virus-host interactions and coevolution by monitoring virome dynamics along a millennium-long land reclamation chronosequence.<br><br>METHODS: We collected 24 soil samples from 8 stages of a millennium-long land reclamation chronosequence, including non-reclamation, and reclamation periods of 10, 50, 100, 300, 500, 700, and 1000&#x202f;years. We characterized their metagenomes, and identified DNA viruses within these metagenomes.<br><br>RESULTS: Our findings reveal a significant shift in viral community composition after 50&#x202f;years of land reclamation, but soil viral diversity reached a stable phase approximately 300&#x202f;years after the initial reclamation. Analysis of the virus-host network showed a scale-free degree distribution and a reduction in complexity over time, with generalist viruses emerging as key facilitators of horizontal gene transfer.<br><br>CONCLUSION: These findings highlight the integral role of viruses, especially generalist types, in mediating gene exchanges between viruses and hosts, thereby influencing the coevolutionary dynamics in soil ecosystems over significant timescales. This study offers novel insights into long-term virus-host interactions, showing how the virome responds to environmental changes, driving shifts in various microbial functions in reclaimed land.},
}
@article {pmid38949703,
year = {2024},
author = {Saula, AY and Knight, G and Bowness, R},
title = {Within-Host Mathematical Models of Antibiotic Resistance.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2833},
number = {},
pages = {79-91},
pmid = {38949703},
issn = {1940-6029},
mesh = {*Bacteria/genetics/drug effects ; Humans ; *Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Models, Theoretical ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Host-Pathogen Interactions/genetics ; },
abstract = {Mathematical models have been used to study the spread of infectious diseases from person to person. More recently studies are developing within-host modeling which provides an understanding of how pathogens-bacteria, fungi, parasites, or viruses-develop, spread, and evolve inside a single individual and their interaction with the host's immune system.Such models have the potential to provide a more detailed and complete description of the pathogenesis of diseases within-host and identify other influencing factors that may not be detected otherwise. Mathematical models can be used to aid understanding of the global antibiotic resistance (ABR) crisis and identify new ways of combating this threat.ABR occurs when bacteria respond to random or selective pressures and adapt to new environments through the acquisition of new genetic traits. This is usually through the acquisition of a piece of DNA from other bacteria, a process called horizontal gene transfer (HGT), the modification of a piece of DNA within a bacterium, or through. Bacteria have evolved mechanisms that enable them to respond to environmental threats by mutation, and horizontal gene transfer (HGT): conjugation; transduction; and transformation. A frequent mechanism of HGT responsible for spreading antibiotic resistance on the global scale is conjugation, as it allows the direct transfer of mobile genetic elements (MGEs). Although there are several MGEs, the most important MGEs which promote the development and rapid spread of antimicrobial resistance genes in bacterial populations are plasmids and transposons. Each of the resistance-spread-mechanisms mentioned above can be modeled allowing us to understand the process better and to define strategies to reduce resistance.},
}
@article {pmid38948848,
year = {2024},
author = {Lv, C and Abdullah, M and Chen, W and Zhou, N and Cheng, Z and Chen, Y and Li, M and Simpson, KW and Elsaadi, A and Zhu, Y and Lipkin, SM and Chang, YF},
title = {Genomic characterization of Escherichia coli harbor a polyketide synthase (pks) island associated with colorectal cancer (CRC) development.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.06.16.599199},
pmid = {38948848},
issn = {2692-8205},
abstract = {The E. coli strain harboring the polyketide synthase (Pks) island encodes the genotoxin colibactin, a secondary metabolite reported to have severe implications for human health and for the progression of colorectal cancer. The present study involved whole-genome-wide comparison and phylogenetic analysis of pks harboring E. coli isolates to gain insight into the distribution and evolution of these organism. Fifteen E. coli strains isolated from patients with ulcerative colitis were sequenced, 13 of which harbored pks islands. In addition, 2,654 genomes from the public database were also screened for pks harboring E. coli genomes, 158 of which were pks -positive isolates. Whole-genome-wide comparison and phylogenetic analysis revealed that 171 (158+13) pks -positive isolates belonged to phylogroup B2, and most of the isolates associated to sequence types ST73 and ST95. One isolate from an ulcerative colitis (UC) patient was of the sequence type ST8303. The maximum likelihood tree based on the core genome of pks -positive isolates revealed horizontal gene transfer across sequence types and serotypes. Virulome and resistome analyses revealed the preponderance of virulence genes and a reduced number of antimicrobial genes in Pks -positive isolates. This study strongly contributes to understanding the evolution of pks islands in E. coli .},
}
@article {pmid38947372,
year = {2024},
author = {Gómez-Gaviria, M and Contreras-López, LM and Aguilera-Domínguez, JI and Mora-Montes, HM},
title = {Strategies of Pharmacological Repositioning for the Treatment of Medically Relevant Mycoses.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {2641-2658},
pmid = {38947372},
issn = {1178-6973},
abstract = {Fungal infections represent a worldwide concern for public health, due to their prevalence and significant increase in cases each year. Among the most frequent mycoses are those caused by members of the genera Candida, Cryptococcus, Aspergillus, Histoplasma, Pneumocystis, Mucor, and Sporothrix, which have been treated for years with conventional antifungal drugs, such as flucytosine, azoles, polyenes, and echinocandins. However, these microorganisms have acquired the ability to evade the mechanisms of action of these drugs, thus hindering their treatment. Among the most common evasion mechanisms are alterations in sterol biosynthesis, modifications of drug transport through the cell wall and membrane, alterations of drug targets, phenotypic plasticity, horizontal gene transfer, and chromosomal aneuploidies. Taking into account these problems, some research groups have sought new therapeutic alternatives based on drug repositioning. Through repositioning, it is possible to use existing pharmacological compounds for which their mechanism of action is already established for other diseases, and thus exploit their potential antifungal activity. The advantage offered by these drugs is that they may be less prone to resistance. In this article, a comprehensive review was carried out to highlight the most relevant repositioning drugs to treat fungal infections. These include antibiotics, antivirals, anthelmintics, statins, and anti-inflammatory drugs.},
}
@article {pmid38946899,
year = {2024},
author = {Ji, J and Zhu, Y and Zhao, F and Zhang, J and Yao, B and Zhu, M and Yu, Y and Zhang, J and Fu, Y},
title = {Co-colonization of different species harboring KPC or NDM carbapenemase in the same host gut: insight of resistance evolution by horizontal gene transfer.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1416454},
pmid = {38946899},
issn = {1664-302X},
abstract = {INTRODUCTION: The dissemination of carbapenem-resistant Enterobacteriales (CRE) in nosocomial settings is primarily associated with the horizontal transfer of plasmids. However, limited research has focused on the in-host transferability of carbapenem resistance. In this study, ten isolates were collected from gut specimens of five individuals, each hosting two different species, including Escherichia coli, Klebsiella pneumoniae, Klebsiella aerogenes, Enterobacter cloacae, or Citrobacter koseri.<br><br>METHODS: Species identification and antimicrobial susceptibility were determined by MALDI-TOF MS and broth microdilution method. Carbapenemase genes were detected and localized using PCR, S1-PFGE and southern blot. The transferability of carbapenemase genes between species was investigated through filter mating experiments, and the genetic contexts of the plasmids were analyzed using whole genome sequencing.<br><br>RESULTS AND DISCUSSION: Our results revealed that each of the ten isolates harbored a carbapenemase gene, including bla NDM-5, bla NDM-1, or bla KPC-2, on a plasmid. Five different plasmids were successfully transferred to recipient cells of E. coli, K. pneumoniae or A. baumannii by transconjugation. The genetic contexts of the carbapenemase gene were remarkably similar between the two CRE isolates from each individual. This study highlights the potential for interspecies plasmid transmission in human gut, emphasizing the colonization of CRE as a significant risk factor for the dissemination of carbapenemase genes within the host. These findings underscore the need for appropriate intestinal CRE screening and colonization prevention.},
}
@article {pmid38944065,
year = {2024},
author = {Marchetti, A and Orlando, M and Bombardi, L and Fusco, S and Mangiagalli, M and Lotti, M},
title = {Evolutionary history and activity towards oligosaccharides and polysaccharides of GH3 glycosidases from an Antarctic marine bacterium.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {133449},
doi = {10.1016/j.ijbiomac.2024.133449},
pmid = {38944065},
issn = {1879-0003},
abstract = {Glycoside hydrolases (GHs) are pivotal in the hydrolysis of the glycosidic bonds of sugars, which are the main carbon and energy sources. The genome of Marinomonas sp. ef1, an Antarctic bacterium, contains three GHs belonging to family 3. These enzymes have distinct architectures and low sequence identity, suggesting that they originated from separate horizontal gene transfer events. M-GH3_A and M-GH3_B, were found to differ in cold adaptation and substrate specificity. M-GH3_A is a bona fide cold-active enzyme since it retains 20 % activity at 10 °C and exhibits poor long-term thermal stability. On the other hand, M-GH3_B shows mesophilic traits with very low activity at 10 °C (< 5 %) and higher long-term thermal stability. Substrate specificity assays highlight that M-GH3_A is a promiscuous β-glucosidase mainly active on cellobiose and cellotetraose, whereas M-GH3_B is a β-xylosidase active on xylan and arabinoxylan. Structural analysis suggests that such functional differences are due to their differently shaped active sites. The active site of M-GH3_A is wider but has a narrower entrance compared to that of M-GH3_B. Genome-based prediction of metabolic pathways suggests that Marinomonas sp. ef1 can use monosaccharides derived from the GH3-catalyzed hydrolysis of oligosaccharides either as a carbon source or for producing osmolytes.},
}
@article {pmid38942826,
year = {2024},
author = {Boukouvala, S and Kontomina, E and Olbasalis, I and Patriarcheas, D and Tzimotoudis, D and Arvaniti, K and Manolias, A and Tsatiri, MA and Basdani, D and Zekkas, S},
title = {Insights into the genomic and functional divergence of NAT gene family to serve microbial secondary metabolism.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {14905},
pmid = {38942826},
issn = {2045-2322},
support = {3712//Hellenic Foundation for Research and Innovation (H.F.R.I.)/ ; MIS-5000432//State Scholarships Foundation (&#x399;&#x39a;&#x3a5;)/ ; },
mesh = {*Multigene Family ; *Secondary Metabolism/genetics ; *Bacteria/genetics/metabolism ; Archaea/genetics/metabolism ; Phylogeny ; Arylamine N-Acetyltransferase/genetics/metabolism ; Fungi/genetics ; Genomics/methods ; Gene Transfer, Horizontal ; },
abstract = {Microbial NAT enzymes, which employ acyl-CoA to acylate aromatic amines and hydrazines, have been well-studied for their role in xenobiotic metabolism. Some homologues have also been linked to secondary metabolism, but this function of NAT enzymes is not as well-known. For this comparative study, we surveyed sequenced microbial genomes to update the list of formally annotated NAT genes, adding over 4000 new sequences (mainly bacterial, but also archaeal, fungal and protist) and portraying a broad but not universal distribution of NATs in the microbiocosmos. Localization of NAT sequences within microbial gene clusters was not a rare finding, and this association was evident across all main types of biosynthetic gene clusters (BGCs) implicated in secondary metabolism. Interrogation of the MIBiG database for experimentally characterized clusters with NAT genes further supports that secondary metabolism must be a major function for microbial NAT enzymes and should not be overlooked by researchers in the field. We also show that NAT sequences can be associated with bacterial plasmids potentially involved in horizontal gene transfer. Combined, our computational predictions and MIBiG literature findings reveal the extraordinary functional diversification of microbial NAT genes, prompting further research into their role in predicted BGCs with as yet uncharacterized function.},
}
@article {pmid38942019,
year = {2024},
author = {Mason, B and Hayward, DC and Moya, A and Cooke, I and Sorenson, A and Brunner, R and Andrade, N and Huerlimann, R and Bourne, DG and Schaeffer, P and Grinblat, M and Ravasi, T and Ueda, N and Tang, SL and Ball, EE and Miller, DJ},
title = {Microbiome manipulation by corals and other Cnidaria via quorum quenching.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.05.073},
pmid = {38942019},
issn = {1879-0445},
abstract = {A dynamic mucous layer containing numerous micro-organisms covers the surface of corals and has multiple functions including both removal of sediment and "food gathering."[1] It is likely to also act as the primary barrier to infection; various proteins and compounds with antimicrobial activity have been identified in coral mucus, though these are thought to be largely or exclusively of microbial origin. As in Hydra,[2] anti-microbial peptides (AMPs) are likely to play major roles in regulating the microbiomes of corals.[3][,][4] Some eukaryotes employ a complementary but less obvious approach to manipulate their associated microbiome by interfering with quorum signaling, effectively preventing bacteria from coordinating gene expression across a population. Our investigation of immunity in the reef-building coral Acropora millepora,[5] however, led to the discovery of a coral gene referred to here as AmNtNH1 that can inactivate a range of acyl homoserine lactones (AHLs), common bacterial quorum signaling molecules, and is induced on immune challenge of adult corals and expressed during the larval settlement process. Closely related proteins are widely distributed within the Scleractinia (hard corals) and some other cnidarians, with multiple paralogs in Acropora, but their closest relatives are bacterial, implying that these are products of one or more lateral gene transfer events post-dating the cnidarian-bilaterian divergence. The deployment by corals of genes used by bacteria to compete with other bacteria reflects a mechanism of microbiome manipulation previously unknown in Metazoa but that may apply more generally.},
}
@article {pmid38941922,
year = {2024},
author = {Li, B and Ni, S and Liu, Y and Lin, J and Wang, X},
title = {The histone-like nucleoid-structuring protein encoded by the plasmid pMBL6842 regulates both plasmid stability and host physiology of Pseudoalteromonas rubra SCSIO 6842.},
journal = {Microbiological research},
volume = {286},
number = {},
pages = {127817},
doi = {10.1016/j.micres.2024.127817},
pmid = {38941922},
issn = {1618-0623},
abstract = {Plasmids orchestrate bacterial adaptation across diverse environments and facilitate lateral gene transfer within bacterial communities. Their presence can perturb host metabolism, creating a competitive advantage for plasmid-free cells. Plasmid stability hinges on efficient replication and partition mechanisms. While plasmids commonly encode histone-like nucleoid-structuring (H-NS) family proteins, the precise influence of plasmid-encoded H-NS proteins on stability remains elusive. In this study, we examined the conjugative plasmid pMBL6842, harboring the hns gene, and observed its positive regulation of parAB transcription, critical for plasmid segregation. Deletion of hns led to rapid plasmid loss, which was remedied by hns complementation. Further investigations unveiled adverse effects of hns overexpression on the bacterial host. Transcriptome analysis revealed hns's role in regulating numerous bacterial genes, impacting both host growth and swimming motility in the presence of the hns gene. Therefore, our study unveils the multifaceted roles of H-NS in both plasmid stability and host physiology, underscoring its biological significance and paving the way for future inquiries into the involvement of H-NS in horizontal gene transfer events.},
}
@article {pmid38940556,
year = {2024},
author = {Sun, W-S and Torrens, G and Ter Beek, J and Cava, F and Berntsson, RP-A},
title = {Breaking barriers: pCF10 type 4 secretion system relies on a self-regulating muramidase to modulate the cell wall.},
journal = {mBio},
volume = {},
number = {},
pages = {e0048824},
doi = {10.1128/mbio.00488-24},
pmid = {38940556},
issn = {2150-7511},
abstract = {Conjugative type 4 secretion systems (T4SSs) are the main driver for the spread of antibiotic resistance genes and virulence factors in bacteria. To deliver the DNA substrate to recipient cells, it must cross the cell envelopes of both donor and recipient bacteria. In the T4SS from the enterococcal conjugative plasmid pCF10, PrgK is known to be the active cell wall degrading enzyme. It has three predicted extracellular hydrolase domains: metallo-peptidase (LytM), soluble lytic transglycosylase (SLT), and cysteine, histidine-dependent amidohydrolases/peptidases (CHAP). Here, we report the structure of the LytM domain and show that its active site is degenerate and lacks the active site metal. Furthermore, we show that only the predicted SLT domain is functional in vitro and that it unexpectedly has a muramidase instead of a lytic transglycosylase activity. While we did not observe any peptidoglycan hydrolytic activity for the LytM or CHAP domain, we found that these domains downregulated the SLT muramidase activity. The CHAP domain was also found to be involved in PrgK dimer formation. Furthermore, we show that PrgK interacts with PrgL, which likely targets PrgK to the rest of the T4SS. The presented data provides important information for understanding the function of Gram-positive T4SSs.IMPORTANCEAntibiotic resistance is a large threat to human health and is getting more prevalent. One of the major contributors to the spread of antibiotic resistance among different bacteria is type 4 secretion systems (T4SS). However, mainly T4SSs from Gram-negative bacteria have been studied in detail. T4SSs from Gram-positive bacteria, which stand for more than half of all hospital-acquired infections, are much less understood. The significance of our research is in identifying the function and regulation of a cell wall hydrolase, a key component of the pCF10 T4SS from Enterococcus faecalis. This system is one of the best-studied Gram-positive T4SSs, and this added knowledge aids in our understanding of horizontal gene transfer in E. faecalis as well as other medically relevant Gram-positive bacteria.},
}
@article {pmid38940543,
year = {2024},
author = {Jian, J and Wang, Z and Chen, C and Workman, CT and Fang, X and Larsen, TO and Guo, J and Sonnenschein, EC},
title = {Two high-quality Prototheca zopfii genomes provide new insights into their evolution as obligate algal heterotrophs and their pathogenicity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0414823},
doi = {10.1128/spectrum.04148-23},
pmid = {38940543},
issn = {2165-0497},
abstract = {UNLABELLED: The majority of the nearly 10,000 described species of green algae are photoautotrophs; however, some species have lost their ability to photosynthesize and become obligate heterotrophs that rely on parasitism for survival. Two high-quality genomes of the heterotrophic algae Prototheca zopfii Pz20 and Pz23 were obtained using short- and long-read genomic as well as transcriptomic data. The genome sizes were 31.2 Mb and 31.3 Mb, respectively, and contig N50 values of 1.99 Mb and 1.26 Mb. Although P. zopfii maintained its plastid genome, the transition to heterotrophy led to a reduction in both plastid and nuclear genome size, including the loss of photosynthesis-related genes from both the nuclear and plastid genomes and the elimination of genes encoding for carotenoid oxygenase and pheophorbide an oxygenase. The loss of genes, including basic leucine-zipper (bZIP) transcription factors, flavin adenine dinucleotide-linked oxidase, and helicase, could have played a role in the transmission of autotrophy to heterotrophs and in the processes of abiotic stress resistance and pathogenicity. A total of 66 (1.37%) and 73 (1.49%) genes were identified as potential horizontal gene transfer events in the two P. zopfii genomes, respectively. Genes for malate synthase and isocitrate lyase, which are horizontally transferred from bacteria, may play a pivotal role in carbon and nitrogen metabolism as well as the pathogenicity of Prototheca and non-photosynthetic organisms. The two high-quality P. zopfii genomes provide new insights into their evolution as obligate heterotrophs and pathogenicity.<br><br>IMPORTANCE: The genus Prototheca, characterized by its heterotrophic nature and pathogenicity, serves as an exemplary model for investigating pathobiology. The limited understanding of the protothecosis infectious disease is attributed to the lack of genomic resources. Using HiFi long-read sequencing, both nuclear and plastid genomes were generated for two strains of P. zopfii. The findings revealed a concurrent reduction in both plastid and nuclear genome size, accompanied by the loss of genes associated with photosynthesis, carotenoid oxygenase, basic leucine-zipper (bZIP) transcription factors, and others. The analysis of horizontal gene transfer revealed the presence of 1.37% and 1.49% bacterial genes, including malate synthase and isocitrate lyase, which play crucial roles in carbon and nitrogen metabolism, as well as pathogenicity and obligate heterotrophy. The two high-quality P. zopfii genomes represent valuable resources for investigating their adaptation and evolution as obligate heterotrophs, as well as for developing future prevention and treatment strategies against protothecosis.},
}
@article {pmid38940156,
year = {2024},
author = {Curry, KD and Yu, FB and Vance, SE and Segarra, S and Bhaya, D and Chikhi, R and Rocha, EPC and Treangen, TJ},
title = {Reference-free structural variant detection in microbiomes via long-read co-assembly graphs.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {Supplement_1},
pages = {i58-i67},
doi = {10.1093/bioinformatics/btae224},
pmid = {38940156},
issn = {1367-4811},
support = {//Ken Kennedy Institute Recruiting/ ; //Rice University Wagoner Foreign Study Scholarship/ ; P01-AI152999/GF/NIH HHS/United States ; //National Institute of Allergy and Infectious Diseases/ ; IIS-2239114//NSF/ ; //NSF/ ; EF-2126387//MIM Universal Rules of Live/ ; //European Union's Horizon 2020/ ; 872539//Marie Sk&#x142;odowska-Curie/ ; //Carnegie Institution for Science/ ; //Department of Energy Joint Genome Institute/ ; //Office of Science/ ; //Department of Energy/ ; 2023333162//NSF/ ; },
mesh = {*Microbiota/genetics ; *Metagenome ; *Genome, Bacterial ; Metagenomics/methods ; Gene Transfer, Horizontal ; Bacteria/genetics ; Algorithms ; },
abstract = {MOTIVATION: The study of bacterial genome dynamics is vital for understanding the mechanisms underlying microbial adaptation, growth, and their impact on host phenotype. Structural variants (SVs), genomic alterations of 50 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to the absence of clear reference genomes and the presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing all metagenomic samples in a series (time or other metric) into a single co-assembly graph. The log fold change in graph coverage between successive samples is then calculated to call SVs that are thriving or declining.<br><br>RESULTS: We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, particularly as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between successive time and temperature samples, suggesting host advantage. Our approach leverages previous work in assembly graph structural and coverage patterns to provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial gene flux.<br><br>rhea is open source and available at: https://github.com/treangenlab/rhea.},
}
@article {pmid38936370,
year = {2024},
author = {Yu, T and Xu, X and Liu, Y and Wang, X and Wu, S and Qiu, Z and Liu, X and Pan, X and Gu, C and Wang, S and Dong, L and Li, W and Yao, X},
title = {Multi-omics signatures reveal genomic and functional heterogeneity of Cutibacterium acnes in normal and diseased skin.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2024.06.002},
pmid = {38936370},
issn = {1934-6069},
abstract = {Cutibacterium acnes is the most abundant bacterium of the human skin microbiome since adolescence, participating in both skin homeostasis and diseases. Here, we demonstrate individual and niche heterogeneity of C. acnes from 1,234 isolate genomes. Skin disease (atopic dermatitis and acne) and body site shape genomic differences of C. acnes, stemming from horizontal gene transfer and selection pressure. C. acnes harbors characteristic metabolic functions, fewer antibiotic resistance genes and virulence factors, and a more stable genome compared with Staphylococcus epidermidis. Integrated genome, transcriptome, and metabolome analysis at the strain level unveils the functional characteristics of C. acnes. Consistent with the transcriptome signature, C. acnes in a sebum-rich environment induces toxic and pro-inflammatory effects on keratinocytes. L-carnosine, an anti-oxidative stress metabolite, is up-regulated in the C. acnes metabolome from atopic dermatitis and attenuates skin inflammation. Collectively, our study reveals the joint impact of genes and the microenvironment on C. acnes function.},
}
@article {pmid38936366,
year = {2024},
author = {Garric, S and Ratin, M and Marie, D and Foulon, V and Probert, I and Rodriguez, F and Six, C},
title = {Impaired photoacclimation in a kleptoplastidic dinoflagellate reveals physiological limits of early stages of endosymbiosis.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.05.066},
pmid = {38936366},
issn = {1879-0445},
abstract = {Dinophysis dinoflagellates are predators of Mesodinium ciliates, from which they retain only the plastids of cryptophyte origin. The absence of nuclear photosynthetic cryptophyte genes in Dinophysis raises intriguing physiological and evolutionary questions regarding the functional dynamics of these temporary kleptoplastids within a foreign cellular environment. In an experimental setup including two light conditions, the comparative analysis with Mesodinium rubrum and the cryptophyte Teleaulax amphioxeia revealed that Dinophysis acuminata possessed a smaller and less dynamic functional photosynthetic antenna for green light, a function performed by phycoerythrin. We showed that the lack of the cryptophyte nucleus prevented the synthesis of the phycoerythrin α subunit, thereby hindering the formation of a complete phycoerythrin in Dinophysis. In particular, biochemical analyses showed that Dinophysis acuminata synthesized a poorly stable, incomplete phycoerythrin composed of chromophorylated β subunits, with impaired performance. We show that, consequently, a continuous supply of new plastids is crucial for growth and effective photoacclimation in this organism. Transcriptome analyses revealed that all examined strains of Dinophysis spp. have acquired the cryptophyte pebA and pebB genes through horizontal gene transfer, suggesting a potential ability to synthesize the phycobilin pigments bound to the cryptophyte phycoerythrin. By emphasizing that a potential long-term acquisition of the cryptophyte plastid relies on establishing genetic independence for essential functions such as light harvesting, this study highlights the intricate molecular challenges inherent in the enslavement of organelles and the processes involved in the diversification of photosynthetic organisms through endosymbiosis.},
}
@article {pmid38936185,
year = {2024},
author = {Hu, CJ and Lv, YQ and Xian, WD and Jiao, JY and Lian, ZH and Tan, S and Li, MM and Luo, ZH and Liu, ZT and Lv, AP and Liu, L and Ali, M and Liu, WQ and Li, WJ},
title = {Multi-omics insights into the function and evolution of sodium benzoate biodegradation pathway in Benzoatithermus flavus gen. nov., sp. nov. from hot spring.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {135017},
doi = {10.1016/j.jhazmat.2024.135017},
pmid = {38936185},
issn = {1873-3336},
abstract = {Biodegradation stands as an eco-friendly and effective approach for organic contaminant remediation. However, research on microorganisms degrading sodium benzoate contaminants in extreme environments remains limited. In this study, we report to display the isolation of a novel hot spring enriched cultures with sodium benzoate (400 mg/L) as the sole carbon source. The results revealed that the phylum Pseudomonadota was the potential sodium benzoate degrader and a novel genus within the family Geminicoccaceae of this phylum. The isolated strain was named Benzoatithermus flavus SYSU G07066[T] and was isolated from HNT-2 hot spring samples. Genomic analysis revealed that SYSU G07066[T] carried benABC genes and physiological experiments indicated the ability to utilize sodium benzoate as a sole carbon source for growth, which was further confirmed by transcriptomic data with expression of benABC. Phylogenetic analysis suggested that Horizontal Gene Transfer (HGT) plays a significant role in acquiring sodium benzoate degradation capability among prokaryotes, and SYSU G07066[T] might have acquired benABC genes through HGT from the family Acetobacteraceae. The discovery of the first microorganism with sodium benzoate degradation function from a hot spring enhances our understanding of the diverse functions within the family Geminicoccaceae. This study unearths the first novel genus capable of efficiently degrading sodium benzoate and its evolution history at high temperatures, holding promising industrial applications, and provides a new perspective for further exploring the application potential of hot spring "microbial dark matter".},
}
@article {pmid38936038,
year = {2024},
author = {Wang, F and Huang, W and Zhang, M and Zhang, Q and Luo, Y and Chen, J and Su, Y and Huang, H and Fang, F and Luo, J},
title = {Disinfectant polyhexamethylene guanidine triggered simultaneous efflux pump antibiotic- and metal-resistance genes propagation during sludge anaerobic digestion.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {357},
number = {},
pages = {124453},
doi = {10.1016/j.envpol.2024.124453},
pmid = {38936038},
issn = {1873-6424},
abstract = {The environmental transmission of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) exerted devastating threats to global public health, and their interactions with other emerging contaminants (ECs) have raised increasing concern. This study investigated that the abundances of ARGs and MRGs with the predominant type of efflux pump were simultaneously increased (8.4-59.1%) by disinfectant polyhexamethylene guanidine (PHMG) during waste activated sludge (WAS) anaerobic digestion. The aggregation of the same microorganisms (i.e., Hymenobacter and Comamonas) and different host bacteria (i.e., Azoarcus and Thauera) were occurred upon exposure to PHMG, thereby increasing the co-selection and propagation of MRGs and ARGs by vertical gene transfer. Moreover, PHMG enhanced the process of horizontal gene transfer (HGT), facilitating their co-transmission by the same mobile genetic elements (20.2-223.7%). Additionally, PHMG up-regulated the expression of critical genes (i.e., glnB, trpG and gspM) associated with the HGT of ARGs and MRGs (i.e., two-component regulatory system and quorum sensing) and exocytosis system (i.e., bacterial secretion system). Structural equation model analysis further verified that the key driver for the simultaneous enrichment of ARGs and MRGs under PHMG stress was microbial community structure. The study gives new insights into the aggravated environmental risks and mechanisms of ECs in sludge digestion system, providing guidance for subsequent regulation and control of ECs.},
}
@article {pmid38936019,
year = {2024},
author = {Liu, Y and Song, X and Hou, X and Wang, Y and Cao, X},
title = {Effect of Mn-HA on ARGs and MRGs in nitrogen-culturing sludge.},
journal = {Journal of environmental management},
volume = {365},
number = {},
pages = {121615},
doi = {10.1016/j.jenvman.2024.121615},
pmid = {38936019},
issn = {1095-8630},
abstract = {The simultaneous escalation in ARGs (antibiotic resistance genes) and MRGs (metal resistance genes) further complicates the intricate network of factors contributing to the proliferation of microbial resistance. Manganese, which has been reported to affect the resistance of bacteria to antibiotics and metals, plays a vital role in microbial nitrogen metabolism. Moreover, nitrifying and denitrifying populations are potential hosts for ARGs. In this study, manganese was introduced in its prevalent organic chelated form in the environment (Manganese humus chelates, Mn-HA) to a N metabolism sludge to explore the effect of manganese on MRGs and ARGs dissemination. Metagenomics results revealed that manganese availability enhances nitrogen metabolism, while a decrease in ARGs was noted which may be attributed to the inhibition of horizontal gene transfer (HGT), reflected in the reduced integrase -encoded gene int. Population analysis revealed that nitrifier and denitrifier genus harbor MRGs and ARGs, indicating that nitrifier and denitrifier are hosts of MRGs and ARGs. This raises the question of whether the prevalence of ARGs is always increased in metal-contained environments.},
}
@article {pmid38935608,
year = {2024},
author = {Randriantseheno, LN and Andrianaivoarimanana, V and Pizarro-Cerdá, J and Wagner, DM and Rajerison, M},
title = {Review of genotyping methods for Yersinia pestis in Madagascar.},
journal = {PLoS neglected tropical diseases},
volume = {18},
number = {6},
pages = {e0012252},
doi = {10.1371/journal.pntd.0012252},
pmid = {38935608},
issn = {1935-2735},
mesh = {*Yersinia pestis/genetics/classification/isolation &amp; purification ; Madagascar/epidemiology ; *Plague/microbiology/epidemiology ; Humans ; Animals ; Genotype ; Genotyping Techniques/methods ; },
abstract = {BACKGROUND: Plague, a zoonotic disease caused by Yersinia pestis, was responsible for 3 historical human pandemics that killed millions of people. It remains endemic in rodent populations in Africa, Asia, North America, and South America but human plague is rare in most of these locations. However, human plague is still highly prevalent in Madagascar, which typically records a significant part of all annual global cases. This has afforded an opportunity to study contemporary human plague in detail using various typing methods for Y. pestis.<br><br>AIM: This review aims to summarize the methods that have been used to type Y. pestis in Madagascar along with the major discoveries that have been made using these approaches.<br><br>METHODS: Pubmed and Google Scholar were used to search for the keywords: "typing Yersinia pestis Madagascar," "evolution Yersinia pestis Madagascar," and "diversity Yersinia pestis Madagascar." Eleven publications were relevant to our topic and further information was retrieved from references cited in those publications.<br><br>RESULTS: The history of Y. pestis typing in Madagascar can be divided in 2 periods: the pre-genomics and genomics eras. During the pre-genomics era, ribotyping, direct observation of plasmid content and plasmid restriction fragment length polymorphisms (RFLP) were employed but only revealed a limited amount of diversity among Malagasy Y. pestis strains. Extensive diversity only started to be revealed in the genomics era with the use of clustered regularly interspaced palindromic repeats (CRISPR), multiple-locus variable number tandem repeats (VNTR) analysis (MLVA), and single-nucleotide polymorphisms (SNPs) discovered from whole genome sequences. These higher-resolution genotyping methods have made it possible to highlight the distribution and persistence of genotypes in the different plague foci of Madagascar (Mahajanga and the Central and Northern Highlands) by genotyping strains from the same locations across years, to detect transfers between foci, to date the emergence of genotypes, and even to document the transmission of antimicrobial resistant (AMR) strains during a pneumonic plague outbreak. Despite these discoveries, there still remain topics that deserve to be explored, such as the contribution of horizontal gene transfer to the evolution of Malagasy Y. pestis strains and the evolutionary history of Y. pestis in Madagascar.<br><br>CONCLUSIONS: Genotyping of Y. pestis has yielded important insights on plague in Madagascar, particularly since the advent of whole-genome sequencing (WGS). These include a better understanding of plague persistence in the environment, antimicrobial AMR and multi-drug resistance in Y. pestis, and the person-to-person spread of pneumonic plague. Considering that human plague is still a significant public health threat in Madagascar, these insights can be useful for controlling and preventing human plague in Madagascar and elsewhere, and also are relevant for understanding the historical pandemics and the possible use of Y. pestis as a biological weapon.},
}
@article {pmid38935220,
year = {2024},
author = {Parra, B and Lutz, VT and Brøndsted, L and Carmona, JL and Palomo, A and Nesme, J and Van Hung Le, V and Smets, BF and Dechesne, A},
title = {Characterization and Abundance of Plasmid-Dependent Alphatectivirus Bacteriophages.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {85},
pmid = {38935220},
issn = {1432-184X},
support = {101026675//European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant/ ; 002200000279//VRID Postdoctorado from Vicerrector&#xed;a de Investigaci&#xf3;n y Desarrollo, Universidad de Concepci&#xf3;n/ ; P-PhanFARE (23046)//Villum Fonden/ ; },
mesh = {*Plasmids/genetics ; *Wastewater/virology/microbiology ; *Bacteriophages/genetics/isolation &amp; purification/physiology/classification ; Genome, Viral ; Escherichia coli/virology/genetics ; Host Specificity ; Pseudomonas putida/virology/genetics ; Salmonella enterica/virology/genetics ; Phylogeny ; },
abstract = {Antimicrobial resistance (AMR) is a major public health threat, exacerbated by the ability of bacteria to rapidly disseminate antimicrobial resistance genes (ARG). Since conjugative plasmids of the incompatibility group P (IncP) are ubiquitous mobile genetic elements that often carry ARG and are broad-host-range, they are important targets to prevent the dissemination of AMR. Plasmid-dependent phages infect plasmid-carrying bacteria by recognizing components of the conjugative secretion system as receptors. We sought to isolate plasmid-dependent phages from wastewater using an avirulent strain of Salmonella enterica carrying the conjugative IncP plasmid pKJK5. Irrespective of the site, we only obtained bacteriophages belonging to the genus Alphatectivirus. Eleven isolates were sequenced, their genomes analyzed, and their host range established using S. enterica, Escherichia coli, and Pseudomonas putida carrying diverse conjugative plasmids. We confirmed that Alphatectivirus are abundant in domestic and hospital wastewater using culture-dependent and culture-independent approaches. However, these results are not consistent with their low or undetectable occurrence in metagenomes. Therefore, overall, our results emphasize the importance of performing phage isolation to uncover diversity, especially considering the potential of plasmid-dependent phages to reduce the spread of ARG carried by conjugative plasmids, and to help combat the AMR crisis.},
}
@article {pmid38934605,
year = {2024},
author = {Burcham, ZM},
title = {Comparative genomic analysis of an emerging Pseudomonadaceae member, Thiopseudomonas alkaliphila.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0415723},
doi = {10.1128/spectrum.04157-23},
pmid = {38934605},
issn = {2165-0497},
abstract = {Thiopseudomonas alkaliphila, an organism recently classified within the Pseudomonadaceae family, has been detected in diverse sources such as human tissues, animal guts, industrial fermenters, and decomposition environments, suggesting a diverse ecological role. However, a large knowledge gap exists in how T. alkaliphila functions. In this comparative genomic analysis, adaptations indicative of habitat specificity among strains and genomic similarity to known opportunistic pathogens are revealed. Genomic investigation reveals a core metabolic utilization of multiple oxidative and non-oxidative catabolic pathways, suggesting adaptability to varied environments and carbon sources. The genomic repertoire of T. alkaliphila includes secondary metabolites, such as antimicrobials and siderophores, indicative of its involvement in microbial competition and resource acquisition. Additionally, the presence of transposases, prophages, plasmids, and Clustered Regularly Interspaced Short Palindromic Repeats-Cas systems in T. alkaliphila genomes suggests mechanisms for horizontal gene transfer and defense against viral predation. This comprehensive genomic analysis expands our understanding on the ecological functions, community interactions, and potential virulence of T. alkaliphila, while emphasizing its adaptability and diverse capabilities across environmental and host-associated ecosystems.IMPORTANCEAs the microbial world continues to be explored, new organisms will emerge with beneficial and/or pathogenetic impact. Thiopseudomonas alkaliphila is a species originally isolated from clinical human tissue and fluid samples but has not been attributed to disease. Since its classification, T. alkaliphila has been found in animal guts, animal waste, decomposing remains, and biogas fermentation reactors. This is the first study to provide an in-depth view of the metabolic potential of publicly available genomes belonging to this species through a comparative genomics and draft pangenome calculation approach. It was found that T. alkaliphila is metabolically versatile and likely adapts to diverse energy sources and environments, which may make it useful for bioremediation and in industrial settings. A range of virulence factors and antibiotic resistances were also detected, suggesting T. alkaliphila may operate as an undescribed opportunistic pathogen.},
}
@article {pmid38930473,
year = {2024},
author = {Otero-Olarra, JE and Díaz-Cárdenas, G and Aguilera-Arreola, MG and Curiel-Quesada, E and Pérez-Valdespino, A},
title = {Aeromonas trota Is Highly Refractory to Acquire Exogenous Genetic Material.},
journal = {Microorganisms},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/microorganisms12061091},
pmid = {38930473},
issn = {2076-2607},
abstract = {Aeromonas trota is sensitive to most antibiotics and the sole species of this genus susceptible to ampicillin. This susceptibility profile could be related to its inability to acquire exogenous DNA. In this study, A. trota isolates were analyzed to establish their capacity to incorporate foreign DNA. Fourteen strains were identified as A. trota by multilocus phylogenetic analysis (MLPA). Minimal inhibitory concentrations of antibiotics (MIC) were assessed, confirming the susceptibility to most antibiotics tested. To explore their capacity to be transformed, A. trota strains were used as recipients in different horizontal transfer assays. Results showed that around fifty percent of A. trota strains were able to incorporate pBAMD1-2 and pBBR1MCS-3 plasmids after conjugal transfer. In all instances, conjugation frequencies were very low. Interestingly, several isoforms of plasmid pBBR1MCS-3 were observed in transconjugants. Strains could not receive pAr-32, a native plasmid from A. salmonicida. A. trota strains were unable to receive DNA by means of electroporation, natural transformation or vesiduction. These results confirm that A. trota species are extremely refractory to horizontal gene transfer, which could be associated to plasmid instability resulting from oligomerization or to the presence of defense systems against exogenous genetic material in their genomes. To explain the poor results of horizontal gene transfer (HGT), selected genomes were sequenced and analyzed, revealing the presence of defense systems, which could prevent the stable incorporation of exogenous DNA in A. trota.},
}
@article {pmid38927231,
year = {2024},
author = {Amábile-Cuevas, CF and Lund-Zaina, S},
title = {Non-Canonical Aspects of Antibiotics and Antibiotic Resistance.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/antibiotics13060565},
pmid = {38927231},
issn = {2079-6382},
abstract = {The understanding of antibiotic resistance, one of the major health threats of our time, is mostly based on dated and incomplete notions, especially in clinical contexts. The "canonical" mechanisms of action and pharmacodynamics of antibiotics, as well as the methods used to assess their activity upon bacteria, have not changed in decades; the same applies to the definition, acquisition, selective pressures, and drivers of resistance. As a consequence, the strategies to improve antibiotic usage and overcome resistance have ultimately failed. This review gathers most of the "non-canonical" notions on antibiotics and resistance: from the alternative mechanisms of action of antibiotics and the limitations of susceptibility testing to the wide variety of selective pressures, lateral gene transfer mechanisms, ubiquity, and societal factors maintaining resistance. Only by having a "big picture" view of the problem can adequate strategies to harness resistance be devised. These strategies must be global, addressing the many aspects that drive the increasing prevalence of resistant bacteria aside from the clinical use of antibiotics.},
}
@article {pmid38927226,
year = {2024},
author = {Gestels, Z and Abdellati, S and Kenyon, C and Manoharan-Basil, SS},
title = {Ciprofloxacin Concentrations 100-Fold Lower than the MIC Can Select for Ciprofloxacin Resistance in Neisseria subflava: An In Vitro Study.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/antibiotics13060560},
pmid = {38927226},
issn = {2079-6382},
support = {Unknown//PRESTIP/ ; },
abstract = {Neisseria gonorrhoeae can acquire antimicrobial resistance (AMR) through horizontal gene transfer (HGT) from other Neisseria spp. such as commensals like Neisseria subflava. Low doses of antimicrobials in food could select for AMR in N. subflava, which could then be transferred to N. gonorrhoeae. In this study, we aimed to determine the lowest concentration of ciprofloxacin that can induce ciprofloxacin resistance (minimum selection concentration-MSC) in a N. subflava isolate (ID-Co000790/2, a clinical isolate collected from a previous community study conducted at ITM). In this study, Neisseria subflava was serially passaged on gonococcal (GC) medium agar plates containing ciprofloxacin concentrations ranging from 1:100 to 1:10,000 below its ciprofloxacin MIC (0.006 µg/mL) for 6 days. After 6 days of serial passaging at ciprofloxacin concentrations of 1/100th of the MIC, 24 colonies emerged on the plate containing 0.06 µg/mL ciprofloxacin, which corresponds to the EUCAST breakpoint for N. gonorrhoeae. Their ciprofloxacin MICs were between 0.19 to 0.25 µg/mL, and whole genome sequencing revealed a missense mutation T91I in the gyrA gene, which has previously been found to cause reduced susceptibility to fluoroquinolones. The N. subflava MSCde novo was determined to be 0.06 ng/mL (0.00006 µg/mL), which is 100×-fold lower than the ciprofloxacin MIC. The implications of this finding are that the low concentrations of fluoroquinolones found in certain environmental samples, such as soil, river water, and even the food we eat, may be able to select for ciprofloxacin resistance in N. subflava.},
}
@article {pmid38927197,
year = {2024},
author = {Yaikhan, T and Suwannasin, S and Singkhamanan, K and Chusri, S and Pomwised, R and Wonglapsuwan, M and Surachat, K},
title = {Genomic Characterization of Multidrug-Resistant Enterobacteriaceae Clinical Isolates from Southern Thailand Hospitals: Unraveling Antimicrobial Resistance and Virulence Mechanisms.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/antibiotics13060531},
pmid = {38927197},
issn = {2079-6382},
support = {B13F670075//the NSRF via the Program Management Unit for Human Resources &amp; Institutional Development, Research Innovation/ ; //the Postdoctoral Fellowship from Prince of Songkla University/ ; B13F660074//the NSRF via the Program Management Unit for Human Resources &amp; Institutional Development, Research and Innovation/ ; },
abstract = {The emergence and spread of antimicrobial resistance (AMR) among Enterobacteriaceae pose significant threats to global public health. In this study, we conducted a short-term surveillance effort in Southern Thailand hospitals to characterize the genomic diversity, AMR profiles, and virulence factors of Enterobacteriaceae strains. We identified 241 carbapenem-resistant Enterobacteriaceae, of which 12 were selected for whole-genome sequencing (WGS) and genome analysis. The strains included Proteus mirabilis, Serratia nevei, Klebsiella variicola, Klebsiella aerogenes, Klebsiella indica, Klebsiella grimontii, Phytobacter ursingii, Phytobacter palmae, Kosakonia spp., and Citrobacter freundii. The strains exhibited high levels of multidrug resistance, including resistance to carbapenem antibiotics. Whole-genome sequencing revealed a diverse array of antimicrobial resistance genes (ARGs), with strains carrying genes for ß-lactamase, efflux pumps, and resistance to other antibiotic classes. Additionally, stress response, metal tolerance, and virulence-associated genes were identified, highlighting the adaptability and pathogenic potential of these strains. A plasmid analysis identified several plasmid replicons, including IncA/C2, IncFIB(K), and Col440I, as well as several plasmids identical to those found globally, indicating the potential for the horizontal gene transfer of ARGs. Importantly, this study also identified a novel species of Kosakonia spp. PSU27, adding to the understanding of the genetic diversity and resistance mechanisms of Enterobacteriaceae in Southern Thailand. The results reported in this study highlight the critical importance of implementing effective antimicrobial management programs and developing innovative treatment approaches to urgently tackle AMR.},
}
@article {pmid38927185,
year = {2024},
author = {Peng, J and Feng, J and Ji, H and Kong, X and Hong, J and Zhu, L and Qian, H},
title = {Emergence of Rarely Reported Extensively Drug-Resistant Salmonella Enterica Serovar Paratyphi B among Patients in East China.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/antibiotics13060519},
pmid = {38927185},
issn = {2079-6382},
support = {National Major S&amp;T Projects(2018ZX10714-002)//Ministry of Science and Technology of the People's Republic of China/ ; Ym2023040//Jiangsu Preventive Medicine Association/ ; },
abstract = {BACKGROUND: In recent years, global concern over increasing multidrug resistance (MDR) among various Salmonella serotypes has grown significantly. However, reports on MDR Salmonella Paratyphi B remain scarce, let alone the extensively drug-resistant (XDR) strains.<br><br>METHODS: In this retrospective study, we investigated the isolates of Salmonella Paratyphi B in Jiangsu Province over the past decade and carried out antimicrobial susceptibility tests, then the strains were sequenced and bioinformatics analyses were performed.<br><br>RESULTS: 27 Salmonella Paratyphi B strains were identified, of which the predominant STs were ST42 (11), ST86 (10), and ST2814 (5). Among these strains, we uncovered four concerning XDR Salmonella Paratyphi B ST2814 strains (4/5) which were previously unreported. These alarmingly resistant isolates showed resistance to all three major antibiotic classes for Salmonella treatment and even the last resort treatment tigecycline. Bioinformatics analysis revealed high similarity between the plasmids harbored by these XDR strains and diverse Salmonella serotypes and Escherichia coli from China and neighboring regions. Notably, these four plasmids carried the ramAp gene responsible for multiple antibiotic resistance by regulating the AcrAB-TolC pump, predominantly originating from China. Additionally, a distinct MDR ST42(1/11) strain with an ICE on chromosome was also identified. Furthermore, phylogenetic analysis of global ST42/ST2814 isolates highlighted the regional specificity of these strains, with Jiangsu isolates clustering together with domestic isolates and XDR ST2814 forming a distinct branch, suggesting adaptation to local antibiotic pressures.<br><br>CONCLUSIONS: This research underscores the pressing need for closely monitoring the MDR/XDR Salmonella Paratyphi B, particularly the emerging ST2814 strains in Jiangsu Province, to effectively curb its spread and protect public health. Moreover, surveillance should be strengthened across different ecological niches and genera to track resistance genes and horizontal gene transfer elements under the concept of "ONE HEALTH".},
}
@article {pmid38926391,
year = {2024},
author = {Brown, CL and Maile-Moskowitz, A and Lopatkin, AJ and Xia, K and Logan, LK and Davis, BC and Zhang, L and Vikesland, PJ and Pruden, A},
title = {Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5412},
pmid = {38926391},
issn = {2041-1723},
support = {1545756//National Science Foundation (NSF)/ ; 2004751//National Science Foundation (NSF)/ ; 2125798//National Science Foundation (NSF)/ ; 4813//Water Research Foundation (WRF)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Sewage/microbiology ; *Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/metabolism ; Water Purification/methods ; Metagenomics/methods ; Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid/methods ; Drug Resistance, Bacterial/genetics ; Selection, Genetic ; },
abstract = {Activated sludge is the centerpiece of biological wastewater treatment, as it facilitates removal of sewage-associated pollutants, fecal bacteria, and pathogens from wastewater through semi-controlled microbial ecology. It has been hypothesized that horizontal gene transfer facilitates the spread of antibiotic resistance genes within the wastewater treatment plant, in part because of the presence of residual antibiotics in sewage. However, there has been surprisingly little evidence to suggest that sewage-associated antibiotics select for resistance at wastewater treatment plants via horizontal gene transfer or otherwise. We addressed the role of sewage-associated antibiotics in promoting antibiotic resistance using lab-scale sequencing batch reactors fed field-collected wastewater, metagenomic sequencing, and our recently developed bioinformatic tool Kairos. Here, we found confirmatory evidence that fluctuating levels of antibiotics in sewage are associated with horizontal gene transfer of antibiotic resistance genes, microbial ecology, and microdiversity-level differences in resistance gene fate in activated sludge.},
}
@article {pmid38922012,
year = {2024},
author = {Kerek, &#xc1; and Németh, V and Szabó, &#xc1; and Papp, M and Bányai, K and Kardos, G and Kaszab, E and Bali, K and Nagy, Z and Süth, M and Jerzsele, &#xc1;},
title = {Monitoring Changes in the Antimicrobial-Resistance Gene Set (ARG) of Raw Milk and Dairy Products in a Cattle Farm, from Production to Consumption.},
journal = {Veterinary sciences},
volume = {11},
number = {6},
pages = {},
doi = {10.3390/vetsci11060265},
pmid = {38922012},
issn = {2306-7381},
support = {RRF-2.3.1-21-2022-00001//National Recovery Fund/ ; },
abstract = {Raw milk and dairy products can serve as potential vectors for transmissible bacterial, viral and protozoal diseases, alongside harboring antimicrobial-resistance genes. This study monitors the changes in the antimicrobial-resistance gene pool in raw milk and cheese, from farm to consumer, utilizing next-generation sequencing. Five parallel sampling runs were conducted to assess the resistance gene pool, as well as phage or plasmid carriage and potential mobility. In terms of taxonomic composition, in raw milk the Firmicutes phylum made up 41%, while the Proteobacteria phylum accounted for 58%. In fresh cheese, this ratio shifted to 93% Firmicutes and 7% Proteobacteria. In matured cheese, the composition was 79% Firmicutes and 21% Proteobacteria. In total, 112 antimicrobial-resistance genes were identified. While a notable reduction in the resistance gene pool was observed in the freshly made raw cheese compared to the raw milk samples, a significant growth in the resistance gene pool occurred after one month of maturation, surpassing the initial gene frequency. Notably, the presence of extended-spectrum beta-lactamase (ESBL) genes, such as OXA-662 (100% coverage, 99.3% identity) and OXA-309 (97.1% coverage, 96.2% identity), raised concerns; these genes have a major public health relevance. In total, nineteen such genes belonging to nine gene families (ACT, CMY, EC, ORN, OXA, OXY, PLA, RAHN, TER) have been identified. The largest number of resistance genes were identified against fluoroquinolone drugs, which determined efflux pumps predominantly. Our findings underscore the importance of monitoring gene pool variations throughout the product pathway and the potential for horizontal gene transfer in raw products. We advocate the adoption of a new approach to food safety investigations, incorporating next-generation sequencing techniques.},
}
@article {pmid38918632,
year = {2024},
author = {Mei, Z and Wang, F and Bhosle, A and Dong, D and Mehta, R and Ghazi, A and Zhang, Y and Liu, Y and Rinott, E and Ma, S and Rimm, EB and Daviglus, M and Willett, WC and Knight, R and Hu, FB and Qi, Q and Chan, AT and Burk, RD and Stampfer, MJ and Shai, I and Kaplan, RC and Huttenhower, C and Wang, DD},
title = {Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {38918632},
issn = {1546-170X},
support = {R00DK119412//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01NR01999//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01AG077489//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; P30DK046200//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 897161//American Heart Association (American Heart Association, Inc.)/ ; 209933838//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; R24DK110499//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; },
abstract = {The association of gut microbial features with type 2 diabetes (T2D) has been inconsistent due in part to the complexity of this disease and variation in study design. Even in cases in which individual microbial species have been associated with T2D, mechanisms have been unable to be attributed to these associations based on specific microbial strains. We conducted a comprehensive study of the T2D microbiome, analyzing 8,117 shotgun metagenomes from 10 cohorts of individuals with T2D, prediabetes, and normoglycemic status in the United States, Europe, Israel and China. Dysbiosis in 19 phylogenetically diverse species was associated with T2D (false discovery rate < 0.10), for example, enriched Clostridium bolteae and depleted Butyrivibrio crossotus. These microorganisms also contributed to community-level functional changes potentially underlying T2D pathogenesis, for example, perturbations in glucose metabolism. Our study identifies within-species phylogenetic diversity for strains of 27 species that explain inter-individual differences in T2D risk, such as Eubacterium rectale. In some cases, these were explained by strain-specific gene carriage, including loci involved in various mechanisms of horizontal gene transfer and novel biological processes underlying metabolic risk, for example, quorum sensing. In summary, our study provides robust cross-cohort microbial signatures in a strain-resolved manner and offers new mechanistic insights into T2D.},
}
@article {pmid38436262,
year = {2024},
author = {Harmer, CJ and Hall, RM},
title = {IS26 and the IS26 family: versatile resistance gene movers and genome reorganizers.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {88},
number = {2},
pages = {e0011922},
doi = {10.1128/mmbr.00119-22},
pmid = {38436262},
issn = {1098-5557},
support = {GNT1194879//DHAC | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {*DNA Transposable Elements/genetics ; *Gram-Negative Bacteria/genetics ; Genome, Bacterial ; Drug Resistance, Bacterial/genetics ; Transposases/metabolism/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {SUMMARYIn Gram-negative bacteria, the insertion sequence IS26 is highly active in disseminating antibiotic resistance genes. IS26 can recruit a gene or group of genes into the mobile gene pool and support their continued dissemination to new locations by creating pseudo-compound transposons (PCTs) that can be further mobilized by the insertion sequence (IS). IS26 can also enhance expression of adjacent potential resistance genes. IS26 encodes a DDE transposase but has unique properties. It forms cointegrates between two separate DNA molecules using two mechanisms. The well-known copy-in (replicative) route generates an additional IS copy and duplicates the target site. The recently discovered and more efficient and targeted conservative mechanism requires an IS in both participating molecules and does not generate any new sequence. The unit of movement for PCTs, known as a translocatable unit or TU, includes only one IS26. TU formed by homologous recombination between the bounding IS26s can be reincorporated via either cointegration route. However, the targeted conservative reaction is key to generation of arrays of overlapping PCTs seen in resistant pathogens. Using the copy-in route, IS26 can also act on a site in the same DNA molecule, either inverting adjacent DNA or generating an adjacent deletion plus a circular molecule carrying the DNA segment lost and an IS copy. If reincorporated, these circular molecules create a new PCT. IS26 is the best characterized IS in the IS26 family, which includes IS257/IS431, ISSau10, IS1216, IS1006, and IS1008 that are also implicated in spreading resistance genes in Gram-positive and Gram-negative pathogens.},
}
@article {pmid38918467,
year = {2024},
author = {Grodner, B and Shi, H and Farchione, O and Vill, AC and Ntekas, I and Diebold, PJ and Wu, DT and Chen, CY and Kim, DM and Zipfel, WR and Brito, IL and De Vlaminck, I},
title = {Spatial mapping of mobile genetic elements and their bacterial hosts in complex microbiomes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {38918467},
issn = {2058-5276},
support = {1DP2AI138242//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 1R33CA235302//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 1R33CA235302//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; S10OD018516//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 1R33CA235302//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
abstract = {The exchange of mobile genetic elements (MGEs) facilitates the spread of functional traits including antimicrobial resistance within bacterial communities. Tools to spatially map MGEs and identify their bacterial hosts in complex microbial communities are currently lacking, limiting our understanding of this process. Here we combined single-molecule DNA fluorescence in situ hybridization (FISH) with multiplexed ribosomal RNA-FISH to enable simultaneous visualization of both MGEs and bacterial taxa. We spatially mapped bacteriophage and antimicrobial resistance (AMR) plasmids and identified their host taxa in human oral biofilms. This revealed distinct clusters of AMR plasmids and prophage, coinciding with densely packed regions of host bacteria. Our data suggest spatial heterogeneity in bacterial taxa results in heterogeneous MGE distribution within the community, with MGE clusters resulting from horizontal gene transfer hotspots or expansion of MGE-carrying strains. Our approach can help advance the study of AMR and phage ecology in biofilms.},
}
@article {pmid38917629,
year = {2024},
author = {Liu, F and Shen, Y and Hou, Y and Wu, J and Ting, Y and Nie, C and Tong, M},
title = {Elimination of representative antibiotic-resistant bacteria, antibiotic resistance genes and ciprofloxacin from water via photoactivation of periodate using FeS2.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {134982},
doi = {10.1016/j.jhazmat.2024.134982},
pmid = {38917629},
issn = {1873-3336},
abstract = {The propagation of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) induced by the release of antibiotics poses great threats to ecological safety and human health. In this study, periodate (PI)/FeS2/simulated sunlight (SSL) system was employed to remove representative ARB, ARGs and antibiotics in water. 1 × 10[7] CFU mL[-1] of gentamycin-resistant Escherichia coli was effectively disinfected below limit of detection in PI/FeS2/SSL system under different water matrix and in real water samples. Sulfadiazine-resistant Pseudomonas and Gram-positive Bacillus subtilis could also be efficiently sterilized. Theoretical calculation showed that (110) facet was the most reactive facet on FeS2 to activate PI for the generation of reactive species (·OH, ·O2[-], h[+] and Fe(IV)=O) to damage cell membrane and intracellular enzyme defense system. Both intracellular and extracellular ARGs could be degraded and the expression levels of multidrug resistance-related genes were downregulated during the disinfection process. Thus, horizontal gene transfer (HGT) of ARB was inhibited. Moreover, PI/FeS2/SSL system could disinfect ARB in a continuous flow reactor and in an enlarged reactor under natural sunlight irradiation. PI/FeS2/SSL system could also effectively degrade the HGT-promoting antibiotic (ciprofloxacin) via hydroxylation and ring cleavage process. Overall, PI/FeS2/SSL exhibited great promise for the elimination of antibiotic resistance from water.},
}
@article {pmid38915079,
year = {2024},
author = {Wu, CS and Wang, RJ and Chaw, SM},
title = {Integration of large and diverse angiosperm DNA fragments into Asian Gnetum mitogenomes.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {140},
pmid = {38915079},
issn = {1741-7007},
support = {No. 2022B1111040003//Guangdong Provincial Key R&amp;D Programme/ ; },
mesh = {*Phylogeny ; *Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Gnetum/genetics ; DNA, Plant/genetics ; Evolution, Molecular ; Magnoliopsida/genetics ; },
abstract = {BACKGROUND: Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms in West African, South American, and Southeast Asian rainforests. Only a single acquisition of an angiosperm mitochondrial intron has been documented to date in Asian Gnetum mitogenomes. We wanted to develop a more comprehensive understanding of frequency and fragment length distribution of such events as well as their evolutionary history in this genus.<br><br>RESULTS: We sequenced and assembled mitogenomes from five Asian Gnetum species. These genomes vary remarkably in size and foreign DNA content. We identified 15 mitochondrion-derived and five plastid-derived (MTPT) foreign genes. Our phylogenetic analyses strongly indicate that these foreign genes were transferred from diverse eudicots-mostly from the Rubiaceae genus Coptosapelta and ten genera of Malpighiales. This indicates that Asian Gnetum has experienced multiple independent HGT events. Patterns of sequence evolution strongly suggest DNA-mediated transfer between mitochondria as the primary mechanism giving rise to these HGT events. Most Asian Gnetum species are lianas and often entwined with sympatric angiosperms. We therefore propose that close apposition of Gnetum and angiosperm stems presents opportunities for interspecific cell-to-cell contact through friction and wounding, leading to HGT.<br><br>CONCLUSIONS: Our study reveals that multiple HGT events have resulted in massive amounts of angiosperm mitochondrial DNA integrated into Asian Gnetum mitogenomes. Gnetum and its neighboring angiosperms are often entwined with each other, possibly accounting for frequent HGT between these two phylogenetically remote lineages.},
}
@article {pmid38914331,
year = {2024},
author = {Haffiez, N and Kalantar, E and Zakaria, BS and Azizi, SMM and Farner, JM and Dhar, BR},
title = {Impact of aging of primary and secondary polystyrene nanoplastics on the transmission of antibiotic resistance genes in anaerobic digestion.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {174213},
doi = {10.1016/j.scitotenv.2024.174213},
pmid = {38914331},
issn = {1879-1026},
abstract = {Sewage sludge is a significant reservoir of nano/microplastics (NPs/MPs) and antibiotic resistance genes (ARGs). Research has revealed that NPs/MPs may exert an inhibitory effect on anaerobic digestion (AD) of sludge. Moreover, NPs/MPs can influence microbial community diversity and composition, potentially increasing ARGs dissemination. The morphological changes to NPs/MPs surface due to aging contribute to modifying hydrophobic properties. To date, there is limited comprehension regarding how various surface properties of NPs influence ARGs dissemination during AD. This study investigated the impact of primary aged/non-aged and secondary aged/non-aged polystyrene nanoplastics (PSNPs) on ARGs and mobile genetic elements (MGEs) propagation during AD. The findings indicated that the UV-aging process resulted in surface oxidation and distinct morphological characteristics in both primary and secondary PSNPs, while the surface oxidation effect was more pronounced in the secondary aged PSNPs. High concentrations (150 μg/L) of primary and secondary PSNPs inhibited methane production, with secondary PSNPs causing greater inhibition by 16 to 20 % compared to control. In contrast, low concentration (25 μg/L) had negligible or slightly positive effects on methane production. PSNPs at 150 μg/L reduced total VFA concentration, indicating an inhibitory effect on the fermentation step in the AD process. Primary and secondary PSNPs exhibited changes in EPS characteristics. ARGs abundance was enriched in reactors amended with PSNPs, with the highest abundance of 8.54 × 10[5] copies/g sludge observed in the secondary aged PSNPs (150 μg/L) reactor. Reactors exposed to aged PSNPs exhibited a relatively higher abundance of ARGs compared to reactors exposed to non-aged PSNPs. Exposure to PSNPs increased the microbial community diversity within the digesters and triggered the enrichment of Comamonadaceae and Syntrophaceae, belonging to Proteobacteria phylum. On the other hand, archaeal communities tended to shift towards hydrogenotrophic methanogens in PSNPs reactors. The correlation analysis showed that Comamonadaceae were positively correlated with the majority of ARGs and intl1. A positive correlation was observed between MGEs and most ARGs, suggesting that the increased proliferation of ARGs under PSNPs exposure may be linked to the abundance of MGEs, which in turn promotes the growth of hosts carrying ARGs. These findings suggest that aged and non-aged NPs could substantially impact the spread of ARGs and MGEs, which also led to notable alterations in the composition of the microbial community. Overall, this study provides valuable insights into the multifaceted impacts of PSNPs with various characteristics on AD processes, microbial communities, and ARGs proliferation, highlighting the urgent need for comprehensive assessments of NPs pollutants in the environment.},
}
@article {pmid38913753,
year = {2024},
author = {Maier, JL and Gin, C and Callahan, B and Sheriff, EK and Duerkop, BA and Kleiner, M},
title = {Pseudo-pac site sequences used by phage P22 in generalized transduction of Salmonella.},
journal = {PLoS pathogens},
volume = {20},
number = {6},
pages = {e1012301},
doi = {10.1371/journal.ppat.1012301},
pmid = {38913753},
issn = {1553-7374},
abstract = {Salmonella enterica Serovar Typhimurium (Salmonella) and its bacteriophage P22 are a model system for the study of horizontal gene transfer by generalized transduction. Typically, the P22 DNA packaging machinery initiates packaging when a short sequence of DNA, known as the pac site, is recognized on the P22 genome. However, sequences similar to the pac site in the host genome, called pseudo-pac sites, lead to erroneous packaging and subsequent generalized transduction of Salmonella DNA. While the general genomic locations of the Salmonella pseudo-pac sites are known, the sequences themselves have not been determined. We used visualization of P22 sequencing reads mapped to host Salmonella genomes to define regions of generalized transduction initiation and the likely locations of pseudo-pac sites. We searched each genome region for the sequence with the highest similarity to the P22 pac site and aligned the resulting sequences. We built a regular expression (sequence match pattern) from the alignment and used it to search the genomes of two P22-susceptible Salmonella strains-LT2 and 14028S-for sequence matches. The final regular expression successfully identified pseudo-pac sites in both LT2 and 14028S that correspond with generalized transduction initiation sites in mapped read coverages. The pseudo-pac site sequences identified in this study can be used to predict locations of generalized transduction in other P22-susceptible hosts or to initiate generalized transduction at specific locations in P22-susceptible hosts with genetic engineering. Furthermore, the bioinformatics approach used to identify the Salmonella pseudo-pac sites in this study could be applied to other phage-host systems.},
}
@article {pmid38878435,
year = {2024},
author = {Zhang, X and Ma, L and Zhang, XX},
title = {Neglected risks of enhanced antimicrobial resistance and pathogenicity in anaerobic digestion during transition from thermophilic to mesophilic.},
journal = {Journal of hazardous materials},
volume = {475},
number = {},
pages = {134886},
doi = {10.1016/j.jhazmat.2024.134886},
pmid = {38878435},
issn = {1873-3336},
mesh = {Anaerobiosis ; *Drug Resistance, Bacterial/genetics ; Temperature ; Methane/metabolism ; Bacteria/genetics/pathogenicity/metabolism/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Virulence Factors/genetics ; Gene Transfer, Horizontal ; Enterobacteriaceae/genetics/pathogenicity/drug effects/metabolism ; Genes, Bacterial ; },
abstract = {Minimization of antibiotic resistance genes (ARGs) and potential pathogenic antibiotic-resistant bacteria (PARB) during anaerobic digestion (AD) is significantly impacted by temperature. However, knowledge on how ARGs and PARB respond to temperature transition from thermophilic to mesophilic is limited. Here, we combined metagenomic-based with culture-based approaches and revealed the risks of antimicrobial resistance and pathogenicity during transition from 55 °C to 35 °C for AD, with strategies of sharp (ST, one-step by 20 °C/d) and mild (MT, step-wise by 1 °C/d). Results indicated a lower decrease in methane production with MT (by 38.9%) than ST (by 88.8%). Phenotypic assays characterized a significant propagation of multi-resistant lactose-fermenting Enterobacteriaceae and indicator pathogens after both transitions, especially via ST. Further genomic evidence indicated a significant increase of ARGs (29.4-fold), virulence factor genes (1.8-fold) and PARB (65.3-fold) after ST, while slight enrichment via MT. Bacterial succession and enhanced horizontal transfer mediated by mobile genetic elements promoted ARG propagation in AD during transition, which was synchronously exacerbated through horizontal transfer mechanisms mediated by cellular physiological responses (oxidative stress, membrane permeability, bacterial conjugation and transformation) and co-selection mechanisms of biomethanation metabolic functions (acidogenesis and acetogenesis). This study reveals temperature-dependent resistome and pathogenicity development in AD, facilitating microbial risk control.},
}
@article {pmid38771049,
year = {2024},
author = {Muñoz-Gutiérrez, I and Cantu, L and Shanahan, J and Girguis, M and de la Cruz, M and Mota-Bravo, L},
title = {Cryptic environmental conjugative plasmid recruits a novel hybrid transposon resulting in a new plasmid with higher dispersion potential.},
journal = {mSphere},
volume = {9},
number = {6},
pages = {e0025224},
doi = {10.1128/msphere.00252-24},
pmid = {38771049},
issn = {2379-5042},
support = {GM136498//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Plasmids/genetics ; *DNA Transposable Elements/genetics ; *Escherichia coli/genetics/drug effects ; *Conjugation, Genetic ; *Anti-Bacterial Agents/pharmacology ; Lakes/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; },
abstract = {UNLABELLED: Cryptic conjugative plasmids lack antibiotic-resistance genes (ARGs). These plasmids can capture ARGs from the vast pool of the environmental metagenome, but the mechanism to recruit ARGs remains to be elucidated. To investigate the recruitment of ARGs by a cryptic plasmid, we sequenced and conducted mating experiments with Escherichia coli SW4848 (collected from a lake) that has a cryptic IncX (IncX4) plasmid and an IncF (IncFII/IncFIIB) plasmid with five genes that confer resistance to aminoglycosides (strA and strB), sulfonamides (sul2), tetracycline [tet(A)], and trimethoprim (dfrA5). In a conjugation experiment, a novel hybrid Tn21/Tn1721 transposon of 22,570 bp (designated Tn7714) carrying the five ARG mobilized spontaneously from the IncF plasmid to the cryptic IncX plasmid. The IncF plasmid was found to be conjugative when it was electroporated into E. coli DH10B (without the IncX plasmid). Two parallel conjugations with the IncF and the new IncX (carrying the novel Tn7714 transposon) plasmids in two separate E. coli DH10B as donors and E. coli J53 as the recipient revealed that the conjugation rate of the new IncX plasmid (with the novel Tn7714 transposon and five ARGs) is more than two orders of magnitude larger than the IncF plasmid. For the first time, this study shows experimental evidence that cryptic environmental plasmids can capture and transfer transposons with ARGs to other bacteria, creating novel multidrug-resistant conjugative plasmids with higher dispersion potential.<br><br>IMPORTANCE: Cryptic conjugative plasmids are extrachromosomal DNA molecules without antibiotic-resistance genes (ARGs). Environmental bacteria carrying cryptic plasmids with a high conjugation rate threaten public health because they can capture clinically relevant ARGs and rapidly spread them to pathogenic bacteria. However, the mechanism to recruit ARG by cryptic conjugative plasmids in environmental bacteria has not been observed experimentally. Here, we document the first translocation of a transposon with multiple clinically relevant ARGs to a cryptic environmental conjugative plasmid. The new multidrug-resistant conjugative plasmid has a conjugation rate that is two orders of magnitude higher than the original plasmid that carries the ARG (i.e., the new plasmid from the environment can spread ARG more than two orders of magnitude faster). Our work illustrates the importance of studying the mobilization of ARGs in environmental bacteria. It sheds light on how cryptic conjugative plasmids recruit ARGs, a phenomenon at the root of the antibiotic crisis.},
}
@article {pmid38911822,
year = {2024},
author = {Banerjee, P and Eulenstein, O and Friedberg, I},
title = {Discovering genomic islands in unannotated bacterial genomes using sequence embedding.},
journal = {Bioinformatics advances},
volume = {4},
number = {1},
pages = {vbae089},
pmid = {38911822},
issn = {2635-0041},
abstract = {MOTIVATION: Genomic islands (GEIs) are clusters of genes in bacterial genomes that are typically acquired by horizontal gene transfer. GEIs play a crucial role in the evolution of bacteria by rapidly introducing genetic diversity and thus helping them adapt to changing environments. Specifically of interest to human health, many GEIs contain pathogenicity and antimicrobial resistance genes. Detecting GEIs is, therefore, an important problem in biomedical and environmental research. There have been many previous studies for computationally identifying GEIs. Still, most of these studies rely on detecting anomalies in the unannotated nucleotide sequences or on a fixed set of known features on annotated nucleotide sequences.<br><br>RESULTS: Here, we present TreasureIsland, which uses a new unsupervised representation of DNA sequences to predict GEIs. We developed a high-precision boundary detection method featuring an incremental fine-tuning of GEI borders, and we evaluated the accuracy of this framework using a new comprehensive reference dataset, Benbow. We show that TreasureIsland's accuracy rivals other GEI predictors, enabling efficient and faster identification of GEIs in unannotated bacterial genomes.<br><br>TreasureIsland is available under an MIT license at: https://github.com/FriedbergLab/GenomicIslandPrediction.},
}
@article {pmid38910035,
year = {2024},
author = {Zarlenga, DS and Hoberg, EP and Thompson, P and Rosenthal, B},
title = {Trichinella: Becoming a parasite.},
journal = {Veterinary parasitology},
volume = {},
number = {},
pages = {110220},
doi = {10.1016/j.vetpar.2024.110220},
pmid = {38910035},
issn = {1873-2550},
abstract = {Phylogenetic evidence indicates that free-living nematodes gave rise to parasitic nematodes where parasitism evolved independently at least 15 times. The high level of genetic and biological diversity among parasites dictates an equally high level of diversity in the transition to parasitism. We previously hypothesized that horizontal gene transfer (HGT) played an important role in the evolution of parasitism among early ancestors of Trichinella, mediated by an interplay of ecological and evolutionary pathways that contributed to persistence and diversification. We propose that host selection may have been associated with the metabolism of ammonia and engender a new paradigm whereby the reprogrammed nurse cell is capable of generating cyanate thereby enabling the importance of the Trichinella cyanase in the longevity of the cell. Parasites and parasitism have revealed considerable resilience against a backdrop of climate change and environmental perturbation. Here we provide a putative link between key periods in the evolution of Trichinella and major geological and climatological events dating back 500 million years. A useful lens for exploring such ideas, the Stockholm Paradigm, integrates Ecological Fitting (a foundation for host colonization and diversification), the Oscillation Hypothesis (recurring shifts between trends in generalization and specialization relative to host range), the Geographic Mosaic Theory of Coevolution (microevolutionary co-adaptive processes), and the Taxon Pulse Hypothesis (alternating events of biotic expansion i.e., exploitation in evolutionary and ecological time). Here we examine how one or more of these interactive theories, in a phylogenetic-historical context and in conjunction with HGT, may help explain the scope and depth of diversity among Trichinella genotypes.},
}
@article {pmid38908181,
year = {2024},
author = {Wu, Y and Niu, Q and Liu, Y and Zheng, X and Long, M and Chen, Y},
title = {Chlorinated organophosphorus flame retardants induce the propagation of antibiotic resistance genes in sludge fermentation systems: Insight of chromosomal mutation and microbial traits.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {134971},
doi = {10.1016/j.jhazmat.2024.134971},
pmid = {38908181},
issn = {1873-3336},
abstract = {Waste activated sludge (WAS) is a critical reservoir for antibiotic resistance genes (ARGs) due to the prevalent misuse of antibiotics. Horizontal gene transfer (HGT) is the primary mechanism for ARGs spread through mobile genetic elements (MGEs). However, the role of non-antibiotic organophosphorus flame retardants (Cl-OFRs) in ARG transmission in the WAS fermentation system remains unclear. This study examines the effects of tris(2-chloroethyl) phosphate (TCEP), a representative Cl-OFR, on ARG dynamics in WAS fermentation using molecular docking and metagenomic analysis. The results showed a 33.4 % increase in ARG abundance in the presence of TCEP. Interestingly, HGT did not appear to be the primary mechanism of ARG dissemination under TCEP stress, as evidenced by a 2.51 % decrease in MGE abundance. TCEP binds to sludge through hydrogen bonds with a binding energy of - 3.6 kJ/mol, leading to microbial damage and an increase in the proportion of non-viable cells. This interaction prompts a microbial shift toward Firmicutes with thick cell walls, which are significant ARG carriers. Additionally, TCEP induces chromosomal mutations through oxidative stress and the SOS response, contributing to ARG formation. Microorganisms also develop multidrug resistance mechanisms to expel TCEP and mitigate its toxicity. This study provides a comprehensive understanding of Cl-OFRs effects on the ARGs fates in WAS fermentation system and offers guidance for the safe and efficient treatment of Cl-OFRs and WAS.},
}
@article {pmid38906294,
year = {2024},
author = {Yao, S and Yu, J and Zhang, T and Xie, J and Yan, C and Ni, X and Guo, B and Cui, C},
title = {Comprehensive analysis of distribution characteristics and horizontal gene transfer elements of blaNDM-1-carrying bacteria.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {173907},
doi = {10.1016/j.scitotenv.2024.173907},
pmid = {38906294},
issn = {1879-1026},
abstract = {The worldwide dissemination of New Delhi metallo-β-lactamase-1 (NDM-1), which mediates resistance to almost all clinical β-lactam antibiotics, is a major public health problem. The global distribution, species, sources, and potential transfer risk of blaNDM-1-carrying bacteria are unclear. Results of a comprehensive analysis of literature in 2010-2022 showed that a total of 6002 blaNDM-1 carrying bacteria were widely distributed around 62 countries with a high trend in the coastal areas. Opportunistic pathogens or pathogens like Klebsiella sp., Escherichia sp., Acinetobacter sp. and Pseudomonas sp. were the four main species indicating the potential microbial risk. Source analysis showed that 86.45 % of target bacteria were isolated from the source of hospital (e.g., Hospital patients and wastewater) and little from surface water (5.07 %) and farms (3.98 %). A plasmid-encoded blaNDM-1Acinetobacter sp. with the resistance mechanisms of antibiotic efflux pump, antibiotic target change and antibiotic degradation was isolated from the wastewater of a typical tertiary hospital. Insertion sequences (IS3 and IS30) located in the adjacent 5 kbp of blaNDM-1-bleMBL gene cluster indicating the transposon-mediated horizontal gene transfer risk. These results showed that the worldwide spread of blaNDM-1-carrying bacteria and its potential horizontal gene transfer risk deserve good control.},
}
@article {pmid38905247,
year = {2024},
author = {Mohamed, DS and Abd El-Baky, RM and El-Mokhtar, MA and Ghanem, SK and Yahia, R and Alqahtani, AM and Abourehab, MAS and Ahmed, EF},
title = {Influence of selected non-antibiotic pharmaceuticals on antibiotic resistance gene transfer in Escherichia coli.},
journal = {PloS one},
volume = {19},
number = {6},
pages = {e0304980},
pmid = {38905247},
issn = {1932-6203},
mesh = {*Escherichia coli/drug effects/genetics ; *Gene Transfer, Horizontal ; *Plasmids/genetics ; Metoclopramide/pharmacology ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics/drug effects ; Conjugation, Genetic ; Drug Resistance, Microbial/genetics/drug effects ; },
abstract = {BACKGROUND: Antibiotic resistance genes (ARGs) transfer rapidly among bacterial species all over the world contributing to the aggravation of antibiotic resistance crisis. Antibiotics at sub-inhibitory concentration induce horizontal gene transfer (HRT) between bacteria, especially through conjugation. The role of common non-antibiotic pharmaceuticals in the market in disseminating antibiotic resistance is not well studied.<br><br>OBJECTIVES: In this work, we indicated the effect of some commonly used non-antibiotic pharmaceuticals including antiemetic (metoclopramide HCl) and antispasmodics (hyoscine butyl bromide and tiemonium methyl sulfate) on the plasmid-mediated conjugal transfer of antibiotic resistance genes between pathogenic E. coli in the gastric intestinal tract (GIT).<br><br>METHODS: Broth microdilution assay was used to test the antibacterial activity of the tested non-antibiotic pharmaceuticals. A conjugation mating system was applied in presence of the studied non-antibiotic pharmaceuticals to test their effect on conjugal transfer frequency. Plasmid extraction and PCR were performed to confirm the conjugation process. Transmission electron microscopy (TEM) was used for imaging the effect of non-antibiotic pharmaceuticals on bacterial cells.<br><br>RESULTS: No antibacterial activity was reported for the used non-antibiotic pharmaceuticals. Plasmid-mediated conjugal transfer between isolates was induced by metoclopramide HCl but suppressed by hyoscine butyl bromide. Tiemonium methylsulfate slightly promoted conjugal transfer. Aggregation between cells and periplasmic bridges was clear in the case of metoclopramide HCl while in presence of hyoscine butyl bromide little affinity was observed.<br><br>CONCLUSION: This study indicates the contribution of non-antibiotic pharmaceuticals to the dissemination and evolution of antibiotic resistance at the community level. Metoclopramide HCl showed an important role in the spread of antibiotic resistance.},
}
@article {pmid38904756,
year = {2024},
author = {Kaur, J and Verma, H and Kaur, J and Lata, P and Dhingra, GG and Lal, R},
title = {In Silico Analysis of the Phylogenetic and Physiological Characteristics of Sphingobium indicum B90A: A Hexachlorocyclohexane-Degrading Bacterium.},
journal = {Current microbiology},
volume = {81},
number = {8},
pages = {233},
pmid = {38904756},
issn = {1432-0991},
mesh = {*Phylogeny ; *Sphingomonadaceae/genetics/metabolism/classification ; *Genome, Bacterial ; *Hexachlorocyclohexane/metabolism ; *Computer Simulation ; *Biodegradation, Environmental ; Genomic Islands ; Gene Transfer, Horizontal ; },
abstract = {The study focuses on the in silico genomic characterization of Sphingobium indicum B90A, revealing a wealth of genes involved in stress response, carbon monoxide oxidation, β-carotene biosynthesis, heavy metal resistance, and aromatic compound degradation, suggesting its potential as a bioremediation agent. Furthermore, genomic adaptations among nine Sphingomonad strains were explored, highlighting shared core genes via pangenome analysis, including those related to the shikimate pathway and heavy metal resistance. The majority of genes associated with aromatic compound degradation, heavy metal resistance, and stress response were found within genomic islands across all strains. Sphingobium indicum UT26S exhibited the highest number of genomic islands, while Sphingopyxis alaskensis RB2256 had the maximum fraction of its genome covered by genomic islands. The distribution of lin genes varied among the strains, indicating diverse genetic responses to environmental pressures. Additionally, in silico evidence of horizontal gene transfer (HGT) between plasmids pSRL3 and pISP3 of the Sphingobium and Sphingomonas genera, respectively, has been provided. The manuscript offers novel insights into strain B90A, highlighting its role in horizontal gene transfer and refining evolutionary relationships among Sphingomonad strains. The discovery of stress response genes and the czcABCD operon emphasizes the potential of Sphingomonads in consortia development, supported by genomic island analysis.},
}
@article {pmid38904697,
year = {2024},
author = {Bhattacharjee, A and Singh, AK},
title = {Delineating the Acquired Genetic Diversity and Multidrug Resistance in Alcaligenes from Poultry Farms and Nearby Soil.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {38904697},
issn = {1976-3794},
support = {OLP-2035//Council for Scientific and Industrial Research/ ; OLP-2081//Council for Scientific and Industrial Research/ ; GPP-0423//DST-SERB/ ; },
abstract = {Alcaligenes faecalis is one of the most important and clinically significant environmental pathogens, increasing in importance due to its isolation from soil and nosocomial environments. The Gram-negative soil bacterium is associated with skin endocarditis, bacteremia, dysentery, meningitis, endophthalmitis, urinary tract infections, and pneumonia in patients. With emerging antibiotic resistance in A. faecalis, it has become crucial to understand the origin of such resistance genes within this clinically significant environmental and gut bacterium. In this research, we studied the impact of antibiotic overuse in poultry and its effect on developing resistance in A. faecalis. We sampled soil and faecal materials from five poultry farms, performed whole genome sequencing &amp; analysis and identified four strains of A. faecalis. Furthermore, we characterized the genes in the genomic islands of A. faecalis isolates. We found four multidrug-resistant A. faecalis strains that showed resistance against vancomycin (MIC >1000 μg/ml), ceftazidime (50 μg/ml), colistin (50 μg/ml) and ciprofloxacin (50 μg/ml). From whole genome comparative analysis, we found more than 180 resistance genes compared to the reference sequence. Parts of our assembled contigs were found to be similar to different bacteria which included pbp1A and pbp2 imparting resistance to amoxicillin originally a part of Helicobacter and Bordetella pertussis. We also found the Mycobacterial insertion element IS6110 in the genomic islands of all four genomes. This prominent insertion element can be transferred and induce resistance to other bacterial genomes. The results thus are crucial in understanding the transfer of resistance genes in the environment and can help in developing regimes for antibiotic use in the food and poultry industry.},
}
@article {pmid38903782,
year = {2024},
author = {Ott, LC and Mellata, M},
title = {Short-chain fatty acids inhibit bacterial plasmid transfer through conjugation in vitro and in ex vivo chicken tissue explants.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1414401},
doi = {10.3389/fmicb.2024.1414401},
pmid = {38903782},
issn = {1664-302X},
abstract = {The animal gut acts as a potent reservoir for spreading and maintaining conjugative plasmids that confer antimicrobial resistance (AMR), fitness, and virulence attributes. Interventions that inhibit the continued emergence and expansion of AMR and virulent strains in agricultural and clinical environments are greatly desired. This study aims to determine the presence and efficacy of short-chain fatty acids (SCFA) inhibitory effects on the conjugal transfer of AMR plasmids. In vitro broth conjugations were conducted between donor Escherichia coli strains carrying AMP plasmids and the plasmid-less Escherichia coli HS-4 recipient strain. Conjugations were supplemented with ddH2O or SCFAs at 1, 0.1, 0.01, or 0.001 molar final concentration. The addition of SCFAs completely inhibited plasmid transfer at 1 and 0.1 molar and significantly (p < 0.05) reduced transfer at 0.01 molar, regardless of SCFA tested. In explant models for the chicken ceca, either ddH2O or a final concentration of 0.025 M SCFAs were supplemented to the explants infected with donor and recipient E. coli. In every SCFA tested, significant decreases in transconjugant populations compared to ddH2O-treated control samples were observed with minimal effects on donor and recipient populations. Finally, significant reductions in transconjugants for plasmids of each incompatibility type (IncP1ε, IncFIβ, and IncI1) tested were detected. This study demonstrates for the first time the broad inhibition ability of SCFAs on bacterial plasmid transfer and eliminates AMR with minimal effect on bacteria. Implementing interventions that increase the concentrations of SCFAs in the gut may be a viable method to reduce the risk, incidence, and rate of AMR emergence in agricultural and human environments.},
}
@article {pmid38903098,
year = {2024},
author = {Sastre-Dominguez, J and DelaFuente, J and Toribio-Celestino, L and Herencias, C and Herrador-Gomez, P and Costas, C and Hernandez-Garcia, M and Canton, R and Rodriguez-Beltran, J and Santos-Lopez, A and San Millan, A},
title = {Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.03.01.582297},
pmid = {38903098},
abstract = {Plasmids are extrachromosomal genetic elements commonly found in bacteria. Plasmids are known to fuel bacterial evolution through horizontal gene transfer (HGT), but recent analyses indicate that they can also promote intragenomic adaptations. However, the role of plasmids as catalysts of bacterial evolution beyond HGT remains poorly explored. In this study, we investigate the impact of a widespread conjugative plasmid, pOXA-48, on the evolution of various multidrug-resistant clinical enterobacteria. Combining experimental and within-patient evolution analyses, we unveil that plasmid pOXA-48 promotes bacterial evolution through the transposition of plasmid-encoded insertion sequence 1 (IS1) elements. Specifically, IS1-mediated gene inactivations expedite the adaptation rate of clinical strains in vitro and foster within-patient adaptation in the gut microbiota. We decipher the mechanism underlying the plasmid-mediated surge in IS1 transposition, revealing a negative feedback loop regulated by the genomic copy number of IS1. Given the overrepresentation of IS elements in bacterial plasmids, our findings propose that plasmid-mediated IS transposition represents a crucial mechanism for swift bacterial adaptation.},
}
@article {pmid38902796,
year = {2024},
author = {Chaudhari, NM and Pérez-Carrascal, OM and Overholt, WA and Totsche, KU and Küsel, K},
title = {Genome streamlining in Parcubacteria transitioning from soil to groundwater.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {41},
pmid = {38902796},
issn = {2524-6372},
abstract = {BACKGROUND: To better understand the influence of habitat on the genetic content of bacteria, with a focus on members of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil via seepage waters to groundwater on genomic composition of ultra-small Parcubacteria, the dominating CPR class in seepage waters, using genome resolved metagenomics.<br><br>RESULTS: Bacterial metagenome-assembled genomes (MAGs), (318 total, 32 of Parcubacteria) were generated from seepage waters and compared directly to groundwater counterparts. The estimated average genome sizes of members of major phyla Proteobacteria, Bacteroidota and Cand. Patescibacteria (Candidate Phyla Radiation - CPR bacteria) were significantly higher in soil-seepage water as compared to their groundwater counterparts. Seepage water Parcubacteria (Paceibacteria) exhibited 1.18-fold greater mean genome size and 2-fold lower mean proportion of pseudogenes than those in groundwater. Bacteroidota and Proteobacteria also showed a similar trend of reduced genomes in groundwater compared to seepage. While exploring gene loss and adaptive gains in closely related CPR lineages in groundwater, we identified a membrane protein, and a lipoglycopeptide resistance gene unique to a seepage Parcubacterium genome. A nitrite reductase gene was also identified and was unique to the groundwater Parcubacteria genomes, likely acquired from other planktonic microbes via horizontal gene transfer.<br><br>CONCLUSIONS: Overall, our data suggest that bacteria in seepage waters, including ultra-small Parcubacteria, have significantly larger genomes and higher metabolic enrichment than their groundwater counterparts, highlighting possible genome streamlining of the latter in response to habitat selection in an oligotrophic environment.},
}
@article {pmid38901473,
year = {2024},
author = {Walt, HK and Ahn, SJ and Hoffmann, FG},
title = {Horizontally transferred glycoside hydrolase 26 may aid hemipteran insects in plant tissue digestion.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108134},
doi = {10.1016/j.ympev.2024.108134},
pmid = {38901473},
issn = {1095-9513},
abstract = {Glycoside hydrolases are enzymes that break down complex carbohydrates into simple sugars by catalyzing the hydrolysis of glycosidic bonds. There have been multiple instances of adaptive horizontal gene transfer of genes belonging to various glycoside hydrolase families from microbes to insects, as glycoside hydrolases can metabolize constituents of the carbohydrate-rich plant cell wall. In this study, we characterize the horizontal transfer of a gene from the glycoside hydrolase family 26 (GH26) from bacteria to insects of the order Hemiptera. Our phylogenies trace the horizontal gene transfer to the common ancestor of the superfamilies Pentatomoidea and Lygaeoidea, which include stink bugs and seed bugs. After horizontal transfer, the gene was assimilated into the insect genome as indicated by the gain of an intron, and a eukaryotic signal peptide. Subsequently, the gene has undergone independent losses and expansions in copy number in multiple lineages, suggesting an adaptive role of GH26s in some insects. Finally, we measured tissue-level gene expression of multiple stink bugs and the large milkweed bug using publicly available RNA-seq datasets. We found that the GH26 genes are highly expressed in tissues associated with plant digestion, especially in the principal salivary glands of the stink bugs. Our results are consistent with the hypothesis that this horizontally transferred GH26 was co-opted by the insect to aid in plant tissue digestion and that this HGT event was likely adaptive.},
}
@article {pmid38896653,
year = {2024},
author = {Elliott, JFK and McLeod, DV and Taylor, TB and Westra, ER and Gandon, S and Watson, BNJ},
title = {Conditions for the spread of CRISPR-Cas immune systems into bacterial populations.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae108},
pmid = {38896653},
issn = {1751-7370},
abstract = {Bacteria contain a wide variety of innate and adaptive immune systems which provide protection to the host against invading genetic material, including bacteriophages (phages). It is becoming increasingly clear that bacterial immune systems are frequently lost and gained through horizontal gene transfer (HGT). However, how and when new immune systems can become established in a bacterial population has remained largely unstudied. We developed a joint epidemiological and evolutionary model that predicts the conditions necessary for the spread of a CRISPR-Cas immune system into a bacterial population lacking this system. We find that whether bacteria carrying CRISPR-Cas will spread (increase in frequency) into a bacterial population depends on the abundance of phages and the difference in the frequency of phage resistance mechanisms between bacteria carrying a CRISPR-Cas immune system, and those not (denoted as ${f}
_{\Delta }
$). Specifically, the abundance of cells carrying CRISPR-Cas will increase if there is a higher proportion of phage resistance (either via CRISPR-Cas immunity or surface modification) in the CRISPR-Cas possessing population than in the cells lacking CRISPR-Cas. We experimentally validated these predictions using Pseudomonas aeruginosa PA14 and phage DMS3vir as a model. Specifically, by varying the initial ratios of different strains of bacteria that carry alternative forms of phage resistance we confirmed that the spread of cells carrying CRISPR-Cas through a population can be predicted based on phage density and the relative frequency of resistance phenotypes. Understanding which conditions promote the spread of CRISPR-Cas systems helps to predict when and where these defences can establish in bacterial populations after a horizontal gene transfer event, both in ecological and clinical contexts.},
}
@article {pmid38896471,
year = {2024},
author = {Lerminiaux, N and Mitchell, R and Katz, K and Fakharuddin, K and McGill, E and Mataseje, L},
title = {Plasmid genomic epidemiology of carbapenem-hydrolysing class D β-lactamase (CDHL)-producing Enterobacterales in Canada, 2010-2021.},
journal = {Microbial genomics},
volume = {10},
number = {6},
pages = {},
doi = {10.1099/mgen.0.001257},
pmid = {38896471},
issn = {2057-5858},
mesh = {*beta-Lactamases/genetics ; *Plasmids/genetics ; Canada/epidemiology ; Humans ; *Carbapenems/pharmacology ; *Whole Genome Sequencing ; *Bacterial Proteins/genetics ; *Enterobacteriaceae Infections/microbiology/epidemiology ; Enterobacteriaceae/genetics/drug effects/classification ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Cross Infection/microbiology/epidemiology ; },
abstract = {Carbapenems are last-resort antibiotics for treatment of infections caused by multidrug-resistant Enterobacterales, but carbapenem resistance is a rising global threat due to the acquisition of carbapenemase genes. Oxacillinase-48 (bla OXA-48)-type carbapenemases are increasing in abundance in Canada and elsewhere; these genes are frequently found on mobile genetic elements and are associated with specific transposons. This means that alongside clonal dissemination, bla OXA-48-type genes can spread through plasmid-mediated horizontal gene transfer. We applied whole genome sequencing to characterize 249 bla OXA-48-type-producing Enterobacterales isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short- and long-read sequencing, we obtained 70 complete and circular bla OXA-48-type-encoding plasmids. Using MOB-suite, four major plasmids clustered were identified, and we further estimated a plasmid cluster for 91.9 % (147/160) of incomplete bla OXA-48-type-encoding contigs. We identified different patterns of carbapenemase mobilization across Canada, including horizontal transmission of bla OXA-181/IncX3 plasmids (75/249, 30.1 %) and bla OXA-48/IncL/M plasmids (47/249, 18.9 %), and both horizontal transmission and clonal transmission of bla OXA-232 for Klebsiella pneumoniae ST231 on ColE2-type/ColKP3 plasmids (25/249, 10.0 %). Our findings highlight the diversity of OXA-48-type plasmids and indicate that multiple plasmid clusters and clonal transmission have contributed to bla OXA-48-type spread and persistence in Canada.},
}
@article {pmid38896033,
year = {2024},
author = {Huang, B and Xiao, Y and Zhang, Y},
title = {Asgard archaeal selenoproteome reveals a roadmap for the archaea-to-eukaryote transition of selenocysteine incorporation machinery.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae111},
pmid = {38896033},
issn = {1751-7370},
abstract = {Selenocysteine (Sec) is encoded by the UGA codon that normally functions as a stop signal and is specifically incorporated into selenoproteins via a unique recoding mechanism. The translational recoding of UGA as Sec is directed by an unusual RNA structure, the Sec insertion sequence (SECIS) element. Although archaea and eukaryotes adopt a similar Sec encoding machinery, the SECIS elements have no similarities to each other with regard to sequence and structure. We analyzed more than 400 Asgard archaeal genomes to examine the occurrence of both Sec encoding system and selenoproteins in this archaeal superphylum, the closest prokaryotic relatives of eukaryotes. A comprehensive map of Sec utilization trait has been generated, providing the most detailed understanding of the use of this nonstandard amino acid in Asgard archaea so far. By characterizing the selenoproteomes of all organisms, several selenoprotein-rich phyla and species were identified. Most Asgard archaeal selenoprotein genes possess eukaryotic SECIS-like structures with varying degrees of diversity. Moreover, euryarchaeal SECIS elements might originate from Asgard archaeal SECIS elements via lateral gene transfer, indicating a complex and dynamic scenario of the evolution of SECIS element within archaea. Finally, a roadmap for the transition of eukaryotic SECIS elements from archaea was proposed, and selenophosphate synthetase may serve as a potential intermediate for the generation of ancestral eukaryotic SECIS element. Our results offer new insights into a deeper understanding of the evolution of Sec insertion machinery.},
}
@article {pmid38895488,
year = {2024},
author = {Ellison, TJ and Ellison, CK},
title = {DNA binding is rate-limiting for natural transformation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.06.06.597730},
pmid = {38895488},
abstract = {UNLABELLED: Bacteria take up environmental DNA using dynamic appendages called type IV pili (T4P) to elicit horizontal gene transfer in a process called natural transformation. Natural transformation is widespread amongst bacteria yet determining how different factors universally contribute to or limit this process across species has remained challenging. Here we show that Acinetobacter baylyi , the most naturally transformable species, is highly transformable due to its ability to robustly bind nonspecific DNA via a dedicated orphan minor pilin, FimT. We show that, compared to its homologues, A. baylyi FimT contains multiple positively charged residues that additively promote DNA binding efficiency. Expression of A. baylyi FimT in a closely related Acinetobacter pathogen is sufficient to substantially improve its capacity for natural transformation, demonstrating that T4P-DNA binding is a rate-limiting step in this process. These results demonstrate the importance of T4P-DNA binding efficiency in driving natural transformation, establishing a key factor limiting horizontal gene transfer.<br><br>IMPORTANCE: Natural transformation is a multi-step, broadly conserved mechanism for horizontal gene transfer in which bacteria take up exogenous DNA from the environment and integrate it into their genome by homologous recombination. A complete picture of the factors that limit this behavior remain unclear due to variability between bacterial systems. In this manuscript, we provide clear and direct evidence that DNA binding by type IV pili prior to DNA uptake is a rate-limiting step of natural transformation. We show that increasing DNA binding in antibiotic resistant Acinetobacter pathogens can boost their transformation rates by 100-fold. In addition to expanding our understanding of the factors that limit transformation in the environment, these results will also contribute to a deeper understanding of the spread of antibiotic resistance genes in relevant human pathogens.},
}
@article {pmid38895369,
year = {2024},
author = {Klein, JA and Predeus, AV and Greissl, AR and Clark-Herrera, MM and Cruz, E and Cundiff, JA and Haeberle, AL and Howell, M and Lele, A and Robinson, DJ and Westerman, TL and Wrande, M and Wright, SJ and Green, NM and Vallance, BA and McClelland, M and Mejia, A and Goodman, AG and Elfenbein, JR and Knodler, LA},
title = {Pathogenic diversification of the gut commensal Providencia alcalifaciens via acquisition of a second type III secretion system.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.06.07.595826},
pmid = {38895369},
abstract = {Providencia alcalifaciens is a Gram-negative bacterium found in a wide variety of water and land environments and organisms. It has been isolated as part of the gut microbiome of animals and insects, as well as from stool samples of patients with diarrhea. Specific P. alcalifaciens strains encode gene homologs of virulence factors found in other pathogenic members of the same Enterobacterales order, such as Salmonella enterica serovar Typhimurium and Shigella flexneri. Whether these genes are also pathogenic determinants in P. alcalifaciens is not known. Here we have used P. alcalifaciens 205/92, a clinical isolate, with in vitro and in vivo infection models to investigate P. alcalifaciens -host interactions at the cellular level. Our particular focus was the role of two type III secretion systems (T3SS) belonging to the Inv-Mxi/Spa family. T3SS 1b is widespread in Providencia spp. and encoded on the chromosome. T3SS 1a is encoded on a large plasmid that is present in a subset of P. alcalifaciens strains, which are primarily isolates from diarrheal patients. Using a combination of electron and fluorescence microscopy and gentamicin protection assays we show that P. alcalifaciens 205/92 is internalized into eukaryotic cells, rapidly lyses its internalization vacuole and proliferates in the cytosol. This triggers caspase-4 dependent inflammasome responses in gut epithelial cells. The requirement for the T3SS 1a in entry, vacuole lysis and cytosolic proliferation is host-cell type specific, playing a more prominent role in human intestinal epithelial cells as compared to macrophages. In a bovine ligated intestinal loop model, P. alcalifaciens colonizes the intestinal mucosa, inducing mild epithelial damage with negligible fluid accumulation. No overt role for T3SS 1a or T3SS 1b was seen in the calf infection model. However, T3SS 1b was required for the rapid killing of Drosophila melanogaster . We propose that the acquisition of two T3SS by horizontal gene transfer has allowed P. alcalifaciens to diversify its host range, from a highly virulent pathogen of insects to an opportunistic gastrointestinal pathogen of animals.},
}
@article {pmid38891015,
year = {2024},
author = {Zhou, H and Lu, Z and Liu, X and Bie, X and Xue, F and Tang, S and Feng, Q and Cheng, Y and Yang, J},
title = {Environmentally Relevant Concentrations of Tetracycline Promote Horizontal Transfer of Antimicrobial Resistance Genes via Plasmid-Mediated Conjugation.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
pmid = {38891015},
issn = {2304-8158},
support = {32272295//National Natural Science Foundation of China/ ; BE2022684//Jiangsu Provincial Key Research and Development Program/ ; KJ2024017//the Science and Technology Project of Jiangsu Provincial Administration for Market Regulation/ ; },
abstract = {The ubiquitous presence of antimicrobial-resistant organisms and antimicrobial resistance genes (ARGs) constitutes a major threat to global public safety. Tetracycline (TET) is a common antimicrobial agent that inhibits bacterial growth and is frequently detected in aquatic environments. Although TET may display coselection for resistance, limited knowledge is available on whether and how it might influence plasmid-mediated conjugation. Subinhibitory concentrations (3.9-250 ng/mL) of TET promoted horizontal gene transfer (HGT) via the mobilizable plasmid pVP52-1 from the donor Vibrio parahaemolyticus NJIFDCVp52 to the recipient Escherichia coli EC600 by 1.47- to 3.19-fold. The transcription levels of tetracycline resistance genes [tetA, tetR(A)], conjugation-related genes (traA, traD), outer membrane protein genes (ompA, ompK, ompV), reactive oxygen species (ROS)-related genes (oxyR, rpoS), autoinducer-2 (AI-2) synthesis gene (luxS), and SOS-related genes (lexA, recA) in the donor and recipient were significantly increased. Furthermore, the overproduced intracellular ROS generation and increased cell membrane permeability under TET exposure stimulated the conjugative transfer of ARGs. Overall, this study provides important insights into the contributions of TET to the spread of antimicrobial resistance.},
}
@article {pmid38888367,
year = {2024},
author = {Li, X and Gallardo, O and August, E and Dassa, B and Court, DL and Stavans, J and Arbel-Goren, R},
title = {Stability and gene strand bias of lambda prophages and chromosome organization in Escherichia coli.},
journal = {mBio},
volume = {},
number = {},
pages = {e0207823},
doi = {10.1128/mbio.02078-23},
pmid = {38888367},
issn = {2150-7511},
abstract = {Temperate phage-mediated horizontal gene transfer is a potent driver of genetic diversity in the evolution of bacteria. Most lambdoid prophages in Escherichia coli are integrated into the chromosome with the same orientation with respect to the direction of chromosomal replication, and their location on the chromosome is far from homogeneous. To better understand these features, we studied the interplay between lysogenic and lytic states of phage lambda in both native and inverted integration orientations at the wild-type integration site as well as at other sites on the bacterial chromosome. Measurements of free phage released by spontaneous induction showed that the stability of lysogenic states is affected by location and orientation along the chromosome, with stronger effects near the origin of replication. Competition experiments and range expansions between lysogenic strains with opposite orientations and insertion loci indicated that there are no major differences in growth. Moreover, measurements of the level of transcriptional bursts of the cI gene coding for the lambda phage repressor using single-molecule fluorescence in situ hybridization resulted in similar levels of transcription for both orientations and prophage location. We postulate that the preference for a given orientation and location is a result of a balance between the maintenance of lysogeny and the ability to lyse.IMPORTANCEThe integration of genetic material of temperate bacterial viruses (phages) into the chromosomes of bacteria is a potent evolutionary force, allowing bacteria to acquire in one stroke new traits and restructure the information in their chromosomes. Puzzlingly, this genetic material is preferentially integrated in a particular orientation and at non-random sites on the bacterial chromosome. The work described here reveals that the interplay between the maintenance of the stability of the integrated phage, its ability to excise, and its localization along the chromosome plays a key role in setting chromosomal organization in Escherichia coli.},
}
@article {pmid38884912,
year = {2024},
author = {Libante, V and Dechêne-Tempier, M and Leblond-Bourget, N and Payot, S},
title = {Detection and Quantification of Conjugative Transfer of Mobile Genetic Elements Carrying Antibiotic Resistance Genes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2815},
number = {},
pages = {79-91},
pmid = {38884912},
issn = {1940-6029},
mesh = {*Conjugation, Genetic ; *Interspersed Repetitive Sequences/genetics ; Gene Transfer, Horizontal ; Streptococcus suis/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Polymerase Chain Reaction/methods ; Genes, Bacterial ; },
abstract = {Multidrug resistance, due to acquired antimicrobial resistance genes, is increasingly reported in the zoonotic pathogen Streptococcus suis. Most of these resistance genes are carried by chromosomal Mobile Genetic Elements (MGEs), in particular, Integrative and Conjugative Elements (ICEs) and Integrative and Mobilizable Elements (IMEs). ICEs and IMEs frequently form tandems or nested composite elements, which make their identification difficult. To evaluate their mobility, it is necessary to (i) select the suitable donor-recipient pairs for mating assays, (ii) do PCR excision tests to confirm that the genetic element is able to excise from the chromosome as a circular intermediate, and (iii) evaluate the transfer of the genetic element by conjugation by doing mating assays. In addition to a dissemination of resistance genes between S. suis strains, MGEs can lead to a spreading of resistance genes in the environment and toward pathogenic bacteria. This propagation had to be considered in a One Health perspective.},
}
@article {pmid38884260,
year = {2024},
author = {Wang, S and Jiang, Y and Che, L and Wang, RH and Li, SC},
title = {Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae515},
pmid = {38884260},
issn = {1362-4962},
support = {20220814183301001//Shenzhen Science and Technology Program/ ; 9667242//Applied Research/ ; 9440262//Hong Kong Innovation and Technology Fund/ ; },
abstract = {Horizontal gene transfer (HGT) phenomena pervade the gut microbiome and significantly impact human health. Yet, no current method can accurately identify complete HGT events, including the transferred sequence and the associated deletion and insertion breakpoints from shotgun metagenomic data. Here, we develop LocalHGT, which facilitates the reliable and swift detection of complete HGT events from shotgun metagenomic data, delivering an accuracy of 99.4%-verified by Nanopore data-across 200 gut microbiome samples, and achieving an average F1 score of 0.99 on 100 simulated data. LocalHGT enables a systematic characterization of HGT events within the human gut microbiome across 2098 samples, revealing that multiple recipient genome sites can become targets of a transferred sequence, microhomology is enriched in HGT breakpoint junctions (P-value = 3.3e-58), and HGTs can function as host-specific fingerprints indicated by the significantly higher HGT similarity of intra-personal temporal samples than inter-personal samples (P-value = 4.3e-303). Crucially, HGTs showed potential contributions to colorectal cancer (CRC) and acute diarrhoea, as evidenced by the enrichment of the butyrate metabolism pathway (P-value = 3.8e-17) and the shigellosis pathway (P-value = 5.9e-13) in the respective associated HGTs. Furthermore, differential HGTs demonstrated promise as biomarkers for predicting various diseases. Integrating HGTs into a CRC prediction model achieved an AUC of 0.87.},
}
@article {pmid38882494,
year = {2024},
author = {Xu, X and Feng, Q and Zhang, T and Gao, Y and Cheng, Q and Zhang, W and Wu, Q and Xu, K and Li, Y and Nguyen, N and Taft, DH and Mills, DA and Lemay, DG and Zhu, W and Mao, S and Zhang, A and Xu, K and Liu, J},
title = {Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life.},
journal = {iMeta},
volume = {3},
number = {2},
pages = {e169},
pmid = {38882494},
issn = {2770-596X},
abstract = {The infant gut microbiome is increasingly recognized as a reservoir of antibiotic resistance genes, yet the assembly of gut resistome in infants and its influencing factors remain largely unknown. We characterized resistome in 4132 metagenomes from 963 infants in six countries and 4285 resistance genes were observed. The inherent resistome pattern of healthy infants (N = 272) could be distinguished by two stages: a multicompound resistance phase (Months 0-7) and a tetracycline-mupirocin-β-lactam-dominant phase (Months 8-14). Microbial taxonomy explained 40.7% of the gut resistome of healthy infants, with Escherichia (25.5%) harboring the most resistance genes. In a further analysis with all available infants (N = 963), we found age was the strongest influencer on the resistome and was negatively correlated with the overall resistance during the first 3 years (p < 0.001). Using a random-forest approach, a set of 34 resistance genes could be used to predict age (R [2] = 68.0%). Leveraging microbial host inference analyses, we inferred the age-dependent assembly of infant resistome was a result of shifts in the gut microbiome, primarily driven by changes in taxa that disproportionately harbor resistance genes across taxa (e.g., Escherichia coli more frequently harbored resistance genes than other taxa). We performed metagenomic functional profiling and metagenomic assembled genome analyses whose results indicate that the development of gut resistome was driven by changes in microbial carbohydrate metabolism, with an increasing need for carbohydrate-active enzymes from Bacteroidota and a decreasing need for Pseudomonadota during infancy. Importantly, we observed increased acquired resistance genes over time, which was related to increased horizontal gene transfer in the developing infant gut microbiome. In summary, infant age was negatively correlated with antimicrobial resistance gene levels, reflecting a composition shift in the gut microbiome, likely driven by the changing need for microbial carbohydrate metabolism during early life.},
}
@article {pmid38880617,
year = {2024},
author = {Miyoshi, SI and Amako, K and Muraoka, M and Morinaga, H and Ueba, S},
title = {Mobile genetic elements associated with utilization of dichloromethane and methanol as energy sources in Cupriavidus metallidurans.},
journal = {Journal of microorganism control},
volume = {29},
number = {2},
pages = {55-65},
doi = {10.4265/jmc.29.2_55},
pmid = {38880617},
issn = {2758-6391},
mesh = {*Methanol/metabolism ; *Cupriavidus/genetics/metabolism/drug effects ; *Methylene Chloride/metabolism ; *Interspersed Repetitive Sequences/genetics ; Energy Metabolism/drug effects/genetics ; Genome, Bacterial/genetics ; Gene Transfer, Horizontal ; },
abstract = {Cupriavidus metallidurans strain PD11 isolated from laboratory waste drainage can use C1 compounds, such as dichloromethane (DCM) and methanol, as a sole carbon and energy source. However, strain CH34 (a type-strain) cannot grow in the medium supplemented with DCM. In the present study, we aimed to unravel the genetic elements underlying the utilization of C1 compounds by strain PD11. The genome subtraction approach indicated that only strain PD11 had several genes highly homologous to those of Herminiimonas arsenicoxydans strain ULPAs1. Moreover, a series of polymerase chain reaction (PCR) to detect the orthologs of H. arsenicoxydans genes and the comparative study of the genomes of three strains revealed that the 87.9 kb DNA fragment corresponding to HEAR1959 to HEAR2054 might be horizontally transferred to strain PD11. The 87.9 kb DNA fragment identified was found to contain three genes whose products were putatively involved in the metabolism of formaldehyde, a common intermediate of DCM and methanol. In addition, reverse transcription PCR analysis showed that all three genes were significantly expressed when strain PD11 was cultivated in the presence of DCM or methanol. These findings suggest that strain PD11 can effectively utilize the C1 compounds because of transfer of the mobile genetic elements from other bacterial species, for instance, from H. arsenicoxydans.},
}
@article {pmid38880337,
year = {2024},
author = {Sugimoto, TN and Jouraku, A and Mitsuhashi, W},
title = {Search for genes gained by horizontal gene transfer in an entomopoxvirus, with special reference to the analysis of the transfer of an ABC transporter gene.},
journal = {Virus research},
volume = {},
number = {},
pages = {199418},
doi = {10.1016/j.virusres.2024.199418},
pmid = {38880337},
issn = {1872-7492},
abstract = {Although it is generally believed that large DNA viruses capture genes by horizontal gene transfer (HGT), the detailed manner of such transfer has not been fully elucidated. Here, we searched for genes in the coleopteran entomopoxvirus (EV) Anomala cuprea entomopoxvirus (ACEV) that might have been gained by HGT. We classified the potential source organisms for HGT into three categories: the host A. cuprea; other organisms, including viruses unrelated to EVs; and organisms with uncertain host attribution. Of the open reading frames (ORFs) of the ACEV genome, 2.1% were suggested to have been gained from the host by ACEV or its recent ancestor via HGT; 8.7% were possibly from organisms other than the host, and 3.7% were possibly from the third category of organisms via HGT. The analysis showed that ACEV contains some interesting ORFs obtained by HGT, including a large ATP-binding cassette protein (ABC transporter) ORF and a tenascin ORF (IDs ACV025 and ACV123, respectively). We then performed a detailed analysis of the HGT of the ACEV large ABC transporter ORF-the largest of the ACEV ORFs. mRNA sequences obtained by RNA-seq from fat bodies-sites of ACEV replication-and midgut tissues-sites of initial infection-of the virus's host A. cuprea larvae were subjected to BLAST analysis. One type of ABC transporter ORF from the fat bodies and two types from the midgut tissues, one of which was identical to that in the fat bodies, had the greatest identity to the ABC transporter ORF of ACEV. The two types from the host had high levels of identity to each other (approximately 95% nucleotide sequence identity), strongly suggesting that the host ABC transporter group consisting of the two types was the origin of ACV025. We then determined the sequence (12,381 bp) containing a full-length gene of the A. cuprea ABC transporter. It turned out to be a transcription template for the abovementioned mRNA found in both tissues. In addition, we determined a large part (ca. 6.9 kb) of the template sequence for the mRNA found only in the midgut tissues. The results showed that the ACEV ABC transporter ORF is missing parts corresponding to introns of the host ABC transporter genes, indicating that the ORF was likely acquired by HGT in the form of mRNA. The presence of definite duplicated sequences adjacent to the ACEV ABC transporter genes-a sign of LINE-1 retrotransposon-mediated HGT-was not observed. An approximately 2-month ACV025 transcription experiment suggested that the transporter sequence is presumed to be continuously functional. The amino acid sequence of ACV025 suggests that its product might function in the regulation of phosphatide in the host-cell membranes.},
}
@article {pmid38878503,
year = {2024},
author = {Hu, Q and Zhang, L and Yang, R and Tang, J and Dong, G},
title = {Quaternary ammonium biocides promote conjugative transfer of antibiotic resistance gene in structure- and species-dependent manner.},
journal = {Environment international},
volume = {189},
number = {},
pages = {108812},
doi = {10.1016/j.envint.2024.108812},
pmid = {38878503},
issn = {1873-6750},
mesh = {*Disinfectants/pharmacology ; *Quaternary Ammonium Compounds/pharmacology ; *Escherichia coli/drug effects/genetics ; *Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; },
abstract = {The linkage between biocides and antibiotic resistance has been widely suggested in laboratories and various environments. However, the action mechanism of biocides on antibiotic resistance genes (ARGs) spread is still unclear. Thus, 6 quaternary ammonium biocides (QACs) with different bonded substituents or alkyl chain lengths were selected to assess their effects on the conjugation transfer of ARGs in this study. Two conjugation models with the same donor (E. coli DH5α (RP4)) into two receptors, E. coli MG1655 and pathogenic S. sonnei SE6-1, were constructed. All QACs were found to significantly promote intra- and inter-genus conjugative transfer of ARGs, and the frequency was highly impacted by their structure and receptors. At the same environmental exposure level (4 × 10[-1] mg/L), didecyl dimethyl ammonium chloride (DDAC (C10)) promoted the most frequency of conjugative transfer, while benzathine chloride (BEC) promoted the least. With the same donor, the enhanced frequency of QACs of intra-transfer is higher than inter-transfer. Then, the acquisition mechanisms of two receptors were further determined using biochemical combined with transcriptome analysis. For the recipient E. coli, the promotion of the intragenus conjugative transfer may be associated with increased cell membrane permeability, reactive oxygen species (ROS) production and proton motive force (PMF)-induced enhancement of flagellar motility. Whereas, the increase of cell membrane permeability and decreased flagellar motility due to PMF disruption but encouraged biofilm formation, maybe the main reasons for promoting intergenus conjugative transfer in the recipient S. sonnei. As one pathogenic bacterium, S. sonnei was first found to acquire ARGs by biocide exposure.},
}
@article {pmid38878444,
year = {2024},
author = {Li, W and Zeng, J and Zheng, N and Ge, C and Li, Y and Yao, H},
title = {Polyvinyl chloride microplastics in the aquatic environment enrich potential pathogenic bacteria and spread antibiotic resistance genes in the fish gut.},
journal = {Journal of hazardous materials},
volume = {475},
number = {},
pages = {134817},
doi = {10.1016/j.jhazmat.2024.134817},
pmid = {38878444},
issn = {1873-3336},
abstract = {Microplastics and antibiotics coexist in aquatic environments, especially in freshwater aquaculture areas. However, as the second largest production of polyvinyl chloride (PVC) in the world, the effects of co-exposure to microplastics particles and antibiotics on changes in antibiotic resistance gene (ARG) profiles and the microbial community structure of aquatic organism gut microorganisms are poorly understood. Therefore, in this study, carp (Cyprinus carpio) were exposed to single or combined PVC microplastic contamination and oxytetracycline (OTC) or sulfamethazine (SMZ) for 8 weeks. PVC microplastics can enrich potential pathogenic bacteria, such as Enterobacter and Acinetobacter, among intestinal microorganisms. The presence of PVC microplastics enhanced the selective enrichment and dissemination risk of ARGs. PVC microplastics combined with OTC (OPVC) treatment significantly increased the abundance of tetracycline resistance genes (1.40-fold) compared with that in the OTC exposure treatment, revealing an obvious co-selection effect. However, compared with those in the control group, the total abundance of ARGs and MGEs in the OPVC treatment groups were significantly lower, which was correlated with the reduced abundances of the potential host Enterobacter. Overall, our results emphasized the diffusion and spread of ARGs are more influenced by PVC microplastics than by antibiotics, which may lead to antibiotic resistance in aquaculture.},
}
@article {pmid38878442,
year = {2024},
author = {Ma, Y and Xu, S and Huang, Y and Du, J and Wang, J and Gao, B and Song, J and Ma, S and Jia, H and Zhan, S},
title = {The mechanism differences between sulfadiazine degradation and antibiotic resistant bacteria inactivation by iron-based graphitic biochar and peroxydisulfate system.},
journal = {Journal of hazardous materials},
volume = {475},
number = {},
pages = {134907},
doi = {10.1016/j.jhazmat.2024.134907},
pmid = {38878442},
issn = {1873-3336},
abstract = {In this study, the activation of peroxydisulfate (PS) by K2FeO4-activation biochar (KFeB) and acid-picking K2FeO4-activation biochar (AKFeB) was investigated to reveal the mechanism differences between iron site and graphitic structure in sulfadiazine (SDZ) degradation and ARB inactivation, respectively. KFeB/PS and AKFeB/PS systems had similar degradation property towards SDZ, but only KFeB/PS system showed excellent bactericidal property. The mechanism study demonstrated that dissolved SDZ was degraded through electron transfer pathway mediated by graphitic structure, while suspended ARB was inactivated through free radicals generated by iron-activated PS, accompanied by excellent removal on antibiotic resistance genes (ARGs). The significant decrease in conjugative transfer frequency indicated the reduced horizontal gene transfer risk of ARGs after treatment with KFeB/PS system. Transcriptome data suggested that membrane protein channel disruption and adenosine triphosphate synthesis inhibition were key reasons for conjugative transfer frequency reduction. Continuous flow reactor of KFeB/PS system can efficiently remove antibiotics and ARB, implying the potential application in practical wastewater purification. In conclusion, this study provides novel insights for classified and collaborative control of antibiotics and ARB by carbon-based catalysts driven persulfate advanced oxidation technology.},
}
@article {pmid38878434,
year = {2024},
author = {Chen, MM and Zhang, YQ and Cheng, LC and Zhao, FJ and Wang, P},
title = {Photoaged nanoplastics with multienzyme-like activities significantly shape the horizontal transfer of antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {475},
number = {},
pages = {134884},
doi = {10.1016/j.jhazmat.2024.134884},
pmid = {38878434},
issn = {1873-3336},
abstract = {Nanoplastics (NPs), identified as emerging pollutants, pose a great risk to environment and global public health, exerting profound influences on the prevalence and dissemination of antibiotic resistance genes (ARGs). Despite evidence suggesting that nano-sized plastic particles can facilitate the horizontal gene transfer (HGT) of ARGs, it is imperative to explore strategies for inhibiting the transfer of ARGs. Currently, limited information exists regarding the characteristics of environmentally aged NPs and their impact on ARGs propagation. Herein, we investigated the impact of photo-aged NPs on the transfer of ARG-carrying plasmids into Escherichia coli (E. coli) cells. Following simulated sunlight irradiation, photo-aged nano-sized polystyrene plastics (PS NPs) exhibited multiple enzyme-like activities, including peroxidase (POD) and oxidase (OXD), leading to a burst of reactive oxygen species (ROS). At relatively low concentrations (0.1, 1 μg/mL), both pristine and aged PS NPs facilitated the transfer of pUC19 and pHSG396 plasmids within E. coli due to moderate ROS production and enhanced cell membrane permeability. Intriguingly, at relatively high concentrations (5, 10 μg/mL), aged PS NPs significantly suppressed plasmids transformation. The non-unidirectional impact of aged PS NPs involved the overproduction of ROS (•OH and •O2[-]) via nanozyme activity, directly degrading ARGs and damaging plasmid structure. Additionally, oxidative damage to bacteria resulted from the presence of much toxic free radicals, causing physical damage to cell membranes, reduction of the SOS response and restriction of adenosine-triphosphate (ATP) supply, ultimately leading to inactivation of recipient cells. This study unveils the intrinsic multienzyme-like activity of environmentally aged NPs, highlighting their potential to impede the transfer and dissemination of ARGs.},
}
@article {pmid38878274,
year = {2024},
author = {Vidal-Quist, JC and Ortego, F and Rombauts, S and Hernández-Crespo, P},
title = {The genome-wide response of Dermatophagoides pteronyssinus to cystatin A, a peptidase inhibitor from human skin, sheds light on its digestive physiology and allergenicity.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.12931},
pmid = {38878274},
issn = {1365-2583},
abstract = {The digestive physiology of house dust mites (HDMs) is particularly relevant for their allergenicity since many of their allergens participate in digestion and are excreted into faecal pellets, a main source of exposure for allergic subjects. To gain insight into the mite dietary digestion, the genome of the HDM Dermatophagoides pteronyssinus was screened for genes encoding peptidases (n = 320), glycosylases (n = 77), lipases and esterases (n = 320), peptidase inhibitors (n = 65) and allergen-related proteins (n = 52). Basal gene expression and transcriptional responses of mites to dietary cystatin A, a cysteine endopeptidase inhibitor with previously shown antinutritional effect on mites, were analysed by RNAseq. The ingestion of cystatin A resulted in significant regulation of different cysteine endopeptidase and glycosylase genes. One Der p 1-like and two cathepsin B-like cysteine endopeptidase genes of high basal expression were induced, which suggests their prominent role in proteolytic digestion together with major allergen Der p 1. A number of genes putatively participating in the interaction of mites with their microbiota and acquired by horizontal gene transfer were repressed, including genes encoding the peptidase Der p 38, two 1,3-beta-glucanases, a lysozyme and a GH19 chitinase. Finally, the disruption of mite digestion resulted in the regulation of up to 17 allergen and isoallergen genes. Altogether, our results shed light on the putative role of specific genes in digestion and illustrate the connection between the digestive physiology of HDM and allergy.},
}
@article {pmid38876022,
year = {2024},
author = {Sivalingam, P and Sabatino, R and Sbaffi, T and Corno, G and Fontaneto, D and Borgomaneiro, G and Rogora, M and Crotti, E and Mapelli, F and Borin, S and Pilar, AL and Eckert, EM and Di Cesare, A},
title = {Anthropogenic pollution may enhance natural transformation in water, favouring the spread of antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {475},
number = {},
pages = {134885},
doi = {10.1016/j.jhazmat.2024.134885},
pmid = {38876022},
issn = {1873-3336},
abstract = {Aquatic ecosystems are crucial in the antimicrobial resistance cycle. While intracellular DNA has been extensively studied to understand human activity's impact on antimicrobial resistance gene (ARG) dissemination, extracellular DNA is frequently overlooked. This study examines the effect of anthropogenic water pollution on microbial community diversity, the resistome, and ARG dissemination. We analyzed intracellular and extracellular DNA from wastewater treatment plant effluents and lake surface water by shotgun sequencing. We also conducted experiments to evaluate anthropogenic pollution's effect on transforming extracellular DNA (using Gfp-plasmids carrying ARGs) within a natural microbial community. Chemical analysis showed treated wastewater had higher anthropogenic pollution-related parameters than lake water. The richness of microbial community, antimicrobial resistome, and high-risk ARGs was greater in treated wastewaters than in lake waters both for intracellular and extracellular DNA. Except for the high-risk ARGs, richness was significantly higher in intracellular than in extracellular DNA. Several ARGs were associated with mobile genetic elements and located on plasmids. Furthermore, Gfp-plasmid transformation within a natural microbial community was enhanced by anthropogenic pollution levels. Our findings underscore anthropogenic pollution's pivotal role in shaping microbial communities and their antimicrobial resistome. Additionally, it may facilitate ARG dissemination through extracellular DNA plasmid uptake.},
}
@article {pmid38871331,
year = {2024},
author = {Wang, X and Li, J and Pan, X},
title = {How micro-/nano-plastics influence the horizontal transfer of antibiotic resistance genes - A review.},
journal = {The Science of the total environment},
volume = {944},
number = {},
pages = {173881},
doi = {10.1016/j.scitotenv.2024.173881},
pmid = {38871331},
issn = {1879-1026},
abstract = {Plastic debris such as microplastics (MPs) and nanoplastics (NPTs), along with antibiotic resistance genes (ARGs), are pervasive in the environment and are recognized as significant global health and ecological concerns. Micro-/nano-plastics (MNPs) have been demonstrated to favor the spread of ARGs by enhancing the frequency of horizontal gene transfer (HGT) through various pathways. This paper comprehensively and systematically reviews the current study with focus on the influence of plastics on the HGT of ARGs. The critical role of MNPs in the HGT of ARGs has been well illustrated in sewage sludge, livestock farms, constructed wetlands and landfill leachate. A summary of the performed HGT assay and the underlying mechanism of plastic-mediated transfer of ARGs is presented in the paper. MNPs could facilitate or inhibit HGT of ARGs, and their effects depend on the type, size, and concentration. This review provides a comprehensive insight into the effects of MNPs on the HGT of ARGs, and offers suggestions for further study. Further research should attempt to develop a standard HGT assay and focus on investigating the impact of different plastics, including the oligomers they released, under real environmental conditions on the HGT of ARGs.},
}
@article {pmid38871190,
year = {2024},
author = {Skalny, M and Rokowska, A and Szuwarzynski, M and Gajewska, M and Dziewit, L and Bajda, T},
title = {Nanoscale surface defects of goethite governing DNA adsorption process and formation of the Goethite-DNA conjugates.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {142602},
doi = {10.1016/j.chemosphere.2024.142602},
pmid = {38871190},
issn = {1879-1298},
abstract = {In urbanized areas, extracellular DNA (exDNA) is suspected of carrying genes with undesirable traits like virulence genes (VGs) or antibiotic resistance genes (ARGs), which can spread through horizontal gene transfer (HGT). Hence, it is crucial to develop novel approaches for the mitigation of exDNA in the environment. Our research explores the role of goethite, a common iron mineral with high adsorption capabilities, in exDNA adsorption processes. We compare well-crystalline, semi-crystalline, and nano goethites with varying particle sizes to achieve various specific surface areas (SSAs) (18.7 - 161.6 m[2]/g) and porosities. We conducted batch adsorption experiments using DNA molecules of varying chain lengths (DNA sizes: < 11 Kb, < 6 Kb, and < 3 Kb) and assessed the impact of Ca[2+] and biomacromolecules on the adsorption efficacy and mechanisms. Results show that porosity and pore structure significantly influence DNA adsorption capacity. Goethite with well-developed meso- and macroporosity demonstrated enhanced DNA adsorption. The accumulation of DNA on the goethite interface led to substantial aggregation in the system, thus the formation of DNA-goethite conjugates, indicating the bridging between mineral particles. DNA chain length, the presence of Ca[2+], and the biomacromolecule matrix also affected the adsorption capacity and mechanism. Interactions between DNA and positively charged biomacromolecules or Ca[2+] led to DNA compaction, allowing greater DNA accumulation in pores. However, a high concentration of biomacromolecules led to the saturation of the goethite surface, inhibiting DNA adsorption. AFM imaging of goethite particles after adsorption suggested the formation of the DNA multilayer. The study advances understanding of the environmental behavior of exDNA and its interaction with iron oxyhydroxides, offering insights into developing more effective methods for ARGs removal in wastewater treatment plants. By manipulating the textural properties of goethite, it's possible to enhance exDNA removal, potentially reducing the spread of biocontamination in urban and industrial environments.},
}
@article {pmid38870897,
year = {2024},
author = {Kennedy, NW and Comstock, LE},
title = {Mechanisms of bacterial immunity, protection, and survival during interbacterial warfare.},
journal = {Cell host &amp; microbe},
volume = {32},
number = {6},
pages = {794-803},
doi = {10.1016/j.chom.2024.05.006},
pmid = {38870897},
issn = {1934-6069},
mesh = {*Bacteria/immunology/genetics ; *Bacterial Toxins/metabolism/immunology ; Gene Transfer, Horizontal ; Humans ; Microbial Viability ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/metabolism/genetics ; },
abstract = {Most bacteria live in communities, often with closely related strains and species with whom they must compete for space and resources. Consequently, bacteria have acquired or evolved mechanisms to antagonize competitors through the production of antibacterial toxins. Similar to bacterial systems that combat phage infection and mechanisms to thwart antibiotics, bacteria have also acquired and evolved features to protect themselves from antibacterial toxins. Just as there is a large body of research identifying and characterizing antibacterial proteins and toxin delivery systems, studies of bacterial mechanisms to resist and survive assault from competitors' weapons have also expanded tremendously. Emerging data are beginning to reveal protective processes and mechanisms that are as diverse as the toxins themselves. Protection against antibacterial toxins can be acquired by horizontal gene transfer, receptor or target alteration, induction of protective functions, physical barriers, and other diverse processes. Here, we review recent studies in this rapidly expanding field.},
}
@article {pmid38870889,
year = {2024},
author = {Zhang, P and Wang, Y and Lin, H and Liang, J and Wang, J and Bai, Y and Qu, J and Wang, A},
title = {Bacterial evolution in Biofiltration of drinking water treatment plant: Different response of phage and plasmid to varied water sources.},
journal = {Water research},
volume = {259},
number = {},
pages = {121887},
doi = {10.1016/j.watres.2024.121887},
pmid = {38870889},
issn = {1879-2448},
abstract = {Biofiltration in drinking water treatment (BDWT) are popular as it holds promise as an alternative to chemical treatments, yet our understanding of the key drivers and trends underlying bacterial evolution within this process remains limited. While plasmids and phages are recognized as the main vectors of horizontal gene transfer (HGT), their roles in shaping bacterial evolution in BDWT remain largely unknown. Here we leverage global metagenomic data to unravel the primary forces driving bacterial evolution in BDWT. Our results revealed that the primary vector of HGT varies depending on the type of source water (groundwater and surface water). Both plasmids and phages accelerated bacterial evolution in BDWT by enhancing genetic diversity within species, but they drove contrasting evolutionary trends in functional redundancy in different source water types. Specifically, trends towards and away from functional redundancy (indicated as gene-protein ratio) were observed in surface-water and groundwater biofilters, respectively. Virulent phages drove bacterial evolution through synergistic interactions with bacterial species capable of natural transformation and with certain natural compounds that disrupt bacterial cytoplasmic membranes. Genes relating to water purification (such as Mn(II)-oxidizing genes), microbial risks (antibiotic resistance genes), and chemical risk (polycyclic aromatic hydrocarbons) were enriched via HGT in BDWT, highlighting the necessity for heighted focus on these useful and risky objects. Overall, these discoveries enhance our understanding of bacterial evolution in BDWT and have implications for the optimization of water treatment strategies.},
}
@article {pmid38861577,
year = {2024},
author = {Elsen, S and Simon, V and Attrée, I},
title = {Cross-regulation and cross-talk of conserved and accessory two-component regulatory systems orchestrate Pseudomonas copper resistance.},
journal = {PLoS genetics},
volume = {20},
number = {6},
pages = {e1011325},
doi = {10.1371/journal.pgen.1011325},
pmid = {38861577},
issn = {1553-7404},
abstract = {Bacteria use diverse strategies and molecular machinery to maintain copper homeostasis and to cope with its toxic effects. Some genetic elements providing copper resistance are acquired by horizontal gene transfer; however, little is known about how they are controlled and integrated into the central regulatory network. Here, we studied two copper-responsive systems in a clinical isolate of Pseudomonas paraeruginosa and deciphered the regulatory and cross-regulation mechanisms. To do so, we combined mutagenesis, transcriptional fusion analyses and copper sensitivity phenotypes. Our results showed that the accessory CusRS two-component system (TCS) responds to copper and activates both its own expression and that of the adjacent nine-gene operon (the pcoA2 operon) to provide resistance to elevated levels of extracellular copper. The same locus was also found to be regulated by two core-genome-encoded TCSs-the copper-responsive CopRS and the zinc-responsive CzcRS. Although the target palindromic sequence-ATTCATnnATGTAAT-is the same for the three response regulators, transcriptional outcomes differ. Thus, depending on the operon/regulator pair, binding can result in different activation levels (from none to high), with the systems demonstrating considerable plasticity. Unexpectedly, although the classical CusRS and the noncanonical CopRS TCSs rely on distinct signaling mechanisms (kinase-based vs. phosphatase-based), we discovered cross-talk in the absence of the cognate sensory kinases. This cross-talk occurred between the proteins of these two otherwise independent systems. The cusRS-pcoA2 locus is part of an Integrative and Conjugative Element, and was found in other Pseudomonas strains where its expression could provide copper resistance under appropriate conditions. The results presented here illustrate how acquired genetic elements can become part of endogenous regulatory networks, providing a physiological advantage. They also highlight the potential for broader effects of accessory regulatory proteins through interference with core regulatory proteins.},
}
@article {pmid38853947,
year = {2024},
author = {Wendt, GR and Collins, JJ},
title = {Horizontal gene transfer of a functional cki homolog in the human pathogen Schistosoma mansoni.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38853947},
abstract = {Schistosomes are parasitic flatworms responsible for the neglected tropical disease schistosomiasis, causing devastating morbidity and mortality in the developing world. The parasites are protected by a skin-like tegument, and maintenance of this tegument is controlled by a schistosome ortholog of the tumor suppressor TP53. To understand mechanistically how p53-1 controls tegument production, we identified a cyclin dependent kinase inhibitor homolog (cki) that was co-expressed with p53-1. RNA interference of cki resulted in a hyperproliferation phenotype, that, in combination with p53-1 RNA interference yielded abundant tumor-like growths, indicating that cki and p53-1 are bona fide tumor suppressors in Schistosoma mansoni. Interestingly, cki homologs are widely present throughout parasitic flatworms but evidently absent from their free-living ancestors, suggesting this cki homolog came from an ancient horizontal gene transfer event. This in turn implies that the evolution of parasitism in flatworms may have been aided by a highly unusual means of metazoan genetic inheritance.},
}
@article {pmid38843310,
year = {2024},
author = {Coelho, MA and David-Palma, M and Shea, T and Bowers, K and McGinley-Smith, S and Mohammad, AW and Gnirke, A and Yurkov, AM and Nowrousian, M and Sun, S and Cuomo, CA and Heitman, J},
title = {Comparative genomics of the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis.},
journal = {PLoS biology},
volume = {22},
number = {6},
pages = {e3002682},
doi = {10.1371/journal.pbio.3002682},
pmid = {38843310},
issn = {1545-7885},
abstract = {In exploring the evolutionary trajectories of both pathogenesis and karyotype dynamics in fungi, we conducted a large-scale comparative genomic analysis spanning the Cryptococcus genus, encompassing both global human fungal pathogens and nonpathogenic species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species, covering virtually all known diversity within these genera. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at preadaptive pathogenic potential, our analysis found evidence of gene gain (via horizontal gene transfer) and gene loss in pathogenic Cryptococcus species, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the 2 genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5, or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion-fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus. Instead, Cryptococcus species with less than 14 chromosomes showed reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Overall, our findings advance our understanding of genetic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.},
}
@article {pmid38754416,
year = {2024},
author = {Benz, F and Camara-Wilpert, S and Russel, J and Wandera, KG and Čepaitė, R and Ares-Arroyo, M and Gomes-Filho, JV and Englert, F and Kuehn, JA and Gloor, S and Mestre, MR and Cuénod, A and Aguilà-Sans, M and Maccario, L and Egli, A and Randau, L and Pausch, P and Rocha, EPC and Beisel, CL and Madsen, JS and Bikard, D and Hall, AR and Sørensen, SJ and Pinilla-Redondo, R},
title = {Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans.},
journal = {Cell host &amp; microbe},
volume = {32},
number = {6},
pages = {875-886.e9},
doi = {10.1016/j.chom.2024.04.016},
pmid = {38754416},
issn = {1934-6069},
mesh = {*CRISPR-Cas Systems ; *Plasmids/genetics ; *Klebsiella pneumoniae/genetics ; *Conjugation, Genetic ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; Bacteriophages/genetics ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Plasmid-encoded type IV-A CRISPR-Cas systems lack an acquisition module, feature a DinG helicase instead of a nuclease, and form ribonucleoprotein complexes of unknown biological functions. Type IV-A3 systems are carried by conjugative plasmids that often harbor antibiotic-resistance genes and their CRISPR array contents suggest a role in mediating inter-plasmid conflicts, but this function remains unexplored. Here, we demonstrate that a plasmid-encoded type IV-A3 system co-opts the type I-E adaptation machinery from its host, Klebsiella pneumoniae (K. pneumoniae), to update its CRISPR array. Furthermore, we reveal that robust interference of conjugative plasmids and phages is elicited through CRISPR RNA-dependent transcriptional repression. By silencing plasmid core functions, type IV-A3 impacts the horizontal transfer and stability of targeted plasmids, supporting its role in plasmid competition. Our findings shed light on the mechanisms and ecological function of type IV-A3 systems and demonstrate their practical efficacy for countering antibiotic resistance in clinically relevant strains.},
}
@article {pmid38842312,
year = {2024},
author = {Klepa, MS and diCenzo, GC and Hungria, M},
title = {Comparative genomic analysis of Bradyrhizobium strains with natural variability in the efficiency of nitrogen fixation, competitiveness, and adaptation to stressful edaphoclimatic conditions.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0026024},
doi = {10.1128/spectrum.00260-24},
pmid = {38842312},
issn = {2165-0497},
abstract = {Bradyrhizobium is known for fixing atmospheric nitrogen in symbiosis with agronomically important crops. This study focused on two groups of strains, each containing eight natural variants of the parental strains, Bradyrhizobium japonicum SEMIA 586 (=CNPSo 17) or Bradyrhizobium diazoefficiens SEMIA 566 (=CNPSo 10). CNPSo 17 and CNPSo 10 were used as commercial inoculants for soybean crops in Brazil at the beginning of the crop expansion in the southern region in the 1960s-1970s. Variants derived from these parental strains were obtained in the late 1980s through a strain selection program aimed at identifying elite strains adapted to a new cropping frontier in the central-western Cerrado region, with a higher capacity of biological nitrogen fixation (BNF) and competitiveness. Here, we aimed to detect genetic variations possibly related to BNF, competitiveness for nodule occupancy, and adaptation to the stressful conditions of the Brazilian Cerrado soils. High-quality genome assemblies were produced for all strains. The core genome phylogeny revealed that strains of each group are closely related, as confirmed by high average nucleotide identity values. However, variants accumulated divergences resulting from horizontal gene transfer, genomic rearrangements, and nucleotide polymorphisms. The B. japonicum group presented a larger pangenome and a higher number of nucleotide polymorphisms than the B. diazoefficiens group, possibly due to its longer adaptation time to the Cerrado soil. Interestingly, five strains of the B. japonicum group carry two plasmids. The genetic variability found in both groups is discussed considering the observed differences in their BNF capacity, competitiveness for nodule occupancy, and environmental adaptation.IMPORTANCEToday, Brazil is a global leader in the study and use of biological nitrogen fixation with soybean crops. As Brazilian soils are naturally void of soybean-compatible bradyrhizobia, strain selection programs were established, starting with foreign isolates. Selection searched for adaptation to the local edaphoclimatic conditions, higher efficiency of nitrogen fixation, and strong competitiveness for nodule occupancy. We analyzed the genomes of two parental strains of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens and eight variant strains derived from each parental strain. We detected two plasmids in five strains and several genetic differences that might be related to adaptation to the stressful conditions of the soils of the Brazilian Cerrado biome. We also detected genetic variations in specific regions that may impact symbiotic nitrogen fixation. Our analysis contributes to new insights into the evolution of Bradyrhizobium, and some of the identified differences may be applied as genetic markers to assist strain selection programs.},
}
@article {pmid38839049,
year = {2024},
author = {Middlebrook, EA and Katani, R and Fair, JM},
title = {OrthoPhyl - Streamlining large scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkae119},
pmid = {38839049},
issn = {2160-1836},
abstract = {There are a staggering number of publicly available bacterial genome sequences (at writing, 2.0 million assemblies in NCBI's GenBank alone), and the deposition rate continues to increase. This wealth of data begs for phylogenetic analyses to place these sequences within an evolutionary context. A phylogenetic placement not only aids in taxonomic classification, but informs the evolution of novel phenotypes, targets of selection, and horizontal gene transfer. Building trees from multi-gene codon alignments is a laborious task that requires bioinformatic expertise, rigorous curation of orthologs, and heavy computation. Compounding the problem is the lack of tools that can streamline these processes for building trees from large scale genomic data. Here we present OrthoPhyl, which takes bacterial genome assemblies and reconstructs trees from whole genome codon alignments. The analysis pipeline can analyze an arbitrarily large number of input genomes (>1200 tested here) by identifying a diversity spanning subset of assemblies and using these genomes to build gene models to infer orthologs in the full dataset. To illustrate the versatility of OrthoPhyl, we show three use-cases: E. coli/Shigella, Brucella/Ochrobactrum, and the order Rickettsiales. We compare trees generated with OrthoPhyl to trees generated with kSNP3 and GToTree along with published trees using alternative methods. We show that OrthoPhyl trees are consistent with other methods while incorporating more data, allowing for greater numbers of input genomes, and more flexibility of analysis.},
}
@article {pmid38830804,
year = {2024},
author = {Amirfard, KD and Moriyama, M and Suzuki, S and Sano, D},
title = {Effect of environmental factors on conjugative transfer of antibiotic resistance genes in aquatic settings.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxae129},
pmid = {38830804},
issn = {1365-2672},
abstract = {Antimicrobial-resistance genes (ARGs) are spread among bacteria by horizontal gene transfer (HGT), however, the effect of environmental factors on the dynamics of the ARG in water environments has not been very well understood. In this systematic review, we employed the regression tree algorithm to identify the environmental factors that facilitate/inhibit the transfer of ARGs via conjugation in planktonic/biofilm-formed bacterial cells based on the results of past relevant research. Escherichia coli strains were the most studied genus for conjugation experiments as donor/recipient in the intra-genera category. Conversely, Pseudomonas spp., Acinetobacter spp., and Salmonella spp. were studied primarily as recipients across inter-genera bacteria. The conjugation efficiency (ce) was found to be highly dependent on the incubation period. Some antibiotics, such as nitrofurantoin (at ≥ 0.2 µg ml -1) and kanamycin (at ≥ 9.5 mg l -1) as well as metallic compounds like mercury (II) chloride (HgCl2, ≥ 3 µmol l -1), and vanadium (III) chloride (VCl3, ≥ 50 µmol l -1) had enhancing effect on conjugation. The highest ce value (-0.90 log10) was achieved at 15-19 °C, with linoleic acid concentrations < 8 mg l -1, a recognized conjugation inhibitor. Identifying critical environmental factors affecting ARG dissemination in aquatic environments will accelerate strategies to control their proliferation and combat antibiotic resistance.},
}
@article {pmid38830497,
year = {2024},
author = {Zhang, X and Li, P and Wang, J and Fu, D and Zhao, B and Dong, W and Liu, Y},
title = {Comparative genomic and phylogenetic analyses of mitochondrial genomes of hawthorn (Crataegus spp.) in Northeast China.},
journal = {International journal of biological macromolecules},
volume = {272},
number = {Pt 1},
pages = {132795},
doi = {10.1016/j.ijbiomac.2024.132795},
pmid = {38830497},
issn = {1879-0003},
abstract = {Hawthorn (Crataegus spp.) plants are major sources of health food and medicines. Twenty species and seven variations of Crataegus are present in China. A variety of unique Crataegus species was found in their natural distribution in northeast China. In the present study, we assembled and annotated the mitochondrial genomes of five Crataegus species from northeastern China. The sizes of the newly sequenced mitochondrial genomes ranged from 245,907 bp to 410,837 bp. A total of 45-55 genes, including 12-19 transfer RNA genes, three ribosomal RNA genes, and 29-33 protein-coding genes (PCGs) were encoded by these mitochondrial genomes. Seven divergent hotspot regions were identified by comparative analyses: atp6, nad3, ccmFN, matR, nad1, nad5, and rps1. The most conserved genes among the Crataegus species, according to the whole-genome correlation analysis, were nad1, matR, nad5, ccmFN, cox1, nad4, trnQ-TTG, trnK-TTT, trnE-TTC, and trnM-CAT. Horizontal gene transfer between organellar genomes was common in Crataegus plants. Based on the phylogenetic trees of mitochondrial PCGs, C. maximowiczii, C. maximowiczii var. ninganensis, and C. bretschneideri shared similar maternal relationships. This study improves Crataegus mitochondrial genome resources and offers important insights into the taxonomy and species identification of this genus.},
}
@article {pmid38830094,
year = {2024},
author = {Attah, V and Milner, DS and Fang, Y and Yan, X and Leonard, G and Heitman, J and Talbot, NJ and Richards, TA},
title = {Duplication and neofunctionalization of a horizontally transferred xyloglucanase as a facet of the Red Queen coevolutionary dynamic.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {24},
pages = {e2218927121},
doi = {10.1073/pnas.2218927121},
pmid = {38830094},
issn = {1091-6490},
support = {PLP-2014-147//Leverhulme Trust/ ; URF/R/191005//Royal Society (The Royal Society)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Glycoside Hydrolases/metabolism/genetics ; *Phylogeny ; Phytophthora/pathogenicity/genetics ; Plant Diseases/microbiology/parasitology ; Evolution, Molecular ; Gene Duplication ; },
abstract = {Oomycete protists share phenotypic similarities with fungi, including the ability to cause plant diseases, but branch in a distant region of the tree of life. It has been suggested that multiple horizontal gene transfers (HGTs) from fungi-to-oomycetes contributed to the evolution of plant-pathogenic traits. These HGTs are predicted to include secreted proteins that degrade plant cell walls, a barrier to pathogen invasion and a rich source of carbohydrates. Using a combination of phylogenomics and functional assays, we investigate the diversification of a horizontally transferred xyloglucanase gene family in the model oomycete species Phytophthora sojae. Our analyses detect 11 xyloglucanase paralogs retained in P. sojae. Using heterologous expression in yeast, we show consistent evidence that eight of these paralogs have xyloglucanase function, including variants with distinct protein characteristics, such as a long-disordered C-terminal extension that can increase xyloglucanase activity. The functional variants analyzed subtend a phylogenetic node close to the fungi-to-oomycete transfer, suggesting the horizontally transferred gene was a bona fide xyloglucanase. Expression of three xyloglucanase paralogs in Nicotiana benthamiana triggers high-reactive oxygen species (ROS) generation, while others inhibit ROS responses to bacterial immunogens, demonstrating that the paralogs differentially stimulate pattern-triggered immunity. Mass spectrometry of detectable enzymatic products demonstrates that some paralogs catalyze the production of variant breakdown profiles, suggesting that secretion of variant xyloglucanases increases efficiency of xyloglucan breakdown as well as diversifying the damage-associated molecular patterns released. We suggest that this pattern of neofunctionalization and the variant host responses represent an aspect of the Red Queen host-pathogen coevolutionary dynamic.},
}
@article {pmid38827508,
year = {2024},
author = {Tang, N and Wei, D and Zeng, Y and Zhang, G and Wang, C and Feng, J and Song, Y},
title = {Understanding the rapid spread of antimicrobial resistance genes mediated by IS26.},
journal = {mLife},
volume = {3},
number = {1},
pages = {101-109},
pmid = {38827508},
issn = {2770-100X},
abstract = {Insertion sequences (ISs) promote the transmission of antimicrobial resistance genes (ARGs) across bacterial populations. However, their contributions and dynamics during the transmission of resistance remain unclear. In this study, we selected IS26 as a representative transposable element to decipher the relationship between ISs and ARGs and to investigate their transfer features and transmission trends. We retrieved 2656 translocatable IS 26 -bounded units with ARGs (tIS26-bUs-ARGs) in complete bacterial genomes from the NCBI RefSeq database. In total, 124 ARGs spanning 12 classes of antibiotics were detected, and the average contribution rate of IS26 to these genes was 41.2%. We found that IS 26 -bounded units (IS26-bUs) mediated extensive ARG dissemination within the bacteria of the Gammaproteobacteria class, showing strong transfer potential between strains, species, and even phyla. The IS26-bUs expanded in bacterial populations over time, and their temporal expansion trend was significantly correlated with antibiotic usage. This wide dissemination could be due to the nonspecific target site preference of IS26. Finally, we experimentally confirmed that the introduction of a single copy of IS26 could lead to the formation of a composite transposon mediating the transmission of "passenger" genes. These observations extend our knowledge of the IS26 and provide new insights into the mediating role of ISs in the dissemination of antibiotic resistance.},
}
@article {pmid38823616,
year = {2024},
author = {Peng, J and Wang, D and He, P and Wei, P and Zhang, L and Lan, W and Zhang, X and Guan, J and Chen, Y and Li, W and Zheng, Y and Li, Y and Chen, W and Zhao, Z and Jiang, L and Zhou, L},
title = {Seasonal Dynamics of Antibiotic Resistance Genes and Mobile Genetic Elements in a Subtropical Coastal Ecosystem: Implications for Environmental Health Risks.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119298},
doi = {10.1016/j.envres.2024.119298},
pmid = {38823616},
issn = {1096-0953},
abstract = {Antibiotic resistance poses a considerable global public health concern, leading to heightened rates of illness and mortality. However, the impact of seasonal variations and environmental factors on the health risks associated with antibiotic resistance genes (ARGs) and their assembly mechanisms is not fully understood. Based on metagenomic sequencing, this study investigated the antibiotic resistome, mobile genetic elements (MGEs), and microbiomes in a subtropical coastal ecosystem of the Beibu Gulf, China, over autumn and winter, and explored the factors influencing seasonal changes in ARG and MGE abundance and diversity. Results indicated that ARG abundance and diversity were higher in winter than in autumn, with beta-lactam and multidrug resistance genes being the most diverse and abundant, respectively. Similarly, MGE abundance and diversity increased in winter and were strongly correlated with ARGs. In contrast, more pronounced associations between microbial communities, especially archaea, and the antibiotic resistome were observed in autumn than in winter. The co-occurrence network identified multiple interactions between MGEs and various multidrug efflux pumps in winter, suggesting a potential for ARG dissemination. Multivariate correlation analyses and path modeling indicated that environmental factors driving microbial community changes predominantly influenced antibiotic resistome assembly in autumn, while the relative importance of MGEs increased significantly in winter. These findings suggest an elevated health risk associated with antimicrobial resistance in the Beibu Gulf during winter, attributed to the dissemination of ARGs by horizontal gene transfer. The observed seasonal variations highlight the dynamic nature of antibiotic resistance dissemination in coastal ecosystems, emphasizing the need for comprehensive surveillance and management measures to address the growing threat of antimicrobial resistance in vulnerable environments.},
}
@article {pmid38820540,
year = {2024},
author = {Morel-Letelier, I and Yuen, B and Kück, AC and Camacho-García, YE and Petersen, JM and Lara, M and Leray, M and Eisen, JA and Osvatic, JT and Gros, O and Wilkins, LGE},
title = {Adaptations to nitrogen availability drive ecological divergence of chemosynthetic symbionts.},
journal = {PLoS genetics},
volume = {20},
number = {5},
pages = {e1011295},
doi = {10.1371/journal.pgen.1011295},
pmid = {38820540},
issn = {1553-7404},
abstract = {Bacterial symbionts, with their shorter generation times and capacity for horizontal gene transfer (HGT), play a critical role in allowing marine organisms to cope with environmental change. The closure of the Isthmus of Panama created distinct environmental conditions in the Tropical Eastern Pacific (TEP) and Caribbean, offering a "natural experiment" for studying how closely related animals evolve and adapt under environmental change. However, the role of bacterial symbionts in this process is often overlooked. We sequenced the genomes of endosymbiotic bacteria in two sets of sister species of chemosymbiotic bivalves from the genera Codakia and Ctena (family Lucinidae) collected on either side of the Isthmus, to investigate how differing environmental conditions have influenced the selection of symbionts and their metabolic capabilities. The lucinid sister species hosted different Candidatus Thiodiazotropha symbionts and only those from the Caribbean had the genetic potential for nitrogen fixation, while those from the TEP did not. Interestingly, this nitrogen-fixing ability did not correspond to symbiont phylogeny, suggesting convergent evolution of nitrogen fixation potential under nutrient-poor conditions. Reconstructing the evolutionary history of the nifHDKT operon by including other lucinid symbiont genomes from around the world further revealed that the last common ancestor (LCA) of Ca. Thiodiazotropha lacked nif genes, and populations in oligotrophic habitats later re-acquired the nif operon through HGT from the Sedimenticola symbiont lineage. Our study suggests that HGT of the nif operon has facilitated niche diversification of the globally distributed Ca. Thiodiazotropha endolucinida species clade. It highlights the importance of nitrogen availability in driving the ecological diversification of chemosynthetic symbiont species and the role that bacterial symbionts may play in the adaptation of marine organisms to changing environmental conditions.},
}
@article {pmid38819554,
year = {2024},
author = {Hellmuth, M and Stadler, PF},
title = {The Theory of Gene Family Histories.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2802},
number = {},
pages = {1-32},
pmid = {38819554},
issn = {1940-6029},
mesh = {*Phylogeny ; *Multigene Family ; *Gene Transfer, Horizontal ; *Evolution, Molecular ; Models, Genetic ; Computational Biology/methods ; },
abstract = {Most genes are part of larger families of evolutionary-related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene family histories, i.e., the precise dating of evolutionary events relative to phylogenetic tree of the underlying species has remained a challenging topic despite their importance as a basis for detailed investigations into adaptation and functional evolution of individual members of the gene family. The identification of orthologs, moreover, is a particularly important subproblem of the more general setting considered here. In the last few years, an extensive body of mathematical results has appeared that tightly links orthology, a formal notion of best matches among genes, and horizontal gene transfer. The purpose of this chapter is to broadly outline some of the key mathematical insights and to discuss their implication for practical applications. In particular, we focus on tree-free methods, i.e., methods to infer orthology or horizontal gene transfer as well as gene trees, species trees, and reconciliations between them without using a priori knowledge of the underlying trees or statistical models for the inference of phylogenetic trees. Instead, the initial step aims to extract binary relations among genes.},
}
@article {pmid38818484,
year = {2022},
author = {Zhou, Z and Liu, Y and Anantharaman, K and Li, M},
title = {The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis.},
journal = {mLife},
volume = {1},
number = {4},
pages = {374-381},
pmid = {38818484},
issn = {2770-100X},
abstract = {The division of organisms on the Tree of Life into either a three-domain (3D) tree or a two-domain (2D) tree has been disputed for a long time. Ever since the discovery of Archaea by Carl Woese in 1977 using 16S ribosomal RNA sequence as the evolutionary marker, there has been a great advance in our knowledge of not only the growing diversity of Archaea but also the evolutionary relationships between different lineages of living organisms. Here, we present this perspective to summarize the progress of archaeal diversity and changing notion of the Tree of Life. Meanwhile, we provide the latest progress in genomics/physiology-based discovery of Asgard archaeal lineages as the closest relative of Eukaryotes. Furthermore, we propose three major directions for future research on exploring the "next one" closest Eukaryote relative, deciphering the function of archaeal eukaryotic signature proteins and eukaryogenesis from both genomic and physiological aspects, and understanding the roles of horizontal gene transfer, viruses, and mobile elements in eukaryogenesis.},
}
@article {pmid38818268,
year = {2023},
author = {Konstantinidis, KT},
title = {Sequence-discrete species for prokaryotes and other microbes: A historical perspective and pending issues.},
journal = {mLife},
volume = {2},
number = {4},
pages = {341-349},
pmid = {38818268},
issn = {2770-100X},
abstract = {Whether prokaryotes, and other microorganisms, form distinct clusters that can be recognized as species remains an issue of paramount theoretical as well as practical consequence in identifying, regulating, and communicating about these organisms. In the past decade, comparisons of thousands of genomes of isolates and hundreds of metagenomes have shown that prokaryotic diversity may be predominantly organized in such sequence-discrete clusters, albeit organisms of intermediate relatedness between the identified clusters are also frequently found. Accumulating evidence suggests, however, that the latter "intermediate" organisms show enough ecological and/or functional distinctiveness to be considered different species. Notably, the area of discontinuity between clusters often-but not always-appears to be around 85%-95% genome-average nucleotide identity, consistently among different taxa. More recent studies have revealed remarkably similar diversity patterns for viruses and microbial eukaryotes as well. This high consistency across taxa implies a specific mechanistic process that underlies the maintenance of the clusters. The underlying mechanism may be a substantial reduction in the efficiency of homologous recombination, which mediates (successful) horizontal gene transfer, around 95% nucleotide identity. Deviations from the 95% threshold (e.g., species showing lower intraspecies diversity) may be caused by ecological differentiation that imposes barriers to otherwise frequent gene transfer. While this hypothesis that clusters are driven by ecological differentiation coupled to recombination frequency (i.e., higher recombination within vs. between groups) is appealing, the supporting evidence remains anecdotal. The data needed to rigorously test the hypothesis toward advancing the species concept are also outlined.},
}
@article {pmid38817968,
year = {2024},
author = {Zhao, Y and Ding, WJ and Xu, L and Sun, JQ},
title = {A comprehensive comparative genomic analysis revealed that plant growth promoting traits are ubiquitous in strains of Stenotrophomonas.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1395477},
doi = {10.3389/fmicb.2024.1395477},
pmid = {38817968},
issn = {1664-302X},
abstract = {Stenotrophomonas strains, which are often described as plant growth promoting (PGP) bacteria, are ubiquitous in many environments. A total of 213 genomes of strains of Stenotrophomonas were analyzed using comparative genomics to better understand the ecological roles of these bacteria in the environment. The pan-genome of the 213 strains of Stenotrophomonas consists of 27,186 gene families, including 710 core gene families, 11,039 unique genes and 15,437 accessory genes. Nearly all strains of Stenotrophomonas harbor the genes for GH3-family cellulose degradation and GH2- and GH31-family hemicellulose hydrolase, as well as intact glycolysis and tricarboxylic acid cycle pathways. These abilities suggest that the strains of this genus can easily obtain carbon and energy from the environment. The Stenotrophomonas strains can respond to oxidative stress by synthesizing catalase, superoxide dismutase, methionine sulfoxide reductase, and disulfide isomerase, as well as managing their osmotic balance by accumulating potassium and synthesizing compatible solutes, such as betaine, trehalose, glutamate, and proline. Each Stenotrophomonas strain also contains many genes for resistance to antibiotics and heavy metals. These genes that mediate stress tolerance increase the ability of Stenotrophomonas strains to survive in extreme environments. In addition, many functional genes related to attachment and plant colonization, growth promotion and biocontrol were identified. In detail, the genes associated with flagellar assembly, motility, chemotaxis and biofilm formation enable the strains of Stenotrophomonas to effectively colonize host plants. The presence of genes for phosphate-solubilization and siderophore production and the polyamine, indole-3-acetic acid, and cytokinin biosynthetic pathways confer the ability to promote plant growth. These strains can produce antimicrobial compounds, chitinases, lipases and proteases. Each Stenotrophomonas genome contained 1-9 prophages and 17-60 genomic islands, and the genes related to antibiotic and heavy metal resistance and the biosynthesis of polyamines, indole-3-acetic acid, and cytokinin may be acquired by horizontal gene transfer. This study demonstrates that strains of Stenotrophomonas are highly adaptable for different environments and have strong potential for use as plant growth-promoting bacteria.},
}
@article {pmid38817813,
year = {2023},
author = {Li, L and Zhang, T},
title = {Roadmap to tackle antibiotic resistance in the environment under the One Health framework.},
journal = {mLife},
volume = {2},
number = {3},
pages = {224-228},
pmid = {38817813},
issn = {2770-100X},
abstract = {Antibiotic resistance has been recognized as a major challenge worldwide for humans. "One Health" has been recognized as a key concept for containment of antibiotic resistance. Under the framework, the role of the environment in the development of antibiotic resistance genes (ARGs) has become increasingly obvious. Despite numerous efforts, response to antibiotic resistance is considered to be inadequate, which is probably due to the lack of a clear roadmap. Here, we propose a "One Health" roadmap to combat antibiotic resistance in the environment through (1) understanding environmental resistome. The environmental gene pool has long been recognized as the single largest reservoir of both known and novel ARGs. (2) Standardizing ARG quantification. Systematic joint efforts based on standardized quantification are urgently needed to understand the true tempospatial profiles of the environmental resistome. (3) Identifying mechanisms of resistome development. Horizontal gene transfer and co-selection have been recognized as the two main mechanisms contributing to the environmental resistome. (4) Establishing a risk-assessment framework. The first critical step for large-scale cost-effective targeted ARG management in the environment is the risk assessment to identify the priority ARGs for control. (5) Formulating regulatory standards. By correlating the environmental ARG profile with public health, we may identify the indicator ARGs that can be integrated into current environmental quality standards. (6) Developing control strategies. Systematic analysis of available control technologies is required to identify the most feasible ones to curtail the spread of ARGs in the environment. The proposed roadmap under the "One Health" framework provides a guide to tackle antibiotic resistance in the environment.},
}
@article {pmid38816863,
year = {2024},
author = {Pontes, A and Paraíso, F and Silva, M and Lagoas, C and Aires, A and Brito, PH and Rosa, CA and Lachance, MA and Sampaio, JP and Gonçalves, C and Gonçalves, P},
title = {Extensive remodeling of sugar metabolism through gene loss and horizontal gene transfer in a eukaryotic lineage.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {128},
pmid = {38816863},
issn = {1741-7007},
support = {UIDB/04378/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0140/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-EVL/1100/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-EVL/0604/2021//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2023.09581.CPCA.A1//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.15871.CPCA.A2//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04378/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0140/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-EVL/1100/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-EVL/0604/2021//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2023.09581.CPCA.A1//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.15871.CPCA.A2//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; #406564/2022-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 0457499/2014-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 313088/2020-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 408733/2021//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; #406564/2022-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq process numbers 0457499/2014-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 313088/2020-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 408733/2021//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; APQ-01525-14//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; APQ-02552-15//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; APQ-01525-14//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; APQ-02552-15//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; },
mesh = {*Gene Transfer, Horizontal ; Phylogeny ; Carbohydrate Metabolism/genetics ; Sugars/metabolism ; Evolution, Molecular ; Genome, Fungal ; },
abstract = {BACKGROUND: In yeasts belonging to the subphylum Saccharomycotina, genes encoding components of the main metabolic pathways, like alcoholic fermentation, are usually conserved. However, in fructophilic species belonging to the floral Wickerhamiella and Starmerella genera (W/S clade), alcoholic fermentation was uniquely shaped by events of gene loss and horizontal gene transfer (HGT).<br><br>RESULTS: Because HGT and gene losses were first identified when only eight W/S-clade genomes were available, we collected publicly available genome data and sequenced the genomes of 36 additional species. A total of 63 genomes, representing most of the species described in the clade, were included in the analyses. Firstly, we inferred the phylogenomic tree of the clade and inspected the genomes for the presence of HGT-derived genes involved in fructophily and alcoholic fermentation. We predicted nine independent HGT events and several instances of secondary loss pertaining to both pathways. To investigate the possible links between gene loss and acquisition events and evolution of sugar metabolism, we conducted phenotypic characterization of 42 W/S-clade species including estimates of sugar consumption rates and fermentation byproduct formation. In some instances, the reconciliation of genotypes and phenotypes yielded unexpected results, such as the discovery of fructophily in the absence of the cornerstone gene (FFZ1) and robust alcoholic fermentation in the absence of the respective canonical pathway.<br><br>CONCLUSIONS: These observations suggest that reinstatement of alcoholic fermentation in the W/S clade triggered a surge of innovation that goes beyond the utilization of xenologous enzymes, with fructose metabolism playing a key role.},
}
@article {pmid38813783,
year = {2024},
author = {Wolyniak, MJ and Frazier, RH and Gemborys, PK and Loehr, HE},
title = {Malate dehydrogenase: a story of diverse evolutionary radiation.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20230076},
pmid = {38813783},
issn = {1744-1358},
support = {//Hampden-Sydney College Office of Undergraduate Research/ ; },
abstract = {Malate dehydrogenase (MDH) is a ubiquitous enzyme involved in cellular respiration across all domains of life. MDH's ubiquity allows it to act as an excellent model for considering the history of life and how the rise of aerobic respiration and eukaryogenesis influenced this evolutionary process. Here, we present the diversity of the MDH family of enzymes across bacteria, archaea, and eukarya, the relationship between MDH and lactate dehydrogenase (LDH) in the formation of a protein superfamily, and the connections between MDH and endosymbiosis in the formation of mitochondria and chloroplasts. The development of novel and powerful DNA sequencing techniques has challenged some of the conventional wisdom underlying MDH evolution and suggests a history dominated by gene duplication, horizontal gene transfer, and cryptic endosymbiosis events and adaptation to a diverse range of environments across all domains of life over evolutionary time. The data also suggest a superfamily of proteins that do not share high levels of sequential similarity but yet retain strong conservation of core function via key amino acid residues and secondary structural components. As DNA sequencing and 'big data' analysis techniques continue to improve in the life sciences, it is likely that the story of MDH will continue to refine as more examples of superfamily diversity are recovered from nature and analyzed.},
}
@article {pmid38811160,
year = {2024},
author = {Breidenstein, A and Lamy, A and Bader, CP and Sun, WS and Wanrooij, PH and Berntsson, RP},
title = {PrgE: an OB-fold protein from plasmid pCF10 with striking differences to prototypical bacterial SSBs.},
journal = {Life science alliance},
volume = {7},
number = {8},
pages = {},
pmid = {38811160},
issn = {2575-1077},
mesh = {*Plasmids/genetics ; *DNA-Binding Proteins/metabolism/genetics/chemistry ; *Bacterial Proteins/genetics/metabolism/chemistry ; *Enterococcus faecalis/genetics/metabolism ; *DNA, Single-Stranded/metabolism/genetics ; Protein Binding ; Conjugation, Genetic/genetics ; Type IV Secretion Systems/genetics/metabolism ; Models, Molecular ; Gene Transfer, Horizontal ; DNA, Bacterial/genetics/metabolism ; },
abstract = {A major pathway for horizontal gene transfer is the transmission of DNA from donor to recipient cells via plasmid-encoded type IV secretion systems (T4SSs). Many conjugative plasmids encode for a single-stranded DNA-binding protein (SSB) together with their T4SS. Some of these SSBs have been suggested to aid in establishing the plasmid in the recipient cell, but for many, their function remains unclear. Here, we characterize PrgE, a proposed SSB from the Enterococcus faecalis plasmid pCF10. We show that PrgE is not essential for conjugation. Structurally, it has the characteristic OB-fold of SSBs, but it has very unusual DNA-binding properties. Our DNA-bound structure shows that PrgE binds ssDNA like beads on a string supported by its N-terminal tail. In vitro studies highlight the plasticity of PrgE oligomerization and confirm the importance of the N-terminus. Unlike other SSBs, PrgE binds both double- and single-stranded DNA equally well. This shows that PrgE has a quaternary assembly and DNA-binding properties that are very different from the prototypical bacterial SSB, but also different from eukaryotic SSBs.},
}
@article {pmid38818326,
year = {2022},
author = {Da Cunha, V and Gaïa, M and Forterre, P},
title = {The expanding Asgard archaea and their elusive relationships with Eukarya.},
journal = {mLife},
volume = {1},
number = {1},
pages = {3-12},
pmid = {38818326},
issn = {2770-100X},
abstract = {The discovery of Asgard archaea and the exploration of their diversity over the last 6 years have deeply impacted the scientific community working on eukaryogenesis, rejuvenating an intense debate on the topology of the universal tree of life (uTol). Here, we discuss how this debate is impacted by two recent publications that expand the number of Asgard lineages and eukaryotic signature proteins (ESPs). We discuss some of the main difficulties that can impair the phylogenetic reconstructions of the uTol and suggest that the debate about its topology is not settled. We notably hypothesize the existence of horizontal gene transfers between ancestral Asgards and proto-eukaryotes that could result in the observed abnormal behaviors of some Asgard ESPs and universal marker proteins. This hypothesis is relevant regardless of the scenario considered regarding eukaryogenesis. It implies that the Asgards were already diversified before the last eukaryotic common ancestor and shared the same biotopes with proto-eukaryotes. We suggest that some Asgards might be still living in symbiosis today with modern Eukarya.},
}
@article {pmid38810941,
year = {2024},
author = {Zhang, Y and Liu, M and Zhang, J and Wu, J and Hong, L and Zhu, L and Long, J},
title = {Large-scale comparative analysis reveals phylogenomic preference of blaNDM-1 and blaKPC-2 transmission among Klebsiella pneumoniae.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107225},
doi = {10.1016/j.ijantimicag.2024.107225},
pmid = {38810941},
issn = {1872-7913},
abstract = {blaNDM-1 and blaKPC-2 are responsible for the global rise of carbapenem-resistant K. pneumoniae, posing a great challenge to public health. However, the impact of phylogenetic factors on blaNDM-1 and blaKPC-2 dissemination is not yet fully understood. Here, we established a global dataset of 4051 blaNDM-1+ or 10223 blaKPC-2+ K. pneumoniae genomes and compared their transmission mode on a global scale. The results showed that blaNDM-1+ K. pneumoniae genomes exhibited a broader geographical distribution and higher ST richness than blaKPC-2+, indicating higher transmissibility of the blaNDM-1 gene. Furthermore, blaNDM-1+ genomes displayed significant difference in ST lineage, antibiotic resistance genes composition, virulence genes composition, genetic environments with blaKPC-2+, suggesting their distinct dissemination mechanism. blaNDM-1+ genomes were predominantly associated with ST147 and ST16, whereas blaKPC-2+ genomes were mainly found in ST11 and ST258. Significantly different accessory genes were identified between blaNDM-1+ and blaKPC-2+ genomes. The preference for blaKPC-2 distribution across certain countries, ST lineages, and genetic environments underscores vertical spread as the primary mechanism driving the expansion of blaKPC-2. In contrast to blaKPC-2+, blaNDM-1+ genomes did not display such a strong preference, confirming that the blaNDM-1 dissemination mainly depended on horizontal gene transfer. Overall, our study demonstrates different phylogenetic drivers of blaNDM-1 and blaKPC-2 dissemination, providing new insights into their global transmission dynamic.},
}
@article {pmid38808732,
year = {2024},
author = {He, J and Yang, Z and Wang, M and Jia, R and Chen, S and Liu, M and Zhao, X and Yang, Q and Wu, Y and Zhang, S and Huang, J and Ou, X and Sun, D and Tian, B and He, Y and Wu, Z and Cheng, A and Zhu, D},
title = {Integrative and conjugative elements of Pasteurella multocida: Prevalence and signatures in population evolution.},
journal = {Virulence},
volume = {15},
number = {1},
pages = {2359467},
doi = {10.1080/21505594.2024.2359467},
pmid = {38808732},
issn = {2150-5608},
mesh = {*Pasteurella multocida/genetics/classification ; *Gene Transfer, Horizontal ; Animals ; *Phylogeny ; *Pasteurella Infections/microbiology/epidemiology/transmission ; *Genome, Bacterial ; DNA Transposable Elements ; Conjugation, Genetic ; Evolution, Molecular ; Poultry/microbiology ; Prevalence ; High-Throughput Nucleotide Sequencing ; },
abstract = {Pasteurella multocida (P. multocida) is a bacterial pathogen responsible for a range of infections in humans and various animal hosts, causing significant economic losses in farming. Integrative and conjugative elements (ICEs) are important horizontal gene transfer elements, potentially enabling host bacteria to enhance adaptability by acquiring multiple functional genes. However, the understanding of ICEs in P. multocida and their impact on the transmission of this pathogen remains limited. In this study, 42 poultry-sourced P. multocida genomes obtained by high-throughput sequencing together with 393 publicly available P. multocida genomes were used to analyse the horizontal transfer of ICEs. Eighty-two ICEs were identified in P. multocida, including SXT/R391 and Tn916 subtypes, as well as three subtypes of ICEHin1056 family, with the latter being widely prevalent in P. multocida and carrying multiple resistance genes. The correlations between insertion sequences and resistant genes in ICEs were also identified, and some ICEs introduced the carbapenem gene blaOXA-2 and the bleomycin gene bleO to P. multocida. Phylogenetic and collinearity analyses of these bioinformatics found that ICEs in P. multocida were transmitted vertically and horizontally and have evolved with host specialization. These findings provide insight into the transmission and evolution mode of ICEs in P. multocida and highlight the importance of understanding these elements for controlling the spread of antibiotic resistance.},
}
@article {pmid38808121,
year = {2024},
author = {Haimlich, S and Fridman, Y and Khandal, H and Savaldi-Goldstein, S and Levy, A},
title = {Widespread horizontal gene transfer between plants and bacteria.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae073},
pmid = {38808121},
issn = {2730-6151},
abstract = {Plants host a large array of commensal bacteria that interact with the host. The growth of both bacteria and plants is often dependent on nutrients derived from the cognate partners, and the bacteria fine-tune host immunity against pathogens. This ancient interaction is common in all studied land plants and is critical for proper plant health and development. We hypothesized that the spatial vicinity and the long-term relationships between plants and their microbiota may promote cross-kingdom horizontal gene transfer (HGT), a phenomenon that is relatively rare in nature. To test this hypothesis, we analyzed the Arabidopsis thaliana genome and its extensively sequenced microbiome to detect events of horizontal transfer of full-length genes that transferred between plants and bacteria. Interestingly, we detected 75 unique genes that were horizontally transferred between plants and bacteria. Plants and bacteria exchange in both directions genes that are enriched in carbohydrate metabolism functions, and bacteria transferred to plants genes that are enriched in auxin biosynthesis genes. Next, we provided a proof of concept for the functional similarity between a horizontally transferred bacterial gene and its Arabidopsis homologue in planta. The Arabidopsis DET2 gene is essential for biosynthesis of the brassinosteroid phytohormones, and loss of function of the gene leads to dwarfism. We found that expression of the DET2 homologue from Leifsonia bacteria of the Actinobacteria phylum in the Arabidopsis det2 background complements the mutant and leads to normal plant growth. Together, these data suggest that cross-kingdom HGT events shape the metabolic capabilities and interactions between plants and bacteria.},
}
@article {pmid38802023,
year = {2024},
author = {Ji, W and Ma, J and Zheng, Z and Al-Herrawy, AZ and Xie, B and Wu, D},
title = {Algae blooms with resistance in fresh water: Potential interplay between Microcystis and antibiotic resistance genes.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {173528},
doi = {10.1016/j.scitotenv.2024.173528},
pmid = {38802023},
issn = {1879-1026},
abstract = {Microcystis, a type of cyanobacteria known for producing microcystins (MCs), is experiencing a global increase in blooms. They have been recently recognized as potential contributors to the widespread of antibiotic resistance genes (ARGs). By reviewing approximately 150 pieces of recent studies, a hypothesis has been formulated suggesting that significant fluctuations in MCs concentrations and microbial community structure during Microcystis blooms could influence the dynamics of waterborne ARGs. Among all MCs, microcystin-LR (MC-LR) is the most widely distributed worldwide, notably abundant in reservoirs during summer. MCs inhibit protein phosphatases or increase reactive oxygen species (ROS), inducing oxidative stresses, enhancing membrane permeability, and causing DNA damage. This further enhances selective pressures and horizontal gene transfer (HGT) chances of ARGs. The mechanisms by which Microcystis regulates ARG dissemination have been systematically organized for the first time, focusing on the secretion of MCs and the alterations of bacterial community structure. However, several knowledge gaps remain, particularly concerning how MCs interfere with the electron transport chain and how Microcystis facilitates HGT of ARGs. Concurrently, the predominance of Microcystis forming the algal microbial aggregates is considered a hotspot for preserving and transferring ARGs. Yet, Microcystis can deplete the nutrients from other taxa within these aggregates, thereby reducing the density of ARG-carrying bacteria. Therefore, further studies are needed to explore the 'symbiotic - competitive' relationships between Microcystis and ARG-hosting bacteria under varied nutrient conditions. Addressing these knowledge gaps is crucial to understand the impacts of the algal aggregates on dynamics of waterborne antibiotic resistome, and underscores the need for effective control of Microcystis to curb the spread of antibiotic resistance. Constructed wetlands and photocatalysis represent advantageous strategies for halting the spread of ARGs from the perspective of Microcystis blooms, as they can effectively control Microcystis and MCs while maintaining the stability of aquatic ecosystem.},
}
@article {pmid38789482,
year = {2024},
author = {Puginier, C and Libourel, C and Otte, J and Skaloud, P and Haon, M and Grisel, S and Petersen, M and Berrin, JG and Delaux, PM and Dal Grande, F and Keller, J},
title = {Phylogenomics reveals the evolutionary origins of lichenization in chlorophyte algae.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4452},
pmid = {38789482},
issn = {2041-1723},
mesh = {*Lichens/genetics/microbiology ; *Phylogeny ; *Symbiosis/genetics ; *Chlorophyta/genetics ; Gene Transfer, Horizontal ; Evolution, Molecular ; Biological Evolution ; Transcriptome ; Glycoside Hydrolases/genetics/metabolism ; Genomics ; },
abstract = {Mutualistic symbioses have contributed to major transitions in the evolution of life. Here, we investigate the evolutionary history and the molecular innovations at the origin of lichens, which are a symbiosis established between fungi and green algae or cyanobacteria. We de novo sequence the genomes or transcriptomes of 12 lichen algal symbiont (LAS) and closely related non-symbiotic algae (NSA) to improve the genomic coverage of Chlorophyte algae. We then perform ancestral state reconstruction and comparative phylogenomics. We identify at least three independent gains of the ability to engage in the lichen symbiosis, one in Trebouxiophyceae and two in Ulvophyceae, confirming the convergent evolution of the lichen symbioses. A carbohydrate-active enzyme from the glycoside hydrolase 8 (GH8) family was identified as a top candidate for the molecular-mechanism underlying lichen symbiosis in Trebouxiophyceae. This GH8 was acquired in lichenizing Trebouxiophyceae by horizontal gene transfer, concomitantly with the ability to associate with lichens fungal symbionts (LFS) and is able to degrade polysaccharides found in the cell wall of LFS. These findings indicate that a combination of gene family expansion and horizontal gene transfer provided the basis for lichenization to evolve in chlorophyte algae.},
}
@article {pmid38789462,
year = {2024},
author = {Wranne, MS and Karami, N and Sriram, KK and Jaén-Luchoro, D and Yazdanshenas, S and Lin, YL and Kabbinale, A and Flach, CF and Westerlund, F and Åhrén, C},
title = {Comparison of CTX-M encoding plasmids present during the early phase of the ESBL pandemic in western Sweden.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {11880},
pmid = {38789462},
issn = {2045-2322},
support = {C4A 2020-02518//V&#xe4;stra G&#xf6;talandsregionen/ ; ALF-965000//V&#xe4;stra G&#xf6;talandsregionen/ ; 2021-00922//Svenska Forskningsr&#xe5;det Formas/ ; 634890//EU Horizon 2020 program BeyondSeq/ ; },
mesh = {Sweden/epidemiology ; *Plasmids/genetics ; *beta-Lactamases/genetics ; *Escherichia coli/genetics ; Humans ; Pandemics ; Escherichia coli Infections/epidemiology/microbiology ; Gene Transfer, Horizontal ; Escherichia coli Proteins/genetics ; Whole Genome Sequencing ; },
abstract = {Plasmids encoding blaCTX-M genes have greatly shaped the evolution of E. coli producing extended-spectrum beta-lactamases (ESBL-E. coli) and adds to the global threat of multiresistant bacteria by promoting horizontal gene transfer (HGT). Here we screened the similarity of 47 blaCTX-M -encoding plasmids, from 45 epidemiologically unrelated and disperse ESBL-E. coli strains, isolated during the early phase (2009-2014) of the ESBL pandemic in western Sweden. Using optical DNA mapping (ODM), both similar and rare plasmids were identified. As many as 57% of the plasmids formed five ODM-plasmid groups of at least three similar plasmids per group. The most prevalent type (28%, IncIl, pMLST37) encoded blaCTX-M-15 (n = 10), blaCTX-M-3 (n = 2) or blaCTX-M-55 (n = 1). It was found in isolates of various sequence types (STs), including ST131. This could indicate ongoing local HGT as whole-genome sequencing only revealed similarities with a rarely reported, IncIl plasmid. The second most prevalent type (IncFII/FIA/FIB, F1:A2:B20) harboring blaCTX-M-27, was detected in ST131-C1-M27 isolates, and was similar to plasmids previously reported for this subclade. The results also highlight the need for local surveillance of plasmids and the importance of temporospatial epidemiological links so that detection of a prevalent plasmid is not overestimated as a potential plasmid transmission event in outbreak investigations.},
}
@article {pmid38788585,
year = {2024},
author = {Liu, T and Lee, S and Kim, M and Fan, P and Boughton, RK and Boucher, C and Jeong, KC},
title = {A study at the wildlife-livestock interface unveils the potential of feral swine as a reservoir for extended-spectrum β-lactamase-producing Escherichia coli.},
journal = {Journal of hazardous materials},
volume = {473},
number = {},
pages = {134694},
doi = {10.1016/j.jhazmat.2024.134694},
pmid = {38788585},
issn = {1873-3336},
abstract = {Wildlife is known to serve as carriers and sources of antimicrobial resistance (AMR). Due to their unrestricted movements and behaviors, they can spread antimicrobial resistant bacteria among livestock, humans, and the environment, thereby accelerating the dissemination of AMR. Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is one of major concerns threatening human and animal health, yet transmission mechanisms at the wildlife-livestock interface are not well understood. Here, we investigated the mechanisms of ESBL-producing bacteria spreading across various hosts, including cattle, feral swine, and coyotes in the same habitat range, as well as from environmental samples over a two-year period. We report a notable prevalence and clonal dissemination of ESBL-producing E. coli in feral swine and coyotes, suggesting their persistence and adaptation within wildlife hosts. In addition, in silico studies showed that horizontal gene transfer, mediated by conjugative plasmids and insertion sequences elements, may play a key role in spreading the ESBL genes among these bacteria. Furthermore, the shared gut resistome of cattle and feral swine suggests the dissemination of antibiotic resistance genes at the wildlife-livestock interface. Taken together, our results suggest that feral swine may serve as a reservoir of ESBL-producing E. coli.},
}
@article {pmid38788579,
year = {2024},
author = {Zhou, CS and Cao, GL and Liu, BF and Liu, W and Ma, WL and Ren, NQ},
title = {Deciphering the reduction of antibiotic resistance genes (ARGs) during medium-chain fatty acids production from waste activated sludge: Driven by inhibition of ARGs transmission and shift of microbial community.},
journal = {Journal of hazardous materials},
volume = {473},
number = {},
pages = {134676},
doi = {10.1016/j.jhazmat.2024.134676},
pmid = {38788579},
issn = {1873-3336},
abstract = {Medium-chain fatty acids (MCFAs) production from waste activated sludge (WAS) by chain extension (CE) is a promising technology. However, the effects and mechanisms of CE process on the fate of antibiotic resistance genes (ARGs) remain unclear. In this study, the results showed that the removal efficiency of ARGs was 81.15 % in CE process, suggesting its efficacy in reducing environmental risks. Further, the observed decrease in mobile genetic elements (MGEs) indicated that CE process restricted the horizontal gene transfer (HGT). Complementing this, the increase in soluble organic matters and extracellular 16 S rDNA confirmed that MCFAs production caused bacterial damage. Decreased intracellular ARGs and increased extracellular ARGs further revealed that MCFAs production impaired ARGs hosts, thereby limiting the vertical gene transfer (VGT) of ARGs. Shift of microbial community combined with co-occurrence network analysis demonstrated that functional bacteria without host potential for ARGs were enriched, but potential ARGs and MGEs hosts decreased, showing the role of functional bacterial phylogeny and selection pressure of MCFAs in reducing ARGs. Finally, partial least squares path model was used to systematic verify the mechanism of ARGs removal in CE process, which was attributed to the inhibition of ARGs transmission (HGT and VGT) and shift of microbial community.},
}
@article {pmid38786183,
year = {2024},
author = {Sabtcheva, S and Stoikov, I and Ivanov, IN and Donchev, D and Lesseva, M and Georgieva, S and Teneva, D and Dobreva, E and Christova, I},
title = {Genomic Characterization of Carbapenemase-Producing Enterobacter hormaechei, Serratia marcescens, Citrobacter freundii, Providencia stuartii, and Morganella morganii Clinical Isolates from Bulgaria.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {5},
pages = {},
pmid = {38786183},
issn = {2079-6382},
abstract = {Carbapenemase-producing Enterobacter spp. Serratia marcescens, Citrobacter freundii, Providencia spp., and Morganella morganii (CP-ESCPM) are increasingly identified as causative agents of nosocomial infections but are still not under systematic genomic surveillance. In this study, using a combination of whole-genome sequencing and conjugation experiments, we sought to elucidate the genomic characteristics and transferability of resistance genes in clinical CP-ESCPM isolates from Bulgaria. Among the 36 sequenced isolates, NDM-1 (12/36), VIM-4 (11/36), VIM-86 (8/36), and OXA-48 (7/36) carbapenemases were identified; two isolates carried both NDM-1 and VIM-86. The majority of carbapenemase genes were found on self-conjugative plasmids. IncL plasmids were responsible for the spread of OXA-48 among E. hormaechei, C. freundii, and S. marcescens. IncM2 plasmids were generally associated with the spread of NDM-1 in C. freundii and S. marcescens, and also of VIM-4 in C. freundii. IncC plasmids were involved in the spread of the recently described VIM-86 in P. stuartii isolates. IncC plasmids carrying blaNDM-1 and blaVIM-86 were observed too. blaNDM-1 was also detected on IncX3 in S. marcescens and on IncT plasmid in M. morganii. The significant resistance transfer rates we observed highlight the role of the ESCPM group as a reservoir of resistance determinants and stress the need for strengthening infection control measures.},
}
@article {pmid38786161,
year = {2024},
author = {Lamichhane, J and Choi, BI and Stegman, N and Fontes Noronha, M and Wolfe, AJ},
title = {Macrolide Resistance in the Aerococcus urinae Complex: Implications for Integrative and Conjugative Elements.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {5},
pages = {},
pmid = {38786161},
issn = {2079-6382},
support = {Pathnostics//Pathnostics/ ; },
abstract = {The recognition of the Aerococcus urinae complex (AUC) as an emerging uropathogen has led to growing concerns due to a limited understanding of its disease spectrum and antibiotic resistance profiles. Here, we investigated the prevalence of macrolide resistance within urinary AUC isolates, shedding light on potential genetic mechanisms. Phenotypic testing revealed a high rate of macrolide resistance: 45%, among a total of 189 urinary AUC isolates. Genomic analysis identified integrative and conjugative elements (ICEs) as carriers of the macrolide resistance gene ermA, suggesting horizontal gene transfer as a mechanism of resistance. Furthermore, comparison with publicly available genomes of related pathogens revealed high ICE sequence homogeneity, highlighting the potential for cross-species dissemination of resistance determinants. Understanding mechanisms of resistance is crucial for developing effective surveillance strategies and improving antibiotic use. Furthermore, the findings underscore the importance of considering the broader ecological context of resistance dissemination, emphasizing the need for community-level surveillance to combat the spread of antibiotic resistance within the urinary microbiome.},
}
@article {pmid38786130,
year = {2024},
author = {Monecke, S and Burgold-Voigt, S and Braun, SD and Diezel, C and Liebler-Tenorio, EM and Müller, E and Nassar, R and Reinicke, M and Reissig, A and Senok, A and Ehricht, R},
title = {Characterisation of PVL-Positive Staphylococcus argenteus from the United Arab Emirates.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {5},
pages = {},
pmid = {38786130},
issn = {2079-6382},
support = {13GW0456//Federal Ministry of Education and Research/ ; 13N15717//Federal Ministry of Education and Research/ ; },
abstract = {Staphylococcus argenteus is a recently described staphylococcal species that is related to Staphylococcus aureus but lacks the staphyloxanthin operon. It is able to acquire both resistance markers such as the SCCmec elements and mobile genetic elements carrying virulence-associated genes from S. aureus. This includes those encoding the Panton-Valentine leukocidin (PVL), which is associated mainly with severe and/or recurrent staphylococcal skin and soft tissue infections. Here, we describe the genome sequences of two PVL-positive, mecA-negative S. argenteus sequence type (ST) 2250 isolates from the United Arab Emirates in detail. The isolates were found in a dental clinic in the United Arab Emirates (UAE). Both were sequenced using Oxford Nanopore Technology (ONT). This demonstrated the presence of temperate bacteriophages in the staphylococcal genomes, including a PVL prophage. It was essentially identical to the published sequence of phiSa2wa_st78 (GenBank NC_055048), a PVL phage from an Australian S. aureus clonal complex (CC) 88 isolate. Besides the PVL prophage, one isolate carried another prophage and the second isolate carried two additional prophages, whereby the region between these two prophages was inverted. This "flipped" region comprised about 1,083,000 bp, or more than a third of the strain's genome, and it included the PVL prophage. Prophages were induced by Mitomycin C treatment and subjected to transmission electron microscopy (TEM). This yielded, in accordance to the sequencing results, one or, respectively, two distinct populations of icosahedral phages. It also showed prolate phages which presumptively might be identified as the PVL phage. This observation highlights the significance bacteriophages have as agents of horizontal gene transfer as well as the need for monitoring emerging staphylococcal strains, especially in cosmopolitan settings such as the UAE.},
}
@article {pmid38783378,
year = {2024},
author = {Brattig, N and Bergquist, R and Vienneau, D and Zhou, XN},
title = {Geography and health: role of human translocation and access to care.},
journal = {Infectious diseases of poverty},
volume = {13},
number = {1},
pages = {37},
pmid = {38783378},
issn = {2049-9957},
mesh = {Humans ; *Health Services Accessibility ; Animals ; *Zoonoses/epidemiology ; COVID-19/transmission/epidemiology ; Communicable Diseases/epidemiology/transmission ; SARS-CoV-2 ; Geography ; },
abstract = {Natural, geographical barriers have historically limited the spread of communicable diseases. This is no longer the case in today's interconnected world, paired with its unprecedented environmental and climate change, emphasising the intersection of evolutionary biology, epidemiology and geography (i.e. biogeography). A total of 14 articles of the special issue entitled "Geography and health: role of human translocation and access to care" document enhanced disease transmission of diseases, such as malaria, leishmaniasis, schistosomiasis, COVID-19 (Severe acute respiratory syndrome corona 2) and Oropouche fever in spite of spatiotemporal surveillance. High-resolution satellite images can be used to understand spatial distributions of transmission risks and disease spread and to highlight the major avenue increasing the incidence and geographic range of zoonoses represented by spill-over transmission of coronaviruses from bats to pigs or civets. Climate change and globalization have increased the spread and establishment of invasive mosquitoes in non-tropical areas leading to emerging outbreaks of infections warranting improved physical, chemical and biological vector control strategies. The translocation of pathogens and their vectors is closely connected with human mobility, migration and the global transport of goods. Other contributing factors are deforestation with urbanization encroaching into wildlife zones. The destruction of natural ecosystems, coupled with low income and socioeconomic status, increase transmission probability of neglected tropical and zoonotic diseases. The articles in this special issue document emerging or re-emerging diseases and surveillance of fever symptoms. Health equity is intricately connected to accessibility to health care and the targeting of healthcare resources, necessitating a spatial approach. Public health comprises successful disease management integrating spatial surveillance systems, including access to sanitation facilities. Antimicrobial resistance caused, e.g. by increased use of antibiotics in health, agriculture and aquaculture, or acquisition of resistance genes, can be spread by horizontal gene transfer. This editorial reviews the key findings of this 14-article special issue, identifies important gaps relevant to our interconnected world and makes a number of specific recommendations to mitigate the transmission risks of infectious diseases in the post-COVID-19 pandemic era.},
}
@article {pmid38783210,
year = {2024},
author = {Han, D and Ma, S and He, C and Yang, Y and Li, P and Lu, L},
title = {Unveiling the genetic architecture and transmission dynamics of a novel multidrug-resistant plasmid harboring blaNDM-5 in E. Coli ST167: implications for antibiotic resistance management.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {178},
pmid = {38783210},
issn = {1471-2180},
support = {2022B1154//Health Projects of Zhongshan City/ ; 2018B1081//Health Projects of Zhongshan City/ ; },
mesh = {*Plasmids/genetics ; *Escherichia coli/genetics/drug effects ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *beta-Lactamases/genetics ; Humans ; *Escherichia coli Infections/microbiology/transmission ; *Microbial Sensitivity Tests ; China ; Gene Transfer, Horizontal ; Carbapenems/pharmacology ; },
abstract = {BACKGROUND: The emergence of multidrug-resistant (MDR) Escherichia coli strains poses significant challenges in clinical settings, particularly when these strains harbor New Delhi metallo-ß-lactamase (NDM) gene, which confer resistance to carbapenems, a critical class of last-resort antibiotics. This study investigates the genetic characteristics and implications of a novel blaNDM-5-carrying plasmid pNDM-5-0083 isolated from an E. coli strain GZ04-0083 from clinical specimen in Zhongshan, China.<br><br>RESULTS: Phenotypic and genotypic evaluations confirmed that the E. coli ST167 strain GZ04-0083 is a multidrug-resistant organism, showing resistance to diverse classes of antibiotics including &#xdf;-lactams, carbapenems, fluoroquinolones, aminoglycosides, and sulfonamides, while maintaining susceptibility to monobactams. Investigations involving S1 pulsed-field gel electrophoresis, Southern blot analysis, and conjugation experiments, alongside genomic sequencing, confirmed the presence of the blaNDM-5 gene within a 146-kb IncFIB plasmid pNDM-5-0083. This evidence underscores a significant risk for the horizontal transfer of resistance genes among bacterial populations. Detailed annotations of genetic elements-such as resistance genes, transposons, and insertion sequences-and comparative BLAST analyses with other blaNDM-5-carrying plasmids, revealed a unique architectural configuration in the pNDM-5-0083. The MDR region of this plasmid shares a conserved gene arrangement (repA-IS15DIV-blaNDM-5-bleMBL-IS91-suI2-aadA2-dfrA12) with three previously reported plasmids, indicating a potential for dynamic genetic recombination and evolution within the MDR region. Additionally, the integration of virulence factors, including the iro and sit gene clusters and enolase, into its genetic architecture poses further therapeutic challenges by enhancing the strain's pathogenicity through improved host tissue colonization, immune evasion, and increased infection severity.<br><br>CONCLUSIONS: The detailed identification and characterization of pNDM-5-0083 enhance our understanding of the mechanisms facilitating the spread of carbapenem resistance. This study illuminates the intricate interplay among various genetic elements within the novel blaNDM-5-carrying plasmid, which are crucial for the stability and mobility of resistance genes across bacterial populations. These insights highlight the urgent need for ongoing surveillance and the development of effective strategies to curb the proliferation of antibiotic resistance.},
}
@article {pmid38783209,
year = {2024},
author = {Gevin, M and Latifi, A and Talla, E},
title = {The modular architecture of sigma factors in cyanobacteria: a framework to assess their diversity and understand their evolution.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {512},
pmid = {38783209},
issn = {1471-2164},
support = {ANR-21-CE20-0025-01//Agence Nationale de la Recherche/ ; ANR-21-CE20-0025-01//Agence Nationale de la Recherche/ ; ANR-21-CE20-0025-01//Agence Nationale de la Recherche/ ; },
mesh = {*Sigma Factor/genetics/metabolism ; *Evolution, Molecular ; *Cyanobacteria/genetics/metabolism ; *Phylogeny ; Bacterial Proteins/genetics/metabolism ; Genetic Variation ; },
abstract = {BACKGROUND: Bacterial RNA polymerase holoenzyme requires sigma70 factors to start transcription by identifying promoter elements. Cyanobacteria possess multiple sigma70 factors to adapt to a wide variety of ecological niches. These factors are grouped into two categories: primary sigma factor initiates transcription of housekeeping genes during normal growth conditions, while alternative sigma factors initiate transcription of specific genes under particular conditions. However, the present classification does not consider the modular organization of their structural domains, introducing therefore multiple functional and structural biases. A comprehensive analysis of this protein family in cyanobacteria is needed to address these limitations.<br><br>RESULTS: We investigated the structure and evolution of sigma70 factors in cyanobacteria, analyzing their modular architecture and variation among unicellular, filamentous, and heterocyst-forming morphotypes. 4,193 sigma70 homologs were found with 59 distinct modular patterns, including six essential and 29 accessory domains, such as DUF6596. 90% of cyanobacteria typically have 5 to 17 sigma70 homologs and this number likely depends on the strain morphotype, the taxonomic order and the genome size. We classified sigma70 factors into 12 clans and 36 families. According to taxonomic orders and phenotypic traits, the number of homologs within the 14 main families was variable, with the A.1 family including the primary sigma factor since this family was found in all cyanobacterial species. The A.1, A.5, C.1, E.1, J.1, and K.1 families were found to be key sigma families that distinguish heterocyst-forming strains. To explain the diversification and evolution of sigma70, we propose an evolutionary scenario rooted in the diversification of a common ancestor of the A1 family. This scenario is characterized by evolutionary events including domain losses, gains, insertions, and modifications. The high occurrence of the DUF6596 domain in bacterial sigma70 proteins, and its association with the highest prevalence observed in Actinobacteria, suggests that this domain might be important for sigma70 function. It also implies that the domain could have emerged in Actinobacteria and been transferred through horizontal gene transfer.<br><br>CONCLUSION: Our analysis provides detailed insights into the modular domain architecture of sigma70, introducing a novel robust classification. It also proposes an evolutionary scenario explaining their diversity across different taxonomical orders.},
}
@article {pmid38781445,
year = {2024},
author = {Vuruputoor, VS and Starovoitov, A and Cai, Y and Liu, Y and Rahmatpour, N and Hedderson, TA and Wilding, N and Wegrzyn, JL and Goffinet, B},
title = {Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkae104},
pmid = {38781445},
issn = {2160-1836},
abstract = {The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana is presented here. Assembled from 73x nanopore long reads and 163x BGI-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes (BUSCO: C:94.8%[D:13.9%]). This genome holds two genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants and are thus interpreted as resulting from two unique horizontal gene transfers from microbes. Further, Physcomitrellopsis africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens, but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses, during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily "short" timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant Physcomitrellopsis africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events.},
}
@article {pmid38777914,
year = {2024},
author = {Zhang, F and Shi, X and Xu, J and Yuan, W and Li, Z},
title = {Tandem gene duplication selected by activation of horizontally transferred gene in bacteria.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {340},
pmid = {38777914},
issn = {1432-0614},
support = {2020YFA0908000//The National Key R&amp;D Program of China/ ; TSBICIP-CXRC-001//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project/ ; 2060302//Key project at central government level: The ability establishment of sustainable use for valuable Chinese medicine resource/ ; },
mesh = {*Gene Duplication ; *Gene Transfer, Horizontal ; *Escherichia coli/genetics/metabolism ; *Plasmids/genetics ; Bacteria/genetics/metabolism ; Gene Dosage ; Recombination, Genetic ; },
abstract = {Horizontal gene transfer occurs frequently in bacteria, but the mechanism driving activation and optimization of the expression of horizontally transferred genes (HTGs) in new recipient strains is not clear. Our previous study found that spontaneous tandem DNA duplication resulted in rapid activation of HTGs. Here, we took advantage of this finding to develop a novel technique for tandem gene duplication, named tandem gene duplication selected by activation of horizontally transferred gene in bacteria (TDAH), in which tandem duplication was selected by the activation of horizontally transferred selectable marker gene. TDAH construction does not contain any reported functional elements based on homologous or site-specific recombination and DNA amplification. TDAH only contains an essential selectable marker for copy number selection and 9-bp-microhomology border sequences for precise illegitimate recombination. One transformation and 3 days were enough to produce a high-copy strain, so its procedure is simple and fast. Without subsequent knockout of the endogenous recombination system, TDAH could also generate the relatively stable high-copy tandem duplication for plasmid-carried and genome-integrated DNA. TDAH also showed an excellent capacity for increase gene expression and worked well in different industrial bacteria. We also applied TDAH to select the optimal high copy number of ribA for vitamin B2 production in E. coli; the yield was improved by 3.5 times and remained stable even after 12 subcultures. TDAH is a useful tool for recombinant protein production and expression optimization of biosynthetic pathways. KEY POINTS: • We develop a novel and efficient technique (TDAH) for tandem gene duplication in bacterium. TDAH is based on the mechanism of HTG rapid activation. TDAH does not contain any reported functional elements based on homologous recombination and DNA amplification. TDAH only contains an essential selectable marker for copy number selection, so its construction and procedure are very simple and fast. • TDAH is the first reported selected and stable tandem-gene-duplication technique in which the selected high-copy plasmid-carried and genome-integrated DNA could remain stable without the subsequent knockout of recombination system. • TDAH showed an excellent capacity for regulating gene expression and worked well in different industrial bacteria, indicating it is a useful tool for recombinant protein production and expression optimization of biosynthetic pathways. • TDAH was applied to select the optimal high copy number of ribA for vitamin B2 production in E. coli; the yield was improved by 3.5-fold and remained stable even after 12 subcultures.},
}
@article {pmid38772228,
year = {2024},
author = {Xu, M and Gao, P and Gao, Y and Xiong, SJ and Chen, HQ and Shen, XX},
title = {Impacts of microplastic type on the fate of antibiotic resistance genes and horizontal gene transfer mechanism during anaerobic digestion.},
journal = {Journal of environmental management},
volume = {360},
number = {},
pages = {121090},
doi = {10.1016/j.jenvman.2024.121090},
pmid = {38772228},
issn = {1095-8630},
abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) are important pollutants in waste activated sludge (WAS), but their interactions during anaerobic digestion (AD) still need to be further explored. This study investigated variations in ARGs, mobile genetic elements (MGEs), and host bacteria during AD under the pressure of polyamide (PA), polyethylene (PE), and polypropylene (PP). The results showed that the MPs increased methane production by 11.7-35.5%, and decreased ARG abundance by 5.6-24.6%. Correlation analysis showed that the decrease of MGEs (plasmid, prophage, etc.) promoted the decrease of the abundance of multidrug, aminoglycoside and tetracycline resistance genes. Metagenomic annotation revealed that the reduction of key host bacteria (Arenimonas, Lautropia, etc.) reduced the abundance of major ARGs (rsmA, rpoB2, etc.). Moreover, PP MPs contributed to a reduction in the abundance of functional genes related to the production of reactive oxygen species, ATP synthesis, and cell membrane permeability, which was conducive to reducing the potential for horizontal gene transfer of ARGs. These findings provide insights into the treatment of organic waste containing MPs.},
}
@article {pmid38772218,
year = {2024},
author = {Kang, J and Zhang, C and Wan, S and Li, W and Zhao, W and Li, L and Shang, Y and Du, XD and Liu, D and Yao, H},
title = {Prevalence and characterization of aminoglycoside resistance gene aph(2")-If-carrying Campylobacter jejuni.},
journal = {International journal of food microbiology},
volume = {419},
number = {},
pages = {110747},
doi = {10.1016/j.ijfoodmicro.2024.110747},
pmid = {38772218},
issn = {1879-3460},
abstract = {Campylobacter jejuni is recognized as a significant foodborne pathogen, and recent studies have indicated a rising trend of aminoglycosides resistance gene aph(2″)-If among C. jejuni isolates from food-producing animals in China. However, systematic information about aph(2″)-If-positive C. jejuni from food-producing animals and other sources worldwide based on whole-genome analysis remains a knowledge gap. In this study, we aimed to analyze the worldwide distribution, genetic environment and phylogenetic tree of aph(2″)-If by utilizing Whole Genome Sequencing (WGS) data obtained, coupled with information in the GenBank database. A total of 160C. jejuni isolates in the GenBank database and 14C. jejuni isolates in our laboratory carrying aph(2″)-If gene were performed for further analysis. WGS analysis revealed the global distribution of aph(2″)-If among C. jejuni from 6 countries. Multilocus Sequence Typing(MLST) results indicated that 70 STs were involved in the dissemination of aph(2″)-If, with ST10086 being the predominant ST. Whole-genome Multilocus Sequence Typing(wg-MLST) analysis according to times, countries, and origins of C. jejuni isolation further demonstrated a close relationship between aph(2″)-If carrying C. jejuni isolates from farm and food. The findings also revealed the existence of 32 distinct types of genetic environments surrounding aph(2″)-If among these isolates. Notably, Type 30, characterized by the arrangement ISsag10-deoD-ant(9)-hp-hp-aph(2″)-If, emerged as the predominant genetic environment. In conclusion, our analysis provides the inaugural perspective on the worldwide distribution of aph(2″)-If. This resistance gene demonstrates horizontal transferability and regional diffusion in a clonal pattern. The close association observed among aph(2″)-If-positive C. jejuni strains isolated from poultry, food, and clinical environments underscores the potential for zoonotic transmission from these isolates.},
}
@article {pmid38771034,
year = {2024},
author = {Chong, TN and Shapiro, L},
title = {Bacterial cell differentiation enables population level survival strategies.},
journal = {mBio},
volume = {},
number = {},
pages = {e0075824},
doi = {10.1128/mbio.00758-24},
pmid = {38771034},
issn = {2150-7511},
abstract = {Clonal reproduction of unicellular organisms ensures the stable inheritance of genetic information. However, this means of reproduction lacks an intrinsic basis for genetic variation, other than spontaneous mutation and horizontal gene transfer. To make up for this lack of genetic variation, many unicellular organisms undergo the process of cell differentiation to achieve phenotypic heterogeneity within isogenic populations. Cell differentiation is either an inducible or obligate program. Induced cell differentiation can occur as a response to a stimulus, such as starvation or host cell invasion, or it can be a stochastic process. In contrast, obligate cell differentiation is hardwired into the organism's life cycle. Whether induced or obligate, bacterial cell differentiation requires the activation of a signal transduction pathway that initiates a global change in gene expression and ultimately results in a morphological change. While cell differentiation is considered a hallmark in the development of multicellular organisms, many unicellular bacteria utilize this process to implement survival strategies. In this review, we describe well-characterized cell differentiation programs to highlight three main survival strategies used by bacteria capable of differentiation: (i) environmental adaptation, (ii) division of labor, and (iii) bet-hedging.},
}
@article {pmid38618896,
year = {2024},
author = {Peng, X and Zhou, J and Lan, Z and Tan, R and Chen, T and Shi, D and Li, H and Yang, Z and Zhou, S and Jin, M and Li, JW and Yang, D},
title = {Carbonaceous particulate matter promotes the horizontal transfer of antibiotic resistance genes.},
journal = {Environmental science. Processes &amp; impacts},
volume = {26},
number = {5},
pages = {915-927},
doi = {10.1039/d3em00547j},
pmid = {38618896},
issn = {2050-7895},
mesh = {*Particulate Matter/analysis ; *Gene Transfer, Horizontal ; *Air Pollutants/analysis ; Drug Resistance, Microbial/genetics ; Particle Size ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; },
abstract = {There is growing concern about the transfer of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in airborne particulate matter. In this study, we investigated the effects of various types of carbonaceous particulate matter (CPM) on the transfer of ARGs in vitro. The results showed that CPM promoted the transfer of ARGs, which was related to the concentration and particle size. Compared with the control group, the transfer frequency was 95.5, 74.7, 65.4, 14.7, and 3.8 times higher in G (graphene), CB (carbon black), NGP (nanographite powder), GP1.6 (graphite powder 1.6 micron), and GP45 (graphite powder 45 micron) groups, respectively. Moreover, the transfer frequency gradually increased with the increase in CPM concentration, while there was a negative relationship between the CPM particle size and conjugative transfer frequency. In addition, the results showed that CPM could promote the transfer of ARGs by increasing ROS, as well as activating the SOS response and expression of conjugative transfer-related genes (trbBp, trfAp, korA, kroB, and trbA). These findings are indicative of the potential risk of CPM for the transfer of ARGs in the environment, enriching our understanding of environmental pollution and further raising awareness of environmental protection.},
}
@article {pmid38770060,
year = {2024},
author = {Tamayo-Leiva, J and Alcorta, J and Sepúlveda, F and Fuentes-Alburquenque, S and Arroyo, JI and González-Pastor, JE and Díez, B},
title = {Structure and dispersion of the conjugative mobilome in surface ocean bacterioplankton.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae059},
pmid = {38770060},
issn = {2730-6151},
abstract = {Mobile genetic elements (MGEs), collectively referred to as the "mobilome", can have a significant impact on the fitness of microbial communities and therefore on ecological processes. Marine MGEs have mainly been associated with wide geographical and phylogenetic dispersal of adaptative traits. However, whether the structure of this mobilome exhibits deterministic patterns in the natural community is still an open question. The aim of this study was to characterize the structure of the conjugative mobilome in the ocean surface bacterioplankton by searching the publicly available marine metagenomes from the TARA Oceans survey, together with molecular markers, such as relaxases and type IV coupling proteins of the type IV secretion system (T4SS). The T4SS machinery was retrieved in more abundance than relaxases in the surface marine bacterioplankton. Moreover, among the identified MGEs, mobilizable elements were the most abundant, outnumbering self-conjugative sequences. Detection of a high number of incomplete T4SSs provides insight into possible strategies related to trans-acting activity between MGEs, and accessory functions of the T4SS (e.g. protein secretion), allowing the host to maintain a lower metabolic burden in the highly dynamic marine system. Additionally, the results demonstrate a wide geographical dispersion of MGEs throughout oceanic regions, while the Southern Ocean appears segregated from other regions. The marine mobilome also showed a high similarity of functions present in known plasmid databases. Moreover, cargo genes were mostly related to DNA processing, but scarcely associated with antibiotic resistance. Finally, within the MGEs, integrative and conjugative elements showed wider marine geographic dispersion than plasmids.},
}
@article {pmid38769479,
year = {2024},
author = {Talat, A and Khan, F and Khan, AU},
title = {Genome analyses of colistin-resistant high-risk blaNDM-5 producing Klebsiella pneumoniae ST147 and Pseudomonas aeruginosa ST235 and ST357 in clinical settings.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {174},
pmid = {38769479},
issn = {1471-2180},
mesh = {*Klebsiella pneumoniae/genetics/drug effects/isolation &amp; purification ; *Pseudomonas aeruginosa/genetics/drug effects/isolation &amp; purification ; *Colistin/pharmacology ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Whole Genome Sequencing ; *Microbial Sensitivity Tests ; *Pseudomonas Infections/microbiology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Genome, Bacterial/genetics ; *Klebsiella Infections/microbiology ; Gene Transfer, Horizontal ; India ; beta-Lactamases/genetics ; Plasmids/genetics ; },
abstract = {BACKGROUND: Colistin is a last-resort antibiotic used in extreme cases of multi-drug resistant (MDR) Gram-negative bacterial infections. Colistin resistance has increased in recent years and often goes undetected due to the inefficiency of predominantly used standard antibiotic susceptibility tests (AST). To address this challenge, we aimed to detect the prevalence of colistin resistance strains through both Vitek®2 and broth micro-dilution. We investigated 1748 blood, tracheal aspirate, and pleural fluid samples from the Intensive Care Unit (ICU), Neonatal Intensive Care Unit (NICU), and Tuberculosis and Respiratory Disease centre (TBRD) in an India hospital. Whole-genome sequencing (WGS) of extremely drug-resitant (XDR) and pan-drug resistant (PDR) strains revealed the resistance mechanisms through the Resistance Gene Identifier (RGI.v6.0.0) and Snippy.v4.6.0. Abricate.v1.0.1, PlasmidFinder.v2.1, MobileElementFinder.v1.0.3 etc. detected virulence factors, and mobile genetic elements associated to uncover the pathogenecity and the role of horizontal gene transfer (HGT).<br><br>RESULTS: This study reveals compelling insights into colistin resistance among global high-risk clinical isolates: Klebsiella pneumoniae ST147 (16/20), Pseudomonas aeruginosa ST235 (3/20), and ST357 (1/20). Vitek&#xae;2 found 6 colistin-resistant strains (minimum inhibitory concentrations, MIC&#x2009;=&#x2009;4&#x2009;&#x3bc;g/mL), while broth microdilution identified 48 (MIC&#x2009;=&#x2009;32-128&#x2009;&#x3bc;g/mL), adhering to CLSI guidelines. Despite the absence of mobile colistin resistance (mcr) genes, mechanisms underlying colistin resistance included mgrB deletion, phosphoethanolamine transferases arnT, eptB, ompA, and mutations in pmrB (T246A, R256G) and eptA (V50L, A135P, I138V, C27F) in K. pneumoniae. P. aeruginosa harbored phosphoethanolamine transferases basS/pmrb, basR, arnA, cprR, cprS, alongside pmrB (G362S), and parS (H398R) mutations. Both strains carried diverse clinically relevant antimicrobial resistance genes (ARGs), including plasmid-mediated blaNDM-5 (K. pneumoniae ST147) and chromosomally mediated blaNDM-1 (P. aeruginosa ST357).<br><br>CONCLUSION: The global surge in MDR, XDR and PDR bacteria necessitates last-resort antibiotics such as colistin. However, escalating resistance, particularly to colistin, presents a critical challenge. Inefficient colistin resistance detection methods, including Vitek2, alongside limited surveillance resources, accentuate the need for improved strategies. Whole-genome sequencing revealed alarming colistin resistance among K. pneumoniae and P. aeruginosa in an Indian hospital. The identification of XDR and PDR strains underscores urgency for enhanced surveillance and infection control. SNP analysis elucidated resistance mechanisms, highlighting the complexity of combatting resistance.},
}
@article {pmid38767750,
year = {2024},
author = {S, V and T, J and E, AP and A, MHA},
title = {Antibiotic resistance of heterotrophic bacteria from the sediments of adjoining high Arctic fjords, Svalbard.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {38767750},
issn = {1678-4405},
abstract = {Antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) are now considered major global threats. The Kongsfjorden and Krossfjorden are the interlinked fjords in the Arctic that are currently experiencing the effects of climate change and receiving input of pollutants from distant and regional sources. The present study focused on understanding the prevalence of antibiotic resistance of retrievable heterotrophic bacteria from the sediments of adjacent Arctic fjords Kongsfjorden and Krossfjorden. A total of 237 bacterial isolates were tested against 16 different antibiotics. The higher resistance observed towards Extended Spectrum β-lactam antibiotic (ESBL) includes ceftazidime (45.56%) followed by trimethoprim (27%) and sulphamethizole (24.05%). The extent of resistance was meagre against tetracycline (2.53%) and gentamycin (2.95%). The 16S rRNA sequencing analysis identified that Proteobacteria (56%) were the dominant antibiotic resistant phyla, followed by Firmicutes (35%), Actinobacteria (8%) and Bacteroidetes. The dominant resistant bacterial isolates are Bacillus cereus (10%), followed by Alcaligenes faecalis (6.47%), Cytobacillus firmus (5.75%) Salinibacterium sp. (5%) and Marinobacter antarcticus (5%). Our study reveals the prevalence of antibiotic resistance showed significant differences in both the inner and outer fjords of Kongsfjorden and Krossfjorden (p < 0.05). This may be the input of antibiotic resistance bacteria released into the fjords from the preserved permafrost due to the melting of glaciers, horizontal gene transfer, and human influence in the Arctic region act as a selection pressure for the development and dissemination of more antibiotic resistant bacteria in Arctic fjords.},
}
@article {pmid38765968,
year = {2024},
author = {Mancuso, CP and Baker, JS and Qu, E and Tripp, AD and Balogun, IO and Lieberman, TD},
title = {Intraspecies warfare restricts strain coexistence in human skin microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.07.592803},
pmid = {38765968},
abstract = {Determining why only a fraction of encountered or applied bacterial strains engraft in a given person's microbiome is crucial for understanding and engineering these communities [1] . Previous work has established that metabolism can determine colonization success in vivo [2-4] , but relevance of bacterial warfare in preventing engraftment has been less explored. Here, we demonstrate that intraspecies warfare presents a significant barrier to strain transmission in the skin microbiome by profiling 14,884 pairwise interactions between Staphylococcus epidermidis cultured from eighteen human subjects from six families. We find that intraspecies antagonisms are abundant; these interactions are mechanistically diverse, independent of the relatedness between strains, and consistent with rapid evolution via horizontal gene transfer. Ability to antagonize more strains is associated with reaching a higher fraction of the on-person S. epidermidis community. Moreover, antagonisms are significantly depleted among strains residing on the same person relative to random assemblages. Two notable exceptions, in which bacteria evolved to become sensitive to antimicrobials found on the same host, are explained by mutations that provide phage resistance, contextualizing the importance of warfare among other lethal selective pressures. Taken together, our results emphasize that accounting for intraspecies bacterial warfare is essential to the design of long-lasting probiotic therapeutics.},
}
@article {pmid38695519,
year = {2024},
author = {Garrido, V and Arrieta-Gisasola, A and Migura-García, L and Laorden, L and Grilló, MJ},
title = {Multidrug resistance in Salmonella isolates of swine origin: mobile genetic elements and plasmids associated with cephalosporin resistance with potential transmission to humans.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {5},
pages = {e0026424},
doi = {10.1128/aem.00264-24},
pmid = {38695519},
issn = {1098-5336},
support = {IIQ14061.RI1//Direcci&#xf3;n General de Industria, Energia y Proyectos Estrategicos S3, Gobierno de Navarra (Department of Industry of the Government of Navarra)/ ; PA20/03//Centres de Recerca de Catalunya (CERCA)/ ; Grant PIF-19/290//Basque Country University (UPV/EHU)/ ; },
mesh = {Animals ; Swine/microbiology ; *Plasmids/genetics ; *Salmonella/genetics/drug effects/isolation &amp; purification ; *Interspersed Repetitive Sequences ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Humans ; Cephalosporin Resistance/genetics ; Salmonella Infections, Animal/microbiology ; Spain ; Swine Diseases/microbiology ; Cephalosporins/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {The emergence of foodborne Salmonella strains carrying antimicrobial resistance (AMR) in mobile genetic elements (MGE) is a significant public health threat in a One Health context requiring continuous surveillance. Resistance to ciprofloxacin and cephalosporins is of particular concern. Since pigs are a relevant source of foodborne Salmonella for human beings, we studied transmissible AMR genes and MGE in a collection of 83 strains showing 9 different serovars and 15 patterns of multidrug resistant (MDR) previously isolated from pigs raised in the conventional breeding system of Northern Spain. All isolates were susceptible to ciprofloxacin and three isolates carried blaCMY-2 or blaCTX-M-9 genes responsible for cefotaxime resistance. Filter mating experiments showed that the two plasmids carrying blaCTX-M-9 were conjugative while that carrying blaCMY-2 was self-transmissible by transformation. Whole-genome sequencing and comparative analyses were performed on the isolates and plasmids. The IncC plasmid pSB109, carrying blaCMY-2, was similar to one found in S. Reading from cattle, indicating potential horizontal transfer between serovars and animal sources. The IncHI2 plasmids pSH102 in S. Heidelberg and pSTM45 in S. Typhimurium ST34, carrying blaCTX-M-9, shared similar backbones and two novel "complex class 1 integrons" containing different AMR and heavy metal genes. Our findings emphasize the importance of sequencing techniques to identify emerging AMR regions in conjugative and stable plasmids from livestock production. The presence of MGE carrying clinically relevant AMR genes raises public health concerns, requiring monitoring to mitigate the emergence of bacteria carrying AMR genes and subsequent spread through animals and food.IMPORTANCEThe emergence of foodborne Salmonella strains carrying antimicrobial resistance (AMR) in mobile genetic elements (MGE) is a significant public health threat in a One Health context. Since pigs are a relevant source of foodborne Salmonella for humans, in this study, we investigate different aspects of AMR in a collection of 83 Salmonella showing nine different serovars and 15 patterns of multidrug resistant (MDR) isolated from pigs raised in the conventional breeding system. Our findings emphasize the importance of sequencing techniques to identify emerging AMR regions in conjugative and stable plasmids from livestock production. The presence of MGE carrying clinically relevant AMR genes raises public health concerns, requiring monitoring to mitigate the emergence of bacteria carrying AMR genes and subsequent spread through animals and food.},
}
@article {pmid38626826,
year = {2024},
author = {Zhang, J and Zhao, L and Wang, W and Zhang, Q and Wang, XT and Xing, DF and Ren, NQ and Lee, DJ and Chen, C},
title = {Large language model for horizontal transfer of resistance gene: From resistance gene prevalence detection to plasmid conjugation rate evaluation.},
journal = {The Science of the total environment},
volume = {931},
number = {},
pages = {172466},
doi = {10.1016/j.scitotenv.2024.172466},
pmid = {38626826},
issn = {1879-1026},
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Pseudomonas/genetics ; },
abstract = {The burgeoning issue of plasmid-mediated resistance genes (ARGs) dissemination poses a significant threat to environmental integrity. However, the prediction of ARGs prevalence is overlooked, especially for emerging ARGs that are potentially evolving gene exchange hotspot. Here, we explored to classify plasmid or chromosome sequences and detect resistance gene prevalence by using DNABERT. Initially, the DNABERT fine-tuned in plasmid and chromosome sequences followed by multilayer perceptron (MLP) classifier could achieve 0.764 AUC (Area under curve) on external datasets across 23 genera, outperforming 0.02 AUC than traditional statistic-based model. Furthermore, Escherichia, Pseudomonas single genera based model were also be trained to explore its predict performance to ARGs prevalence detection. By integrating K-mer frequency attributes, our model could boost the performance to predict the prevalence of ARGs in an external dataset in Escherichia with 0.0281-0.0615 AUC and Pseudomonas with 0.0196-0.0928 AUC. Finally, we established a random forest model aimed at forecasting the relative conjugation transfer rate of plasmids with 0.7956 AUC, drawing on data from existing literature. It identifies the plasmid's repression status, cellular density, and temperature as the most important factors influencing transfer frequency. With these two models combined, they provide useful reference for quick and low-cost integrated evaluation of resistance gene transfer, accelerating the process of computer-assisted quantitative risk assessment of ARGs transfer in environmental field.},
}
@article {pmid38765680,
year = {2024},
author = {Tan, BSY and Mohan, L and Watthanaworawit, W and Ngamprasertchai, T and Nosten, FH and Ling, C and Bifani, P},
title = {Detection of florfenicol resistance in opportunistic Acinetobacter spp. infections in rural Thailand.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1368813},
pmid = {38765680},
issn = {1664-302X},
abstract = {Florfenicol (Ff) is an antimicrobial agent belonging to the class amphenicol used for the treatment of bacterial infections in livestock, poultry, and aquaculture (animal farming). It inhibits protein synthesis. Ff is an analog of chloramphenicol, an amphenicol compound on the WHO essential medicine list that is used for the treatment of human infections. Due to the extensive usage of Ff in animal farming, zoonotic pathogens have developed resistance to this antimicrobial agent. There are numerous reports of resistance genes from organisms infecting or colonizing animals found in human pathogens, suggesting a possible exchange of genetic materials. One of these genes is floR, a gene that encodes for an efflux pump that removes Ff from bacterial cells, conferring resistance against amphenicol, and is often associated with mobile genetic elements and other resistant determinants. In this study, we analyzed bacterial isolates recovered in rural Thailand from patients and environmental samples collected for disease monitoring. Whole genome sequencing was carried out for all the samples collected. Speciation and genome annotation was performed revealing the presence of the floR gene in the bacterial genome. The minimum inhibitory concentration (MIC) was determined for Ff and chloramphenicol. Chromosomal and phylogenetic analyses were performed to investigate the acquisition pattern of the floR gene. The presence of a conserved floR gene in unrelated Acinetobacter spp. isolated from human bacterial infections and environmental samples was observed, suggesting multiple and independent inter-species genetic exchange of drug-resistant determinants. The floR was found to be in the variable region containing various mobile genetic elements and other antibiotic resistance determinants; however, no evidence of HGT could be found. The floR gene identified in this study is chromosomal for all isolates. The study highlights a plausible impact of antimicrobials used in veterinary settings on human health. Ff shares cross-resistance with chloramphenicol, which is still in use in several countries. Furthermore, by selecting for floR-resistance genes, we may be selecting for and facilitating the zoonotic and reverse zoonotic exchange of other flanking resistance markers between human and animal pathogens or commensals with detrimental public health consequences.},
}
@article {pmid38760381,
year = {2024},
author = {Nguyen, Q and Nguyen, YTP and Ha, TT and Tran, DTN and Voong, PV and Chau, V and Nguyen, PLN and Le, NTQ and Nguyen, LPH and Nguyen, TTN and Trinh, TV and Carrique-Mas, JJ and Baker, S and Thwaites, G and Rabaa, MA and Choisy, M and Chung, HT and Pham, DT},
title = {Genomic insights unveil the plasmid transfer mechanism and epidemiology of hypervirulent Klebsiella pneumoniae in Vietnam.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4187},
pmid = {38760381},
issn = {2041-1723},
support = {222983/Z/21/Z//Wellcome Trust (Wellcome)/ ; 0010734//Oxford University | John Fell Fund, University of Oxford (John Fell OUP Research Fund)/ ; },
mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/isolation &amp; purification ; Vietnam/epidemiology ; Humans ; *Plasmids/genetics ; *Klebsiella Infections/epidemiology/microbiology ; *Phylogeny ; *Whole Genome Sequencing ; Virulence/genetics ; Adult ; Female ; Gene Transfer, Horizontal ; Male ; Genome, Bacterial ; Middle Aged ; Anti-Bacterial Agents/pharmacology ; Child ; Genomics ; Drug Resistance, Bacterial/genetics ; },
abstract = {Hypervirulent Klebsiella pneumoniae (hvKp) is a significant cause of severe invasive infections in Vietnam, yet data on its epidemiology, population structure and dynamics are scarce. We screened hvKp isolates from patients with bloodstream infections (BSIs) at a tertiary infectious diseases hospital in Vietnam and healthy individuals, followed by whole genome sequencing and plasmid analysis. Among 700 BSI-causing Kp strains, 100 (14.3%) were hvKp. Thirteen hvKp isolates were identified from 350 rectal swabs of healthy adults; none from 500 rectal swabs of healthy children. The hvKp isolates were genetically diverse, encompassing 17 sequence types (STs), predominantly ST23, ST86 and ST65. Among the 113 hvKp isolates, 14 (12.6%) carried at least one antimicrobial resistance (AMR) gene, largely mediated by IncFII, IncR, and IncA/C plasmids. Notably, the acquisition of AMR conjugative plasmids facilitated horizontal transfer of the non-conjugative virulence plasmid between K. pneumoniae strains. Phylogenetic analysis demonstrated hvKp isolates from BSIs and human carriage clustered together, suggesting a significant role of intestinal carriage in hvKp transmission. Enhanced surveillance is crucial to understand the factors driving intestinal carriage and hvKp transmission dynamics for informing preventive measures. Furthermore, we advocate the clinical use of our molecular assay for diagnosing hvKp infections to guide effective management.},
}
@article {pmid38756985,
year = {2024},
author = {Roughgarden, J},
title = {Lytic/Lysogenic Transition as a Life-History Switch.},
journal = {Virus evolution},
volume = {10},
number = {1},
pages = {veae028},
pmid = {38756985},
issn = {2057-1577},
abstract = {The transition between lytic and lysogenic life cycles is the most important feature of the life-history of temperate viruses. To explain this transition, an optimal life-history model is offered based a discrete-time formulation of phage/bacteria population dynamics that features infection of bacteria by Poisson sampling of virions from the environment. The time step is the viral latency period. In this model, density-dependent viral absorption onto the bacterial surface produces virus/bacteria coexistence and density dependence in bacterial growth is not needed. The formula for the transition between lytic and lysogenic phases is termed the 'fitness switch'. According to the model, the virus switches from lytic to lysogenic when its population grows faster as prophage than as virions produced by lysis of the infected cells, and conversely for the switch from lysogenic to lytic. A prophage that benefits the bacterium it infects automatically incurs lower fitness upon exiting the bacterial genome, resulting in its becoming locked into the bacterial genome in what is termed here as a 'prophage lock'. The fitness switch qualitatively predicts the ecogeographic rule that environmental enrichment leads to microbialization with a concomitant increase in lysogeny, fluctuating environmental conditions promote virus-mediated horizontal gene transfer, and prophage-containing bacteria can integrate into the microbiome of a eukaryotic host forming a functionally integrated tripartite holobiont. These predictions accord more with the 'Piggyback-the-Winner' hypothesis than with the 'Kill-the-Winner' hypothesis in virus ecology.},
}
@article {pmid38756231,
year = {2024},
author = {Pobeguts, OV and Galaymina, MA and Sikamov, KV and Urazaeva, DR and Avshalumov, AS and Mikhailycheva, MV and Babenko, VV and Smirnov, IP and Gorbachev, AY},
title = {Unraveling the adaptive strategies of Mycoplasma hominis through proteogenomic profiling of clinical isolates.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1398706},
pmid = {38756231},
issn = {2235-2988},
mesh = {Humans ; *Mycoplasma hominis/genetics/metabolism ; *Proteogenomics ; *Mycoplasma Infections/microbiology ; *Adaptation, Physiological ; Biofilms/growth &amp; development ; Genome, Bacterial ; Phenotype ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial/genetics ; },
abstract = {INTRODUCTION: Mycoplasma hominis (M. hominis) belongs to the class Mollicutes, characterized by a very small genome size, reduction of metabolic pathways, including transcription factors, and the absence of a cell wall. Despite this, they adapt well not only to specific niches within the host organism but can also spread throughout the body, colonizing various organs and tissues. The adaptation mechanisms of M. hominis, as well as their regulatory pathways, are poorly understood. It is known that, when adapting to adverse conditions, Mycoplasmas can undergo phenotypic switches that may persist for several generations.<br><br>METHODS: To investigate the adaptive properties of M. hominis related to survival in the host, we conducted a comparative phenotypic and proteogenomic analysis of eight clinical isolates of M. hominis obtained from patients with urogenital infections and the laboratory strain H-34.<br><br>RESULTS: We have shown that clinical isolates differ in phenotypic features from the laboratory strain, form biofilms more effectively and show resistance to ofloxacin. The comparative proteogenomic analysis revealed that, unlike the laboratory strain, the clinical isolates possess several features related to stress survival: they switch carbon metabolism, activating the energetically least advantageous pathway of nucleoside utilization, which allows slowing down cellular processes and transitioning to a starvation state; they reconfigure the repertoire of membrane proteins; they have integrative conjugative elements in their genomes, which are key mediators of horizontal gene transfer. The upregulation of the methylating subunit of the restriction-modification (RM) system type I and the additional components of RM systems found in clinical isolates suggest that DNA methylation may play a role in regulating the adaptation mechanisms of M. hominis in the host organism. It has been shown that based on the proteogenomic profile, namely the genome sequence, protein content, composition of the RM systems and additional subunits HsdM, HsdS and HsdR, composition and number of transposable elements, as well as the sequence of the main variable antigen Vaa, we can divide clinical isolates into two phenotypes: typical colonies (TC), which have a high growth rate, and atypical (aTC) mini-colonies, which have a slow growth rate and exhibit properties similar to persisters.<br><br>DISCUSSION: We believe that the key mechanism of adaptation of M. hominis in the host is phenotypic restructuring, leading to a slowing down cellular processes and the formation of small atypical colonies. This is due to a switch in carbon metabolism and activation the pathway of nucleoside utilization. We hypothesize that DNA methylation may play a role in regulating this switch.},
}
@article {pmid38755134,
year = {2024},
author = {Fujino, T and Sonoda, R and Higashinagata, T and Mishiro-Sato, E and Kano, K and Murakami, H},
title = {Ser/Leu-swapped cell-free translation system constructed with natural/in vitro transcribed-hybrid tRNA set.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4143},
pmid = {38755134},
issn = {2041-1723},
support = {23H05456//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 21K05270//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {*Cell-Free System ; *Protein Biosynthesis ; *Escherichia coli/genetics/metabolism ; RNA, Transfer, Leu/genetics/metabolism ; RNA, Transfer, Ser/metabolism/genetics ; Genetic Code ; RNA, Transfer/genetics/metabolism ; Green Fluorescent Proteins/metabolism/genetics ; Protein Engineering/methods ; Transcription, Genetic ; Anticodon/genetics/metabolism ; },
abstract = {The Ser/Leu-swapped genetic code can act as a genetic firewall, mitigating biohazard risks arising from horizontal gene transfer in genetically modified organisms. Our prior work demonstrated the orthogonality of this swapped code to the standard genetic code using a cell-free translation system comprised of 21 in vitro transcribed tRNAs. In this study, to advance this system for protein engineering, we introduce a natural/in vitro transcribed-hybrid tRNA set. This set combines natural tRNAs from Escherichia coli (excluding Ser, Leu, and Tyr) and in vitro transcribed tRNAs, encompassing anticodon-swapped tRNA[Ser]GAG and tRNA[Leu]GGA. This approach reduces the number of in vitro transcribed tRNAs required from 21 to only 4. In this optimized system, the production of a model protein, superfolder green fluorescent protein, increases to 3.5-fold. With this hybrid tRNA set, the Ser/Leu-swapped cell-free translation system will stand as a potent tool for protein production with reduced biohazard concerns in future biological endeavors.},
}
@article {pmid38755022,
year = {2024},
author = {Figueroa, W and Cazares, D and Cazares, A},
title = {Phage-plasmids: missed links between mobile genetic elements.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2024.04.014},
pmid = {38755022},
issn = {1878-4380},
abstract = {Phages and plasmids are discrete mobile genetic elements (MGEs) with critical roles in gene dissemination across bacteria but limited scope for exchanging DNA between them. By investigating recent gene-sharing events, Pfeifer and Rocha describe how the hybrid elements phage-plasmids (P-Ps) promote gene flow between MGE types and evolve into new ones.},
}
@article {pmid38754503,
year = {2024},
author = {Wei, L and Han, Y and Zheng, J and Xu, X and Zhu, L},
title = {Accelerated dissemination of antibiotic resistant genes via conjugative transfer driven by deficient denitrification in biochar-based biofiltration systems.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {173268},
doi = {10.1016/j.scitotenv.2024.173268},
pmid = {38754503},
issn = {1879-1026},
abstract = {Biofiltration systems harbored and disseminated antibiotic resistance genes (ARGs), when confronting antibiotic-contained wastewater. Biochar, a widely used environmental remediation material, can mitigate antibiotic stress on adjoining microbes by lowering the availability of sorbed antibiotics, and enhance the attachment of denitrifiers. Herein, bench-scale biofiltration systems, packed with commercial biochars, were established to explore the pivotal drivers affecting ARG emergence. Results showed that biofiltration columns, achieving higher TN removal and denitrification capacity, showed a significant decrease in ARG accumulation (p < 0.05). The relative abundance of ARGs (0.014 ± 0.0008) in the attached biofilms decreased to 1/5-folds of that in the control group (0.065 ± 0.004). Functional analysis indicated ARGs' accumulation was less attributed to ARG activation or horizontal gene transfer (HGT) driven by sorbed antibiotics. Most denitrifiers, like Bradyrhizobium, Geothrix, etc., were found to be enriched and host ARGs. Nitrosative stress from deficient denitrification was demonstrated to be the dominant driver for affecting ARG accumulation and dissemination. Metagenomic and metaproteomic analysis revealed that nitrosative stress promoted the conjugative HGT of ARGs mainly via increasing the transmembrane permeability and enhancing the amino acid transport and metabolism, such as cysteine, methionine, and valine metabolism. Overall, this study highlighted the risks of deficient denitrification in promoting ARG transfer and transmission in biofiltration systems and natural ecosystems.},
}
@article {pmid38344902,
year = {2024},
author = {Macesic, N and Dennis, A and Hawkey, J and Vezina, B and Wisniewski, JA and Cottingham, H and Blakeway, LV and Harshegyi, T and Pragastis, K and Badoordeen, GZ and Bass, P and Stewardson, AJ and Dennison, A and Spelman, DW and Jenney, AWJ and Peleg, AY},
title = {Genomic investigation of multispecies and multivariant blaNDM outbreak reveals key role of horizontal plasmid transmission.},
journal = {Infection control and hospital epidemiology},
volume = {45},
number = {6},
pages = {709-716},
doi = {10.1017/ice.2024.8},
pmid = {38344902},
issn = {1559-6834},
mesh = {Humans ; *beta-Lactamases/genetics ; *Plasmids/genetics ; *Disease Outbreaks ; Male ; Female ; Middle Aged ; Aged ; Australia/epidemiology ; Whole Genome Sequencing ; Adult ; Enterobacteriaceae Infections/epidemiology/transmission/microbiology ; Gene Transfer, Horizontal ; Aged, 80 and over ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Genome, Bacterial ; },
abstract = {OBJECTIVES: New Delhi metallo-β-lactamases (NDMs) are major contributors to the spread of carbapenem resistance globally. In Australia, NDMs were previously associated with international travel, but from 2019 we noted increasing incidence of NDM-positive clinical isolates. We investigated the clinical and genomic epidemiology of NDM carriage at a tertiary-care Australian hospital from 2016 to 2021.<br><br>METHODS: We identified 49 patients with 84 NDM-carrying isolates in an institutional database, and we collected clinical data from electronic medical record. Short- and long-read whole genome sequencing was performed on all isolates. Completed genome assemblies were used to assess the genetic setting of blaNDM genes and to compare NDM plasmids.<br><br>RESULTS: Of 49 patients, 38 (78%) were identified in 2019-2021 and only 11 (29%) of 38 reported prior travel, compared with 9 (82%) of 11 in 2016-2018 (P = .037). In patients with NDM infection, the crude 7-day mortality rate was 0% and the 30-day mortality rate was 14% (2 of 14 patients). NDMs were noted in 41 bacterial strains (ie, species and sequence type combinations). Across 13 plasmid groups, 4 NDM variants were detected: blaNDM-1, blaNDM-4, blaNDM-5, and blaNDM-7. We noted a change from a diverse NDM plasmid repertoire in 2016-2018 to the emergence of conserved blaNDM-1 IncN and blaNDM-7 IncX3 epidemic plasmids, with interstrain spread in 2019-2021. These plasmids were noted in 19 (50%) of 38 patients and 35 (51%) of 68 genomes in 2019-2021.<br><br>CONCLUSIONS: Increased NDM case numbers were due to local circulation of 2 epidemic plasmids with extensive interstrain transfer. Our findings underscore the challenges of outbreak detection when horizontal transmission of plasmids is the primary mode of spread.},
}
@article {pmid38753980,
year = {2024},
author = {He, Z and Dechesne, A and Schreiber, F and Zhu, YG and Larsson, DGJ and Smets, BF},
title = {Understanding Stimulation of Conjugal Gene Transfer by Nonantibiotic Compounds: How Far Are We?.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.3c06060},
pmid = {38753980},
issn = {1520-5851},
abstract = {A myriad of nonantibiotic compounds is released into the environment, some of which may contribute to the dissemination of antimicrobial resistance by stimulating conjugation. Here, we analyzed a collection of studies to (i) identify patterns of transfer stimulation across groups and concentrations of chemicals, (ii) evaluate the strength of evidence for the proposed mechanisms behind conjugal stimulation, and (iii) examine the plausibility of alternative mechanisms. We show that stimulatory nonantibiotic compounds act at concentrations from 1/1000 to 1/10 of the minimal inhibitory concentration for the donor strain but that stimulation is always modest (less than 8-fold). The main proposed mechanisms for stimulation via the reactive oxygen species/SOS cascade and/or an increase in cell membrane permeability are not unequivocally supported by the literature. However, we identify the reactive oxygen species/SOS cascade as the most likely mechanism. This remains to be confirmed by firm molecular evidence. Such evidence and more standardized and high-throughput conjugation assays are needed to create technologies and solutions to limit the stimulation of conjugal gene transfer and contribute to mitigating global antibiotic resistance.},
}
@article {pmid38752994,
year = {2024},
author = {Ortiz Charneco, G and McDonnell, B and Kelleher, P and Buivydas, A and Dashko, S and de Waal, PP and van Rijswijck, I and van Peij, NNME and Mahony, J and Van Sinderen, D},
title = {Plasmid-mediated horizontal gene mobilisation: Insights from two lactococcal conjugative plasmids.},
journal = {Microbial biotechnology},
volume = {17},
number = {5},
pages = {e14421},
doi = {10.1111/1751-7915.14421},
pmid = {38752994},
issn = {1751-7915},
support = {//dsm-firmenich, Taste, Texture &amp; Health/ ; 12/RC/2273/SFI_/Science Foundation Ireland/Ireland ; 17/SP/4678/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {*Plasmids/genetics ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; Bacterial Proteins/genetics/metabolism ; Lactococcus lactis/genetics ; },
abstract = {The distinct conjugation machineries encoded by plasmids pNP40 and pUC11B represent the most prevalent plasmid transfer systems among lactococcal strains. In the current study, we identified genetic determinants that underpin pNP40- and pUC11B-mediated, high-frequency mobilisation of other, non-conjugative plasmids. The mobilisation frequencies of the smaller, non-conjugative plasmids and the minimal sequences required for their mobilisation were determined, owing to the determination of the oriT sequences of both pNP40 and pUC11B, which allowed the identification of similar sequences in some of the non-conjugative plasmids that were shown to promote their mobilisation. Furthermore, the auxiliary gene mobC, two distinct functional homologues of which are present in several plasmids harboured by the pNP40- and pUC11B-carrying host strains, was observed to confer a high-frequency mobilisation phenotype. These findings provide mechanistic insights into how lactococcal conjugative plasmids achieve conjugation and promote mobilisation of non-conjugative plasmids. Ultimately, these insights would be harnessed to optimise conjugation and mobilisation strategies for the rapid and predictable development of robust and technologically improved strains.},
}
@article {pmid38752745,
year = {2024},
author = {Tomasch, J and Kopejtka, K and Shivaramu, S and Mujakić, I and Koblížek, M},
title = {On the evolution of chromosomal regions with high gene strand bias in bacteria.},
journal = {mBio},
volume = {},
number = {},
pages = {e0060224},
doi = {10.1128/mbio.00602-24},
pmid = {38752745},
issn = {2150-7511},
abstract = {On circular bacterial chromosomes, the majority of genes are coded on the leading strand. This gene strand bias (GSB) ranges from up to 85% in some Bacillota to a little more than 50% in other phyla. The factors determining the extent of the strand bias remain to be found. Here, we report that species in the phylum Gemmatimonadota share a unique chromosome architecture, distinct from neighboring phyla: in a conserved 600-kb region around the terminus of replication, almost all genes were located on the leading strands, while on the remaining part of the chromosome, the strand preference was more balanced. The high strand bias (HSB) region harbors the rRNA clusters, core, and highly expressed genes. Selective pressure for reduction of collisions with DNA replication to minimize detrimental mutations can explain the conservation of essential genes in this region. Repetitive and mobile elements are underrepresented, suggesting reduced recombination frequency by structural isolation from other parts of the chromosome. We propose that the HSB region forms a distinct chromosomal domain. Gemmatimonadota chromosomes evolved mainly by expansion through horizontal gene transfer and duplications outside of the ancient high strand bias region. In support of our hypothesis, we could further identify two Spiroplasma strains on a similar evolutionary path.IMPORTANCEOn bacterial chromosomes, a preferred location of genes on the leading strand has evolved to reduce conflicts between replication and transcription. Despite a vast body of research, the question why bacteria show large differences in their gene strand bias is still not solved. The discovery of "hybrid" chromosomes in different phyla, including Gemmatimonadota, in which a conserved high strand bias is found exclusively in a region at ter, points toward a role of nucleoid structure, additional to replication, in the evolution of strand preferences. A fine-grained structural analysis of the ever-increasing number of available bacterial genomes could help to better understand the forces that shape the sequential and spatial organization of the cell's information content.},
}
@article {pmid38750628,
year = {2024},
author = {Mrnjavac, N and Nagies, FSP and Wimmer, JLE and Kapust, N and Knopp, MR and Trost, K and Modjewski, L and Bremer, N and Mentel, M and Esposti, MD and Mizrahi, I and Allen, JF and Martin, WF},
title = {The radical impact of oxygen on prokaryotic evolution-enzyme inhibition first, uninhibited essential biosyntheses second, aerobic respiration third.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.14906},
pmid = {38750628},
issn = {1873-3468},
support = {1426/23-1//German-Israeli Project Cooperation (DIP)/ ; 2476/2-1//German-Israeli Project Cooperation (DIP)/ ; 96742//Volkswagen Foundation/ ; 101018894//H2020 European Research Council/ ; 1/0457/24//Scientific Grant Agency of the Ministry of Education of the Slovak Republic (VEGA)/ ; MA 1426/21-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Molecular oxygen is a stable diradical. All O2-dependent enzymes employ a radical mechanism. Generated by cyanobacteria, O2 started accumulating on Earth 2.4 billion years ago. Its evolutionary impact is traditionally sought in respiration and energy yield. We mapped 365 O2-dependent enzymatic reactions of prokaryotes to phylogenies for the corresponding 792 protein families. The main physiological adaptations imparted by O2-dependent enzymes were not energy conservation, but novel organic substrate oxidations and O2-dependent, hence O2-tolerant, alternative pathways for O2-inhibited reactions. Oxygen-dependent enzymes evolved in ancestrally anaerobic pathways for essential cofactor biosynthesis including NAD[+], pyridoxal, thiamine, ubiquinone, cobalamin, heme, and chlorophyll. These innovations allowed prokaryotes to synthesize essential cofactors in O2-containing environments, a prerequisite for the later emergence of aerobic respiratory chains.},
}
@article {pmid38747597,
year = {2024},
author = {Stindt, KR and McClean, MN},
title = {Tuning interdomain conjugation to enable in situ population modification in yeasts.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0005024},
doi = {10.1128/msystems.00050-24},
pmid = {38747597},
issn = {2379-5077},
abstract = {The ability to modify and control natural and engineered microbiomes is essential for biotechnology and biomedicine. Fungi are critical members of most microbiomes, yet technology for modifying the fungal members of a microbiome has lagged far behind that for bacteria. Interdomain conjugation (IDC) is a promising approach, as DNA transfer from bacterial cells to yeast enables in situ modification. While such genetic transfers have been known to naturally occur in a wide range of eukaryotes and are thought to contribute to their evolution, IDC has been understudied as a technique to control fungal or fungal-bacterial consortia. One major obstacle to the widespread use of IDC is its limited efficiency. In this work, we manipulated metabolic and physical interactions between genetically tractable Escherichia coli and Saccharomyces cerevisiae to control the incidence of IDC. We test the landscape of population interactions between the bacterial donors and yeast recipients to find that bacterial commensalism leads to maximized IDC, both in culture and in mixed colonies. We demonstrate the capacity of cell-to-cell binding via mannoproteins to assist both IDC incidence and bacterial commensalism in culture and model how these tunable controls can predictably yield a range of IDC outcomes. Furthermore, we demonstrate that these controls can be utilized to irreversibly alter a recipient yeast population, by both "rescuing" a poor-growing recipient population and collapsing a stable population via a novel IDC-mediated CRISPR/Cas9 system.IMPORTANCEFungi are important but often unaddressed members of most natural and synthetic microbial communities. This work highlights opportunities for modifying yeast microbiome populations through bacterial conjugation. While conjugation has been recognized for its capacity to deliver engineerable DNA to a range of cells, its dependence on cell contact has limited its efficiency. Here, we find "knobs" to control DNA transfer, by engineering the metabolic dependence between bacterial donors and yeast recipients and by changing their ability to physically adhere to each other. Importantly, we functionally validate these "knobs" by irreversibly altering yeast populations. We use these controls to "rescue" a failing yeast population, demonstrate the capacity of conjugated CRISPR/Cas9 to depress or collapse populations, and show that conjugation can be easily interrupted by disrupting cell-to-cell binding. These results offer building blocks toward in situ mycobiome editing, with significant implications for clinical treatments of fungal pathogens and other fungal system engineering.},
}
@article {pmid38746121,
year = {2024},
author = {García-Bayona, L and Said, N and Coyne, MJ and Flores, K and Elmekki, NM and Sheahan, ML and Camacho, AG and Hutt, K and Yildiz, FH and Kovács, &#xc1;T and Waldor, MK and Comstock, LE},
title = {A pervasive large conjugative plasmid mediates multispecies biofilm formation in the intestinal microbiota increasing resilience to perturbations.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.29.590671},
pmid = {38746121},
abstract = {Although horizontal gene transfer is pervasive in the intestinal microbiota, we understand only superficially the roles of most exchanged genes and how the mobile repertoire affects community dynamics. Similarly, little is known about the mechanisms underlying the ability of a community to recover after a perturbation. Here, we identified and functionally characterized a large conjugative plasmid that is one of the most frequently transferred elements among Bacteroidales species and is ubiquitous in diverse human populations. This plasmid encodes both an extracellular polysaccharide and fimbriae, which promote the formation of multispecies biofilms in the mammalian gut. We use a hybridization-based approach to visualize biofilms in clarified whole colon tissue with unprecedented 3D spatial resolution. These biofilms increase bacterial survival to common stressors encountered in the gut, increasing strain resiliency, and providing a rationale for the plasmid's recent spread and high worldwide prevalence.},
}
@article {pmid38743630,
year = {2024},
author = {Dewar, AE and Hao, C and Belcher, LJ and Ghoul, M and West, SA},
title = {Bacterial lifestyle shapes pangenomes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {21},
pages = {e2320170121},
doi = {10.1073/pnas.2320170121},
pmid = {38743630},
issn = {1091-6490},
support = {834164//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; },
mesh = {*Genome, Bacterial ; *Bacteria/genetics/classification ; *Phylogeny ; },
abstract = {Pangenomes vary across bacteria. Some species have fluid pangenomes, with a high proportion of genes varying between individual genomes. Other species have less fluid pangenomes, with different genomes tending to contain the same genes. Two main hypotheses have been suggested to explain this variation: differences in species' bacterial lifestyle and effective population size. However, previous studies have not been able to test between these hypotheses because the different features of lifestyle and effective population size are highly correlated with each other, and phylogenetically conserved, making it hard to disentangle their relative importance. We used phylogeny-based analyses, across 126 bacterial species, to tease apart the causal role of different factors. We found that pangenome fluidity was lower in i) host-associated compared with free-living species and ii) host-associated species that are obligately dependent on a host, live inside cells, and are more pathogenic and less motile. In contrast, we found no support for the competing hypothesis that larger effective population sizes lead to more fluid pangenomes. Effective population size appears to correlate with pangenome variation because it is also driven by bacterial lifestyle, rather than because of a causal relationship.},
}
@article {pmid38742878,
year = {2024},
author = {Mies, US and Hervé, V and Kropp, T and Platt, K and Sillam-Dussès, D and Šobotník, J and Brune, A},
title = {Genome reduction and horizontal gene transfer in the evolution of Endomicrobia-rise and fall of an intracellular symbiosis with termite gut flagellates.},
journal = {mBio},
volume = {},
number = {},
pages = {e0082624},
doi = {10.1128/mbio.00826-24},
pmid = {38742878},
issn = {2150-7511},
abstract = {Bacterial endosymbionts of eukaryotic hosts typically experience massive genome reduction, but the underlying evolutionary processes are often obscured by the lack of free-living relatives. Endomicrobia, a family-level lineage of host-associated bacteria in the phylum Elusimicrobiota that comprises both free-living representatives and endosymbionts of termite gut flagellates, are an excellent model to study evolution of intracellular symbionts. We reconstructed 67 metagenome-assembled genomes (MAGs) of Endomicrobiaceae among more than 1,700 MAGs from the gut microbiota of a wide range of termites. Phylogenomic analysis confirmed a sister position of representatives from termites and ruminants, and allowed to propose eight new genera in the radiation of Endomicrobiaceae. Comparative genome analysis documented progressive genome erosion in the new genus Endomicrobiellum, which comprises all flagellate endosymbionts characterized to date. Massive gene losses were accompanied by the acquisition of new functions by horizontal gene transfer, which led to a shift from a glucose-based energy metabolism to one based on sugar phosphates. The breakdown of glycolysis and many anabolic pathways for amino acids and cofactors in several subgroups was compensated by the independent acquisition of new uptake systems, including an ATP/ADP antiporter, from other gut microbiota. The putative donors are mostly flagellate endosymbionts from other bacterial phyla, including several, hitherto unknown lineages of uncultured Alphaproteobacteria, documenting the importance of horizontal gene transfer in the convergent evolution of these intracellular symbioses. The loss of almost all biosynthetic capacities in some lineages of Endomicrobiellum suggests that their originally mutualistic relationship with flagellates is on its decline.IMPORTANCEUnicellular eukaryotes are frequently colonized by bacterial and archaeal symbionts. A prominent example are the cellulolytic gut flagellates of termites, which harbor diverse but host-specific bacterial symbionts that occur exclusively in termite guts. One of these lineages, the so-called Endomicrobia, comprises both free-living and endosymbiotic representatives, which offers the unique opportunity to study the evolutionary processes underpinning the transition from a free-living to an intracellular lifestyle. Our results revealed a progressive gene loss in energy metabolism and biosynthetic pathways, compensated by the acquisition of new functions via horizontal gene transfer from other gut bacteria, and suggest the eventual breakdown of an initially mutualistic symbiosis. Evidence for convergent evolution of unrelated endosymbionts reflects adaptations to the intracellular environment of termite gut flagellates.},
}
@article {pmid38741889,
year = {2024},
author = {Carrera Páez, LC and Olivier, M and Gambino, AS and Poklepovich, T and Aguilar, AP and Quiroga, MP and Centrón, D},
title = {Sporadic clone Escherichia coli ST615 as a vector and reservoir for dissemination of crucial antimicrobial resistance genes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1368622},
pmid = {38741889},
issn = {2235-2988},
mesh = {*Escherichia coli/genetics/drug effects ; *Plasmids/genetics ; Humans ; *Escherichia coli Infections/microbiology ; *beta-Lactamases/genetics ; *Gene Transfer, Horizontal ; *Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Escherichia coli Proteins/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Latin America ; Drug Resistance, Bacterial/genetics ; },
abstract = {There is scarce information concerning the role of sporadic clones in the dissemination of antimicrobial resistance genes (ARGs) within the nosocomial niche. We confirmed that the clinical Escherichia coli M19736 ST615 strain, one of the first isolates of Latin America that harbors a plasmid with an mcr-1 gene, could receive crucial ARG by transformation and conjugation using as donors critical plasmids that harbor bla CTX-M-15, bla KPC-2, bla NDM-5, bla NDM-1, or aadB genes. Escherichia coli M19736 acquired bla CTX-M-15, bla KPC-2, bla NDM-5, bla NDM-1, and aadB genes, being only blaNDM-1 maintained at 100% on the 10th day of subculture. In addition, when the evolved MDR-E. coli M19736 acquired sequentially bla CTX-M-15 and bla NDM-1 genes, the maintenance pattern of the plasmids changed. In addition, when the evolved XDR-E. coli M19736 acquired in an ulterior step the paadB plasmid, a different pattern of the plasmid's maintenance was found. Interestingly, the evolved E. coli M19736 strains disseminated simultaneously the acquired conjugative plasmids in different combinations though selection was ceftazidime in all cases. Finally, we isolated and characterized the extracellular vesicles (EVs) from the native and evolved XDR-E. coli M19736 strains. Interestingly, EVs from the evolved XDR-E. coli M19736 harbored bla CTX-M-15 though the pDCAG1-CTX-M-15 was previously lost as shown by WGS and experiments, suggesting that EV could be a relevant reservoir of ARG for susceptible bacteria. These results evidenced the genetic plasticity of a sporadic clone of E. coli such as ST615 that could play a relevant transitional link in the clinical dynamics and evolution to multidrug/extensively/pandrug-resistant phenotypes of superbugs within the nosocomial niche by acting simultaneously as a vector and reservoir of multiple ARGs which later could be disseminated.},
}
@article {pmid38741746,
year = {2024},
author = {Ghaly, TM and Gillings, MR and Rajabal, V and Paulsen, IT and Tetu, SG},
title = {Horizontal gene transfer in plant microbiomes: integrons as hotspots for cross-species gene exchange.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1338026},
pmid = {38741746},
issn = {1664-302X},
abstract = {Plant microbiomes play important roles in plant health and fitness. Bacterial horizontal gene transfer (HGT) can influence plant health outcomes, driving the spread of both plant growth-promoting and phytopathogenic traits. However, community dynamics, including the range of genetic elements and bacteria involved in this process are still poorly understood. Integrons are genetic elements recently shown to be abundant in plant microbiomes, and are associated with HGT across broad phylogenetic boundaries. They facilitate the spread of gene cassettes, small mobile elements that collectively confer a diverse suite of adaptive functions. Here, we analysed 5,565 plant-associated bacterial genomes to investigate the prevalence and functional diversity of integrons in this niche. We found that integrons are particularly abundant in the genomes of Pseudomonadales, Burkholderiales, and Xanthomonadales. In total, we detected nearly 9,000 gene cassettes, and found that many could be involved in plant growth promotion or phytopathogenicity, suggesting that integrons might play a role in bacterial mutualistic or pathogenic lifestyles. The rhizosphere was enriched in cassettes involved in the transport and metabolism of diverse substrates, suggesting that they may aid in adaptation to this environment, which is rich in root exudates. We also found that integrons facilitate cross-species HGT, which is particularly enhanced in the phyllosphere. This finding may provide an ideal opportunity to promote plant growth by fostering the spread of genes cassettes relevant to leaf health. Together, our findings suggest that integrons are important elements in plant microbiomes that drive HGT, and have the potential to facilitate plant host adaptation.},
}
@article {pmid38741126,
year = {2024},
author = {Blanco-Melo, D and Campbell, MA and Zhu, H and Dennis, TPW and Modha, S and Lytras, S and Hughes, J and Gatseva, A and Gifford, RJ},
title = {A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {120},
pmid = {38741126},
issn = {1474-760X},
support = {MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; *Vertebrates/genetics/virology ; *Genome ; *Fossils ; *Phylogeny ; Evolution, Molecular ; Humans ; Gene Transfer, Horizontal ; Viruses/genetics ; Genomics/methods ; Endogenous Retroviruses/genetics ; DNA Transposable Elements ; },
abstract = {BACKGROUND: Genomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (EVEs)-virus-derived sequences that can dramatically impact host biology and serve as a virus fossil record. In this study, we introduce a database-integrated genome screening (DIGS) approach to investigate the dark genome in silico, focusing on EVEs found within vertebrate genomes.<br><br>RESULTS: Using DIGS on 874 vertebrate genomes, we uncover approximately 1.1 million EVE sequences, with over 99% originating from endogenous retroviruses or transposable elements that contain EVE DNA. We show that the remaining 6038 sequences represent over a thousand distinct horizontal gene transfer events across 10 virus families, including some that have not previously been reported as EVEs. We explore the genomic and phylogenetic characteristics of non-retroviral EVEs and determine their rates of acquisition during vertebrate evolution. Our study uncovers novel virus diversity, broadens knowledge of virus distribution among vertebrate hosts, and provides new insights into the ecology and evolution of vertebrate viruses.<br><br>CONCLUSIONS: We comprehensively catalog and analyze EVEs within 874 vertebrate genomes, shedding light on the distribution, diversity, and long-term evolution of viruses and reveal their extensive impact on vertebrate genome evolution. Our results demonstrate the power of linking a relational database management system to a similarity search-based screening pipeline for in silico exploration of the dark genome.},
}
@article {pmid38738821,
year = {2024},
author = {Liao, L and Qin, Q and Yi, D and Lai, Q and Cong, B and Zhang, H and Shao, Z and Zhang, J and Chen, B},
title = {Evolution and adaptation of terrestrial plant-associated Plantibacter species into remote marine environments.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17385},
doi = {10.1111/mec.17385},
pmid = {38738821},
issn = {1365-294X},
support = {2022YFC2807501//National Key Research and Development Program of China/ ; 2023YFC2812600//National Key Research and Development Program of China/ ; 41976224//National Natural Science Foundation of China/ ; },
abstract = {Microbes are thought to be distributed and circulated around the world, but the connection between marine and terrestrial microbiomes remains largely unknown. We use Plantibacter, a representative genus associated with plants, as our research model to investigate the global distribution and adaptation of plant-related bacteria in plant-free environments, particularly in the remote Southern Ocean and the deep Atlantic Ocean. The marine isolates and their plant-associated relatives shared over 98% whole-genome average nucleotide identity (ANI), indicating recent divergence and ongoing speciation from plant-related niches to marine environments. Comparative genomics revealed that the marine strains acquired new genes via horizontal gene transfer from non-Plantibacter species and refined existing genes through positive selection to improve adaptation to new habitats. Meanwhile, marine strains retained the ability to interact with plants, such as modifying root system architecture and promoting germination. Furthermore, Plantibacter species were found to be widely distributed in marine environments, revealing an unrecognized phenomenon that plant-associated microbiomes have colonized the ocean, which could serve as a reservoir for plant growth-promoting microbes. This study demonstrates the presence of an active reservoir of terrestrial plant growth-promoting bacteria in remote marine systems and advances our understanding of the microbial connections between plant-associated and plant-free environments at the genome level.},
}
@article {pmid38736754,
year = {2024},
author = {Singh, H and Gibb, B and Abdi, R},
title = {Abundance and diversity of methicillin-resistant bacteria from bathroom surfaces at workplaces using CHROMagar media, 16S, and dnaJ gene sequence typing.},
journal = {International journal of molecular epidemiology and genetics},
volume = {15},
number = {2},
pages = {12-21},
pmid = {38736754},
issn = {1948-1756},
abstract = {University campus communities consist of dynamic and diverse human populations originated from different regions of the country or the world. Their national/global movement to and from campus may contribute to the spread and buildup of methicillin-resistant (MR) bacteria, including MR Staphylococci (MRS) on high-touch surfaces, sinks, and toilets. However, studies on MR bacteria contamination of surfaces, sinks, and toilets are scarce in workplaces outside of healthcare settings. Hence, little is known whether university communities contaminate campus bathrooms by MR bacteria. This study evaluated the abundance, identity, and phylogenetics of MR bacteria grown on CHROMagar MRSA media from bathrooms at workplaces. We collected 21 sink and 21 toilet swab samples from 10 buildings on campus and cultured them on CHROMagar MRSA media, extracted DNA from MR bacteria colonies, sequenced PCR products of 16S and dnaJ primers, determined the sequence identities by BLAST search, and constructed a phylogenetic tree. Of 42 samples, 57.1% (24/42) harbored MR bacteria. MR bacteria were more prevalent on the sink (61.9%) than in the toilet (52.2%) and in male bathrooms (54.2%) than in female bathrooms (41.7%). The colony count on the bathroom surfaces of 42 samples varied in that 42.9% (18/42), 33.3, 14.3, and 9.5% of samples harbored 0, 100, and > 1000 MR bacteria colonies, respectively. Of MR bacteria sequenced, BLAST search and phylogenetic analysis showed that Staphylococcus accounted for 60% of the MR bacteria and the rest were non-Staphylococci. Of Staphylococcus carrying MR (n = 15), 53.3% were S. hemolyticus followed by S. lugdunensis (26.7%), S. epidermidis (8%), and a newly discovered S. borealis in 2020 (4%). Of non-Staphylococci MR bacteria, 20% accounted for Sphingomonas koreensis. Campus bathrooms serve as a reservoir for diverse bacteria carrying MR, which pose a direct risk of infection and a potential source of horizontal gene transfer. To reduce the health risk posed by MR bacteria in high traffic areas such as bathrooms additional environmental monitoring and improved decontamination practices are needed.},
}
@article {pmid38733792,
year = {2024},
author = {Musat, F and Kjeldsen, KU and Rotaru, AE and Chen, SC and Musat, N},
title = {Archaea oxidizing alkanes through alkyl-coenzyme M reductases.},
journal = {Current opinion in microbiology},
volume = {79},
number = {},
pages = {102486},
doi = {10.1016/j.mib.2024.102486},
pmid = {38733792},
issn = {1879-0364},
abstract = {This review synthesizes recent discoveries of novel archaea clades capable of oxidizing higher alkanes, from volatile ones like ethane to longer-chain alkanes like hexadecane. These archaea, termed anaerobic multicarbon alkane-oxidizing archaea (ANKA), initiate alkane oxidation using alkyl-coenzyme M reductases, enzymes similar to the methyl-coenzyme M reductases of methanogenic and anaerobic methanotrophic archaea (ANME). The polyphyletic alkane-oxidizing archaea group (ALOX), encompassing ANME and ANKA, harbors increasingly complex alkane degradation pathways, correlated with the alkane chain length. We discuss the evolutionary trajectory of these pathways emphasizing metabolic innovations and the acquisition of metabolic modules via lateral gene transfer. Additionally, we explore the mechanisms by which archaea couple alkane oxidation with the reduction of electron acceptors, including electron transfer to partner sulfate-reducing bacteria (SRB). The phylogenetic and functional constraints that shape ALOX-SRB associations are also discussed. We conclude by highlighting the research needs in this emerging research field and its potential applications in biotechnology.},
}
@article {pmid38733104,
year = {2024},
author = {Quiñonero-Coronel, MDM and Devos, DP and Garcillán-Barcia, MP},
title = {Specificities and commonalities of the Planctomycetes plasmidome.},
journal = {Environmental microbiology},
volume = {26},
number = {5},
pages = {e16638},
doi = {10.1111/1462-2920.16638},
pmid = {38733104},
issn = {1462-2920},
support = {9733//Moore-Simons Project on the Origin of the Eukaryotic Cell/ ; FPU20/04579//Ministerio de Universidades/ ; PID2020-117923GB-I0//Ministerio de Ciencia e Innovaci&#xf3;n/ ; },
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; Bacteria/genetics/classification ; Bacterial Proteins/genetics ; Conjugation, Genetic ; Phylogeny ; Planctomycetales/genetics ; Evolution, Molecular ; Replication Origin/genetics ; },
abstract = {Plasmids, despite their critical role in antibiotic resistance and modern biotechnology, are understood in only a few bacterial groups in terms of their natural ecological dynamics. The bacterial phylum Planctomycetes, known for its unique molecular and cellular biology, has a largely unexplored plasmidome. This study offers a thorough exploration of the diversity of natural plasmids within Planctomycetes, which could serve as a foundation for developing various genetic research tools for this phylum. Planctomycetes plasmids encode a broad range of biological functions and appear to have coevolved significantly with their host chromosomes, sharing many homologues. Recent transfer events of insertion sequences between cohabiting chromosomes and plasmids were also observed. Interestingly, 64% of plasmid genes are distantly related to either chromosomally encoded genes or have homologues in plasmids from other bacterial groups. The planctomycetal plasmidome is composed of 36% exclusive proteins. Most planctomycetal plasmids encode a replication initiation protein from the Replication Protein A family near a putative iteron-containing replication origin, as well as active type I partition systems. The identification of one conjugative and three mobilizable plasmids suggests the occurrence of horizontal gene transfer via conjugation within this phylum. This comprehensive description enhances our understanding of the plasmidome of Planctomycetes and its potential implications in antibiotic resistance and biotechnology.},
}
@article {pmid38728817,
year = {2024},
author = {Wen, X and Xu, J and Worrich, A and Li, X and Yuan, X and Ma, B and Zou, Y and Wang, Y and Liao, X and Wu, Y},
title = {Priority establishment of soil bacteria in rhizosphere limited the spread of tetracycline resistance genes from pig manure to soil-plant systems based on synthetic communities approach.},
journal = {Environment international},
volume = {187},
number = {},
pages = {108732},
doi = {10.1016/j.envint.2024.108732},
pmid = {38728817},
issn = {1873-6750},
abstract = {The spread of antibiotic resistance genes (ARGs) in agroecosystems through the application of animal manure is a global threat to human and environmental health. However, the adaptability and colonization ability of animal manure-derived bacteria determine the spread pathways of ARG in agroecosystems, which have rarely been studied. Here, we performed an invasion experiment by creating a synthetic communities (SynCom) with ten isolates from pig manure and followed its assembly during gnotobiotic cultivation of a soil-Arabidopsis thaliana (A. thaliana) system. We found that Firmicutes in the SynCom were efficiently filtered out in the rhizosphere, thereby limiting the entry of tetracycline resistance genes (TRGs) into the plant. However, Proteobacteria and Actinobacteria in the SynCom were able to establish in all compartments of the soil-plant system thereby spreading TRGs from manure to soil and plant. The presence of native soil bacteria prevented the establishment of manure-borne bacteria and effectively reduced the spread of TRGs. Achromobacter mucicolens and Pantoea septica were the main vectors for the entry of tetA into plants. Furthermore, doxycycline stress promoted the horizontal gene transfer (HGT) of the conjugative resistance plasmid RP4 within the SynCom in A. thaliana by upregulating the expression of HGT-related mRNAs. Therefore, this study provides evidence for the dissemination pathways of ARGs in agricultural systems through the invasion of manure-derived bacteria and HGT by conjugative resistance plasmids and demonstrates that the priority establishment of soil bacteria in the rhizosphere limited the spread of TRGs from pig manure to soil-plant systems.},
}
@article {pmid38727238,
year = {2024},
author = {Lee, D-H and Lee, K and Kim, Y-S and Cha, C-J},
title = {Comprehensive genomic landscape of antibiotic resistance in Staphylococcus epidermidis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0022624},
doi = {10.1128/msystems.00226-24},
pmid = {38727238},
issn = {2379-5077},
abstract = {UNLABELLED: Staphylococcus epidermidis, a common commensal bacterium found on human skin, can cause infections in clinical settings, and the presence of antibiotic resistance genes (ARGs) impedes the treatment of S. epidermidis infections. However, studies characterizing the ARGs in S. epidermidis with regard to genomic and ecological diversities are limited. Thus, we performed a comprehensive and comparative analysis of 405 high-quality S. epidermidis genomes, including those of 35 environmental isolates from the Han River, to investigate the genomic diversity of antibiotic resistance in this pathogen. Comparative genomic analysis revealed the prevalence of ARGs in S. epidermidis genomes associated with multi-locus sequence types. The genes encoding dihydrofolate reductase (dfrC) and multidrug efflux pump (norA) were genome-wide core ARGs. β-Lactam class ARGs were also highly prevalent in the S. epidermidis genomes, which was consistent with the resistance phenotype observed in river isolates. Furthermore, we identified chloramphenicol acetyltransferase genes (cat) in the plasmid-like sequences of the six river isolates, which have not been reported previously in S. epidermidis genomes. These genes were identical to those harbored by the Enterococcus faecium plasmids and associated with the insertion sequence 6 family transposases, homologous to those found in Staphylococcus aureus plasmids, suggesting the possibility of horizontal gene transfer between these Gram-positive pathogens. Comparison of the ARG and virulence factor profiles between S. epidermidis and S. aureus genomes revealed that these two species were clearly distinguished, suggesting genomic demarcation despite ecological overlap. Our findings provide a comprehensive understanding of the genomic diversity of antibiotic resistance in S. epidermidis.<br><br>IMPORTANCE: A comprehensive understanding of the antibiotic resistance gene (ARG) profiles of the skin commensal bacterium and opportunistic pathogen Staphylococcus epidermidis needs to be documented from a genomic point of view. Our study encompasses a comparative analysis of entire S. epidermidis genomes from various habitats, including those of 35 environmental isolates from the Han River sequenced in this study. Our results shed light on the distribution and diversity of ARGs within different S. epidermidis multi-locus sequence types, providing valuable insights into the ecological and genetic factors associated with antibiotic resistance. A comparison between S. epidermidis and Staphylococcus aureus revealed marked differences in ARG and virulence factor profiles, despite their overlapping ecological niches.},
}
@article {pmid38721599,
year = {2024},
author = {Yang, Z and Chai, Z and Wang, X and Zhang, Z and Zhang, F and Kang, F and Liu, W and Ren, H and Jin, Y and Yue, J},
title = {Comparative genomic analysis provides insights into the genetic diversity and pathogenicity of the genus Brucella.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1389859},
pmid = {38721599},
issn = {1664-302X},
abstract = {Some Brucella spp. are important pathogens. According to the latest prokaryotic taxonomy, the Brucella genus consists of facultative intracellular parasitic Brucella species and extracellular opportunistic or environmental Brucella species. Intracellular Brucella species include classical and nonclassical types, with different species generally exhibiting host preferences. Some classical intracellular Brucella species can cause zoonotic brucellosis, including B. melitensis, B. abortus, B. suis, and B. canis. Extracellular Brucella species comprise opportunistic or environmental species which belonged formerly to the genus Ochrobactrum and thus nowadays renamed as for example Brucella intermedia or Brucella anthropi, which are the most frequent opportunistic human pathogens within the recently expanded genus Brucella. The cause of the diverse phenotypic characteristics of different Brucella species is still unclear. To further investigate the genetic evolutionary characteristics of the Brucella genus and elucidate the relationship between its genomic composition and prediction of phenotypic traits, we collected the genomic data of Brucella from the NCBI Genome database and conducted a comparative genomics study. We found that classical and nonclassical intracellular Brucella species and extracellular Brucella species exhibited differences in phylogenetic relationships, horizontal gene transfer and distribution patterns of mobile genetic elements, virulence factor genes, and antibiotic resistance genes, showing the close relationship between the genetic variations and prediction of phenotypic traits of different Brucella species. Furthermore, we found significant differences in horizontal gene transfer and the distribution patterns of mobile genetic elements, virulence factor genes, and antibiotic resistance genes between the two chromosomes of Brucella, indicating that the two chromosomes had distinct dynamics and plasticity and played different roles in the survival and evolution of Brucella. These findings provide new directions for exploring the genetic evolutionary characteristics of the Brucella genus and could offer new clues to elucidate the factors influencing the phenotypic diversity of the Brucella genus.},
}
@article {pmid38717818,
year = {2024},
author = {Nair, S and Barker, CR and Bird, M and Greig, DR and Collins, C and Painset, A and Chattaway, M and Pickard, D and Larkin, L and Gharbia, S and Didelot, X and Ribeca, P},
title = {Presence of phage-plasmids in multiple serovars of Salmonella enterica.},
journal = {Microbial genomics},
volume = {10},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001247},
pmid = {38717818},
issn = {2057-5858},
mesh = {*Plasmids/genetics ; *Salmonella enterica/virology/genetics ; *Serogroup ; Salmonella Infections/microbiology ; Bacteriophages/genetics/classification ; Salmonella Phages/genetics/classification ; Humans ; Phylogeny ; Gene Transfer, Horizontal ; Retrospective Studies ; },
abstract = {Evidence is accumulating in the literature that the horizontal spread of antimicrobial resistance (AMR) genes mediated by bacteriophages and bacteriophage-like plasmid (phage-plasmid) elements is much more common than previously envisioned. For instance, we recently identified and characterized a circular P1-like phage-plasmid harbouring a bla CTX-M-15 gene conferring extended-spectrum beta-lactamase (ESBL) resistance in Salmonella enterica serovar Typhi. As the prevalence and epidemiological relevance of such mechanisms has never been systematically assessed in Enterobacterales, in this study we carried out a follow-up retrospective analysis of UK Salmonella isolates previously sequenced as part of routine surveillance protocols between 2016 and 2021. Using a high-throughput bioinformatics pipeline we screened 47 784 isolates for the presence of the P1 lytic replication gene repL, identifying 226 positive isolates from 25 serovars and demonstrating that phage-plasmid elements are more frequent than previously thought. The affinity for phage-plasmids appears highly serovar-dependent, with several serovars being more likely hosts than others; most of the positive isolates (170/226) belonged to S. Typhimurium ST34 and ST19. The phage-plasmids ranged between 85.8 and 98.2 kb in size, with an average length of 92.1 kb; detailed analysis indicated a high amount of diversity in gene content and genomic architecture. In total, 132 phage-plasmids had the p0111 plasmid replication type, and 94 the IncY type; phylogenetic analysis indicated that both horizontal and vertical gene transmission mechanisms are likely to be involved in phage-plasmid propagation. Finally, phage-plasmids were present in isolates that were resistant and non-resistant to antimicrobials. In addition to providing a first comprehensive view of the presence of phage-plasmids in Salmonella, our work highlights the need for a better surveillance and understanding of phage-plasmids as AMR carriers, especially through their characterization with long-read sequencing.},
}
@article {pmid38717786,
year = {2024},
author = {Zhang, Y and Wang, J and Yu, J},
title = {PSA: an effective method for predicting horizontal gene transfers through parsimonious phylogenetic networks.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/cla.12578},
pmid = {38717786},
issn = {1096-0031},
support = {NJYT24036//2024 Youth Science and Technology Talent Development Project (Youth Science and Technology Talents) of Education Department of Inner Mongolia Autonomous Region of China/ ; NMGIRT2318//University Youth Science and Technology Talent Development Project (Innovation Group Development Plan) of Inner Mongolia A. R. of China/ ; 2022MS01002//Natural Science Foundation of Inner Mongolia Province/ ; 12002175//National Natural Science Foundation of China/ ; 62002181//National Natural Science Foundation of China/ ; 62061035//National Natural Science Foundation of China/ ; },
abstract = {Horizontal gene transfer (HGT) from one organism to another, according to some researchers, can be abundant in the evolution of species. A phylogenetic network is a network structure that describes the HGTs among species. Several studies have proposed methods to construct phylogenetic networks to predict HGTs based on parsimony values. Existing definitions of parsimony values for a phylogenetic network are based on the assumption that each gene site or segment evolves independently along different trees in the network. However, in the current study, we define a novel parsimony value, denoted the p definition, for phylogenetic networks, considering that a gene as a whole typically evolves along a tree. Using Simulated Annealing, a new method called the Phylogeny with Simulated Annealing (PSA) algorithm is proposed to search for an optimal network based on the p definition. The PSA method is tested on the simulated data. The results reveal that the parsimonious networks constructed using PSA can better represent the evolutionary relationships of species involving HGTs. Additionally, the HGTs predicted using PSA are more accurate than those predicted using other methods. The PSA algorithm is publicly accessible at http://github.com/imustu/sap.},
}
@article {pmid38716477,
year = {2024},
author = {Cheewapat, R and Redkimned, J and Lekuthai, S and Kitti, T and Tasanapak, K and Thanwisai, A and Sitthisak, S and Sornda, T and Impheng, H and Onsurathum, S and Leungtongkam, U and Lamlertthon, S and Kucharoenphaibul, S and Wongwigkarn, J and Singkum, P and Chanchaithong, P and Thummeepak, R},
title = {Genomic Landscape Reveals Chromosomally-Mediated Antimicrobial Resistome and Virulome of a High-Risk International Clone II Acinetobacter baumannii AB073 from Thailand.},
journal = {Global health, epidemiology and genomics},
volume = {2024},
number = {},
pages = {8872463},
pmid = {38716477},
issn = {2054-4200},
mesh = {*Acinetobacter baumannii/genetics/drug effects ; Thailand/epidemiology ; *Acinetobacter Infections/microbiology/epidemiology/drug therapy ; Humans ; Genome, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Drug Resistance, Multiple, Bacterial/genetics ; Carbapenems/pharmacology ; Virulence/genetics ; },
abstract = {This study utilized integrative bioinformatics' tools together with phenotypic assays to understand the whole-genome features of a carbapenem-resistant international clone II Acinetobacter baumannii AB073. Overall, we found the isolate to be resistant to seven antibiotic classes, penicillins, β-lactam/β-lactamase inhibitor combinations, cephalosporins, carbapenems, aminoglycosides, fluoroquinolones, and folate pathway antagonists. These resistance phenotypes are related to various chromosomal-located antibiotic resistance determinants involved in different mechanisms such as reduced permeability, antibiotic target protection, antibiotic target alteration, antibiotic inactivation, and antibiotic efflux. IC2 A. baumannii AB073 could not transfer antibiotic resistance by conjugation experiments. Likewise, mobilome analysis found that AB073 did not carry genetic determinants involving horizontal gene transfer. Moreover, this isolate also carried multiple genes associated with the ability of iron uptake, biofilm formation, immune invasion, virulence regulations, and serum resistance. In addition, the genomic epidemiological study showed that AB073-like strains were successful pathogens widespread in various geographic locations and clinical sources. In conclusion, the comprehensive analysis demonstrated that AB073 contained multiple genomic determinants which were important characteristics to classify this isolate as a successful international clone II obtained from Thailand.},
}
@article {pmid38714248,
year = {2024},
author = {Wang, S and Tian, R and Bi, Y and Meng, F and Zhang, R and Wang, C and Wang, D and Liu, L and Zhang, B},
title = {A review of distribution and functions of extracellular DNA in the environment and wastewater treatment systems.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {142264},
doi = {10.1016/j.chemosphere.2024.142264},
pmid = {38714248},
issn = {1879-1298},
abstract = {Extracellular DNA referred to DNA fragments existing outside the cell, originating from various cell release mechanisms, including active secretion, cell lysis, and phage-mediated processes. Extracellular DNA serves as a vital environmental biomarker, playing crucial ecological and environmental roles in water bodies. This review is summarized the mechanisms of extracellular DNA release, including pathways involving cell lysis, extracellular vesicles, and type IV secretion systems. Then, the extraction and detection methods of extracellular DNA from water, soil, and biofilm are described and analyzed. Finally, we emphasize the role of extracellular DNA in microbial community systems, including its significant contributions to biofilm formation, biodiversity through horizontal gene transfer (HGT), and electron transfer processes. This review offers a comprehensive insight into the sources, distribution, functions, and impacts of extracellular DNA within aquatic environments, aiming to foster further exploration and understanding of extracellular DNA dynamics in aquatic environments as well as other environments.},
}
@article {pmid38714231,
year = {2024},
author = {Wang, YL and Ikuma, K and Brown, AMV and Deonarine, A},
title = {Global survey of hgcA-carrying genomes in marine and freshwater sediments: Insights into mercury methylation processes.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {124117},
doi = {10.1016/j.envpol.2024.124117},
pmid = {38714231},
issn = {1873-6424},
abstract = {Mercury (Hg) methylation is a microbially mediated process that produces methylmercury (MeHg), a bioaccumulative neurotoxin. A highly conserved gene pair, hgcAB, is required for Hg methylation, which provides a basis for identifying Hg methylators and evaluating their genomic composition. In this study, we conducted a large-scale omics analysis in which 281 metagenomic freshwater and marine sediment samples from 46 geographic locations across the globe were queried. Specific objectives were to examine the prevalence of Hg methylators, to identify horizontal gene transfer (HGT) events involving hgcAB within Hg methylator communities, and to identify associations between hgcAB and microbial biochemical functions/genes. Hg methylators from the phyla Desulfobacterota and Bacteroidota were dominant in both freshwater and marine sediments while Firmicutes and methanogens belonging to Euryarchaeota were identified only in freshwater sediments. Novel Hg methylators were found in the Phycisphaerae and Planctomycetia classes within the phylum Planctomycetota, including potential hgcA-carrying anammox metagenome-assembled genomes (MAGs) from Candidatus Brocadiia. HGT of hgcA and hgcB were identified in both freshwater and marine methylator communities. Spearman's correlation analysis of methylator genomes suggested that in addition to sulfide, thiosulfate, sulfite, and ammonia may be important parameters for Hg methylation processes in sediments. Overall, our results indicated that the biochemical drivers of Hg methylation vary between marine and freshwater sites, lending insight into the influence of environmental perturbances, such as a changing climate, on Hg methylation processes.},
}
@article {pmid38712952,
year = {2024},
author = {Fidopiastis, PM and Childs, C and Esin, JJ and Stellern, J and Darin, A and Lorenzo, A and Mariscal, VT and Lorenz, J and Gopan, V and McAnulty, S and Visick, KL},
title = {Corrected and republished from: "Vibrio fischeri Possesses Xds and Dns Nucleases That Differentially Influence Phosphate Scavenging, Aggregation, Competence, and Symbiotic Colonization of Squid".},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0032824},
doi = {10.1128/aem.00328-24},
pmid = {38712952},
issn = {1098-5336},
abstract = {Cells of Vibrio fischeri colonize the light organ of Euprymna scolopes, providing the squid bioluminescence in exchange for nutrients and protection. The bacteria encounter DNA-rich mucus throughout their transition to a symbiotic lifestyle, leading us to hypothesize a role for nuclease activity in the colonization process. In support of this, we detected abundant extracellular nuclease activity in growing cells of V. fischeri. To discover the gene(s) responsible for this activity, we screened a V. fischeri transposon mutant library for nuclease-deficient strains. Interestingly, only one strain, whose transposon insertion mapped to nuclease gene VF_1451, showed a complete loss of nuclease activity in our screens. A database search revealed that VF_1451 is homologous to the nuclease-encoding gene xds in Vibrio cholerae. However, V. fischeri strains lacking xds eventually revealed slight nuclease activity on plates upon prolonged incubation. This led us to hypothesize that a second secreted nuclease, identified through a database search as VF_0437, a homolog of V. cholerae dns, might be responsible for the residual nuclease activity. Here, we show that Xds and/or Dns are involved in essential aspects of V. fischeri biology, including natural transformation, aggregation, and phosphate scavenging. Furthermore, strains lacking either nuclease were outcompeted by the wild type for squid colonization. Understanding the specific role of nuclease activity in the squid colonization process represents an intriguing area of future research.IMPORTANCEFrom soil and water to host-associated secretions such as mucus, environments that bacteria inhabit are awash in DNA. Extracellular DNA (eDNA) is a nutritious resource that microbes dedicate significant energy to exploit. Calcium binds eDNA to promote cell-cell aggregation and horizontal gene transfer. eDNA hydrolysis impacts the construction of and dispersal from biofilms. Strategies in which pathogens use nucleases to avoid phagocytosis or disseminate by degrading host secretions are well-documented; significantly less is known about nucleases in mutualistic associations. This study describes the role of nucleases in the mutualism between Vibrio fischeri and its squid host Euprymna scolopes. We find that nuclease activity is an important determinant of colonization in V. fischeri, broadening our understanding of how microbes establish and maintain beneficial associations.},
}
@article {pmid38712904,
year = {2024},
author = {Muelbaier, H and Arthen, F and Collins, G and Hickler, T and Hohberg, K and Lehmitz, R and Pauchet, Y and Pfenninger, M and Potapov, A and Romahn, J and Schaefer, I and Scheu, S and Schneider, C and Ebersberger, I and Bálint, M},
title = {Genomic evidence for the widespread presence of GH45 cellulases among soil invertebrates.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17351},
doi = {10.1111/mec.17351},
pmid = {38712904},
issn = {1365-294X},
support = {LOEWE/1/10/519/03/03.001(0014)/52//Landes-Offensive zur Entwicklung Wissenschaftlich-&#xf6;konomischer Exzellenz (LOEWE)/ ; BA 4843/4-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Lignocellulose is a major component of vascular plant biomass. Its decomposition is crucial for the terrestrial carbon cycle. Microorganisms are considered primary decomposers, but evidence increases that some invertebrates may also decompose lignocellulose. We investigated the taxonomic distribution and evolutionary origins of GH45 hydrolases, important enzymes for the decomposition of cellulose and hemicellulose, in a collection of soil invertebrate genomes. We found that these genes are common in springtails and oribatid mites. Phylogenetic analysis revealed that cellulase genes were acquired early in the evolutionary history of these groups. Domain architectures and predicted 3D enzyme structures indicate that these cellulases are functional. Patterns of presence and absence of these genes across different lineages prompt further investigation into their evolutionary and ecological benefits. The ubiquity of cellulase genes suggests that soil invertebrates may play a role in lignocellulose decomposition, independently or in synergy with microorganisms. Understanding the ecological and evolutionary implications might be crucial for understanding soil food webs and the carbon cycle.},
}
@article {pmid38712252,
year = {2024},
author = {Buck, CB and Welch, N and Belford, AK and Varsani, A and Pastrana, DV and Tisza, MJ and Starrett, GJ},
title = {Widespread Horizontal Gene Transfer Among Animal Viruses.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.03.25.586562},
pmid = {38712252},
abstract = {The initial objective of this study was to shed light on the evolution of small DNA tumor viruses by analyzing de novo assemblies of publicly available deep sequencing datasets. The survey generated a searchable database of contig snapshots representing more than 100,000 Sequence Read Archive records. Using modern structure-aware search tools, we iteratively broadened the search to include an increasingly wide range of other virus families. The analysis revealed a surprisingly diverse range of chimeras involving different virus groups. In some instances, genes resembling known DNA-replication modules or known virion protein operons were paired with unrecognizable sequences that structural predictions suggest may represent previously unknown replicases and novel virion architectures. Discrete clades of an emerging group called adintoviruses were discovered in datasets representing humans and other primates. As a proof of concept, we show that the contig database is also useful for discovering RNA viruses and candidate archaeal phages. The ancillary searches revealed additional examples of chimerization between different virus groups. The observations support a gene-centric taxonomic framework that should be useful for future virus-hunting efforts.},
}
@article {pmid38710287,
year = {2024},
author = {Zuo, Y and Yang, J and Zhang, H and Li, L and Luo, J and Lv, Y and Yuan, M and Yang, K},
title = {Genome comparison of long-circulating field CnmeGV isolates from the same region.},
journal = {Virus research},
volume = {},
number = {},
pages = {199390},
doi = {10.1016/j.virusres.2024.199390},
pmid = {38710287},
issn = {1872-7492},
abstract = {Cnaphalocrocis medinalis granulovirus (CnmeGV), belonging to Betabaculovirus cnamedinalis, can infect the rice pest, the rice leaf roller. In 1979, a CnmeGV isolate, CnmeGV-EP, was collected from Enping County, China. In 2014, we collected another CnmeGV isolate, CnmeGV-EPDH3, at the same location and obtained the complete virus genome sequence using Illumina and ONT sequencing technologies. By combining these two virus isolates, we updated the genome annotation of CnmeGV and conducted an in-depth analysis of its genome features. CnmeGV genome contains abundant tandem repeat sequences, and the repeating units in the homologous regions (hrs) exhibit overlapping and nested patterns. The genetic variations within EPDH3 population show the high stability of CnmeGV genome, and tandem repeats are the only region of high genetic variation in CnmeGV genome replication. Some defective viral genomes formed by recombination were found within the population. Comparison analysis of the two virus isolates collected from Enping showed that the proteins encoded by the CnmeGV-specific genes were less conserved relative to the baculovirus core genes. At the genomic level, there are a large number of SNPs and InDels between the two virus isolates, especially in and around the bro genes and hrs. Additionally, we discovered that CnmeGV acquired a segment of non-ORF sequence from its host, which does not provide any new proteins but rather serves as redundant genetic material integrated into the viral genome. Furthermore, we observed that the host's transposon piggyBac has inserted into some virus genes. Together, dsDNA viruses could acquire non-coding genetic material from their hosts to expand the size of their genomes. These findings provide new insights into the evolution of dsDNA viruses.},
}
@article {pmid38710286,
year = {2024},
author = {Zhao, F and Wang, J},
title = {Another piece of the puzzle for the human microbiome: the gut virome under dietary modulation.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2024.04.013},
pmid = {38710286},
issn = {1673-8527},
abstract = {The virome is the most abundant and highly variable microbial consortium in the gut. Because of difficulties in isolating and culturing gut viruses and consequently shorting of reference genomes, the virome has remained a relatively elusive aspect of the human microbiome. In recent years, studies on the virome have accumulated growing evidence showing that the virome is diet-modulated and widely involved in regulating health. Here, we review the responses of the gut virome to dietary intake and the potential health implications, presenting changes in the gut viral community, preferences of viral members to particular diets. We further discuss how viral-bacterial interactions and phage lifestyle shifts shape the gut microbiota. We also discuss the specific functions conferred by diet on the gut virome and bacterial community in the context of horizontal gene transfer, as well as the import of new viral members along with the diet. Collating these studies will expand our understanding of the dietary regulation of the gut virome and inspire dietary interventions and health maintenance strategies targeting the gut microbiota.},
}
@article {pmid38707295,
year = {2024},
author = {Cochran, JP and Zhang, L and Parrott, BB and Seaman, JC},
title = {Plasmid size determines adsorption to clay and breakthrough in a saturated sand column.},
journal = {Heliyon},
volume = {10},
number = {9},
pages = {e29679},
pmid = {38707295},
issn = {2405-8440},
abstract = {Horizontal gene transfer (HGT) is a major factor in the spread of antibiotic resistant genes (ARG). Transformation, one mode of HGT, involves the acquisition and expression of extracellular DNA (eDNA). eDNA in soils is degraded rapidly by extracellular nucleases. However, if bound to a clay particle, eDNA can persist for long periods of time without losing its transformation ability. To better understand the mechanism of eDNA persistence in soil, this experiment assessed the effects of 1) clay mineralogy, 2) mixed salt solution, 3) plasmid size on DNA adsorption to clay and 4) breakthrough behavior of three differently sized plasmids in an environmentally relevant solution. Batch test methods were used to determine adsorption trends of three differently sized DNA plasmids, pUC19, pBR322, and pTYB21, to several pure clay minerals, goethite (α-FeOOH), illite, and kaolinite, and one environmental soil sample. Results show not all sorbents have equal adsorption capacity based on surface area with adsorption capacities decreasing from goethite > illite = kaolinite > bulk soil, and low ionic strength solutions will likely not significantly alter sorption trends. Additionally, plasmid DNA size (i.e., length) was shown to be a significant predictor of adsorption efficiency and that size affects DNA breakthrough, with breakthroughs occurring later with larger plasmids. Given that DNA persistence is linked to its adsorption to soil constituents and breakthrough, eDNA size is likely an important contributor to the spread of ARG within natural microbial communities.},
}
@article {pmid38458877,
year = {2024},
author = {Wilson, CG and Pieszko, T and Nowell, RW and Barraclough, TG},
title = {Recombination in bdelloid rotifer genomes: asexuality, transfer and stress.},
journal = {Trends in genetics : TIG},
volume = {40},
number = {5},
pages = {422-436},
doi = {10.1016/j.tig.2024.02.001},
pmid = {38458877},
issn = {0168-9525},
mesh = {Animals ; *Rotifera/genetics/physiology ; *Gene Transfer, Horizontal/genetics ; *Recombination, Genetic ; *Stress, Physiological/genetics ; Reproduction, Asexual/genetics ; Genome/genetics ; Genome, Helminth ; Phylogeny ; Male ; },
abstract = {Bdelloid rotifers constitute a class of microscopic animals living in freshwater habitats worldwide. Several strange features of bdelloids have drawn attention: their ability to tolerate desiccation and other stresses, a lack of reported males across the clade despite centuries of study, and unusually high numbers of horizontally acquired, non-metazoan genes. Genome sequencing is transforming our understanding of their lifestyle and its consequences, while in turn providing wider insights about recombination and genome organisation in animals. Many questions remain, not least how to reconcile apparent genomic signatures of sex with the continued absence of reported males, why bdelloids have so many horizontally acquired genes, and how their remarkable ability to survive stress interacts with recombination and other genomic processes.},
}
@article {pmid38705616,
year = {2024},
author = {Bui, QTN and Kim, HS and Ki, JS},
title = {Polyphyletic origin of saxitoxin biosynthesis genes in the marine dinoflagellate Alexandrium revealed by comparative transcriptomics.},
journal = {Harmful algae},
volume = {134},
number = {},
pages = {102620},
doi = {10.1016/j.hal.2024.102620},
pmid = {38705616},
issn = {1878-1470},
mesh = {*Dinoflagellida/genetics/metabolism ; *Saxitoxin/genetics/biosynthesis ; *Phylogeny ; *Transcriptome ; Gene Expression Profiling ; Evolution, Molecular ; },
abstract = {The marine dinoflagellate Alexandrium is known to form harmful algal blooms, and at least 14 species within the genus can produce saxitoxins (STXs). STX biosynthesis genes (sxt) are individually revealed in toxic dinoflagellates; however, the evolutionary history remains controversial. Herein, we determined the transcriptome sequences of toxic Alexandrium (A. catenella and A. pacificum) and non-toxic Alexandrium (A. fraterculus and A. fragae) and characterized their sxt by focusing on evolutionary events and STX production. Comparative transcriptome analysis revealed higher homology of the sxt in toxic Alexandrium than in non-toxic species. Notably, non-toxic Alexandrium spp. were found to have lost two sxt core genes, namely sxtA4 and sxtG. Expression levels of 28 transcripts related to eight sxt core genes showed that sxtA, sxtG, and sxtI were relatively high (>1.5) in the toxic group compared to the non-toxic group. In contrast, the non-toxic group showed high expression levels in sxtU (1.9) and sxtD (1.7). Phylogenetic tree comparisons revealed distinct evolutionary patterns between 28S rDNA and sxtA, sxtB, sxtI, sxtD, and sxtU. However, similar topology was observed between 28S rDNA, sxtS, and sxtH/T. In the sxtB and sxtI phylogeny trees, toxic Alexandrium and cyanobacteria were clustered together, separating from non-toxic species. These suggest that Alexandrium may acquire sxt genes independently via horizontal gene transfer from toxic cyanobacteria and other multiple sources, demonstrating monocistronic transcripts of sxt in dinoflagellates.},
}
@article {pmid38705297,
year = {2024},
author = {Xu, Q and Ali, S and Afzal, M and Nizami, AS and Han, S and Dar, MA and Zhu, D},
title = {Advancements in bacterial chemotaxis: Utilizing the navigational intelligence of bacteria and its practical applications.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172967},
doi = {10.1016/j.scitotenv.2024.172967},
pmid = {38705297},
issn = {1879-1026},
abstract = {The fascinating world of microscopic life unveils a captivating spectacle as bacteria effortlessly maneuver through their surroundings with astonishing accuracy, guided by the intricate mechanism of chemotaxis. This review explores the complex mechanisms behind this behavior, analyzing the flagellum as the driving force and unraveling the intricate signaling pathways that govern its movement. We delve into the hidden costs and benefits of this intricate skill, analyzing its potential to propagate antibiotic resistance gene while shedding light on its vital role in plant colonization and beneficial symbiosis. We explore the realm of human intervention, considering strategies to manipulate bacterial chemotaxis for various applications, including nutrient cycling, algal bloom and biofilm formation. This review explores the wide range of applications for bacterial capabilities, from targeted drug delivery in medicine to bioremediation and disease control in the environment. Ultimately, through unraveling the intricacies of bacterial movement, we can enhance our comprehension of the intricate web of life on our planet. This knowledge opens up avenues for progress in fields such as medicine, agriculture, and environmental conservation.},
}
@article {pmid38704526,
year = {2024},
author = {Kobakhidze, S and Koulouris, S and Kakabadze, N and Kotetishvili, M},
title = {Genetic recombination-mediated evolutionary interactions between phages of potential industrial importance and prophages of their hosts within or across the domains of Escherichia, Listeria, Salmonella, Campylobacter, and Staphylococcus.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {155},
pmid = {38704526},
issn = {1471-2180},
mesh = {*Prophages/genetics ; *Recombination, Genetic ; Campylobacter/virology/genetics ; Staphylococcus/virology/genetics ; Gene Transfer, Horizontal ; Bacteriophages/genetics/physiology/classification ; Listeria/virology/genetics ; Salmonella/virology/genetics ; Evolution, Molecular ; Bacteria/virology/genetics ; },
abstract = {BACKGROUND: The in-depth understanding of the role of lateral genetic transfer (LGT) in phage-prophage interactions is essential to rationalizing phage applications for human and animal therapy, as well as for food and environmental safety. This in silico study aimed to detect LGT between phages of potential industrial importance and their hosts.<br><br>METHODS: A large array of genetic recombination detection algorithms, implemented in SplitsTree and RDP4, was applied to detect LGT between various Escherichia, Listeria, Salmonella, Campylobacter, Staphylococcus, Pseudomonas, and Vibrio phages and their hosts. PHASTER and RAST were employed respectively to identify prophages across the host genome and to annotate LGT-affected genes with unknown functions. PhageAI was used to gain deeper insights into the life cycle history of recombined phages.<br><br>RESULTS: The split decomposition inferences (bootstrap values: 91.3-100; fit: 91.433-100), coupled with the Phi (0.0-2.836E-12) and RDP4 (P being well below 0.05) statistics, provided strong evidence for LGT between certain Escherichia, Listeria, Salmonella, and Campylobacter virulent phages and prophages of their hosts. The LGT events entailed mainly the phage genes encoding for hypothetical proteins, while some of these genetic loci appeared to have been affected even by intergeneric recombination in specific E. coli and S. enterica virulent phages when interacting with their host prophages. Moreover, it is shown that certain L. monocytogenes virulent phages could serve at least as the donors of the gene loci, involved in encoding for the basal promoter specificity factor, for L. monocytogenes. In contrast, the large genetic clusters were determined to have been simultaneously exchanged by many S. aureus prophages and some Staphylococcus temperate phages proposed earlier as potential therapeutic candidates (in their native or modified state). The above genetic clusters were found to encompass multiple genes encoding for various proteins, such as e.g., phage tail proteins, the capsid and scaffold proteins, holins, and transcriptional terminator proteins.<br><br>CONCLUSIONS: It is suggested that phage-prophage interactions, mediated by LGT (including intergeneric recombination), can have a far-reaching impact on the co-evolutionary trajectories of industrial phages and their hosts especially when excessively present across microbially rich environments.},
}
@article {pmid38704005,
year = {2024},
author = {Lv, B and Jiang, C and Han, Y and Wu, D and Jin, L and Zhu, G and An, T and Shi, J},
title = {Diverse bacterial hosts and potential risk of antibiotic resistomes in ship ballast water revealed by metagenomic binning.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119056},
doi = {10.1016/j.envres.2024.119056},
pmid = {38704005},
issn = {1096-0953},
abstract = {Ship ballast water promoting the long-range migration of antibiotic resistance genes (ARGs) has raised a great concern. This study attempted to reveal ARGs profile in ballast water and decipher their hosts and potential risk using metagenomic approaches. In total, 710 subtypes across 26 ARG types were identified among the ballast water samples from 13 ships of 11 countries and regions, and multidrug resistance genes were the most dominant ARGs. The composition of ARGs were obviously different across samples, and only 5% of the ARG subtypes were shared by all samples. Procrustes analysis showed the bacterial community contributed more than the mobile genetic elements (MGEs) in shaping the antibiotic resistome. Further, 79 metagenome-assembled genomes (46 genera belong to four phyla) were identified as ARG hosts, with predominantly affiliated with the Proteobacteria. Notably, potential human pathogens (Alcaligenes, Mycolicibacterium, Rhodococcus and Pseudomonas) were also recognized as the ARG hosts. Above 30% of the ARGs hosts contained the MGEs simultaneously, supporting a pronounced horizontal gene transfer capability. A total of 43 subtypes (six percent of overall ARGs) of ARGs were assessed with high-risk, of which 23 subtypes belonged to risk Rank I (including rsmA, ugd, etc.) and 20 subtypes to the risk Rank II (including aac(6)-I, sul1, etc.). In addition, antibiotic resistance risk index indicated the risk of ARGs in ballast water from choke points of maritime trade routes was significantly higher than that from other regions. Overall, this study offers insights for risk evaluation and management of antibiotic resistance in ballast water.},
}
@article {pmid38700770,
year = {2024},
author = {Zhang, Y and Ji, Y and Tang, X and Chen, M and Su, J},
title = {Spread of plasmids carrying antibiotic resistance genes in soil-lettuce-snail food chain.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {38700770},
issn = {1614-7499},
support = {41701564//National Natural Science Foundation of China/ ; SNG201613//Science and Technology Program of Suzhou/ ; },
abstract = {Fertilization can change the composition of antibiotic resistance genes(ARGs) and their host bacteria in agricultural fields, while complex microbial activities help ARGs into crops and transmit them to humans through agricultural products.Therefore, this study constructed a farmland food chain with soil-lettuce-snail as a typical structure, added genetically engineered Pseudomonas fluorescens containing multidrug-resistant plasmid RP4 to track its spread in the farmland food chain, and used different fertilization methods to explore its influence on the spread and diffusion of ARGs and intl1 in the farmland food chain. It was found that exogenous Pseudomonas can enter plants from soil and pass into snails' intestines, and there is horizontal gene transfer phenomenon of RP4 plasmid in bacteria. At different interfaces of the constructed food chain, the addition of exogenous drug-resistant bacteria had different effects on the total abundance of ARGs and intl1. Fertilization, especially manure, not only promoted the spread of Pseudomonas aeruginosa and the transfer of RP4 plasmid levels, but also significantly increased the total abundance of ARGs and intl1 at all interfaces of the constructed food chain. The main ARGs host bacteria in the constructed food chain include Proteobacteria, Bacteroides, and Firmicutes, while Flavobacterium of Bacteroides is the unique potential host bacteria of RP4 plasmid. In conclusion, this study provides a reference for the risk assessment of ARGs transmitted to the human body through the food chain, and has important practical significance to reduce the antibiotic resistance contamination of agricultural products and ensure the safety of vegetable basket.},
}
@article {pmid38698002,
year = {2024},
author = {Da Silva Morais, E and Grimaud, GM and Warda, A and Stanton, C and Ross, P},
title = {Genome plasticity shapes the ecology and evolution of Phocaeicola dorei and Phocaeicola vulgatus.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {10109},
pmid = {38698002},
issn = {2045-2322},
support = {BACtheWINNER, Project No. 101054719/ERC_/European Research Council/International ; },
mesh = {*Phylogeny ; *Genome, Bacterial ; Humans ; Gastrointestinal Microbiome/genetics ; Gene Transfer, Horizontal ; Evolution, Molecular ; Genomics/methods ; Bacteroidetes/genetics ; },
abstract = {Phocaeicola dorei and Phocaeicola vulgatus are very common and abundant members of the human gut microbiome and play an important role in the infant gut microbiome. These species are closely related and often confused for one another; yet, their genome comparison, interspecific diversity, and evolutionary relationships have not been studied in detail so far. Here, we perform phylogenetic analysis and comparative genomic analyses of these two Phocaeicola species. We report that P. dorei has a larger genome yet a smaller pan-genome than P. vulgatus. We found that this is likely because P. vulgatus is more plastic than P. dorei, with a larger repertoire of genetic mobile elements and fewer anti-phage defense systems. We also found that P. dorei directly descends from a clade of P. vulgatus¸ and experienced genome expansion through genetic drift and horizontal gene transfer. Overall, P. dorei and P. vulgatus have very different functional and carbohydrate utilisation profiles, hinting at different ecological strategies, yet they present similar antimicrobial resistance profiles.},
}
@article {pmid38696408,
year = {2024},
author = {Aldaihani, R and Heath, LS},
title = {Investigating the nature of prokaryotic genomic island locations within a genome.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0301172},
pmid = {38696408},
issn = {1932-6203},
mesh = {*Genomic Islands ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genome, Archaeal ; Replication Origin/genetics ; Prokaryotic Cells/metabolism ; },
abstract = {Horizontal gene transfer (HGT) is a powerful evolutionary force that considerably shapes the structure of prokaryotic genomes and is associated with genomic islands (GIs). A GI is a DNA segment composed of transferred genes that can be found within a prokaryotic genome, obtained through HGT. Much research has focused on detecting GIs in genomes, but here we pursue a new course, which is identifying possible preferred locations of GIs in the prokaryotic genome. Here, we identify the locations of the GIs within prokaryotic genomes to examine patterns in those locations. Prokaryotic GIs were analyzed according to the genome structure that they are located in, whether it be a circular or a linear genome. The analytical investigations employed are: (1) studying the GI locations in relation to the origin of replication (oriC); (2) exploring the distances between GIs; and (3) determining the distribution of GIs across the genomes. For each of the investigations, the analysis was performed on all of the GIs in the data set. Moreover, to void bias caused by the distribution of the genomes represented, the GIs in one genome from each species and the GIs of the most frequent species are also analyzed. Overall, the results showed that there are preferred sites for the GIs in the genome. In the linear genomes, these sites are usually located in the oriC region and terminus region, while in the circular genomes, they are located solely in the terminus region. These results also showed that the distance distribution between the GIs is almost exponential, which proves that GIs have preferred sites within genomes. The oriC and termniuns are preferred sites for the GIs and a possible natural explanation for this could be connected to the content of the oriC region. Moreover, the content of the GIs in terms of its protein families was studied and the results demonstrated that the majority of frequent protein families are close to identical in each section.},
}
@article {pmid38695851,
year = {2024},
author = {Fang, L and Li, M and Zhang, J and Jia, C and Qiang, Y and He, X and Liu, T and Zhou, Q and Luo, D and Han, Y and Li, Z and Liu, W and Yang, Y and Liu, J and Liu, Z},
title = {Chromosome-level genome assembly of Pedicularis kansuensis illuminates genome evolution of facultative parasitic plant.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e13966},
doi = {10.1111/1755-0998.13966},
pmid = {38695851},
issn = {1755-0998},
support = {CCPTZX2023N04//National Grassland Technology Innovation Center (Preparatory) of China/ ; 32201463//National Natural Science Foundation of China/ ; 32071862//National Natural Science Foundation of China/ ; 2023-NK-147//Qinghai Province Talented Scientists Responsibility System Project/ ; },
abstract = {Parasitic plants have a heterotrophic lifestyle, in which they withdraw all or part of their nutrients from their host through the haustorium. Despite the release of many draft genomes of parasitic plants, the genome evolution related to the parasitism feature of facultative parasites remains largely unknown. In this study, we present a high-quality chromosomal-level genome assembly for the facultative parasite Pedicularis kansuensis (Orobanchaceae), which invades both legume and grass host species in degraded grasslands on the Qinghai-Tibet Plateau. This species has the largest genome size compared with other parasitic species, and expansions of long terminal repeat retrotransposons accounting for 62.37% of the assembly greatly contributed to the genome size expansion of this species. A total of 42,782 genes were annotated, and the patterns of gene loss in P. kansuensis differed from other parasitic species. We also found many mobile mRNAs between P. kansuensis and one of its host species, but these mobile mRNAs could not compensate for the functional losses of missing genes in P. kansuensis. In addition, we identified nine horizontal gene transfer (HGT) events from rosids and monocots, as well as one single-gene duplication events from HGT genes, which differ distinctly from that of other parasitic species. Furthermore, we found evidence for HGT through transferring genomic fragments from phylogenetically remote host species. Taken together, these findings provide genomic insights into the evolution of facultative parasites and broaden our understanding of the diversified genome evolution in parasitic plants and the molecular mechanisms of plant parasitism.},
}
@article {pmid38695606,
year = {2024},
author = {Wang, X-Q and Du, K and Chen, C and Hou, P and Li, W-F and Chen, Y and Li, Q and Zhou, C-Z},
title = {Profiling the interplay and coevolution of Microcystis aeruginosa and cyanosiphophage Mic1.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0029824},
doi = {10.1128/spectrum.00298-24},
pmid = {38695606},
issn = {2165-0497},
abstract = {UNLABELLED: The cyanosiphophage Mic1 specifically infects the bloom-forming Microcystis aeruginosa FACHB 1339 from Lake Chaohu, China. Previous genomic analysis showed that its 92,627 bp double-stranded DNA genome consists of 98 putative open reading frames, 63% of which are of unknown function. Here, we investigated the transcriptome dynamics of Mic1 and its host using RNA sequencing. In the early, middle, and late phases of the 10 h lytic cycle, the Mic1 genes are sequentially expressed and could be further temporally grouped into two distinct clusters in each phase. Notably, six early genes, including gp49 that encodes a TnpB-like transposase, immediately reach the highest transcriptional level in half an hour, representing a pioneer cluster that rapidly regulates and redirects host metabolism toward the phage. An in-depth analysis of the host transcriptomic profile in response to Mic1 infection revealed significant upregulation of a polyketide synthase pathway and a type III-B CRISPR system, accompanied by moderate downregulation of the photosynthesis and key metabolism pathways. The constant increase of phage transcripts and relatively low replacement rate over the host transcripts indicated that Mic1 utilizes a unique strategy to gradually take over a small portion of host metabolism pathways after infection. In addition, genomic analysis of a less-infective Mic1 and a Mic1-resistant host strain further confirmed their dynamic interplay and coevolution via the frequent horizontal gene transfer. These findings provide insights into the mutual benefit and symbiosis of the highly polymorphic cyanobacteria M. aeruginosa and cyanophages.<br><br>IMPORTANCE: The highly polymorphic Microcystis aeruginosa is one of the predominant bloom-forming cyanobacteria in eutrophic freshwater bodies and is infected by diverse and abundant cyanophages. The presence of a large number of defense systems in M. aeruginosa genome suggests a dynamic interplay and coevolution with the cyanophages. In this study, we investigated the temporal gene expression pattern of Mic1 after infection and the corresponding transcriptional responses of its host. Moreover, the identification of a less-infective Mic1 and a Mic1-resistant host strain provided the evolved genes in the phage-host coevolution during the multiple-generation cultivation in the laboratory. Our findings enrich the knowledge on the interplay and coevolution of M. aeruginosa and its cyanophages and lay the foundation for the future application of cyanophage as a potential eco-friendly and bio-safe agent in controlling the succession of harmful cyanobacterial blooms.},
}
@article {pmid38695111,
year = {2024},
author = {Van Etten, J and Stephens, TG and Chille, E and Lipzen, A and Peterson, D and Barry, K and Grigoriev, IV and Bhattacharya, D},
title = {Diverse fates of ancient horizontal gene transfers in extremophilic red algae.},
journal = {Environmental microbiology},
volume = {26},
number = {5},
pages = {e16629},
doi = {10.1111/1462-2920.16629},
pmid = {38695111},
issn = {1462-2920},
support = {80NSSC19K0462/NASA/NASA/United States ; 80NSSC19K1542/NASA/NASA/United States ; },
mesh = {*Gene Transfer, Horizontal ; *Rhodophyta/genetics ; *Extremophiles/genetics ; *Arsenic/metabolism ; Mercury/metabolism ; Stress, Physiological/genetics ; Inactivation, Metabolic/genetics ; Evolution, Molecular ; },
abstract = {Horizontal genetic transfer (HGT) is a common phenomenon in eukaryotic genomes. However, the mechanisms by which HGT-derived genes persist and integrate into other pathways remain unclear. This topic is of significant interest because, over time, the stressors that initially favoured the fixation of HGT may diminish or disappear. Despite this, the foreign genes may continue to exist if they become part of a broader stress response or other pathways. The conventional model suggests that the acquisition of HGT equates to adaptation. However, this model may evolve into more complex interactions between gene products, a concept we refer to as the 'Integrated HGT Model' (IHM). To explore this concept further, we studied specialized HGT-derived genes that encode heavy metal detoxification functions. The recruitment of these genes into other pathways could provide clear examples of IHM. In our study, we exposed two anciently diverged species of polyextremophilic red algae from the Galdieria genus to arsenic and mercury stress in laboratory cultures. We then analysed the transcriptome data using differential and coexpression analysis. Our findings revealed that mercury detoxification follows a 'one gene-one function' model, resulting in an indivisible response. In contrast, the arsH gene in the arsenite response pathway demonstrated a complex pattern of duplication, divergence and potential neofunctionalization, consistent with the IHM. Our research sheds light on the fate and integration of ancient HGTs, providing a novel perspective on the ecology of extremophiles.},
}
@article {pmid38694799,
year = {2024},
author = {Zhang, Y and Xue, G and Wang, F and Zhang, J and Xu, L and Yu, C},
title = {The impact of antibiotic exposure on antibiotic resistance gene dynamics in the gut microbiota of inflammatory bowel disease patients.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1382332},
doi = {10.3389/fmicb.2024.1382332},
pmid = {38694799},
issn = {1664-302X},
abstract = {BACKGROUND: While antibiotics are commonly used to treat inflammatory bowel disease (IBD), their widespread application can disturb the gut microbiota and foster the emergence and spread of antibiotic resistance. However, the dynamic changes to the human gut microbiota and direction of resistance gene transmission under antibiotic effects have not been clearly elucidated.<br><br>METHODS: Based on the Human Microbiome Project, a total of 90 fecal samples were collected from 30 IBD patients before, during and after antibiotic treatment. Through the analysis workflow of metagenomics, we described the dynamic process of changes in bacterial communities and resistance genes pre-treatment, during and post-treatment. We explored potential consistent relationships between gut microbiota and resistance genes, and established gene transmission networks among species before and after antibiotic use.<br><br>RESULTS: Exposure to antibiotics can induce alterations in the composition of the gut microbiota in IBD patients, particularly a reduction in probiotics, which gradually recovers to a new steady state after cessation of antibiotics. Network analyses revealed intra-phylum transfers of resistance genes, predominantly between taxonomically close organisms. Specific resistance genes showed increased prevalence and inter-species mobility after antibiotic cessation.<br><br>CONCLUSION: This study demonstrates that antibiotics shape the gut resistome through selective enrichment and promotion of horizontal gene transfer. The findings provide insights into ecological processes governing resistance gene dynamics and dissemination upon antibiotic perturbation of the microbiota. Optimizing antibiotic usage may help limit unintended consequences like increased resistance in gut bacteria during IBD management.},
}
@article {pmid38694026,
year = {2024},
author = {Reem, A and Almansoob, S and Senan, AM and Kumar Raj, A and Shah, R and Kumar Shrewastwa, M and Kumal, JPP},
title = {Pseudomonas aeruginosa and related antibiotic resistance genes as indicators for wastewater treatment.},
journal = {Heliyon},
volume = {10},
number = {9},
pages = {e29798},
doi = {10.1016/j.heliyon.2024.e29798},
pmid = {38694026},
issn = {2405-8440},
abstract = {This review aims to examine the existence of Pseudomonas aeruginosa (P. aeruginosa) and their antibiotic resistance genes (ARGs) in aquatic settings and the alternative treatment ways. P. aeruginosa in a various aquatic environment have been identified as contaminants with impacts on human health and the environment. P. aeruginosa resistance to multiple antibiotics, such as sulfamethoxazole, ciprofloxacin, quinolone, trimethoprim, tetracycline, vancomycin, as well as specific antibiotic resistance genes including sul1, qnrs, blaVIM, blaTEM, blaCTX, blaAIM-1, tetA, ampC, blaVIM. The development of resistance can occur naturally, through mutations, or via horizontal gene transfer facilitated by sterilizing agents. In addition, an overview of the current knowledge on inactivation of Pseudomonas aeruginosa and ARG and the mechanisms of action of various disinfection processes in water and wastewater (UV chlorine processes, catalytic oxidation, Fenton reaction, and ozonation) is given. An overview of the effects of nanotechnology and the resulting wetlands is also given.},
}
@article {pmid38693917,
year = {2024},
author = {Filgueiras, JPC and Zámocký, M and Turchetto-Zolet, AC},
title = {Unraveling the evolutionary origin of the P5CS gene: a story of gene fusion and horizontal transfer.},
journal = {Frontiers in molecular biosciences},
volume = {11},
number = {},
pages = {1341684},
doi = {10.3389/fmolb.2024.1341684},
pmid = {38693917},
issn = {2296-889X},
abstract = {The accumulation of proline in response to the most diverse types of stress is a widespread defense mechanism. In prokaryotes, fungi, and certain unicellular eukaryotes (green algae), the first two reactions of proline biosynthesis occur through two distinct enzymes, γ-glutamyl kinase (GK E.C. 2.7.2.11) and γ-glutamyl phosphate reductase (GPR E.C. 1.2.1.41), encoded by two different genes, ProB and ProA, respectively. Plants, animals, and a few unicellular eukaryotes carry out these reactions through a single bifunctional enzyme, the Δ[1]-pyrroline-5-carboxylate synthase (P5CS), which has the GK and GPR domains fused. To better understand the origin and diversification of the P5CS gene, we use a robust phylogenetic approach with a broad sampling of the P5CS, ProB and ProA genes, including species from all three domains of life. Our results suggest that the collected P5CS genes have arisen from a single fusion event between the ProA and ProB gene paralogs. A peculiar fusion event occurred in an ancestral eukaryotic lineage and was spread to other lineages through horizontal gene transfer. As for the diversification of this gene family, the phylogeny of the P5CS gene in plants shows that there have been multiple independent processes of duplication and loss of this gene, with the duplications being related to old polyploidy events.},
}
@article {pmid38693486,
year = {2024},
author = {Rork, AM and Bala, AS and Renner, T},
title = {Dynamic evolution of the mTHF gene family associated with primary metabolism across life.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {432},
pmid = {38693486},
issn = {1471-2164},
mesh = {*Evolution, Molecular ; *Phylogeny ; *Methylenetetrahydrofolate Dehydrogenase (NADP)/genetics/metabolism ; *Multigene Family ; Archaea/genetics/metabolism ; Eukaryota/genetics/metabolism ; Metabolic Networks and Pathways/genetics ; Gene Transfer, Horizontal ; },
abstract = {BACKGROUND: The folate cycle of one-carbon (C1) metabolism, which plays a central role in the biosynthesis of nucleotides and amino acids, demonstrates the significance of metabolic adaptation. We investigated the evolutionary history of the methylenetetrahydrofolate dehydrogenase (mTHF) gene family, one of the main drivers of the folate cycle, across life.<br><br>RESULTS: Through comparative genomic and phylogenetic analyses, we found that several lineages of Archaea lacked domains vital for folate cycle function such as the mTHF catalytic and NAD(P)-binding domains of FolD. Within eukaryotes, the mTHF gene family diversified rapidly. For example, several duplications have been observed in lineages including the Amoebozoa, Opisthokonta, and Viridiplantae. In a common ancestor of Opisthokonta, FolD and FTHFS underwent fusion giving rise to the gene MTHFD1, possessing the domains of both genes.<br><br>CONCLUSIONS: Our evolutionary reconstruction of the mTHF gene family associated with a primary metabolic pathway reveals dynamic evolution, including gene birth-and-death, gene fusion, and potential horizontal gene transfer events and/or amino acid convergence.},
}
@article {pmid38692276,
year = {2024},
author = {Li, C and Li, CQ and Chen, ZB and Liu, BQ and Sun, X and Wei, KH and Li, CY and Luan, JB},
title = {Wolbachia symbionts control sex in a parasitoid wasp using a horizontally acquired gene.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.04.035},
pmid = {38692276},
issn = {1879-0445},
abstract = {Host reproduction can be manipulated by bacterial symbionts in various ways. Parthenogenesis induction is the most effective type of reproduction manipulation by symbionts for their transmission. Insect sex is determined by regulation of doublesex (dsx) splicing through transformer2 (tra2) and transformer (tra) interaction. Although parthenogenesis induction by symbionts has been studied since the 1970s, its underlying molecular mechanism is unknown. Here we identify a Wolbachia parthenogenesis-induction feminization factor gene (piff) that targets sex-determining genes and causes female-producing parthenogenesis in the haplodiploid parasitoid Encarsia formosa. We found that Wolbachia elimination repressed expression of female-specific dsx and enhanced expression of male-specific dsx, which led to the production of wasp haploid male offspring. Furthermore, we found that E. formosa tra is truncated and non-functional, and Wolbachia has a functional tra homolog, termed piff, with an insect origin. Wolbachia PIFF can colocalize and interact with wasp TRA2. Moreover, Wolbachia piff has coordinated expression with tra2 and dsx of E. formosa. Our results demonstrate the bacterial symbiont Wolbachia has acquired an insect gene to manipulate the host sex determination cascade and induce parthenogenesis in wasps. This study reveals insect-to-bacteria horizontal gene transfer drives the evolution of animal sex determination systems, elucidating a striking mechanism of insect-microbe symbiosis.},
}
@article {pmid38692255,
year = {2024},
author = {Li, H and Wang, Q and Wang, Y and Liu, Y and Zhou, J and Wang, T and Zhu, L and Guo, J},
title = {EDTA enables to alleviate impacts of metal ions on conjugative transfer of antibiotic resistance genes.},
journal = {Water research},
volume = {257},
number = {},
pages = {121659},
doi = {10.1016/j.watres.2024.121659},
pmid = {38692255},
issn = {1879-2448},
abstract = {Various heavy metals are reported to be able to accelerate horizontal transfer of antibiotic resistance genes (ARGs). In real water environmental settings, ubiquitous complexing agents would affect the environmental behaviors of heavy metal ions due to the formation of metal-organic complexes. However, little is known whether the presence of complexing agents would change horizontal gene transfer due to heavy metal exposure. This study aimed to fill this gap by investigating the impacts of a typical complexing agent ethylenediaminetetraacetic acid (EDTA) on the conjugative transfer of plasmid-mediated ARGs induced by a range of heavy metal ions. At the environmentally relevant concentration (0.64 mg L[-1]) of metal ions, all the tested metal ions (Mg[2+], Ca[2+], Co[2+], Pb[2+], Ni[2+], Cu[2+], and Fe[3+]) promoted conjugative transfer of ARGs, while an inhibitory effect was observed at a relatively higher concentration (3.20 mg L[-1]). In contrast, EDTA (0.64 mg L[-1]) alleviated the effects of metal ions on ARGs conjugation transfer, evidenced by 11 %-66 % reduction in the conjugate transfer frequency. Molecular docking and dynamics simulations disclosed that this is attributed to the stronger binding of metal ions with the lipids in cell membranes. Under metal-EDTA exposure, gene expressions related to oxidative stress response, cell membrane permeability, intercellular contact, energy driving force, mobilization, and channels of plasmid transfer were suppressed compared with the metal ions exposure. This study offers insights into the alleviation mechanisms of complexing agents on ARGs transfer induced by free metal ions.},
}
@article {pmid38497713,
year = {2024},
author = {Tang, X-F and Sun, Y-F and Liang, Y-S and Yang, K-Y and Chen, P-T and Li, H-S and Huang, Y-H and Pang, H},
title = {Metabolism, digestion, and horizontal transfer: potential roles and interaction of symbiotic bacteria in the ladybird beetle Novius pumilus and their prey Icerya aegyptiaca.},
journal = {Microbiology spectrum},
volume = {12},
number = {5},
pages = {e0295523},
doi = {10.1128/spectrum.02955-23},
pmid = {38497713},
issn = {2165-0497},
support = {2023YFD1400600//National Key Research and Development Program of China/ ; 32172472//National Natural Science Foundation of China/ ; 31970439//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Coleoptera/microbiology ; *Symbiosis ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Gene Transfer, Horizontal ; Phylogeny ; Female ; Microbiota ; },
abstract = {In this study, we first time sequenced and analyzed the 16S rRNA gene data of predator ladybird beetles Novius pumilus and globally distributed invasive pest Icerya aegyptiaca at different stages, and combined data with bacterial genome sequences in N. pumilus to explored the taxonomic distribution, alpha and beta diversity, differentially abundant bacteria, co-occurrence network, and putative functions of their microbial community. Our finding revealed that Candidatus Walczuchella, which exhibited a higher abundance in I. aegyptiaca, possessed several genes in essential amino acid biosynthesis and seemed to perform roles in providing nutrients to the host, similar to other obligate symbionts in scale insects. Lactococcus, Serratia, and Pseudomonas, more abundant in N. pumilus, were predicted to have genes related to hydrocarbon, fatty acids, and chitin degradation, which may assist their hosts in digesting the wax shell covering the scale insects. Notably, our result showed that Lactococcus had relatively higher abundances in adults and eggs compared to other stages in N. pumilus, indicating potential vertical transmission. Additionally, we found that Arsenophonus, known to influence sex ratios in whitefly and wasp, may also function in I. aegyptiaca, probably by influencing nutrient metabolism as it similarly had many genes corresponding to vitamin B and essential amino acid biosynthesis. Also, we observed a potential horizontal transfer of Arsenophonus between the scale insect and its predator, with a relatively high abundance in the ladybirds compared to other bacteria from the scale insects.IMPORTANCEThe composition and dynamic changes of microbiome in different developmental stages of ladybird beetles Novius pumilus with its prey Icerya aegyptiaca were detected. We found that Candidatus Walczuchella, abundant in I. aegyptiaca, probably provide nutrients to their host based on their amino acid biosynthesis-related genes. Abundant symbionts in N. pumilus, including Lactococcus, Serratia, and Pseudophonus, may help the host digest the scale insects with their hydrocarbon, fatty acid, and chitin degrading-related genes. A key endosymbiont Arsenophonus may play potential roles in the nutrient metabolisms and sex determination in I. aegyptiaca, and is possibly transferred from the scale insect to the predator.},
}
@article {pmid38692150,
year = {2024},
author = {Cai, Y and Chen, C and Sun, T and Li, G and Wang, W and Zhao, H and An, T},
title = {Mariculture waters as yet another hotbed for the creation and transfer of new antibiotic-resistant pathogenome.},
journal = {Environment international},
volume = {187},
number = {},
pages = {108704},
doi = {10.1016/j.envint.2024.108704},
pmid = {38692150},
issn = {1873-6750},
abstract = {With the rapid growth of aquaculture globally, large amounts of antibiotics have been used to treat aquatic disease, which may accelerate induction and spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in aquaculture environments. Herein, metagenomic and 16S rRNA analyses were used to analyze the potentials and co-occurrence patterns of pathogenome (culturable and unculturable pathogens), antibiotic resistome (ARGs), and mobilome (mobile genetic elements (MGEs)) from mariculture waters near 5000 km coast of South China. Total 207 species of pathogens were identified, with only 10 culturable species. Furthermore, more pathogen species were detected in mariculture waters than those in coastal waters, and mariculture waters were prone to become reservoirs of unculturable pathogens. In addition, 913 subtypes of 21 ARG types were also identified, with multidrug resistance genes as the majority. MGEs including plasmids, integrons, transposons, and insertion sequences were abundantly present in mariculture waters. The co-occurrence network pattern between pathogenome, antibiotic resistome, and mobilome suggested that most of pathogens may be potential multidrug resistant hosts, possibly due to high frequency of horizontal gene transfer. These findings increase our understanding of mariculture waters as reservoirs of antibiotic resistome and mobilome, and as yet another hotbed for creation and transfer of new antibiotic-resistant pathogenome.},
}
@article {pmid38689039,
year = {2024},
author = {Shepherd, MJ and Fu, T and Harrington, NE and Kottara, A and Cagney, K and Chalmers, JD and Paterson, S and Fothergill, JL and Brockhurst, MA},
title = {Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {38689039},
issn = {1740-1534},
abstract = {The ecological and evolutionary mechanisms of antimicrobial resistance (AMR) emergence within patients and how these vary across bacterial infections are poorly understood. Increasingly widespread use of pathogen genome sequencing in the clinic enables a deeper understanding of these processes. In this Review, we explore the clinical evidence to support four major mechanisms of within-patient AMR emergence in bacteria: spontaneous resistance mutations; in situ horizontal gene transfer of resistance genes; selection of pre-existing resistance; and immigration of resistant lineages. Within-patient AMR emergence occurs across a wide range of host niches and bacterial species, but the importance of each mechanism varies between bacterial species and infection sites within the body. We identify potential drivers of such differences and discuss how ecological and evolutionary analysis could be embedded within clinical trials of antimicrobials, which are powerful but underused tools for understanding why these mechanisms vary between pathogens, infections and individuals. Ultimately, improving understanding of how host niche, bacterial species and antibiotic mode of action combine to govern the ecological and evolutionary mechanism of AMR emergence in patients will enable more predictive and personalized diagnosis and antimicrobial therapies.},
}
@article {pmid38688912,
year = {2024},
author = {Yang, QE and Ma, X and Li, M and Zhao, M and Zeng, L and He, M and Deng, H and Liao, H and Rensing, C and Friman, VP and Zhou, S and Walsh, TR},
title = {Evolution of triclosan resistance modulates bacterial permissiveness to multidrug resistance plasmids and phages.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3654},
pmid = {38688912},
issn = {2041-1723},
support = {32100150//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42277436//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Triclosan/pharmacology ; *Plasmids/genetics ; *Klebsiella pneumoniae/drug effects/genetics/virology ; *Bacteriophages/genetics/physiology ; Drug Resistance, Multiple, Bacterial/genetics ; Mutation ; Gene Transfer, Horizontal ; Whole Genome Sequencing ; Evolution, Molecular ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The horizontal transfer of plasmids has been recognized as one of the key drivers for the worldwide spread of antimicrobial resistance (AMR) across bacterial pathogens. However, knowledge remain limited about the contribution made by environmental stress on the evolution of bacterial AMR by modulating horizontal acquisition of AMR plasmids and other mobile genetic elements. Here we combined experimental evolution, whole genome sequencing, reverse genetic engineering, and transcriptomics to examine if the evolution of chromosomal AMR to triclosan (TCS) disinfectant has correlated effects on modulating bacterial pathogen (Klebsiella pneumoniae) permissiveness to AMR plasmids and phage susceptibility. Herein, we show that TCS exposure increases the evolvability of K. pneumoniae to evolve TCS-resistant mutants (TRMs) by acquiring mutations and altered expression of several genes previously associated with TCS and antibiotic resistance. Notably, nsrR deletion increases conjugation permissiveness of K. pneumoniae to four AMR plasmids, and enhances susceptibility to various Klebsiella-specific phages through the downregulation of several bacterial defense systems and changes in membrane potential with altered reactive oxygen species response. Our findings suggest that unrestricted use of TCS disinfectant imposes a dual impact on bacterial antibiotic resistance by augmenting both chromosomally and horizontally acquired AMR mechanisms.},
}
@article {pmid38688811,
year = {2024},
author = {Szczepankowska, AK and Łobocka, M},
title = {Exploring the role of phage plasmids in gene transfers.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2024.04.011},
pmid = {38688811},
issn = {0168-9525},
abstract = {Bacteriophages and plasmids drive horizontal gene transfer (HGT) in bacteria. Phage-plasmids (P-Ps) are hybrids of plasmid and phages. Pfeifer and Rocha recently demonstrated that P-Ps can serve as intermediates in gene exchanges between these two types of elements, identified categories of preferentially transferred genes, and reconstructed gene flows involving phage P1-like P-Ps.},
}
@article {pmid38683832,
year = {2024},
author = {Guillén-Chable, F and Valdez Iuit, JO and Avila Castro, LA and Rosas, C and Merino, E and Rodríguez-Escamilla, Z and Martínez-Núñez, MA},
title = {Geographical distribution of mobile genetic elements in microbial communities along the Yucatan coast.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0301642},
doi = {10.1371/journal.pone.0301642},
pmid = {38683832},
issn = {1932-6203},
mesh = {*Interspersed Repetitive Sequences/genetics ; *Gene Transfer, Horizontal ; *Microbiota/genetics ; Mexico ; Bacteria/genetics/classification ; Proteobacteria/genetics ; },
abstract = {Horizontal gene transfer (HGT) is a well-documented strategy used by bacteria to enhance their adaptability to challenging environmental conditions. Through HGT, a group of conserved genetic elements known as mobile genetic elements (MGEs) is disseminated within bacterial communities. MGEs offer numerous advantages to the host, increasing its fitness by acquiring new functions that help bacteria contend with adverse conditions, including exposure to heavy metal and antibiotics. This study explores MGEs within microbial communities along the Yucatan coast using a metatranscriptomics approach. Prior to this research, nothing was known about the coastal Yucatan's microbial environmental mobilome and HGT processes between these bacterial communities. This study reveals a positive correlation between MGEs and antibiotic resistance genes (ARGs) along the Yucatan coast, with higher MGEs abundance in more contaminated sites. The Proteobacteria and Firmicutes groups exhibited the highest number of MGEs. It's important to highlight that the most abundant classes of MGEs might not be the ones most strongly linked to ARGs, as observed for the recombination/repair class. This work presents the first geographical distribution of the environmental mobilome in Yucatan Peninsula mangroves.},
}
@article {pmid38683670,
year = {2024},
author = {Ferrari, E and Di Benedetto, G and Firrincieli, A and Presentato, A and Frascari, D and Cappelletti, M},
title = {Unravelling the role of the group 6 soluble di-iron monooxygenase (SDIMO) SmoABCD in alkane metabolism and chlorinated alkane degradation.},
journal = {Microbial biotechnology},
volume = {17},
number = {5},
pages = {e14453},
pmid = {38683670},
issn = {1751-7915},
mesh = {*Alkanes/metabolism ; *Mixed Function Oxygenases/metabolism/genetics ; Genetic Complementation Test ; Mutagenesis, Insertional ; Biotransformation ; DNA Transposable Elements ; Hydrocarbons, Chlorinated/metabolism ; },
abstract = {Soluble di-iron monooxygenases (SDIMOs) are multi-component enzymes catalysing the oxidation of various substrates. These enzymes are characterized by high sequence and functional diversity that is still not well understood despite their key role in biotechnological processes including contaminant biodegradation. In this study, we analysed a mutant of Rhodoccocus aetherivorans BCP1 (BCP1-2.10) characterized by a transposon insertion in the gene smoA encoding the alpha subunit of the plasmid-located SDIMO SmoABCD. The mutant BCP1-2.10 showed a reduced capacity to grow on propane, lost the ability to grow on butane, pentane and n-hexane and was heavily impaired in the capacity to degrade chloroform and trichloroethane. The expression of the additional SDIMO prmABCD in BCP1-2.10 probably allowed the mutant to partially grow on propane and to degrade it, to some extent, together with the other short-chain n-alkanes. The complementation of the mutant, conducted by introducing smoABCD in the genome as a single copy under a constitutive promoter or within a plasmid under a thiostreptone-inducible promoter, allowed the recovery of the alkanotrophic phenotype as well as the capacity to degrade chlorinated n-alkanes. The heterologous expression of smoABCD allowed a non-alkanotrophic Rhodococcus strain to grow on pentane and n-hexane when the gene cluster was introduced together with the downstream genes encoding alcohol and aldehyde dehydrogenases and a GroEL chaperon. BCP1 smoA gene was shown to belong to the group 6 SDIMOs, which is a rare group of monooxygenases mostly present in Mycobacterium genus and in a few Rhodococcus strains. SmoABCD originally evolved in Mycobacterium and was then acquired by Rhodococcus through horizontal gene transfer events. This work extends the knowledge of the biotechnologically relevant SDIMOs by providing functional and evolutionary insights into a group 6 SDIMO in Rhodococcus and demonstrating its key role in the metabolism of short-chain alkanes and degradation of chlorinated n-alkanes.},
}
@article {pmid38683013,
year = {2024},
author = {Taylor, AJ and Yahara, K and Pascoe, B and Ko, S and Mageiros, L and Mourkas, E and Calland, JK and Puranen, S and Hitchings, MD and Jolley, KA and Kobras, CM and Bayliss, S and Williams, NJ and van Vliet, AHM and Parkhill, J and Maiden, MCJ and Corander, J and Hurst, LD and Falush, D and Keim, P and Didelot, X and Kelly, DJ and Sheppard, SK},
title = {Epistasis, core-genome disharmony, and adaptation in recombining bacteria.},
journal = {mBio},
volume = {},
number = {},
pages = {e0058124},
doi = {10.1128/mbio.00581-24},
pmid = {38683013},
issn = {2150-7511},
abstract = {Recombination of short DNA fragments via horizontal gene transfer (HGT) can introduce beneficial alleles, create genomic disharmony through negative epistasis, and create adaptive gene combinations through positive epistasis. For non-core (accessory) genes, the negative epistatic cost is likely to be minimal because the incoming genes have not co-evolved with the recipient genome and are frequently observed as tightly linked cassettes with major effects. By contrast, interspecific recombination in the core genome is expected to be rare because disruptive allelic replacement is likely to introduce negative epistasis. Why then is homologous recombination common in the core of bacterial genomes? To understand this enigma, we take advantage of an exceptional model system, the common enteric pathogens Campylobacter jejuni and C. coli that are known for very high magnitude interspecies gene flow in the core genome. As expected, HGT does indeed disrupt co-adapted allele pairings, indirect evidence of negative epistasis. However, multiple HGT events enable recovery of the genome's co-adaption between introgressing alleles, even in core metabolism genes (e.g., formate dehydrogenase). These findings demonstrate that, even for complex traits, genetic coalitions can be decoupled, transferred, and independently reinstated in a new genetic background-facilitating transition between fitness peaks. In this example, the two-step recombinational process is associated with C. coli that are adapted to the agricultural niche.IMPORTANCEGenetic exchange among bacteria shapes the microbial world. From the acquisition of antimicrobial resistance genes to fundamental questions about the nature of bacterial species, this powerful evolutionary force has preoccupied scientists for decades. However, the mixing of genes between species rests on a paradox: 0n one hand, promoting adaptation by conferring novel functionality; on the other, potentially introducing disharmonious gene combinations (negative epistasis) that will be selected against. Taking an interdisciplinary approach to analyze natural populations of the enteric bacteria Campylobacter, an ideal example of long-range admixture, we demonstrate that genes can independently transfer across species boundaries and rejoin in functional networks in a recipient genome. The positive impact of two-gene interactions appears to be adaptive by expanding metabolic capacity and facilitating niche shifts through interspecific hybridization. This challenges conventional ideas and highlights the possibility of multiple-step evolution of multi-gene traits by interspecific introgression.},
}
@article {pmid38537404,
year = {2024},
author = {Cui, J and Dong, Y and Chen, Q and Zhang, C and He, K and Hu, G and He, D and Yuan, L},
title = {Horizontal transfer characterization of ColV plasmids in blaCTX-M-bearing avian Escherichia coli.},
journal = {Poultry science},
volume = {103},
number = {5},
pages = {103631},
doi = {10.1016/j.psj.2024.103631},
pmid = {38537404},
issn = {1525-3171},
mesh = {*Escherichia coli/genetics/drug effects ; Animals ; *Escherichia coli Infections/veterinary/microbiology ; *Gene Transfer, Horizontal ; *Poultry Diseases/microbiology ; *Plasmids/genetics ; *Chickens ; *beta-Lactamases/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Extended-spectrum-β-lactamases (ESBLs)-producing Escherichia coli conferred resistance to most β-lactams, except for carbapenems. To date, the transmission mechanism of blaCTX-M, as the most common ESBLs subtype, in E. coli has received sustained attention around the worldwide, but the research on the pathogenicity of blaCTX-M-bearing E. coli is still scarce. The aims of this study were to discern the spread characteristics of ColV (encoding colicin V) plasmids in blaCTX-M-positive E. coli. The multi-drug resistance traits, phylogroups, and ColV plasmid profilings were screened in 76 blaCTX-M-positive E. coli. Thereafter, the genetic profiles of E. coli G12 and GZM7 were determined by whole genome sequencing, conjugation and S1-pulsed-field gel electrophoresis. The median lethal dose was analyzed in E. coli G12 and TG12A, the ColV-plasmid transconjugant of G12. Of all 76 blaCTX-M-bearing E. coli, 67.11% exhibited resistance to at least 2 drugs in addition to ceftiofur, 14.47% carried ColV-positive plasmids, and 53.95% were phylogroup C. Further studies demonstrated that the blaCTX-M-bearing E. coli G12 was assigned to the predominant lineage O78:H4-ST117 of phylogroup G. In addition, its ColV-positive plasmid simultaneously carried multiple resistance genes, and could be independently transferred to confer partial pathogenicity on its host by plasmid mating. E. coli GZM7 was O53:H9-ST23 of phylogroup C, which belonged to another representative lineage of APEC (avian pathogenic E. coli). Its ColV-positive plasmid could complete conjugation with the help of the other coexisting-resistance conjugative plasmid, although it failed to transfer alone. Our findings highlight the flexibly horizontal transfer of ColV plasmids along with multidrug-resistant genes among blaCTX-M-bearing E. coli poses a threat to poultry health and food safety, which contributes to elucidate the concept of "One Health" and deserves particular concern.},
}
@article {pmid38508537,
year = {2024},
author = {Yang, W and Tang, C and Shen, S and Shi, Q and Hu, F},
title = {Spread and evolution of blaKPC-plasmid between Serratia marcescens and Klebsiella pneumoniae.},
journal = {International journal of antimicrobial agents},
volume = {63},
number = {5},
pages = {107149},
doi = {10.1016/j.ijantimicag.2024.107149},
pmid = {38508537},
issn = {1872-7913},
mesh = {*Serratia marcescens/genetics/drug effects/isolation &amp; purification/enzymology ; *Klebsiella pneumoniae/genetics/drug effects ; Humans ; *Plasmids/genetics ; *Microbial Sensitivity Tests ; *beta-Lactamases/genetics ; *Serratia Infections/microbiology/epidemiology ; *Anti-Bacterial Agents/pharmacology ; *Klebsiella Infections/microbiology/epidemiology ; *Whole Genome Sequencing ; Ceftazidime/pharmacology ; Drug Combinations ; Drug Resistance, Multiple, Bacterial/genetics ; Azabicyclo Compounds/pharmacology ; Sputum/microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Carbapenems/pharmacology ; },
abstract = {OBJECTIVES: blaKPC-carrying Enterobacterales have post great challenges to global healthcare systems. In this study, we reported the evolution and spread of blaKPC between Serratia marcescens and Klebsiella pneumoniae.<br><br>METHODS: Four S. marcescens and one K. pneumoniae strains were isolated from the sputum samples of the patient. Antimicrobial susceptibility tests and whole genome sequencing were performed to investigate the phenotype &amp; genotype of strains. Conjugation assays, cloning experiment and kinetic parameters measuring were performed to explore the spread and antimicrobial resistance mechanisms.<br><br>RESULTS: The evolution and transmission of blaKPC-2 occurred during the treatment of ceftazidime-avibactam and trimethoprim-sulfamethoxazole. Analysis of the antimicrobial susceptibility and genetic profiles of the clinical strains showed that blaKPC-2 evolved into blaKPC-71 and blaKPC-44, together with resistance to ceftazidime-avibactam and carbapenems susceptibility recovery under antimicrobial pressure. Cloning and expression of blaKPC-44 &amp; blaKPC-71 in E. coli DH5&#x3b1; showed that KPC-44 and KPC-71 resulted in a 64&#x223c;128-fold increase in the MIC value for ceftazidime-avibactam. Meanwhile, the kinetic assays also showed that the enzyme activity of KPC-44 and KPC-71 towards carbapenems was destroyed and couldn't be inhibited by avibactam. Based on the conjugation assay and whole genome sequence analyses, we provided evolutionary insights into the transmission pathway trace of blaKPC-bearing plasmids between S. marcescens and K. pneumoniae.<br><br>CONCLUSIONS: Mixed-species co-infection is one of the risk factors leading to the spread of plasmids carrying carbapenem-resistant genes, and increased surveillance of multidrug-resistant Enterobacterales is urgently needed.},
}
@article {pmid38682189,
year = {2024},
author = {Almatroudi, A},
title = {Investigating Biofilms: Advanced Methods for Comprehending Microbial Behavior and Antibiotic Resistance.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {29},
number = {4},
pages = {133},
doi = {10.31083/j.fbl2904133},
pmid = {38682189},
issn = {2768-6698},
mesh = {*Biofilms/drug effects/growth &amp; development ; Humans ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Extracellular Polymeric Substance Matrix/metabolism ; Bacteria/genetics/drug effects/metabolism ; },
abstract = {Biofilms, which consist of microorganisms enclosed in an extracellular polymeric material (EPS), hold immense importance in the fields of environmental research, industry, and medicine. They play a significant role in ecosystem dynamics and stability, but they also pose issues such as biofouling, corrosion, and pollution. Biofilms in medical environments are linked to persistent infections and elevated healthcare expenses. The EPS matrix plays a crucial role in maintaining the structural integrity and antibiotic resistance of these structures. The research primarily investigates the role of the EPS matrix in facilitating horizontal gene transfer among biofilm communities, with a particular emphasis on EPS and its impact on this process. The process is recognized as a pivotal mechanism in the emergence of antibiotic resistance, underscoring the crucial function of EPS in the dynamics of biofilms. The analysis also highlights the significant financial constraints caused by biofilms in several industries. Biofilm-associated infections in the healthcare sector result in escalated treatment expenses and extended hospitalization periods. In an industrial context, biofilms have a role in increasing maintenance expenses and product contamination, emphasizing the need for efficient management solutions. This review presents the most recent progress in biofilm research, emphasizing the utilization of sophisticated imaging tools and molecular methodologies. In addition to conventional imaging techniques, the research explores the utilization of sophisticated molecular tools, such as DNA and RNA sequencing, in conjunction with proteomics. These approaches are essential for assessing the genetic and metabolic mechanisms that regulate biofilm development and antibiotic resistance. The review underscores the significance of employing an interdisciplinary methodology in the study of biofilms. By incorporating a range of approaches, such as sophisticated imaging and molecular analysis, a comprehensive understanding of biofilm dynamics may be achieved. This approach also opens up possibilities for developing novel solutions to address the negative impacts of biofilms on health, industry, and the environment.},
}
@article {pmid38678226,
year = {2024},
author = {Alexa, EA and Cobo-Díaz, JF and Renes, E and O Callaghan, TF and Kilcawley, K and Mannion, D and Skibinska, I and Ruiz, L and Margolles, A and Fernández-Gómez, P and Alvarez-Molina, A and Puente-Gómez, P and Crispie, F and López, M and Prieto, M and Cotter, PD and Alvarez-Ordóñez, A},
title = {The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {78},
pmid = {38678226},
issn = {2049-2618},
support = {818368//European Commission under the European Union&#xb4;s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union&#xb4;s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union&#xb4;s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union&#xb4;s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union&#xb4;s Horizon 2020 research and innovation program/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; },
mesh = {*Cheese/microbiology ; *Microbiota/genetics ; *Food Microbiology ; Bacteria/classification/genetics ; Caves/microbiology ; Corynebacterium/genetics ; Longitudinal Studies ; Metagenome ; Lactococcus/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Staphylococcus/genetics/classification ; Food Safety ; },
abstract = {BACKGROUND: Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal study assessing the impact of ripening in three natural caves on the microbiome and resistome succession across three different producers of Cabrales blue-veined cheese.<br><br>RESULTS: Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome. Lactococcus and the former Lactobacillus genus, among other taxa, showed high abundance in cheeses at initial stages of ripening, either coming from the raw material, starter culture used, and/or the environment of processing plants. Along cheese ripening in caves, these taxa were displaced by other bacteria, such as Tetragenococcus, Corynebacterium, Brevibacterium, Yaniella, and Staphylococcus, predominantly originating from cave environments (mainly food contact surfaces), as demonstrated by source-tracking analysis, strain analysis at read level, and the characterization of 613 metagenome-assembled genomes. The high abundance of Tetragenococcus koreensis and Tetragenococcus halophilus detected in cheese has not been found previously in cheese metagenomes. Furthermore, Tetragenococcus showed a high level of horizontal gene transfer with other members of the cheese microbiome, mainly with Lactococcus and Staphylococcus, involving genes related to carbohydrate metabolism functions. The resistome analysis revealed that raw milk and the associated processing environments are a rich reservoir of antimicrobial resistance determinants, mainly associated with resistance to aminoglycosides, tetracyclines, and &#x3b2;-lactam antibiotics and harbored by aerobic gram-negative bacteria of high relevance from a safety point of view, such as Escherichia coli, Salmonella enterica, Acinetobacter, and Klebsiella pneumoniae, and that the displacement of most raw milk-associated taxa by cave-associated taxa during ripening gave rise to a significant decrease in the load of ARGs and, therefore, to a safer end product.<br><br>CONCLUSION: Overall, the cave environments represented an important source of non-starter microorganisms which may play a relevant role in the quality and safety of the end products. Among them, we have identified novel taxa and taxa not previously regarded as being dominant components of the cheese microbiome (Tetragenococcus spp.), providing very valuable information for the authentication of this protected designation of origin artisanal cheese. Video Abstract.},
}
@article {pmid38678007,
year = {2024},
author = {Wang, X and Tang, Y and Yue, X and Wang, S and Yang, K and Xu, Y and Shen, Q and Friman, VP and Wei, Z},
title = {The role of rhizosphere phages in soil health.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae052},
pmid = {38678007},
issn = {1574-6941},
abstract = {While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.},
}
@article {pmid38669903,
year = {2024},
author = {Liu, H and Al-Dhabi, NA and Jiang, H and Liu, B and Qing, T and Feng, B and Ma, T and Tang, W and Zhang, P},
title = {Toward nitrogen recovery: Co-cultivation of microalgae and bacteria enhances the production of high-value nitrogen-rich cyanophycin.},
journal = {Water research},
volume = {256},
number = {},
pages = {121624},
doi = {10.1016/j.watres.2024.121624},
pmid = {38669903},
issn = {1879-2448},
abstract = {The algal-bacterial wastewater treatment process has been proven to be highly efficient in removing nutrients and recovering nitrogen (N). However, the recovery of the valuable N-rich biopolymer, cyanophycin, remains limited. This research explored the synthesis mechanism and recovery potential of cyanophycin within two algal-bacterial symbiotic reactors. The findings reveal that the synergy between algae and bacteria enhances the removal of N and phosphorus. The crude contents of cyanophycin in the algal-bacterial consortia reached 115 and 124 mg/g of mixed liquor suspended solids (MLSS), respectively, showing an increase of 11.7 %-20.4 % (p < 0.001) compared with conventional activated sludge. Among the 170 metagenome-assembled genomes (MAGs) analyzed, 50 were capable of synthesizing cyanophycin, indicating that cyanophycin producers are common in algal-bacterial systems. The compositions of cyanophycin producers in the two algal-bacterial reactors were affected by different lighting initiation time. The study identified two intracellular synthesis pathways for cyanophycin. Approximately 36 MAGs can synthesize cyanophycin de novo using ammonium and glucose, while the remaining 14 MAGs require exogenous arginine for production. Notably, several MAGs with high abundance are capable of assimilating both nitrate and ammonium into cyanophycin, demonstrating a robust N utilization capability. This research also marks the first identification of potential horizontal gene transfer of the cyanophycin synthase encoding gene (cphA) within the wastewater microbial community. This suggests that the spread of cphA could expand the population of cyanophycin producers. The study offers new insights into recycling the high-value N-rich biopolymer cyanophycin, contributing to the advancement of wastewater resource utilization.},
}
@article {pmid38664322,
year = {2024},
author = {Vincent, J and Tenore, A and Mattei, MR and Frunzo, L},
title = {Modelling Plasmid-Mediated Horizontal Gene Transfer in Biofilms.},
journal = {Bulletin of mathematical biology},
volume = {86},
number = {6},
pages = {63},
pmid = {38664322},
issn = {1522-9602},
support = {861088//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; },
mesh = {*Biofilms/growth &amp; development ; *Gene Transfer, Horizontal ; *Plasmids/genetics ; *Mathematical Concepts ; *Models, Biological ; *Models, Genetic ; Conjugation, Genetic ; Anti-Bacterial Agents/pharmacology ; },
abstract = {In this study, we present a mathematical model for plasmid spread in a growing biofilm, formulated as a nonlocal system of partial differential equations in a 1-D free boundary domain. Plasmids are mobile genetic elements able to transfer to different phylotypes, posing a global health problem when they carry antibiotic resistance factors. We model gene transfer regulation influenced by nearby potential receptors to account for recipient-sensing. We also introduce a promotion function to account for trace metal effects on conjugation, based on literature data. The model qualitatively matches experimental results, showing that contaminants like toxic metals and antibiotics promote plasmid persistence by favoring plasmid carriers and stimulating conjugation. Even at higher contaminant concentrations inhibiting conjugation, plasmid spread persists by strongly inhibiting plasmid-free cells. The model also replicates higher plasmid density in biofilm's most active regions.},
}
@article {pmid38658529,
year = {2024},
author = {Xie, O and Zachreson, C and Tonkin-Hill, G and Price, DJ and Lacey, JA and Morris, JM and McDonald, MI and Bowen, AC and Giffard, PM and Currie, BJ and Carapetis, JR and Holt, DC and Bentley, SD and Davies, MR and Tong, SYC},
title = {Overlapping Streptococcus pyogenes and Streptococcus dysgalactiae subspecies equisimilis household transmission and mobile genetic element exchange.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3477},
pmid = {38658529},
issn = {2041-1723},
support = {/WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Streptococcus pyogenes/genetics/isolation &amp; purification/classification ; *Streptococcal Infections/transmission/microbiology ; Humans ; *Streptococcus/genetics/isolation &amp; purification ; *Interspersed Repetitive Sequences/genetics ; *Gene Transfer, Horizontal ; Australia ; Genome, Bacterial/genetics ; Female ; Male ; Child ; Family Characteristics ; Adult ; Child, Preschool ; Adolescent ; Longitudinal Studies ; Drug Resistance, Bacterial/genetics ; Young Adult ; },
abstract = {Streptococcus dysgalactiae subspecies equisimilis (SDSE) and Streptococcus pyogenes share skin and throat niches with extensive genomic homology and horizontal gene transfer (HGT) possibly underlying shared disease phenotypes. It is unknown if cross-species transmission interaction occurs. Here, we conduct a genomic analysis of a longitudinal household survey in remote Australian First Nations communities for patterns of cross-species transmission interaction and HGT. Collected from 4547 person-consultations, we analyse 294 SDSE and 315 S. pyogenes genomes. We find SDSE and S. pyogenes transmission intersects extensively among households and show that patterns of co-occurrence and transmission links are consistent with independent transmission without inter-species interference. We identify at least one of three near-identical cross-species mobile genetic elements (MGEs) carrying antimicrobial resistance or streptodornase virulence genes in 55 (19%) SDSE and 23 (7%) S. pyogenes isolates. These findings demonstrate co-circulation of both pathogens and HGT in communities with a high burden of streptococcal disease, supporting a need to integrate SDSE and S. pyogenes surveillance and control efforts.},
}
@article {pmid38658407,
year = {2024},
author = {Kuwata, K and Sato-Takabe, Y and Nakai, R and Sugimura, Y and Tazato, N and Kunihiro, T and Morohoshi, S and Iwataki, M and Hamasaki, K and Shiozaki, T},
title = {Novel aerobic anoxygenic phototrophic bacterium Jannaschia pagri sp. nov., isolated from seawater around a fish farm.},
journal = {Antonie van Leeuwenhoek},
volume = {117},
number = {1},
pages = {70},
pmid = {38658407},
issn = {1572-9699},
support = {80635839//MEXT Grants-in-Aid for Young Scientists/ ; JP19H04263//JSPS KAKENHI/ ; },
mesh = {*Phylogeny ; *Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; Japan ; Aquaculture ; DNA, Bacterial/genetics ; Photosynthesis ; Bacterial Typing Techniques ; Aerobiosis ; Animals ; Bacteriochlorophyll A/analysis ; },
abstract = {The genus Jannaschia is one of the representatives of aerobic anoxygenic phototrophic (AAP) bacteria, which is a strictly aerobic bacterium, producing a photosynthetic pigment bacteriochlorophyll (BChl) a. However, a part of the genus Jannaschia members have not been confirmed the photosynthetic ability. The partly presence of the ability in the genus Jannaschia could suggest the complexity of evolutionary history for anoxygenic photosynthesis in the genus, which is expected as gene loss and/or horizontal gene transfer. Here a novel AAP bacterium designated as strain AI_62[T] (= DSM 115720[ T] = NBRC 115938[ T]), was isolated from coastal seawater around a fish farm in the Uwa Sea, Japan. Its closest relatives were identified as Jannaschia seohaensis SMK-146[ T] (95.6% identity) and J. formosa 12N15[T] (94.6% identity), which have been reported to produce BChl a. The genomic characteristic of strain AI_62[T] clearly showed the possession of the anoxygenic photosynthesis related gene sets. This could be a useful model organism to approach the evolutionary mystery of anoxygenic photosynthesis in the genus Jannaschia. Based on a comprehensive consideration of both phylogenetic and phenotypic characteristics, we propose the classification of a novel species within the genus Jannaschia, designated as Jannaschia pagri sp. nov. The type strain for this newly proposed species is AI_62[T] (= DSM 115720[ T] = NBRC 115938[ T]).},
}
@article {pmid38657817,
year = {2024},
author = {Gong, W and Guo, L and Huang, C and Xie, B and Jiang, M and Zhao, Y and Zhang, H and Wu, Y and Liang, H},
title = {A systematic review of antibiotics and antibiotic resistance genes (ARGs) in mariculture wastewater: Antibiotics removal by microalgal-bacterial symbiotic system (MBSS), ARGs characterization on the metagenomic.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172601},
doi = {10.1016/j.scitotenv.2024.172601},
pmid = {38657817},
issn = {1879-1026},
abstract = {Antibiotic residues in mariculture wastewater seriously affect the aquatic environment. Antibiotic Resistance Genes (ARGs) produced under antibiotic stress flow through the environment and eventually enter the human body, seriously affecting human health. Microalgal-bacterial symbiotic system (MBSS) can remove antibiotics from mariculture and reduce the flow of ARGs into the environment. This review encapsulates the present scenario of mariculture wastewater, the removal mechanism of MBSS for antibiotics, and the biomolecular information under metagenomic assay. When confronted with antibiotics, there was a notable augmentation in the extracellular polymeric substances (EPS) content within MBSS, along with a concurrent elevation in the proportion of protein (PN) constituents within the EPS, which limits the entry of antibiotics into the cellular interior. Quorum sensing stimulates the microorganisms to produce biological responses (DNA synthesis - for adhesion) through signaling. Oxidative stress promotes gene expression (coupling, conjugation) to enhance horizontal gene transfer (HGT) in MBSS. The microbial community under metagenomic detection is dominated by aerobic bacteria in the bacterial-microalgal system. Compared to aerobic bacteria, anaerobic bacteria had the significant advantage of decreasing the distribution of ARGs. Overall, MBSS exhibits remarkable efficacy in mitigating the challenges posed by antibiotics and resistant genes from mariculture wastewater.},
}
@article {pmid38651513,
year = {2024},
author = {Gomathinayagam, S and Kodiveri Muthukaliannan, G},
title = {Dynamics of antibiotic resistance genes in plasmids and bacteriophages.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/1040841X.2024.2339262},
pmid = {38651513},
issn = {1549-7828},
abstract = {This brief review explores the intricate interplay between bacteriophages and plasmids in the context of antibiotic resistance gene (ARG) dissemination. Originating from studies in the late 1950s, the review traces the evolution of knowledge regarding extrachromosomal factors facilitating horizontal gene transfer and adaptation in bacteria. Analyzing the gene repertoires of plasmids and bacteriophages, the study highlights their contributions to bacterial evolution and adaptation. While plasmids encode essential and accessory genes influencing host characteristics, bacteriophages carry auxiliary metabolic genes (AMGs) that augment host metabolism. The debate on phages carrying ARGs is explored through a critical evaluation of various studies, revealing contrasting findings from researchers. Additionally, the review addresses the interplay between prophages and plasmids, underlining their similarities and divergences. Based on the available literature evidence, we conclude that plasmids generally encode ARGs while bacteriophages typically do not contain ARGs. But extra-chromosomaly present prophages with plasmid characteristics can encode and disseminate ARGs.},
}
@article {pmid38648967,
year = {2024},
author = {Se, J and Xie, Y and Ma, Q and Zhu, L and Fu, Y and Xu, X and Shen, C and Nannipieri, P},
title = {Drying-wetting cycle enhances stress resistance of Escherichia coli O157:H7 in a model soil.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {123988},
doi = {10.1016/j.envpol.2024.123988},
pmid = {38648967},
issn = {1873-6424},
abstract = {Outbreaks of Escherichia coli (E. coli) O157:H7 in farms are often triggered by heavy rains and flooding. Most cells die with the decreasing of soil moisture, while few cells enter a dormant state and then resuscitate after rewetting. The resistance of dormant cells to stress has been extensively studied, whereas the molecular mechanisms of the cross-resistance development of the resuscitated cells are poorly known. We performed a comparative proteomic analysis on O157:H7 before and after undergoing soil dry-wet alternation. A differential expression of 820 proteins was identified in resuscitated cells compared to exponential-phase cells, as determined by proteomics analysis. The GO and KEGG pathway enrichment analyses revealed that up-regulated proteins were associated with oxidative phosphorylation, glycolysis/gluconeogenesis, the citrate cycle (TCA cycle), aminoacyl-tRNA biosynthesis, ribosome activity, and transmembrane transporters, indicating increased energy production and protein synthesis in resuscitated O157:H7. Moreover, proteins related to acid, osmotic, heat, oxidative, antibiotic stress and horizontal gene transfer efficiency were up-regulated, suggesting a potential improvement in stress resistance. Subsequent validation experiments demonstrated that the survival rates of the resuscitated cells were 476.54 and 7786.34 times higher than the exponential-phase cells, with pH levels of 1.5 and 2.5, respectively. Similarly, resuscitated cells showed higher survival rates under osmotic stress, with 7.5%, 15%, and 30% NaCl resulting in survival rates that were 460.58, 1974.55, and 3475.31 times higher. Resuscitated cells also exhibited increased resistance to heat stress, with survival rates 69.64 and 139.72 times higher at 55°C and 90°C, respectively. Furthermore, the horizontal gene transfer (HGT) efficiency of resuscitated cells was significantly higher (153.12-fold) compared to exponential phase cells. This study provides new insights into bacteria behavior under changing soil moisture and this may explain O157:H7 outbreaks following rainfall and flooding, as the dry-wet cycle promotes stress cross-resistance development.},
}
@article {pmid38647527,
year = {2024},
author = {Ruhluel, D and Fisher, L and Barton, TE and Leighton, H and Kumar, S and Morillo, PA and O'Brien, S and Fothergill, JL and Neill, DR},
title = {Secondary messenger signalling influences Pseudomonas aeruginosa adaptation to sinus and lung environments.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae065},
pmid = {38647527},
issn = {1751-7370},
abstract = {Pseudomonas aeruginosa is a cause of chronic respiratory tract infections in people with cystic fibrosis (CF), non-CF bronchiectasis and chronic obstructive pulmonary disease. Prolonged infection allows accumulation of mutations and horizontal gene transfer, increasing the likelihood of adaptive phenotypic traits. Adaptation is proposed to arise first in bacterial populations colonising upper airway environments. Here, we model this process using an experimental evolution approach. P. aeruginosa PAO1, which is not airway adapted, was serially passaged, separately, in media chemically reflective of upper or lower airway environments. To explore whether the CF environment selects for unique traits, we separately passaged PAO1 in airway-mimicking media with or without CF-specific factors. Our findings demonstrated that all airway environments - sinus and lungs, under CF and non-CF conditions - selected for loss of twitching motility, increased resistance to multiple antibiotic classes and a hyper-biofilm phenotype. These traits conferred increased airway colonisation potential in an in vivo model. CF-like conditions exerted stronger selective pressures, leading to emergence of more pronounced phenotypes. Loss of twitching was associated with mutations in type IV pili genes. Type IV pili mediate surface attachment, twitching and induction of cAMP signalling. We additionally identified multiple evolutionary routes to increased biofilm formation involving regulation of cyclic-di-GMP signalling. These included loss of function mutations in bifA and dipA phosphodiesterase genes and activating mutations in the siaA phosphatase. These data highlight that airway environments select for traits associated with sessile lifestyles and suggest upper airway niches support emergence of phenotypes that promote establishment of lung infection.},
}
@article {pmid38643972,
year = {2024},
author = {Kogay, R and Wolf, YI and Koonin, EV},
title = {Defence systems and horizontal gene transfer in bacteria.},
journal = {Environmental microbiology},
volume = {26},
number = {4},
pages = {e16630},
pmid = {38643972},
issn = {1462-2920},
support = {Z01 LM000073/ImNIH/Intramural NIH HHS/United States ; },
mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/virology ; *CRISPR-Cas Systems ; Genome, Bacterial ; Interspersed Repetitive Sequences ; Bacteriophages/genetics ; Evolution, Molecular ; Prophages/genetics ; },
abstract = {Horizontal gene transfer (HGT) is a fundamental process in prokaryotic evolution, contributing significantly to diversification and adaptation. HGT is typically facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages, which often impose fitness costs on their hosts. However, a considerable number of bacterial genes are involved in defence mechanisms that limit the propagation of MGEs, suggesting they may actively restrict HGT. In our study, we investigated whether defence systems limit HGT by examining the relationship between the HGT rate and the presence of 73 defence systems across 12 bacterial species. We discovered that only six defence systems, three of which were different CRISPR-Cas subtypes, were associated with a reduced gene gain rate at the species evolution scale. Hosts of these defence systems tend to have a smaller pangenome size and fewer phage-related genes compared to genomes without these systems. This suggests that these defence mechanisms inhibit HGT by limiting prophage integration. We hypothesize that the restriction of HGT by defence systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and the fitness effect of HGT in bacterial populations.},
}
@article {pmid38643216,
year = {2024},
author = {Bartoš, O and Chmel, M and Swierczková, I},
title = {The overlooked evolutionary dynamics of 16S rRNA revises its role as the "gold standard" for bacterial species identification.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9067},
pmid = {38643216},
issn = {2045-2322},
support = {MO1012//Ministry of Defence, Czech Republic/ ; },
mesh = {RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Biological Evolution ; Sequence Analysis, DNA ; },
abstract = {The role of 16S rRNA has been and largely remains crucial for the identification of microbial organisms. Although 16S rRNA could certainly be described as one of the most studied sequences ever, the current view of it remains somewhat ambiguous. While some consider 16S rRNA to be a variable marker with resolution power down to the strain level, others consider them to be living fossils that carry information about the origin of domains of cellular life. We show that 16S rRNA is clearly an evolutionarily very rigid sequence, making it a largely unique and irreplaceable marker, but its applicability beyond the genus level is highly limited. Interestingly, it seems that the evolutionary rigidity is not driven by functional constraints of the sequence (RNA-protein interactions), but rather results from the characteristics of the host organism. Our results suggest that, at least in some lineages, Horizontal Gene Transfer (HGT) within genera plays an important role for the evolutionary non-dynamics (stasis) of 16S rRNA. Such genera exhibit an apparent lack of diversification at the 16S rRNA level in comparison to the rest of a genome. However, why it is limited specifically and solely to 16S rRNA remains enigmatic.},
}
@article {pmid38642082,
year = {2024},
author = {Singh, CK and Sodhi, KK and Shree, P and Nitin, V},
title = {Heavy Metals as Catalysts in the Evolution of Antimicrobial Resistance and the Mechanisms Underpinning Co-selection.},
journal = {Current microbiology},
volume = {81},
number = {6},
pages = {148},
pmid = {38642082},
issn = {1432-0991},
mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; *Metals, Heavy ; Bacteria/genetics ; *Environmental Pollutants ; },
abstract = {The menace caused by antibiotic resistance in bacteria is acknowledged on a global scale. Concerns over the same are increasing because of the selection pressure exerted by a huge number of different antimicrobial agents, including heavy metals. Heavy metals are non-metabolizable and recalcitrant to degradation, therefore the bacteria can expel the pollutants out of the system and make it less harmful via different mechanisms. The selection of antibiotic-resistant bacteria may be influenced by heavy metals present in environmental reservoirs. Through co-resistance and cross-resistance processes, the presence of heavy metals in the environment can act as co-selecting agents, hence increasing resistance to both heavy metals and antibiotics. The horizontal gene transfer or mutation assists in the selection of mutant bacteria resistant to the polluted environment. Hence, bioremediation and biodegradation are sustainable methods for the natural clean-up of pollutants. This review sheds light on the occurrence of metal and antibiotic resistance in the environment via the co-resistance and cross-resistance mechanisms underpinning co-selection emphasizing the dearth of studies that specifically examine the method of co-selection in clinical settings. Furthermore, it is advised that future research incorporate both culture- and molecular-based methodologies to further our comprehension of the mechanisms underlying bacterial co- and cross-resistance to antibiotics and heavy metals.},
}
@article {pmid38641304,
year = {2024},
author = {Sha, G and Wu, Z and Chen, T and Zhang, G and Shen, J and Zhao, X and Wang, L},
title = {Mechanisms for more efficient antibiotics and antibiotic resistance genes removal during industrialized treatment of over 200 tons of tylosin and spectinomycin mycelial dregs by integrated meta-omics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130715},
doi = {10.1016/j.biortech.2024.130715},
pmid = {38641304},
issn = {1873-2976},
abstract = {To mitigate the environmental risks posed by the accumulation of antibiotic mycelial dregs (AMDs), this study first attempted over 200 tons of mass production fermentation (MP) using tylosin and spectinomycin mycelial dregs alongside pilot-scale fermentation (PS) for comparison, utilizing the integrated-omics and qPCR approaches. Co-fermentation results showed that both antibiotics were effectively removed in all treatments, with an average removal rate of 92%. Antibiotic resistance gene (ARG)-related metabolic pathways showed that rapid degradation of antibiotics was associated with enzymes that inactivate macrolides and aminoglycosides (e.g., K06979, K07027, K05593). Interestingly, MP fermentations with optimized conditions had more efficient ARGs removal because homogenization permitted faster microbial succession, with more stable removal of antibiotic resistant bacteria and mobile genetic elements. Moreover, Bacillus reached 75% and secreted antioxidant enzymes that might inhibit horizontal gene transfer of ARGs. The findings confirmed the advantages of MP fermentation and provided a scientific basis for other AMDs.},
}
@article {pmid38641198,
year = {2024},
author = {Ouzounis, CA},
title = {The Net of Life, a short story: Intricate patterns of gene flows across hundreds of extant genomes, all the way to LUCA.},
journal = {Bio Systems},
volume = {},
number = {},
pages = {105199},
doi = {10.1016/j.biosystems.2024.105199},
pmid = {38641198},
issn = {1872-8324},
abstract = {Over the past quarter-century, the field of evolutionary biology has been transformed by the emergence of complete genome sequences and the conceptual framework known as the 'Net of Life.' This paradigm shift challenges traditional notions of evolution as a tree-like process, emphasizing the complex, interconnected network of gene flow that may blur the boundaries between distinct lineages. In this context, gene loss, rather than horizontal gene transfer, is the primary driver of gene content, with vertical inheritance playing a principal role. The 'Net of Life' not only impacts our understanding of genome evolution but also has profound implications for classification systems, the rapid appearance of new traits, and the spread of diseases. Here, we explore the core tenets of the 'Net of Life' and its implications for genome-scale phylogenetic divergence, providing a comprehensive framework for further investigations in evolutionary biology.},
}
@article {pmid38641137,
year = {2024},
author = {De, R and Jani, M and Azad, RK},
title = {DICEP: An integrative approach to augmenting genomic island detection.},
journal = {Journal of biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jbiotec.2024.04.011},
pmid = {38641137},
issn = {1873-4863},
abstract = {Mobilization of clusters of genes called genomic islands (GIs) across bacterial lineages facilitates dissemination of traits, such as, resistance against antibiotics, virulence or hypervirulence, and versatile metabolic capabilities. Robust delineation of GIs is critical to understanding bacterial evolution that has a vast impact on different life forms. Methods for identification of GIs exploit different evolutionary features or signals encoded within the genomes of bacteria, however, the current state-of-the-art in GI detection still leaves much to be desired. Here, we have taken a combinatorial approach that accounted for GI specific features such as compositional bias, aberrant phyletic pattern, and marker gene enrichment within an integrative framework to delineate GIs in bacterial genomes. Our GI prediction tool, DICEP, was assessed on simulated genomes and well-characterized bacterial genomes. DICEP compared favorably with current GI detection tools on real and synthetic datasets.},
}
@article {pmid38641096,
year = {2024},
author = {Liu, Y and Chu, K and Hua, Z and Li, Q and Lu, Y and Ye, F and Dong, Y and Li, X},
title = {Dynamics of antibiotic resistance genes in the sediments of a water-diversion lake and its human exposure risk behaviour.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172563},
doi = {10.1016/j.scitotenv.2024.172563},
pmid = {38641096},
issn = {1879-1026},
abstract = {The dynamics and exposure risk behaviours of antibiotic resistance genes (ARGs) in the sediments of water-diversion lakes remain poorly understood. In this study, spatiotemporal investigations of ARG profiles in sediments targeting non-water (NWDP) and water diversion periods (WDP) were conducted in Luoma Lake, a typical water-diversion lake, and an innovative dynamics-based risk assessment framework was constructed to evaluate ARG exposure risks to local residents. ARGs in sediments were significantly more abundant in the WDP than in the NWDP, but there was no significant variation in their spatial distribution in either period. Moreover, the pattern of ARG dissemination in sediments was unchanged between the WDP and NWDP, with horizontal gene transfer (HGT) and vertical gene transfer (VGT) contributing to ARG dissemination in both periods. However, water diversion altered the pattern in lake water, with HGT and VGT in the NWDP but only HGT in the WDP, which were critical pathways for the dissemination of ARGs. The significantly lower ARG sediment-water partition coefficient in the WDP indicated that water diversion could shift the fate of ARGs and facilitate their aqueous partitioning. Risk assessment showed that all age groups faced a higher human exposure risk of ARGs (HERA) in the WDP than in the NWDP, with the 45-59 age group having the highest risk. Furthermore, HERA increased overall with the bacterial carrying capacity in the local environment and peaked when the carrying capacity reached three (NWDP) or four (WDP) orders of magnitude higher than the observed bacterial population. HGT and VGT promoted, whereas ODF covering gene mutation and loss mainly reduced HERA in the lake. As the carrying capacity increased, the relative contribution of ODF to HERA remained relatively stable, whereas the dominant mechanism of HERA development shifted from HGT to VGT.},
}
@article {pmid38640666,
year = {2024},
author = {Xie, S and Hamid, N and Zhang, T and Zhang, Z and Peng, L},
title = {Unraveling the nexus: Microplastics, antibiotics, and ARGs interactions, threats and control in aquaculture - A review.},
journal = {Journal of hazardous materials},
volume = {471},
number = {},
pages = {134324},
doi = {10.1016/j.jhazmat.2024.134324},
pmid = {38640666},
issn = {1873-3336},
abstract = {In recent years, aquaculture has expanded rapidly to address food scarcity and provides high-quality aquatic products. However, this growth has led to the release of significant effluents, containing emerging contaminants like antibiotics, microplastics (MPs), and antibiotic resistance genes (ARGs). This study investigated the occurrence and interactions of these pollutants in aquaculture environment. Combined pollutants, such as MPs and coexisting adsorbents, were widespread and could include antibiotics, heavy metals, resistance genes, and pathogens. Elevated levels of chemical pollutants on MPs could lead to the emergence of resistance genes under selective pressure, facilitated by bacterial communities and horizontal gene transfer (HGT). MPs acted as vectors, transferring pollutants into the food web. Various technologies, including membrane technology, coagulation, and advanced oxidation, have been trialed for pollutants removal, each with its benefits and drawbacks. Future research should focus on ecologically friendly treatment technologies for emerging contaminants in aquaculture wastewater. This review provided insights into understanding and addressing newly developing toxins, aiming to develop integrated systems for effective aquaculture wastewater treatment.},
}
@article {pmid38638913,
year = {2024},
author = {Liu, F and Luo, Y and Xu, T and Lin, H and Qiu, Y and Li, B},
title = {Current examining methods and mathematical models of horizontal transfer of antibiotic resistance genes in the environment.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1371388},
pmid = {38638913},
issn = {1664-302X},
abstract = {The increasing prevalence of antibiotic resistance genes (ARGs) in the environment has garnered significant attention due to their health risk to human beings. Horizontal gene transfer (HGT) is considered as an important way for ARG dissemination. There are four general routes of HGT, including conjugation, transformation, transduction and vesiduction. Selection of appropriate examining methods is crucial for comprehensively understanding characteristics and mechanisms of different HGT ways. Moreover, combined with the results obtained from different experimental methods, mathematical models could be established and serve as a powerful tool for predicting ARG transfer dynamics and frequencies. However, current reviews of HGT for ARG spread mainly focus on its influencing factors and mechanisms, overlooking the important roles of examining methods and models. This review, therefore, delineated four pathways of HGT, summarized the strengths and limitations of current examining methods, and provided a comprehensive summing-up of mathematical models pertaining to three main HGT ways of conjugation, transformation and transduction. Finally, deficiencies in current studies were discussed, and proposed the future perspectives to better understand and assess the risks of ARG dissemination through HGT.},
}
@article {pmid38638826,
year = {2024},
author = {Nasrollahian, S and Graham, JP and Halaji, M},
title = {A review of the mechanisms that confer antibiotic resistance in pathotypes of E. coli.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1387497},
pmid = {38638826},
issn = {2235-2988},
abstract = {The dissemination of antibiotic resistance in Escherichia coli poses a significant threat to public health worldwide. This review provides a comprehensive update on the diverse mechanisms employed by E. coli in developing resistance to antibiotics. We primarily focus on pathotypes of E. coli (e.g., uropathogenic E. coli) and investigate the genetic determinants and molecular pathways that confer resistance, shedding light on both well-characterized and recently discovered mechanisms. The most prevalent mechanism continues to be the acquisition of resistance genes through horizontal gene transfer, facilitated by mobile genetic elements such as plasmids and transposons. We discuss the role of extended-spectrum β-lactamases (ESBLs) and carbapenemases in conferring resistance to β-lactam antibiotics, which remain vital in clinical practice. The review covers the key resistant mechanisms, including: 1) Efflux pumps and porin mutations that mediate resistance to a broad spectrum of antibiotics, including fluoroquinolones and aminoglycosides; 2) adaptive strategies employed by E. coli, including biofilm formation, persister cell formation, and the activation of stress response systems, to withstand antibiotic pressure; and 3) the role of regulatory systems in coordinating resistance mechanisms, providing insights into potential targets for therapeutic interventions. Understanding the intricate network of antibiotic resistance mechanisms in E. coli is crucial for the development of effective strategies to combat this growing public health crisis. By clarifying these mechanisms, we aim to pave the way for the design of innovative therapeutic approaches and the implementation of prudent antibiotic stewardship practices to preserve the efficacy of current antibiotics and ensure a sustainable future for healthcare.},
}
@article {pmid38626743,
year = {2024},
author = {Sewell, HL and Criddle, CS and Woo, SG and Kim, S and Müller, JA and Kaster, AK},
title = {Pseudomonas stutzeri KC carries the pdt genes for carbon tetrachloride degradation on an integrative and conjugative element.},
journal = {Microbial physiology},
volume = {},
number = {},
pages = {},
doi = {10.1159/000538783},
pmid = {38626743},
issn = {2673-1673},
abstract = {Pseudomonas stutzeri KC can rapidly degrade carbon tetrachloride (CCl4) to CO2 by a fortuitous reaction with pyridine-2,6-bis(thiocarboxylic acid), a metal chelator encoded by pdt genes. These genes were first identified after a spontaneous mutant, strain CTN1, lost the ability to degrade CCl4. Here we report the complete genome of strain KC and show that these pdt genes are located on an integrative and conjugative element (ICE), designated ICEPsstKC. Comparative genome analyses revealed homologues of pdt genes in genomes of members of other gammaproteobacterial orders. Discrepancies between the tree topologies of the deduced pdt gene products and the host phylogeny based on 16S rRNA provided evidence for horizontal gene transfer (HGT) in several sequenced strains of these orders. In addition to ICEPsstKC, HGT may be have been facilitated by other mobile genetic elements, as indicated by the location of the pdt gene cluster adjacent to fragments of other ICEs and prophages in several genome assemblies. We could here show that the majority of cells from the culture collection DSMZ had lost the ICE. The presence of the pdt gene cluster on mobile genetic elements has important implications for the bioremediation of CCl4 for bioremediation of CCl4 and needs consideration when selecting suitable strains.},
}
@article {pmid38618705,
year = {2024},
author = {Sarkar, S and Anyaso-Samuel, S and Qiu, P and Datta, S},
title = {Multiblock partial least squares and rank aggregation: Applications to detection of bacteriophages associated with antimicrobial resistance in the presence of potential confounding factors.},
journal = {Statistics in medicine},
volume = {},
number = {},
pages = {},
doi = {10.1002/sim.10058},
pmid = {38618705},
issn = {1097-0258},
abstract = {Urban environments, characterized by bustling mass transit systems and high population density, host a complex web of microorganisms that impact microbial interactions. These urban microbiomes, influenced by diverse demographics and constant human movement, are vital for understanding microbial dynamics. We explore urban metagenomics, utilizing an extensive dataset from the Metagenomics &amp; Metadesign of Subways &amp; Urban Biomes (MetaSUB) consortium, and investigate antimicrobial resistance (AMR) patterns. In this pioneering research, we delve into the role of bacteriophages, or "phages"-viruses that prey on bacteria and can facilitate the exchange of antibiotic resistance genes (ARGs) through mechanisms like horizontal gene transfer (HGT). Despite their potential significance, existing literature lacks a consensus on their significance in ARG dissemination. We argue that they are an important consideration. We uncover that environmental variables, such as those on climate, demographics, and landscape, can obscure phage-resistome relationships. We adjust for these potential confounders and clarify these relationships across specific and overall antibiotic classes with precision, identifying several key phages. Leveraging machine learning tools and validating findings through clinical literature, we uncover novel associations, adding valuable insights to our comprehension of AMR development.},
}
@article {pmid38617843,
year = {2024},
author = {Guinet, B and Leobold, M and Herniou, EA and Bloin, P and Burlet, N and Bredlau, J and Navratil, V and Ravallec, M and Uzbekov, R and Kester, K and Gundersen Rindal, D and Drezen, JM and Varaldi, J and Bézier, A},
title = {A novel and diverse family of filamentous DNA viruses associated with parasitic wasps.},
journal = {Virus evolution},
volume = {10},
number = {1},
pages = {veae022},
pmid = {38617843},
issn = {2057-1577},
abstract = {Large dsDNA viruses from the Naldaviricetes class are currently composed of four viral families infecting insects and/or crustaceans. Since the 1970s, particles described as filamentous viruses (FVs) have been observed by electronic microscopy in several species of Hymenoptera parasitoids but until recently, no genomic data was available. This study provides the first comparative morphological and genomic analysis of these FVs. We analyzed the genomes of seven FVs, six of which were newly obtained, to gain a better understanding of their evolutionary history. We show that these FVs share all genomic features of the Naldaviricetes while encoding five specific core genes that distinguish them from their closest relatives, the Hytrosaviruses. By mining public databases, we show that FVs preferentially infect Hymenoptera with parasitoid lifestyle and that these viruses have been repeatedly integrated into the genome of many insects, particularly Hymenoptera parasitoids, overall suggesting a long-standing specialization of these viruses to parasitic wasps. Finally, we propose a taxonomical revision of the class Naldaviricetes in which FVs related to the Leptopilina boulardi FV constitute a fifth family. We propose to name this new family, Filamentoviridae.},
}
@article {pmid38617331,
year = {2024},
author = {Lyulina, AS and Liu, Z and Good, BH},
title = {Linkage equilibrium between rare mutations.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.03.28.587282},
pmid = {38617331},
abstract = {Recombination breaks down genetic linkage by reshuffling existing variants onto new genetic backgrounds. These dynamics are traditionally quantified by examining the correlations between alleles, and how they decay as a function of the recombination rate. However, the magnitudes of these correlations are strongly influenced by other evolutionary forces like natural selection and genetic drift, making it difficult to tease out the effects of recombination. Here we introduce a theoretical framework for analyzing an alternative family of statistics that measure the homoplasy produced by recombination. We derive analytical expressions that predict how these statistics depend on the rates of recombination and recurrent mutation, the strength of negative selection and genetic drift, and the present-day frequencies of the mutant alleles. We find that the degree of homoplasy can strongly depend on this frequency scale, which reflects the underlying timescales over which these mutations occurred. We show how these scaling properties can be used to isolate the effects of recombination, and discuss their implications for the rates of horizontal gene transfer in bacteria.},
}
@article {pmid38615644,
year = {2024},
author = {Fu, X and Gao, J and Wang, Q and Chen, H and Liu, Y and Zeng, L and Yuan, Y and Xu, H},
title = {Mechanisms on the removal of gram-negative/positive antibiotic resistant bacteria and inhibition of horizontal gene transfer by ferrate coupled with peroxydisulfate or peroxymonosulfate.},
journal = {Journal of hazardous materials},
volume = {470},
number = {},
pages = {134254},
doi = {10.1016/j.jhazmat.2024.134254},
pmid = {38615644},
issn = {1873-3336},
abstract = {The existence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) has been a global public environment and health issue. Due to the different cell structures, gram-positive/negative ARB exhibit various inactivation mechanisms in water disinfection. In this study, a gram-negative ARB Escherichia coli DH5α (E. coli DH5α) was used as a horizontal gene transfer (HGT) donor, while a gram-positive ARB Bacillus as a recipient. To develop an efficient and engineering applicable method in water disinfection, ARB and ARGs removal efficiency of Fe(VI) coupled peroxydisulfate (PDS) or peroxymonosulfate (PMS) was compared, wherein hydroxylamine (HA) was added as a reducing agent. The results indicated that Fe(VI)/PMS/HA showed higher disinfection efficiency than Fe(VI)/PDS/HA. When the concentration of each Fe(VI), PMS, HA was 0.48 mM, 5.15 log E. coli DH5α and 3.57 log Bacillus lost cultivability, while the proportion of recovered cells was 0.0017 % and 0.0566 %, respectively, and HGT was blocked. Intracellular tetA was reduced by 2.49 log. Fe(IV) and/or Fe(V) were proved to be the decisive reactive species. Due to the superiority of low cost as well as high efficiency and practicality, Fe(VI)/PMS/HA has significant application potential in ARB, ARGs removal and HGT inhibition, offering a new insight for wastewater treatment.},
}
@article {pmid38609370,
year = {2024},
author = {Quinones-Olvera, N and Owen, SV and McCully, LM and Marin, MG and Rand, EA and Fan, AC and Martins Dosumu, OJ and Paul, K and Sanchez Castaño, CE and Petherbridge, R and Paull, JS and Baym, M},
title = {Diverse and abundant phages exploit conjugative plasmids.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3197},
pmid = {38609370},
issn = {2041-1723},
support = {R35GM133700//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32GM135014//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; IOS-2331228//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; 1764269//NSF | Directorate for Mathematical &amp; Physical Sciences | Division of Mathematical Sciences (DMS)/ ; },
mesh = {*Bacteriophages/genetics ; Wastewater ; Biological Evolution ; Biotechnology ; Cell Membrane ; },
abstract = {Phages exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of phages use chromosomally encoded cell surface structures as receptors, plasmid-dependent phages exploit plasmid-encoded conjugation proteins, making their host range dependent on horizontal transfer of the plasmid. Despite their unique biology and biotechnological significance, only a small number of plasmid-dependent phages have been characterized. Here we systematically search for new plasmid-dependent phages targeting IncP and IncF plasmids using a targeted discovery platform, and find that they are common and abundant in wastewater, and largely unexplored in terms of their genetic diversity. Plasmid-dependent phages are enriched in non-canonical types of phages, and all but one of the 65 phages we isolated were non-tailed, and members of the lipid-containing tectiviruses, ssDNA filamentous phages or ssRNA phages. We show that plasmid-dependent tectiviruses exhibit profound differences in their host range which is associated with variation in the phage holin protein. Despite their relatively high abundance in wastewater, plasmid-dependent tectiviruses are missed by metaviromic analyses, underscoring the continued importance of culture-based phage discovery. Finally, we identify a tailed phage dependent on the IncF plasmid, and find related structural genes in phages that use the orthogonal type 4 pilus as a receptor, highlighting the evolutionarily promiscuous use of these distinct contractile structures by multiple groups of phages. Taken together, these results indicate plasmid-dependent phages play an under-appreciated evolutionary role in constraining horizontal gene transfer via conjugative plasmids.},
}
@article {pmid38608575,
year = {2024},
author = {Xu, Z and Hu, S and Zhao, D and Xiong, J and Li, C and Ma, Y and Li, S and Huang, B and Pan, X},
title = {Molybdenum disulfide nanosheets promote the plasmid-mediated conjugative transfer of antibiotic resistance genes.},
journal = {Journal of environmental management},
volume = {358},
number = {},
pages = {120827},
doi = {10.1016/j.jenvman.2024.120827},
pmid = {38608575},
issn = {1095-8630},
abstract = {The environmental safety of nanoscale molybdenum disulfide (MoS2) has attracted considerable attention, but its influence on the horizontal migration of antibiotic resistance genes and the ecological risks entailed have not been reported. This study addressed the influence of exposure to MoS2 at different concentrations up to 100 mg/L on the conjugative transfer of antibiotic resistance genes carried by RP4 plasmids with two strains of Escherichia coli. As a result, MoS2 facilitated RP4 plasmid-mediated conjugative transfer in a dose-dependent manner. The conjugation of RP4 plasmids was enhanced as much as 7-fold. The promoting effect is mainly attributable to increased membrane permeability, oxidative stress induced by reactive oxygen species, changes in extracellular polymer secretion and differential expression of the genes involved in horizontal gene transfer. The data highlight the distinct dose dependence of the conjugative transfer of antibiotic resistance genes and the need to improve awareness of the ecological and health risks of nanoscale transition metal dichalcogenides.},
}
@article {pmid38608246,
year = {2024},
author = {Yi, S and Zhou, K and Xu, X},
title = {Characterization of erm(B)-Carrying Integrative and Conjugative Elements Transferred from Streptococcus anginosus to Other Streptococci and Enterococci.},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1089/mdr.2023.0342},
pmid = {38608246},
issn = {1931-8448},
abstract = {Integrative and conjugative elements (ICEs) are important vectors of lateral gene transfer and contribute to the evolution of bacterial pathogens. However, studies on the transfer among species and the physiological consequences of ICEs are rare. The objective of this study was to investigate the cross-species transferability of newly identified erm(B)-carried ICE in Streptococcus anginosus San95 and its physiological consequences after transfer. The erm(B)-carried ICE, characterized by a triple serine integrase module, integrated into hsdM genes, thus designated ICESan95_hsdM. Analysis of ICESan95_hsdM revealed 32 additional ICESan95-like ICEs in the available NCBI genome (n = 24) and sequence of clinical isolates (n = 8). Polymerase chain reaction (PCR) was used to evaluate the 467 clinical isolates, of which 84 were positive for core genes (integrase, relaxase, and T4SS genes) of ICESan95_hsdM. Cross-species transfer experiments demonstrated that ICESan95_hsdM could transfer from S. anginosus to different streptococcal and enterococcal recipients. Growth and competitive culture assays showed acquisition of ICESan95_hsdM incurred no fitness cost. Our work discovered a group of ICEs in Streptococci and Enterococci. For the first time, we demonstrated the broad cross-species transferability to different species or genera of ICEs with no fitness cost that enables commensal S. anginosus to deliver antimicrobial resistance genes to other streptococci and enterococci.},
}
@article {pmid38605260,
year = {2024},
author = {Rafiq, MS and Shabbir, MA and Raza, A and Irshad, S and Asghar, A and Maan, MK and Gondal, MA and Hao, H},
title = {CRISPR-Cas System: A New Dawn to Combat Antibiotic Resistance.},
journal = {BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy},
volume = {},
number = {},
pages = {},
pmid = {38605260},
issn = {1179-190X},
support = {32172914//the National Natural Science Foundation of China/ ; 2021YFD1800600//Key Technology Research and Development Program of Shandong Province/ ; . 2662022DKYJC005//the Fundamental Research Funds for the Central Universities/ ; },
abstract = {Antimicrobial resistance (AMR) can potentially harm global public health. Horizontal gene transfer (HGT), which speeds up the emergence of AMR and increases the burden of drug resistance in mobile genetic elements (MGEs), is the primary method by which AMR genes are transferred across bacterial pathogens. New approaches are urgently needed to halt the spread of bacterial diseases and antibiotic resistance. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), an RNA-guided adaptive immune system, protects prokaryotes from foreign DNA like plasmids and phages. This approach may be essential in limiting horizontal gene transfer and halting the spread of antibiotic resistance. The CRISPR-Cas system has been crucial in identifying and understanding resistance mechanisms and developing novel therapeutic approaches. This review article investigates the CRISPR-Cas system's potential as a tool to combat bacterial AMR. Antibiotic-resistant bacteria can be targeted and eliminated by the CRISPR-Cas system. It has been proven to be an efficient method for removing carbapenem-resistant plasmids and regaining antibiotic susceptibility. The CRISPR-Cas system has enormous potential as a weapon against bacterial AMR. It precisely targets and eliminates antibiotic-resistant bacteria, facilitates resistance mechanism identification, and offers new possibilities in diagnostics and therapeutics.},
}
@article {pmid38605009,
year = {2024},
author = {Zorea, A and Pellow, D and Levin, L and Pilosof, S and Friedman, J and Shamir, R and Mizrahi, I},
title = {Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3147},
pmid = {38605009},
issn = {2041-1723},
support = {866530//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; ISF 1947/19//Israel Science Foundation (ISF)/ ; },
abstract = {Plasmids are pivotal in driving bacterial evolution through horizontal gene transfer. Here, we investigated 3467 human gut microbiome samples across continents and disease states, analyzing 11,086 plasmids. Our analyses reveal that plasmid dispersal is predominantly stochastic, indicating neutral processes as the primary driver of their wide distribution. We find that only 20-25% of plasmid DNA is being selected in various disease states, constraining its distribution across hosts. Selective pressures shape specific plasmid segments with distinct ecological functions, influenced by plasmid mobilization lifestyle, antibiotic usage, and inflammatory gut diseases. Notably, these elements are more commonly shared within groups of individuals with similar health conditions, such as Inflammatory Bowel Disease (IBD), regardless of geographic location across continents. These segments contain essential genes such as iron transport mechanisms- a distinctive gut signature of IBD that impacts the severity of inflammation. Our findings shed light on mechanisms driving plasmid dispersal and selection in the human gut, highlighting their role as carriers of vital gene pools impacting bacterial hosts and ecosystem dynamics.},
}
@article {pmid38604355,
year = {2024},
author = {Yin, Z and Liang, J and Zhang, M and Chen, B and Yu, Z and Tian, X and Deng, X and Peng, L},
title = {Pan-genome insights into adaptive evolution of bacterial symbionts in mixed host-microbe symbioses represented by human gut microbiota Bacteroides cellulosilyticus.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172251},
doi = {10.1016/j.scitotenv.2024.172251},
pmid = {38604355},
issn = {1879-1026},
abstract = {Animal hosts harbor diverse assemblages of microbial symbionts that play crucial roles in the host's lifestyle. The link between microbial symbiosis and host development remains poorly understood. In particular, little is known about the adaptive evolution of gut bacteria in host-microbe symbioses. Recently, symbiotic relationships have been categorized as open, closed, or mixed, reflecting their modes of inter-host transmission and resulting in distinct genomic features. Members of the genus Bacteroides are the most abundant human gut microbiota and possess both probiotic and pathogenic potential, providing an excellent model for studying pan-genome evolution in symbiotic systems. Here, we determined the complete genome of an novel clinical strain PL2022, which was isolated from a blood sample and performed pan-genome analyses on a representative set of Bacteroides cellulosilyticus strains to quantify the influence of the symbiotic relationship on the evolutionary dynamics. B. cellulosilyticus exhibited correlated genomic features with both open and closed symbioses, suggesting a mixed symbiosis. An open pan-genome is characterized by abundant accessory gene families, potential horizontal gene transfer (HGT), and diverse mobile genetic elements (MGEs), indicating an innovative gene pool, mainly associated with genomic islands and plasmids. However, massive parallel gene loss, weak purifying selection, and accumulation of positively selected mutations were the main drivers of genome reduction in B. cellulosilyticus. Metagenomic read recruitment analyses showed that B. cellulosilyticus members are globally distributed and active in human gut habitats, in line with predominant vertical transmission in the human gut. However, existence and/or high abundance were also detected in non-intestinal tissues, other animal hosts, and non-host environments, indicating occasional horizontal transmission to new niches, thereby creating arenas for the acquisition of novel genes. This case study of adaptive evolution under a mixed host-microbe symbiosis advances our understanding of symbiotic pan-genome evolution. Our results highlight the complexity of genetic evolution in this unusual intestinal symbiont.},
}
@article {pmid38601936,
year = {2024},
author = {Ortañez, J and Degnan, PH},
title = {Tracking and characterization of a novel conjugative transposon identified by shotgun transposon mutagenesis.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1241582},
pmid = {38601936},
issn = {1664-302X},
abstract = {The horizontal transfer of mobile genetic elements (MGEs) is an essential process determining the functional and genomic diversity of bacterial populations. MGEs facilitate the exchange of fitness determinant genes like antibiotic resistance and virulence factors. Various computational methods exist to identify potential MGEs, but confirming their ability to transfer requires additional experimental approaches. Here, we apply a transposon (Tn) mutagenesis technique for confirming mobilization without the need for targeted mutations. Using this method, we identified two MGEs, including a previously known conjugative transposon (CTn) called BoCTn found in Bacteroides ovatus and a novel CTn, PvCTn, identified in Phocaeicola vulgatus. In addition, Tn mutagenesis and subsequent genetic deletion enabled our characterization of a helix-turn-helix motif gene, BVU3433 which negatively regulates the conjugation efficiency of PvCTn in vitro. Furthermore, our transcriptomics data revealed that BVU3433 plays a crucial role in the repression of PvCTn genes, including genes involved in forming complete conjugation machinery [Type IV Secretion System (T4SS)]. Finally, analysis of individual strain genomes and community metagenomes identified the widespread prevalence of PvCTn-like elements with putative BVU3433 homologs among human gut-associated bacteria. In summary, this Tn mutagenesis mobilization method (TMMM) enables observation of transfer events in vitro and can ultimately be applied in vivo to identify a broader diversity of functional MGEs that may underly the transfer of important fitness determinants.},
}
@article {pmid38601791,
year = {2024},
author = {Babiker, A and Lohsen, S and Van Riel, J and Hjort, K and Weiss, DS and Andersson, DI and Satola, S},
title = {Heteroresistance to piperacillin/tazobactam in Klebsiella pneumoniae is mediated by increased copy number of multiple β-lactamase genes.},
journal = {JAC-antimicrobial resistance},
volume = {6},
number = {2},
pages = {dlae057},
pmid = {38601791},
issn = {2632-1823},
abstract = {BACKGROUND: Piperacillin/tazobactam is a β-lactam/β-lactamase inhibitor combination with a broad spectrum of activity that is often used as empirical and/or targeted therapy among hospitalized patients. Heteroresistance (HR) is a form of antibiotic resistance in which a minority population of resistant cells coexists with a majority susceptible population that has been found to be a cause of antibiotic treatment failure in murine models.<br><br>OBJECTIVES: To determine the prevalence of HR and mechanisms of HR to piperacillin/tazobactam among Klebsiella pneumoniae bloodstream infection (BSI) isolates.<br><br>MATERIALS: From July 2018 to June 2021, K. pneumoniae piperacillin/tazobactam-susceptible BSI isolates were collected from two tertiary hospitals in Atlanta, GA, USA. Only first isolates from each patient per calendar year were included. Population analysis profiling (PAP) and WGS were performed to identify HR and its mechanisms.<br><br>RESULTS: Among 423 K. pneumoniae BSI isolates collected during the study period, 6% (25/423) were found to be HR with a subpopulation surviving above the breakpoint. WGS of HR isolates grown in the presence of piperacillin/tazobactam at concentrations 8-fold that of the MIC revealed copy number changes of plasmid-located &#x3b2;-lactamase genes blaCTX-M-15, blaSHV33, blaOXA-1 and blaTEM-1 by tandem gene amplification or plasmid copy number increase.<br><br>CONCLUSIONS: Prevalence of HR to piperacillin/tazobactam among bloodstream isolates was substantial. The HR phenotype appears to be caused by tandem amplification of &#x3b2;-lactamase genes found on plasmids or plasmid copy number increase. This raises the possibility of dissemination of HR through horizontal gene transfer and requires further study.},
}
@article {pmid38601688,
year = {2024},
author = {Ma, X and Yin, Z and Li, H and Guo, J},
title = {Roles of herbivorous insects salivary proteins.},
journal = {Heliyon},
volume = {10},
number = {7},
pages = {e29201},
pmid = {38601688},
issn = {2405-8440},
abstract = {The intricate relationship between herbivorous insects and plants has evolved over millions of years, central to this dynamic interaction are salivary proteins (SPs), which mediate key processes ranging from nutrient acquisition to plant defense manipulation. SPs, sourced from salivary glands, intestinal regurgitation or acquired through horizontal gene transfer, exhibit remarkable functional versatility, influencing insect development, behavior, and adhesion mechanisms. Moreover, SPs play pivotal roles in modulating plant defenses, to induce or inhibit plant defenses as elicitors or effectors. In this review, we delve into the multifaceted roles of SPs in herbivorous insects, highlighting their diverse impacts on insect physiology and plant responses. Through a comprehensive exploration of SP functions, this review aims to deepen our understanding of plant-insect interactions and foster advancements in both fundamental research and practical applications in plant-insect interactions.},
}
@article {pmid38599270,
year = {2024},
author = {Thibodeau, AJ and Barret, M and Mouchetd, F and Nguyen, VX and Pinelli, E},
title = {"The potential contribution of aquatic wildlife to antibiotic resistance dissemination in freshwater ecosystems: A review".},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {123894},
doi = {10.1016/j.envpol.2024.123894},
pmid = {38599270},
issn = {1873-6424},
abstract = {Antibiotic resistance (AR) is one of the major health threats of our time. The presence of antibiotics in the environment and their continuous release from sewage treatment plants, chemical manufacturing plants and animal husbandry, agriculture and aquaculture, result in constant selection pressure on microbial organisms. This presence leads to the emergence, mobilization, horizontal gene transfer and a selection of antibiotic resistance genes, resistant bacteria and mobile genetic elements. Under these circumstances, aquatic wildlife is impacted in all compartments, including freshwater organisms with partially impermeable microbiota. In this narrative review, recent advancements in terms of occurrence of antibiotics and antibiotic resistance genes in sewage treatment plant effluents source compared to freshwater have been examined, occurrence of antibiotic resistance in wildlife, as well as experiments on antibiotic exposure. Based on this current state of knowledge, we propose the hypothesis that freshwater aquatic wildlife may play a crucial role in the dissemination of antibiotic resistance within the environment. Specifically, we suggest that organisms with high bacterial density tissues, which are partially isolated from the external environment, such as fishes and amphibians, could potentially be reservoirs and amplifiers of antibiotic resistance in the environment, potentially favoring the increase of the abundance of antibiotic resistance genes and resistant bacteria. Potential avenues for further research (trophic transfer, innovative exposure experiment) and action (biodiversity eco-engineering) are finally proposed.},
}
@article {pmid38598950,
year = {2024},
author = {Lei, L and Chen, N and Chen, Z and Zhao, Y and Lin, H and Li, X and Hu, W and Zhang, H and Shi, J and Luo, Y},
title = {Dissemination of antibiotic resistance genes from aboveground sources to groundwater in livestock farms.},
journal = {Water research},
volume = {256},
number = {},
pages = {121584},
doi = {10.1016/j.watres.2024.121584},
pmid = {38598950},
issn = {1879-2448},
abstract = {Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are prevalent in various environments on livestock farms, including livestock waste, soil, and groundwater. Contamination of groundwater by ARB and ARGs in livestock farms is a growing concern as it may have potentially huge risks to human health. However, the source of groundwater-borne ARB and ARGs in animal farms remains largely unknown. In this study, different types of samples including groundwater and its potential contamination sources from aboveground (pig feces, wastewater, and soil) from both working and abandoned swine feedlots in southern China were collected and subjected to metagenomic sequencing and ARB isolation. The source tracking based on metagenomic analysis revealed that 56-95 % of ARGs in groundwater was attributable to aboveground sources. Using metagenomic assembly, we found that 45 ARGs predominantly conferring resistance to aminoglycosides, sulfonamides, and tetracyclines could be transferred from the aboveground sources to groundwater, mostly through plasmid-mediated horizontal gene transfer. Furthermore, the full-length nucleotide sequences of sul1, tetA, and TEM-1 detected in ARB isolates exhibited the close evolutionary relationships between aboveground sources and groundwater. Some isolated strains of antibiotic-resistant Pseudomonas spp. from aboveground sources and groundwater had the high similarity (average nucleotide identity > 99 %). Notably, the groundwater-borne ARGs were identified as mainly carried by bacterial pathogens, potentially posing risks to human and animal health. Overall, this study underscores the dissemination of ARGs from aboveground sources to groundwater in animal farms and associated risks.},
}
@article {pmid38598457,
year = {2024},
author = {Gao, X and Xu, L and Zhong, T and Song, X and Zhang, H and Liu, X and Jiang, Y},
title = {The proliferation of antibiotic resistance genes (ARGs) and microbial communities in industrial wastewater treatment plant treating N,N-dimethylformamide (DMF) by AAO process.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0299740},
pmid = {38598457},
issn = {1932-6203},
abstract = {The excessive use of antibiotics has resulted in the contamination of the environment with antibiotic resistance genes (ARGs), posing a significant threat to public health. Wastewater treatment plants (WWTPs) are known to be reservoirs of ARGs and considered to be hotspots for horizontal gene transfer (HGT) between bacterial communities. However, most studies focused on the distribution and dissemination of ARGs in hospital and urban WWTPs, and little is known about their fate in industrial WWTPs. In this study, collected the 15 wastewater samples containing N,N-dimethylformamide (DMF) from five stages of the anaerobic anoxic aerobic (AAO) process in an industrial WWTPs. The findings revealed a stepwise decrease in DMF and chemical oxygen demand (COD) content with the progression of treatment. However, the number and abundances of ARGs increase in the effluents of biological treatments. Furthermore, the residues of DMF and the treatment process altered the structure of the bacterial community. The correlation analysis indicated that the shift in bacterial community structures might be the main driver for the dynamics change of ARGs. Interestingly, observed that the AAO process may acted as a microbial source and increased the total abundance of ARGs instead of attenuating it. Additionally, found that non-pathogenic bacteria had higher ARGs abundance than pathogenic bacteria in effluents. The study provides insights into the microbial community structure and the mechanisms that drive the variation in ARGs abundance in industrial WWTPs.},
}
@article {pmid38598029,
year = {2024},
author = {Ramnarine, SDBJ and Jayaraman, J and Ramsubhag, A},
title = {Crucifer Lesion-Associated Xanthomonas Strains Show Multi-Resistance to Heavy Metals and Antibiotics.},
journal = {Current microbiology},
volume = {81},
number = {5},
pages = {136},
pmid = {38598029},
issn = {1432-0991},
support = {CRP.5.APR17.45//University of the West Indies, St. Augustine Campus/ ; },
abstract = {Copper resistance in phytopathogens is a major challenge to crop production globally and is known to be driven by excessive use of copper-based pesticides. However, recent studies have shown co-selection of multiple heavy metal and antibiotic resistance genes in bacteria exposed to heavy metal and xenobiotics, which may impact the epidemiology of plant, animal, and human diseases. In this study, multi-resistance to heavy metals and antibiotics were evaluated in local Xanthomonas campestris pv. campestris (Xcc) and co-isolated Xanthomonas melonis (Xmel) strains from infected crucifer plants in Trinidad. Resistance to cobalt, cadmium, zinc, copper, and arsenic (V) was observed in both Xanthomonas species up to 25 mM. Heavy metal resistance (HMR) genes were found on a small plasmid-derived locus with ~ 90% similarity to a Stenotrophomonas spp. chromosomal locus and a X. perforans pLH3.1 plasmid. The co-occurrence of mobile elements in these regions implies their organization on a composite transposon-like structure. HMR genes in Xcc strains showed the lowest similarity to references, and the cus and ars operons appear to be unique among Xanthomonads. Overall, the similarity of HMR genes to Stenotrophomonas sp. chromosomal genomes suggest their origin in this genus or a related organism and subsequent spread through lateral gene transfer events. Further resistome characterization revealed the presence of small multidrug resistance (SMR), multidrug resistance (MDR) efflux pumps, and bla (Xcc) genes for broad biocide resistance in both species. Concurrently, resistance to antibiotics (streptomycin, kanamycin, tetracycline, chloramphenicol, and ampicillin) up to 1000 µg/mL was confirmed.},
}
@article {pmid38597658,
year = {2024},
author = {Schmid, N and Brandt, D and Walasek, C and Rolland, C and Wittmann, J and Fischer, D and Müsken, M and Kalinowski, J and Thormann, K},
title = {An autonomous plasmid as an inovirus phage satellite.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0024624},
doi = {10.1128/aem.00246-24},
pmid = {38597658},
issn = {1098-5336},
abstract = {Bacterial viruses (phages) are potent agents of lateral gene transfer and thus are important drivers of evolution. A group of mobile genetic elements, referred to as phage satellites, exploits phages to disseminate their own genetic material. Here, we isolated a novel member of the family Inoviridae, Shewanella phage Dolos, along with an autonomously replicating plasmid, pDolos. Dolos causes a chronic infection in its host Shewanella oneidensis by phage production with only minor effects on the host cell proliferation. When present, plasmid pDolos hijacks Dolos functions to be predominantly packaged into phage virions and released into the environment and, thus, acts as a phage satellite. pDolos can disseminate further genetic material encoding, e.g., resistances or fluorophores to host cells sensitive to Dolos infection. Given the rather simple requirements of a plasmid for takeover of an inovirus and the wide distribution of phages of this group, we speculate that similar phage-satellite systems are common among bacteria.IMPORTANCEPhage satellites are mobile genetic elements, which hijack phages to be transferred to other host cells. The vast majority of these phage satellites integrate within the host's chromosome, and they all carry remaining phage genes. Here, we identified a novel phage satellite, pDolos, which uses an inovirus for dissemination. pDolos (i) remains as an autonomously replicating plasmid within its host, (ii) does not carry recognizable phage genes, and (iii) is smaller than any other phage satellites identified so far. Thus, pDolos is the first member of a new class of phage satellites, which resemble natural versions of phagemids.},
}
@article {pmid38593892,
year = {2024},
author = {Zheng, B and Wang, G and Qu, Z and Hu, J and Bao, Z and Wang, M},
title = {Glycosaminoglycan lyase: A new competition between bacteria and the pacific white shrimp Litopenaeus vannamei.},
journal = {Developmental and comparative immunology},
volume = {},
number = {},
pages = {105177},
doi = {10.1016/j.dci.2024.105177},
pmid = {38593892},
issn = {1879-0089},
abstract = {Horizontal gene transfer (HGT) is an important evolutionary force in the formation of prokaryotic and eukaryotic genomes. In recent years, many HGT genes horizontally transferred from prokaryotes to eukaryotes have been reported, and most of them are present in arthropods. The Pacific white shrimp Litopenaeus vannamei, an important economic species of arthropod, has close relationships with bacteria, providing a platform for horizontal gene transfer (HGT). In this study, we analyzed bacteria-derived HGT based on a high-quality genome of L. vannamei via a homology search and phylogenetic analysis, and six HGT genes were identified. Among these six horizontally transferred genes, we found one gene (LOC113799989) that contains a bacterial chondroitinase AC structural domain and encodes an unknown glycosaminoglycan (GAG) lyase in L. vannamei. The real-time quantitative PCR results showed that the mRNA expression level of LOC113799989 was highest in the hepatopancreas and heart, and after stimulation by Vibrio parahaemolyticus, its mRNA expression level was rapidly up-regulated within 12 h. Furthermore, after injecting si-RNA and stimulation by V. parahaemolyticus, we found that the experimental group had a higher cumulative mortality rate in 48 h than the control group, indicating that the bacteria-derived GAG lyase can reduce the mortality of shrimp with respect to infection by V. parahaemolyticus and might be related to the resistance of shrimp to bacterial diseases. Our findings contribute to the study of the function of GAGs and provide new insights into GAG-related microbial pathogenesis and host defense mechanisms in arthropods.},
}
@article {pmid38593473,
year = {2024},
author = {Paul, B and Siddaramappa, S},
title = {Comparative analysis of the diversity of trinucleotide repeats in bacterial genomes.},
journal = {Genome},
volume = {},
number = {},
pages = {},
doi = {10.1139/gen-2023-0097},
pmid = {38593473},
issn = {1480-3321},
abstract = {The human gut is the most favorable niche for microbial populations, and few studies have explored the possibilities of horizontal gene transfer between host and pathogen. Trinucleotide repeat (TNR) expansion in humans can cause more than 40 neurodegenerative diseases. Furthermore, TNRs are a type of microsatellite that resides on coding regions can contribute to the synthesis of homopolymeric amino acids. Hence, the present study aims to estimate the occurrence and diversity of TNRs in bacterial genomes available in the NCBI Genome database. Genome-wide analyses revealed that several bacterial genomes contain different types of uninterrupted TNRs. It was found that TNRs are abundant in the genomes of Alcaligenes faecalis, Mycoplasma gallisepticum, Mycoplasma genitalium, Sorangium cellulosum, and Thermus thermophilus. Interestingly, the genome of Bacillus thuringiensis strain YBT-1518 contained 169 uninterrupted ATT repeats. The genome of Leclercia adecarboxylata had 46 uninterrupted CAG repeats, which potentially translate into polyglutamine. In some instances, the TNRs were present in genes that potentially encode essential functions. Similar occurrences in human genes is known to cause genetic disorders. Further analysis of the occurrence of TNRs in bacterial genomes is likely to provide a better understanding of mismatch repair, genetic disorders, host-pathogen interaction, and homopolymeric amino acids.},
}
@article {pmid38591887,
year = {2024},
author = {Ng, WL and Rego, EH},
title = {A nucleoid-associated protein is involved in the emergence of antibiotic resistance by promoting the frequent exchange of the replicative DNA polymerase in Mycobacterium smegmatis.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0012224},
doi = {10.1128/msphere.00122-24},
pmid = {38591887},
issn = {2379-5042},
abstract = {UNLABELLED: Antibiotic resistance in Mycobacterium tuberculosis exclusively originates from chromosomal mutations, either during normal DNA replication or under stress, when the expression of error-prone DNA polymerases increases to repair damaged DNA. To bypass DNA lesions and catalyze error-prone DNA synthesis, translesion polymerases must be able to access the DNA, temporarily replacing the high-fidelity replicative polymerase. The mechanisms that govern polymerase exchange are not well understood, especially in mycobacteria. Here, using a suite of quantitative fluorescence imaging techniques, we discover that in Mycobacterium smegmatis, as in other bacterial species, the replicative polymerase, DnaE1, exchanges at a timescale much faster than that of DNA replication. Interestingly, this fast exchange rate depends on an actinobacteria-specific nucleoid-associated protein (NAP), Lsr2. In cells missing lsr2, DnaE1 exchanges less frequently, and the chromosome is replicated more faithfully. Additionally, in conditions that damage DNA, cells lacking lsr2 load the complex needed to bypass DNA lesions less effectively and, consistently, replicate with higher fidelity but exhibit growth defects. Together, our results show that Lsr2 promotes dynamic flexibility of the mycobacterial replisome, which is critical for robust cell growth and lesion repair in conditions that damage DNA.<br><br>IMPORTANCE: Unlike many other pathogens, Mycobacterium tuberculosis has limited ability for horizontal gene transfer, a major mechanism for developing antibiotic resistance. Thus, the mechanisms that facilitate chromosomal mutagenesis are of particular importance in mycobacteria. Here, we show that Lsr2, a nucleoid-associated protein, has a novel role in DNA replication and mutagenesis in the model mycobacterium Mycobacterium smegmatis. We find that Lsr2 promotes the fast exchange rate of the replicative DNA polymerase, DnaE1, at the replication fork and is important for the effective loading of the DnaE2-ImuA'-ImuB translesion complex. Without lsr2, M. smegmatis replicates its chromosome more faithfully and acquires resistance to rifampin at a lower rate, but at the cost of impaired survival to DNA damaging agents. Together, our work establishes Lsr2 as a potential factor in the emergence of mycobacterial antibiotic resistance.},
}
@article {pmid38591882,
year = {2024},
author = {Xing, Y and Clark, JR and Chang, JD and Zulk, JJ and Chirman, DM and Piedra, F-A and Vaughan, EE and Hernandez Santos, HJ and Patras, KA and Maresso, AW},
title = {Progress toward a vaccine for extraintestinal pathogenic E. coli (ExPEC) II: efficacy of a toxin-autotransporter dual antigen approach.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0044023},
doi = {10.1128/iai.00440-23},
pmid = {38591882},
issn = {1098-5522},
abstract = {Extraintestinal pathogenic Escherichia coli (ExPEC) is a leading cause of worldwide morbidity and mortality, the top cause of antimicrobial-resistant (AMR) infections, and the most frequent cause of life-threatening sepsis and urinary tract infections (UTI) in adults. The development of an effective and universal vaccine is complicated by this pathogen's pan-genome, its ability to mix and match virulence factors and AMR genes via horizontal gene transfer, an inability to decipher commensal from pathogens, and its intimate association and co-evolution with mammals. Using a pan virulome analysis of >20,000 sequenced E. coli strains, we identified the secreted cytolysin α-hemolysin (HlyA) as a high priority target for vaccine exploration studies. We demonstrate that a catalytically inactive pure form of HlyA, expressed in an autologous host using its own secretion system, is highly immunogenic in a murine host, protects against several forms of ExPEC infection (including lethal bacteremia), and significantly lowers bacterial burdens in multiple organ systems. Interestingly, the combination of a previously reported autotransporter (SinH) with HlyA was notably effective, inducing near complete protection against lethal challenge, including commonly used infection strains ST73 (CFT073) and ST95 (UTI89), as well as a mixture of 10 of the most highly virulent sequence types and strains from our clinical collection. Both HlyA and HlyA-SinH combinations also afforded some protection against UTI89 colonization in a murine UTI model. These findings suggest recombinant, inactive hemolysin and/or its combination with SinH warrant investigation in the development of an E. coli vaccine against invasive disease.},
}
@article {pmid38591037,
year = {2024},
author = {Giermasińska-Buczek, K and Gawor, J and Stefańczyk, E and Gągała, U and Żuchniewicz, K and Rekosz-Burlaga, H and Gromadka, R and Łobocka, M},
title = {Interaction of bacteriophage P1 with an epiphytic Pantoea agglomerans strain-the role of the interplay between various mobilome elements.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1356206},
pmid = {38591037},
issn = {1664-302X},
abstract = {P1 is a model, temperate bacteriophage of the 94 kb genome. It can lysogenize representatives of the Enterobacterales order. In lysogens, it is maintained as a plasmid. We tested P1 interactions with the biocontrol P. agglomerans L15 strain to explore the utility of P1 in P. agglomerans genome engineering. A P1 derivative carrying the Tn9 (cm[R]) transposon could transfer a plasmid from Escherichia coli to the L15 cells. The L15 cells infected with this derivative formed chloramphenicol-resistant colonies. They could grow in a liquid medium with chloramphenicol after adaptation and did not contain prophage P1 but the chromosomally inserted cm[R] marker of P1 Tn9 (cat). The insertions were accompanied by various rearrangements upstream of the Tn9 cat gene promoter and the loss of IS1 (IS1L) from the corresponding region. Sequence analysis of the L15 strain genome revealed a chromosome and three plasmids of 0.58, 0.18, and 0.07 Mb. The largest and the smallest plasmid appeared to encode partition and replication incompatibility determinants similar to those of prophage P1, respectively. In the L15 derivatives cured of the largest plasmid, P1 with Tn9 could not replace the smallest plasmid even if selected. However, it could replace the smallest and the largest plasmid of L15 if its Tn9 IS1L sequence driving the Tn9 mobility was inactivated or if it was enriched with an immobile kanamycin resistance marker. Moreover, it could develop lytically in the L15 derivatives cured of both these plasmids. Clearly, under conditions of selection for P1, the mobility of the P1 selective marker determines whether or not the incoming P1 can outcompete the incompatible L15 resident plasmids. Our results demonstrate that P. agglomerans can serve as a host for bacteriophage P1 and can be engineered with the help of this phage. They also provide an example of how antibiotics can modify the outcome of horizontal gene transfer in natural environments. Numerous plasmids of Pantoea strains appear to contain determinants of replication or partition incompatibility with P1. Therefore, P1 with an immobile selective marker may be a tool of choice in curing these strains from the respective plasmids to facilitate their functional analysis.},
}
@article {pmid38587657,
year = {2024},
author = {Gidhi, A and Jha, SK and Kumar, M and Mukhopadhyay, K},
title = {The F-box protein encoding genes of the leaf-rust fungi Puccinia triticina: genome-wide identification, characterization and expression dynamics during pathogenesis.},
journal = {Archives of microbiology},
volume = {206},
number = {5},
pages = {209},
pmid = {38587657},
issn = {1432-072X},
mesh = {Phylogeny ; Puccinia ; *Basidiomycota/genetics ; *F-Box Proteins/genetics ; },
abstract = {The F-box proteins in fungi perform diverse functions including regulation of cell cycle, circadian clock, development, signal transduction and nutrient sensing. Genome-wide analysis revealed 10 F-box genes in Puccinia triticina, the causal organism for the leaf rust disease in wheat and were characterized using in silico approaches for revealing phylogenetic relationships, gene structures, gene ontology, protein properties, sequence analysis and gene expression studies. Domain analysis predicted functional domains like WD40 and LRR at C-terminus along with the obvious presence of F-box motif in N-terminus. MSA showed amino acid replacements, which might be due to nucleotide substitution during replication. Phylogenetic analysis revealed the F-box proteins with similar domains to be clustered together while some sequences were spread out in different clades, which might be due to functional diversity. The clustering of Puccinia triticina GG705409 with Triticum aestivum TaAFB4/TaAFB5 in a single clade suggested the possibilities of horizontal gene transfer during the coevolution of P. triticina and wheat. Gene ontological annotation categorized them into three classes and were functionally involved in protein degradation through the protein ubiquitination pathway. Protein-protein interaction network revealed F-box proteins to interact with other components of the SCF complex involved in protein ubiquitination. Relative expression analysis of five F-box genes in a time course experiment denoted their involvement in leaf rust susceptible wheat plants. This study provides information on structure elucidation of F-box proteins of a basidiomycetes plant pathogenic fungi and their role during pathogenesis.},
}
@article {pmid38587426,
year = {2024},
author = {Bessen, DE and Beall, BW and Hayes, A and Huang, W and DiChiara, JM and Velusamy, S and Tettelin, H and Jolley, KA and Fallon, JT and Chochua, S and Alobaidallah, MSA and Higgs, C and Barnett, TC and Steemson, JT and Proft, T and Davies, MR},
title = {Recombinational exchange of M-fibril and T-pilus genes generates extensive cell surface diversity in the global group A Streptococcus population.},
journal = {mBio},
volume = {},
number = {},
pages = {e0069324},
doi = {10.1128/mbio.00693-24},
pmid = {38587426},
issn = {2150-7511},
abstract = {Among genes present in all group A streptococci (GAS), those encoding M-fibril and T-pilus proteins display the highest levels of sequence diversity, giving rise to the two primary serological typing schemes historically used to define strain. A new genotyping scheme for the pilin adhesin and backbone genes is developed and, when combined with emm typing, provides an account of the global GAS strain population. Cluster analysis based on nucleotide sequence similarity assigns most T-serotypes to discrete pilin backbone sequence clusters, yet the established T-types correspond to only half the clusters. The major pilin adhesin and backbone sequence clusters yield 98 unique combinations, defined as "pilin types." Numerous horizontal transfer events that involve pilin or emm genes generate extensive antigenic and functional diversity on the bacterial cell surface and lead to the emergence of new strains. Inferred pilin genotypes applied to a meta-analysis of global population-based collections of pharyngitis and impetigo isolates reveal highly significant associations between pilin genotypes and GAS infection at distinct ecological niches, consistent with a role for pilin gene products in adaptive evolution. Integration of emm and pilin typing into open-access online tools (pubmlst.org) ensures broad utility for end-users wanting to determine the architecture of M-fibril and T-pilus genes from genome assemblies.IMPORTANCEPrecision in defining the variant forms of infectious agents is critical to understanding their population biology and the epidemiology of associated diseases. Group A Streptococcus (GAS) is a global pathogen that causes a wide range of diseases and displays a highly diverse cell surface due to the antigenic heterogeneity of M-fibril and T-pilus proteins which also act as virulence factors of varied functions. emm genotyping is well-established and highly utilized, but there is no counterpart for pilin genes. A global GAS collection provides the basis for a comprehensive pilin typing scheme, and online tools for determining emm and pilin genotypes are developed. Application of these tools reveals the expansion of structural-functional diversity among GAS via horizontal gene transfer, as evidenced by unique combinations of surface protein genes. Pilin and emm genotype correlations with superficial throat vs skin infection provide new insights on the molecular determinants underlying key ecological and epidemiological trends.},
}
@article {pmid38585972,
year = {2024},
author = {Marin, MG and Wippel, C and Quinones-Olvera, N and Behruznia, M and Jeffrey, BM and Harris, M and Mann, BC and Rosenthal, A and Jacobson, KR and Warren, RM and Li, H and Meehan, CJ and Farhat, MR},
title = {Analysis of the limited M. tuberculosis accessory genome reveals potential pitfalls of pan-genome analysis approaches.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.03.21.586149},
pmid = {38585972},
abstract = {Pan-genome analysis is a fundamental tool in the study of bacterial genome evolution. Benchmarking the accuracy of pan-genome analysis methods is challenging, because it can be significantly influenced by both the methodology used to compare genomes, as well as differences in the accuracy and representativeness of the genomes analyzed. In this work, we curated a collection of 151 Mycobacterium tuberculosis (Mtb) isolates to evaluate sources of variability in pan-genome analysis. Mtb is characterized by its clonal evolution, absence of horizontal gene transfer, and limited accessory genome, making it an ideal test case for this study. Using a state-of-the-art graph-genome approach, we found that a majority of the structural variation observed in Mtb originates from rearrangement, deletion, and duplication of redundant nucleotide sequences. In contrast, we found that pan-genome analyses that focus on comparison of coding sequences (at the amino acid level) can yield surprisingly variable results, driven by differences in assembly quality and the softwares used. Upon closer inspection, we found that coding sequence annotation discrepancies were a major contributor to inflated Mtb accessory genome estimates. To address this, we developed panqc, a software that detects annotation discrepancies and collapses nucleotide redundancy in pan-genome estimates. We characterized the effect of the panqc adjustment on both pan-genome analysis of Mtb and E. coli genomes, and highlight how different levels of genomic diversity are prone to unique biases. Overall, this study illustrates the need for careful methodological selection and quality control to accurately map the evolutionary dynamics of a bacterial species.},
}
@article {pmid38585963,
year = {2024},
author = {Maier, JL and Gin, C and Callahan, B and Sheriff, EK and Duerkop, BA and Kleiner, M},
title = {Pseudo-pac site sequences used by phage P22 in generalized transduction of Salmonella.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.03.25.586692},
pmid = {38585963},
abstract = {UNLABELLED: Salmonella enterica Serovar Typhimurium (Salmonella) and its bacteriophage P22 are a model system for the study of horizontal gene transfer by generalized transduction. Typically, the P22 DNA packaging machinery initiates packaging when a short sequence of DNA, known as the pac site, is recognized on the P22 genome. However, sequences similar to the pac site in the host genome, called pseudo-pac sites, lead to erroneous packaging and subsequent generalized transduction of Salmonella DNA. While the general genomic locations of the Salmonella pseudo-pac sites are known, the sequences themselves have not been determined. We used visualization of P22 sequencing reads mapped to host Salmonella genomes to define regions of generalized transduction initiation and the likely locations of pseudo-pac sites. We searched each genome region for the sequence with the highest similarity to the P22 pac site and aligned the resulting sequences. We built a regular expression (sequence match pattern) from the alignment and used it to search the genomes of two P22-susceptible Salmonella strains-LT2 and 14028S- for sequence matches. The final regular expression successfully identified pseudo-pac sites in both LT2 and 14028S that correspond with generalized transduction initiation sites in mapped read coverages. The pseudo-pac site sequences identified in this study can be used to predict locations of generalized transduction in other P22-susceptible hosts or to initiate generalized transduction at specific locations in P22-susceptible hosts with genetic engineering. Furthermore, the bioinformatics approach used to identify the Salmonella pseudo-pac sites in this study could be applied to other phage-host systems.<br><br>IMPORTANCE: Bacteriophage P22 has been a genetic tool and a key model for the study of generalized transduction in Salmonella since the 1950s, yet certain components of the generalized transduction molecular mechanism remain unknown. Specifically, the locations and sequences of pseudo-pac sites, hypothesized to facilitate packaging of Salmonella DNA by P22, to date have not been determined. In this study, we identified the specific locations and sequences of the pseudo-pac sites frequently recognized by P22 in Salmonella genomes. The identification of highly efficient pseudo-pac sites in Salmonella provides fundamental insights into the sequence specificity necessary for P22 pac site recognition and opens the door to more targeted use of generalized transduction with P22.},
}
@article {pmid38579360,
year = {2024},
author = {Whitfield, GB and Brun, YV},
title = {The type IVc pilus: just a Tad different.},
journal = {Current opinion in microbiology},
volume = {79},
number = {},
pages = {102468},
doi = {10.1016/j.mib.2024.102468},
pmid = {38579360},
issn = {1879-0364},
abstract = {Bacteria utilize type IV pili (T4P) to interact with their environment, where they facilitate processes including motility, adherence, and DNA uptake. T4P require multisubunit, membrane-spanning nanomachines for assembly. The tight adherence (Tad) pili are an Archaea-derived T4P subgroup whose machinery exhibits significant mechanistic and architectural differences from bacterial type IVa and IVb pili. Most Tad biosynthetic genes are encoded in a single locus that is widespread in bacteria due to facile acquisition via horizontal gene transfer. These loci experience extensive structural rearrangements, including the acquisition of novel regulatory or biosynthetic genes, which fine-tune their function. This has permitted their integration into many different bacterial lifestyles, including the Caulobacter crescentus cell cycle, Myxococcus xanthus predation, and numerous plant and mammalian pathogens and symbionts.},
}
@article {pmid38578105,
year = {2024},
author = {Darby, EM and Moran, RA and Holden, E and Morris, T and Harrison, F and Clough, B and McInnes, RS and Schneider, L and Frickel, EM and Webber, MA and Blair, JMA},
title = {Differential development of antibiotic resistance and virulence between Acinetobacter species.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0010924},
doi = {10.1128/msphere.00109-24},
pmid = {38578105},
issn = {2379-5042},
abstract = {UNLABELLED: The two species that account for most cases of Acinetobacter-associated bacteremia in the United Kingdom are Acinetobacter lwoffii, often a commensal but also an emerging pathogen, and Acinetobacter baumannii, a well-known antibiotic-resistant species. While these species both cause similar types of human infection and occupy the same niche, A. lwoffii (unlike A. baumannii) has thus far remained susceptible to antibiotics. Comparatively little is known about the biology of A. lwoffii, and this is the largest study on it conducted to date, providing valuable insights into its behaviour and potential threat to human health. This study aimed to explain the antibiotic susceptibility, virulence, and fundamental biological differences between these two species. The relative susceptibility of A. lwoffii was explained as it encoded fewer antibiotic resistance and efflux pump genes than A. baumannii (9 and 30, respectively). While both species had markers of horizontal gene transfer, A. lwoffii encoded more DNA defense systems and harbored a far more restricted range of plasmids. Furthermore, A. lwoffii displayed a reduced ability to select for antibiotic resistance mutations, form biofilm, and infect both in vivo and in in vitro models of infection. This study suggests that the emerging pathogen A. lwoffii has remained susceptible to antibiotics because mechanisms exist to make it highly selective about the DNA it acquires, and we hypothesize that the fact that it only harbors a single RND system restricts the ability to select for resistance mutations. This provides valuable insights into how development of resistance can be constrained in Gram-negative bacteria.<br><br>IMPORTANCE: Acinetobacter lwoffii is often a harmless commensal but is also an emerging pathogen and is the most common cause of Acinetobacter-derived bloodstream infections in England and Wales. In contrast to the well-studied and often highly drug-resistant A. baumannii, A. lwoffii has remained susceptible to antibiotics. This study explains why this organism has not evolved resistance to antibiotics. These new insights are important to understand why and how some species develop antibiotic resistance, while others do not, and could inform future novel treatment strategies.},
}
@article {pmid38574109,
year = {2024},
author = {Samson, S and Lord, &#xc9; and Makarenkov, V},
title = {Assessing the emergence time of SARS-CoV-2 zoonotic spillover.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0301195},
pmid = {38574109},
issn = {1932-6203},
mesh = {Animals ; Humans ; SARS-CoV-2/genetics ; Phylogeny ; *Chiroptera ; Pangolins/genetics ; *COVID-19/epidemiology ; Bayes Theorem ; Zoonoses/epidemiology ; },
abstract = {Understanding the evolution of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) and its relationship to other coronaviruses in the wild is crucial for preventing future virus outbreaks. While the origin of the SARS-CoV-2 pandemic remains uncertain, mounting evidence suggests the direct involvement of the bat and pangolin coronaviruses in the evolution of the SARS-CoV-2 genome. To unravel the early days of a probable zoonotic spillover event, we analyzed genomic data from various coronavirus strains from both human and wild hosts. Bayesian phylogenetic analysis was performed using multiple datasets, using strict and relaxed clock evolutionary models to estimate the occurrence times of key speciation, gene transfer, and recombination events affecting the evolution of SARS-CoV-2 and its closest relatives. We found strong evidence supporting the presence of temporal structure in datasets containing SARS-CoV-2 variants, enabling us to estimate the time of SARS-CoV-2 zoonotic spillover between August and early October 2019. In contrast, datasets without SARS-CoV-2 variants provided mixed results in terms of temporal structure. However, they allowed us to establish that the presence of a statistically robust clade in the phylogenies of gene S and its receptor-binding (RBD) domain, including two bat (BANAL) and two Guangdong pangolin coronaviruses (CoVs), is due to the horizontal gene transfer of this gene from the bat CoV to the pangolin CoV that occurred in the middle of 2018. Importantly, this clade is closely located to SARS-CoV-2 in both phylogenies. This phylogenetic proximity had been explained by an RBD gene transfer from the Guangdong pangolin CoV to a very recent ancestor of SARS-CoV-2 in some earlier works in the field before the BANAL coronaviruses were discovered. Overall, our study provides valuable insights into the timeline and evolutionary dynamics of the SARS-CoV-2 pandemic.},
}
@article {pmid38572613,
year = {2024},
author = {Moore, KA and Petersen, AP and Zierden, HC},
title = {Microorganism-derived extracellular vesicles: emerging contributors to female reproductive health.},
journal = {Nanoscale},
volume = {},
number = {},
pages = {},
doi = {10.1039/d3nr05524h},
pmid = {38572613},
issn = {2040-3372},
abstract = {Extracellular vesicles (EVs) are cell-derived nanoparticles that carry small molecules, nucleic acids, and proteins long distances in the body facilitating cell-cell communication. Microorganism-derived EVs mediate communication between parent cells and host cells, with recent evidence supporting their role in biofilm formation, horizontal gene transfer, and suppression of the host immune system. As lipid-bound bacterial byproducts, EVs demonstrate improved cellular uptake and distribution in vivo compared to cell-free nucleic acids, proteins, or small molecules, allowing these biological nanoparticles to recapitulate the effects of parent cells and contribute to a range of human health outcomes. Here, we focus on how EVs derived from vaginal microorganisms contribute to gynecologic and obstetric outcomes. As the composition of the vaginal microbiome significantly impacts women's health, we discuss bacterial EVs from both healthy and dysbiotic vaginal microbiota. We also examine recent work done to evaluate the role of EVs from common vaginal bacterial, fungal, and parasitic pathogens in pathogenesis of female reproductive tract disease. We highlight evidence for the role of EVs in women's health, gaps in current knowledge, and opportunities for future work. Finally, we discuss how leveraging the innate interactions between microorganisms and mammalian cells may establish EVs as a novel therapeutic modality for gynecologic and obstetric indications.},
}
@article {pmid38568420,
year = {2024},
author = {Hamrick, GS and Maddamsetti, R and Son, HI and Wilson, ML and Davis, HM and You, L},
title = {Programming Dynamic Division of Labor Using Horizontal Gene Transfer.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.3c00615},
pmid = {38568420},
issn = {2161-5063},
abstract = {The metabolic engineering of microbes has broad applications, including biomanufacturing, bioprocessing, and environmental remediation. The introduction of a complex, multistep pathway often imposes a substantial metabolic burden on the host cell, restraining the accumulation of productive biomass and limiting pathway efficiency. One strategy to alleviate metabolic burden is the division of labor (DOL) in which different subpopulations carry out different parts of the pathway and work together to convert a substrate into a final product. However, the maintenance of different engineered subpopulations is challenging due to competition and convoluted interstrain population dynamics. Through modeling, we show that dynamic division of labor (DDOL), which we define as the DOL between indiscrete populations capable of dynamic and reversible interchange, can overcome these limitations and enable the robust maintenance of burdensome, multistep pathways. We propose that DDOL can be mediated by horizontal gene transfer (HGT) and use plasmid genomics to uncover evidence that DDOL is a strategy utilized by natural microbial communities. Our work suggests that bioengineers can harness HGT to stabilize synthetic metabolic pathways in microbial communities, enabling the development of robust engineered systems for deployment in a variety of contexts.},
}
@article {pmid38568247,
year = {2024},
author = {Fu, S and Iqbal, B and Li, G and Alabbosh, KF and Khan, KA and Zhao, X and Raheem, A and Du, D},
title = {The role of microbial partners in heavy metal metabolism in plants: a review.},
journal = {Plant cell reports},
volume = {43},
number = {4},
pages = {111},
pmid = {38568247},
issn = {1432-203X},
support = {BK20220030//Open Project of the Carbon Peak and Carbon Neutrality Technology Innovation Foundation of Jiangsu Province/ ; 32271587//National Natural Science Foundation of China/ ; 3235041400//National Natural Science Foundation of China/ ; 18JDG039//Senior Talent Foundation of Jiangsu University/ ; RGP2/360/44//Deanship of Scientific Research at King Khalid University Saudi Arabia for funding this work through Large Groups Project/ ; },
mesh = {*Herb-Drug Interactions ; *Metals, Heavy/toxicity ; Protein Processing, Post-Translational ; Soil ; },
abstract = {Heavy metal pollution threatens plant growth and development as well as ecological stability. Here, we synthesize current research on the interplay between plants and their microbial symbionts under heavy metal stress, highlighting the mechanisms employed by microbes to enhance plant tolerance and resilience. Several key strategies such as bioavailability alteration, chelation, detoxification, induced systemic tolerance, horizontal gene transfer, and methylation and demethylation, are examined, alongside the genetic and molecular basis governing these plant-microbe interactions. However, the complexity of plant-microbe interactions, coupled with our limited understanding of the associated mechanisms, presents challenges in their practical application. Thus, this review underscores the necessity of a more detailed understanding of how plants and microbes interact and the importance of using a combined approach from different scientific fields to maximize the benefits of these microbial processes. By advancing our knowledge of plant-microbe synergies in the metabolism of heavy metals, we can develop more effective bioremediation strategies to combat the contamination of soil by heavy metals.},
}
@article {pmid38565359,
year = {2024},
author = {Medeiros, P and Canato, D and Sergio Kimus Braz, A and Campos Paulino, L},
title = {Phylogenetic analyses reveal insights into interdomain horizontal gene transfer of microbial lipases.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108069},
doi = {10.1016/j.ympev.2024.108069},
pmid = {38565359},
issn = {1095-9513},
abstract = {Microbial lipases play a pivotal role in a wide range of biotechnological processes and in the human skin microbiome. However, their evolution remains poorly understood. Accessing the evolutionary process of lipases could contribute to future applications in health and biotechnology. We investigated genetic events associated with the evolutionary trajectory of the microbial family LIP lipases. Using phylogenetic analysis, we identified two distinct horizontal gene transfer (HGT) events from Bacteria to Fungi. Further analysis of human cutaneous mycobiome members such as the lipophilic Malassezia yeasts and CUG-Ser-1 clade (including Candida sp. and other microorganisms associated with cutaneous mycobiota) revealed recent evolutionary processes, with multiple gene duplication events. The Lid region of fungal lipases, crucial for substrate interaction, exhibits varying degrees of conservation among different groups. Our findings suggest the adaptability of the fungal LIP family in various genetic and metabolic contexts and its potential role in niche exploration.},
}
@article {pmid38415983,
year = {2024},
author = {Zhang, M and Yang, B and Shi, J and Wang, Z and Liu, Y},
title = {Host defense peptides mitigate the spread of antibiotic resistance in physiologically relevant condition.},
journal = {Antimicrobial agents and chemotherapy},
volume = {68},
number = {4},
pages = {e0126123},
doi = {10.1128/aac.01261-23},
pmid = {38415983},
issn = {1098-6596},
support = {32222084, 32172907//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Animals ; Cattle ; Humans ; *Conjugation, Genetic ; Plasmids/genetics ; Drug Resistance, Microbial ; *Genes, Bacterial ; Gene Transfer, Horizontal ; Antimicrobial Cationic Peptides/pharmacology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Antibiotic resistance represents a significant challenge to public health and human safety. The primary driver behind the dissemination of antibiotic resistance is the horizontal transfer of plasmids. Current conjugative transfer assay is generally performed in a standardized manner, ignoring the effect of the host environment. Host defense peptides (HDPs) possess a wide range of biological targets and play an essential role in the innate immune system. Herein, we reveal that sub-minimum inhibitory concentrations of HDPs facilitate the conjugative transfer of RP4-7 plasmid in the Luria Broth medium, and this observation is reversed in the RPMI medium, designed to simulate the host environment. Out of these HDPs, indolicidin (Ind), a cationic tridecapeptide from bovine neutrophils, significantly inhibits the conjugation of multidrug resistance plasmids in a dose-dependent manner, including blaNDM- and tet(X4)-bearing plasmids. We demonstrate that the addition of Ind to RPMI medium as the incubation substrate downregulates the expression of conjugation-related genes. In addition, Ind weakens the tricarboxylic acid cycle, impedes the electron transport chain, and disrupts the proton motive force, consequently diminishing the synthesis of adenosine triphosphate and limiting the energy supply. Our findings highlight the importance of the host-like environments for the development of horizontal transfer inhibitors and demonstrate the potential of HDPs in preventing the spread of resistance plasmids.},
}
@article {pmid38565354,
year = {2024},
author = {Li, X and Chen, T and Ren, Q and Lu, J and Cao, S and Liu, C and Li, Y},
title = {Phages in sludge from the A/O wastewater treatment process play an important role in the transmission of ARGs.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172111},
doi = {10.1016/j.scitotenv.2024.172111},
pmid = {38565354},
issn = {1879-1026},
abstract = {Phages can influence the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) through transduction, but their profiles and effects on the transmission of ARGs are unclear, especially in complex swine sludge. In this study, we investigated the characterization of phage and ARG profiles in sludge generated from anoxic/oxic (A/O) wastewater treatment processes on swine farms using metagenomes and viromes. The results demonstrated that 205-221 subtypes of ARGs could be identified in swine sludge, among which sul1, tet(M), and floR were the dominant ARGs, indicating that sludge is an important reservoir of ARGs, especially in sludge tanks. The greater abundance of mobile genetic elements (MGEs) in the sludge (S) could be a significant factor regarding the greater abundance of ARGs in the sludge than in the anoxic (A) and oxic (O) tanks (P < 0.05). However, when we compared the abundances of ARGs and MGEs in the A and O tanks, we observed opposite significant differences (P < 0.05), suggesting that MGEs are not the only factor influencing the abundance of ARGs. The high proportion of lysogenic phages in sludge from the S tank can also have a major impact on the ARG profile. Siphoviridae, Myoviridae, and Podoviridae were the dominant phage families in sludge, and a network diagram of bacteria-ARG-phages revealed that dominant phages and bacteria acted simultaneously as potential hosts for ARGs, which may have led to phage-mediated HGT of ARGs. Therefore, the risk of phage-mediated HGT of ARGs cannot be overlooked.},
}
@article {pmid38564675,
year = {2024},
author = {Lehman, SS and Verhoeve, VI and Driscoll, TP and Beckmann, JF and Gillespie, JJ},
title = {Metagenome diversity illuminates the origins of pathogen effectors.},
journal = {mBio},
volume = {},
number = {},
pages = {e0075923},
doi = {10.1128/mbio.00759-23},
pmid = {38564675},
issn = {2150-7511},
abstract = {Recent metagenome-assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. The discovery of basal lineages (novel families Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles exposed an evolutionary timepoint for the transition to host dependency, which seemingly occurred independent of mitochondrial evolution. Notably, these basal rickettsiae carry the Rickettsiales vir homolog (rvh) type IV secretion system and purportedly use rvh to kill congener microbes rather than parasitize host cells as described for later-evolving rickettsial pathogens. MAG analysis also substantially increased diversity for the genus Rickettsia and delineated a sister lineage (the novel genus Tisiphia) that stands to inform on the emergence of human pathogens from protist and invertebrate endosymbionts. Herein, we probed Rickettsiales MAG and genomic diversity for the distribution of Rickettsia rvh effectors to ascertain their origins. A sparse distribution of most Rickettsia rvh effectors outside of Rickettsiaceae lineages illuminates unique rvh evolution from basal extracellular species and other rickettsial families. Remarkably, nearly every effector was found in multiple divergent forms with variable architectures, indicating profound roles for gene duplication and recombination in shaping effector repertoires in Rickettsia pathogens. Lateral gene transfer plays a prominent role in shaping the rvh effector landscape, as evinced by the discovery of many effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchange between Rickettsia and Legionella species. Our study exemplifies how MAGs can yield insight into pathogen effector origins, particularly how effector architectures might become tailored to the discrete host cell functions of different eukaryotic hosts.IMPORTANCEWhile rickettsioses are deadly vector-borne human diseases, factors distinguishing Rickettsia pathogens from the innumerable bevy of environmental rickettsial endosymbionts remain lacking. Recent metagenome-assembled genome (MAG) studies revealed evolutionary timepoints for rickettsial transitions to host dependency. The rvh type IV secretion system was likely repurposed from congener killing in basal extracellular species to parasitizing host cells in later-evolving pathogens. Our analysis of MAG diversity for over two dozen rvh effectors unearthed their presence in some non-pathogens. However, most effectors were found in multiple divergent forms with variable architectures, indicating gene duplication and recombination-fashioned effector repertoires of Rickettsia pathogens. Lateral gene transfer substantially shaped pathogen effector arsenals, evinced by the discovery of effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchanges between Rickettsia and Legionella species. Our study exemplifies how MAGs yield insight into pathogen effector origins and evolutionary processes tailoring effectors to eukaryotic host cell biology.},
}
@article {pmid38561802,
year = {2024},
author = {Lanoizelet, M and Elkhoury Youhanna, C and Roure, A and Darras, S},
title = {Molecular control of cellulosic fin morphogenesis in ascidians.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {74},
pmid = {38561802},
issn = {1741-7007},
support = {Emergence 2021//Sorbonne Universit&#xe9;/ ; DBM2020//Institut des sciences biologiques/ ; DBM2022//Institut des sciences biologiques/ ; },
abstract = {BACKGROUND: The tunicates form a group of filter-feeding marine animals closely related to vertebrates. They share with them a number of features such as a notochord and a dorsal neural tube in the tadpole larvae of ascidians, one of the three groups that make tunicates. However, a number of typical chordate characters have been lost in different branches of tunicates, a diverse and fast-evolving phylum. Consequently, the tunic, a sort of exoskeleton made of extracellular material including cellulose secreted by the epidermis, is the unifying character defining the tunicate phylum. In the larva of ascidians, the tunic differentiates in the tail into a median fin (with dorsal and ventral extended blades) and a caudal fin.<br><br>RESULTS: Here we have performed experiments in the ascidian Phallusia mammillata to address the molecular control of tunic 3D morphogenesis. We have demonstrated that the tail epidermis medio-lateral patterning essential for peripheral nervous system specification also controls tunic elongation into fins. More specifically, when tail epidermis midline identity was abolished by BMP signaling inhibition, or CRISPR/Cas9 inactivation of the transcription factor coding genes Msx or Klf1/2/4/17, median fin did not form. We postulated that this genetic program should regulate effectors of tunic secretion. We thus analyzed the expression and regulation in different ascidian species of two genes acquired by horizontal gene transfer (HGT) from bacteria, CesA coding for a cellulose synthase and Gh6 coding for a cellulase. We have uncovered an unexpected dynamic history of these genes in tunicates and high levels of variability in gene expression and regulation among ascidians. Although, in Phallusia, Gh6 has a regionalized expression in the epidermis compatible with an involvement in fin elongation, our functional studies indicate a minor function during caudal fin formation only.<br><br>CONCLUSIONS: Our study constitutes an important step in the study of the integration of HGT-acquired genes into developmental networks and a cellulose-based morphogenesis of extracellular material in animals.},
}
@article {pmid38561223,
year = {2024},
author = {LeBleu, VS and Kanasaki, K and Lovisa, S and Alge, JL and Kim, J and Chen, Y and Teng, Y and Gerami-Naini, B and Sugimoto, H and Kato, N and Revuelta, I and Grau, N and Sleeman, JP and Taduri, G and Kizu, A and Rafii, S and Hochedlinger, K and Quaggin, SE and Kalluri, R},
title = {Genetic reprogramming with stem cells regenerates glomerular epithelial podocytes in Alport syndrome.},
journal = {Life science alliance},
volume = {7},
number = {6},
pages = {},
doi = {10.26508/lsa.202402664},
pmid = {38561223},
issn = {2575-1077},
abstract = {Glomerular filtration relies on the type IV collagen (ColIV) network of the glomerular basement membrane, namely, in the triple helical molecules containing the α3, α4, and α5 chains of ColIV. Loss of function mutations in the genes encoding these chains (Col4a3, Col4a4, and Col4a5) is associated with the loss of renal function observed in Alport syndrome (AS). Precise understanding of the cellular basis for the patho-mechanism remains unknown and a specific therapy for this disease does not currently exist. Here, we generated a novel allele for the conditional deletion of Col4a3 in different glomerular cell types in mice. We found that podocytes specifically generate α3 chains in the developing glomerular basement membrane, and that its absence is sufficient to impair glomerular filtration as seen in AS. Next, we show that horizontal gene transfer, enhanced by TGFβ1 and using allogenic bone marrow-derived mesenchymal stem cells and induced pluripotent stem cells, rescues Col4a3 expression and revive kidney function in Col4a3-deficient AS mice. Our proof-of-concept study supports that horizontal gene transfer such as cell fusion enables cell-based therapy in Alport syndrome.},
}
@article {pmid38560215,
year = {2024},
author = {Comba-González, NB and Chaves-Moreno, D and Santamaría-Vanegas, J and Montoya-Castaño, D},
title = {A pan-genomic assessment: Delving into the genome of the marine epiphyte Bacillus altitudinis strain 19_A and other very close Bacillus strains from multiple environments.},
journal = {Heliyon},
volume = {10},
number = {7},
pages = {e27820},
pmid = {38560215},
issn = {2405-8440},
abstract = {Marine macroalgae are the habitat of epiphytic bacteria and provide several conditions for a beneficial biological interaction to thrive. Although Bacillus is one of the most abundant epiphytic genera, genomic information on marine macroalgae-associated Bacillus species remains scarce. In this study, we further investigated our previously published genome of the epiphytic strain Bacillus altitudinis 19_A to find features that could be translated to potential metabolites produced by this microorganism, as well as genes that play a role in its interaction with its macroalgal host. To achieve this goal, we performed a pan-genome analysis of Bacillus sp. and a codon bias assessment, including the genome of the strain Bacillus altitudinis 19_A and 29 complete genome sequences of closely related Bacillus strains isolated from soil, marine environments, plants, extreme environments, air, and food. This genomic analysis revealed that Bacillus altitudinis 19_A possessed unique genes encoding proteins involved in horizontal gene transfer, DNA repair, transcriptional regulation, and bacteriocin biosynthesis. In this comparative analysis, codon bias was not associated with the habitat of the strains studied. Some accessory genes were identified in the Bacillus altitudinis 19_A genome that could be related to its epiphytic lifestyle, as well as gene clusters for the biosynthesis of a sporulation-killing factor and a bacteriocin, showing their potential as a source of antimicrobial peptides. Our results provide a comprehensive view of the Bacillus altitudinis 19_A genome to understand its adaptation to the marine environment and its potential as a producer of bioactive compounds.},
}
@article {pmid38555673,
year = {2024},
author = {Sun, H and Chang, H and Zhu, Y and Li, X and Yang, X and Zhou, X and Wu, D and Ding, J and Liu, Y},
title = {Strong suppression of silver nanoparticles on antibiotic resistome in anammox process.},
journal = {Journal of hazardous materials},
volume = {470},
number = {},
pages = {134128},
doi = {10.1016/j.jhazmat.2024.134128},
pmid = {38555673},
issn = {1873-3336},
abstract = {This study comprehensively deciphered the effect of silver nanoparticles (AgNPs) on anammox flocculent sludge, including nitrogen removal performance, microbial community structure, functional enzyme abundance, antibiotic resistance gene (ARGs) dissemination, and horizontal gene transfer (HGT) mechanisms. After long-term exposure to 0-2.5 mg/L AgNPs for 200 cycles, anammox performance significantly decreased (P < 0.05), while the relative abundances of dominant Ca. Kuenenia and anammox-related enzymes (hzsA, nirK) increased compared to the control (P < 0.05). For antibiotic resistome, ARG abundance hardly changed with 0-0.5 mg/L AgNPs but decreased by approximately 90% with 1.5-2.5 mg/L AgNPs. More importantly, AgNPs effectively inhibited MGE-mediated HGT of ARGs. Additionally, structural equation model (SEM) disclosed the underlying relationship between AgNPs, the antibiotic resistome, and the microbial community. Overall, AgNPs suppressed the anammox-driven nitrogen cycle, regulated the microbial community, and prevented the spread of ARGs in anammox flocs. This study provides a theoretical baseline for an advanced understanding of the ecological roles of nanoparticles and resistance elements in engineered ecosystems.},
}
@article {pmid38554973,
year = {2024},
author = {Song, H and Yoo, JS and Unno, T},
title = {Discerning the dissemination mechanisms of antibiotic resistance genes through whole genome sequencing of extended-spectrum beta-lactamase (ESBL)-producing E. coli isolated from veterinary clinics and farms in South Korea.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172068},
doi = {10.1016/j.scitotenv.2024.172068},
pmid = {38554973},
issn = {1879-1026},
abstract = {Extended-spectrum beta-lactamase (ESBL)-producing bacteria are resistant to most beta-lactams, including third-generation cephalosporins, limiting the treatment methods against the infections they cause. In this study, we performed whole genome sequencing of ESBL-producing E. coli to determine the mechanisms underlying the dissemination of antibiotic resistance genes. We analyzed 141 ESBL-producing isolates which had been collected from 16 veterinary clinics and 16 farms in South Korea. Long- and short-read sequencing platforms were used to obtain high-quality assemblies. The results showed that blaCTX-M is the dominant ESBL gene type found in South Korea. The spread of blaCTX-M appears to have been facilitated by both clonal spread between different host species and conjugation. Most blaCTX-M genes were found associated with diverse mobile genetic elements that may contribute to the chromosomal integration of the genes. Diverse incompatibility groups of blaCTX-M-harboring plasmids were also observed, which allows their spread among a variety of bacteria. Comprehensive whole genome sequence analysis was useful for the identification of the most prevalent types of ESBL genes and their dissemination mechanisms. The results of this study suggest that the propagation of ESBL genes can occur through clonal spread and plasmid-mediated dissemination, and that suitable action plans should be developed to prevent further propagation of these genes.},
}
@article {pmid38554512,
year = {2024},
author = {Qin, J and Qi, X and Li, Y and Tang, Z and Zhang, X and Ru, S and Xiong, JQ},
title = {Bisphenols can promote antibiotic resistance by inducing metabolic adaptations and natural transformation.},
journal = {Journal of hazardous materials},
volume = {470},
number = {},
pages = {134149},
doi = {10.1016/j.jhazmat.2024.134149},
pmid = {38554512},
issn = {1873-3336},
abstract = {Whether bisphenols, as plasticizers, can influence bacterial uptake of antibiotic resistance genes (ARGs) in natural environment, as well as the underlying mechanism remains largely unknown. Our results showed that four commonly used bisphenols (bisphenol A, S, F, and AF) at their environmental relative concentrations can significantly promote transmission of ARGs by 2.97-3.56 times in Acinetobacter baylyi ADP1. Intriguingly, we observed ADP1 acquired resistance by integrating plasmids uptake and cellular metabolic adaptations other than through reactive oxygen species mediated pathway. Metabolic adaptations including upregulation of capsules polysaccharide biosynthesis and intracellularly metabolic enzymes, which enabled formation of thicker capsules for capturing free plasmids, and degradation of accumulated compounds. Simultaneously, genes encoding DNA uptake and translocation machinery were incorporated to enhance natural transformation of antibiotic resistance carrying plasmids. We further exposed aquatic fish to bisphenols for 120 days to monitor their long-term effects in aquatic environment, which showed that intestinal bacteria communities were dominated by a drug resistant microbiome. Our study provides new insight into the mechanism of enhanced natural transformation of ARGs by bisphenols, and highlights the investigations for unexpectedly-elevated antibiotic-resistant risks by structurally related environmental chemicals.},
}
@article {pmid38552150,
year = {2024},
author = {Howard-Varona, C and Lindback, MM and Fudyma, JD and Krongauz, A and Solonenko, NE and Zayed, AA and Andreopoulos, WB and Olson, HM and Kim, YM and Kyle, JE and Del Rio, TG and Adkins, JN and Tfaily, MM and Paul, S and Sullivan, MB and Duhaime, MB},
title = {Environment-specific virocell metabolic reprogramming.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae055},
pmid = {38552150},
issn = {1751-7370},
abstract = {Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell", is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.},
}
@article {pmid38551849,
year = {2024},
author = {Masuda, T and Mareš, J and Shiozaki, T and Inomura, K and Fujiwara, A and Prášil, O},
title = {Crocosphaera watsonii - A widespread nitrogen-fixing unicellular marine cyanobacterium.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.13450},
pmid = {38551849},
issn = {1529-8817},
support = {23-06593S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; JP23H02301//Japan Society for the Promotion of Science/ ; JPMJPR23GA//JST, PRESTO/ ; },
abstract = {Crocosphaera watsonii is a unicellular N2-fixing (diazotrophic) cyanobacterium observed in tropical and subtropical oligotrophic oceans. As a diazotroph, it can be a source of bioavailable nitrogen (N) to the microbial community in N-limited environments, and this may fuel primary production in the regions where it occurs. Crocosphaera watsonii has been the subject of intense study, both in culture and in field populations. Here, we summarize the current understanding of the phylogenetic and physiological diversity of C. watsonii, its distribution, and its ecological niche. Analysis of the relationships among the individual Crocosphaera species and related free-living and symbiotic lineages of diazotrophs based on the nifH gene have shown that the C. watsonii group holds a basal position and that its sequence is more similar to Rippkaea and Zehria than to other Crocosphaera species. This finding warrants further scrutiny to determine if the placement is related to a horizontal gene transfer event. Here, the nifH UCYN-B gene copy number from a recent synthesis effort was used as a proxy for relative C. watsonii abundance to examine patterns of C. watsonii distribution as a function of environmental factors, like iron and phosphorus concentration, and complimented with a synthesis of C. watsonii physiology. Furthermore, we have summarized the current knowledge of C. watsonii with regards to N2 fixation, photosynthesis, and quantitative modeling of physiology. Because N availability can limit primary production, C. watsonii is widely recognized for its importance to carbon and N cycling in ocean ecosystems, and we conclude this review by highlighting important topics for further research on this important species.},
}
@article {pmid38548766,
year = {2024},
author = {Pratt, CJ and Meili, CH and Jones, AL and Jackson, DK and England, EE and Wang, Y and Hartson, S and Rogers, J and Elshahed, MS and Youssef, NH},
title = {Anaerobic fungi in the tortoise alimentary tract illuminate early stages of host-fungal symbiosis and Neocallimastigomycota evolution.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2714},
pmid = {38548766},
issn = {2041-1723},
support = {2029478//National Science Foundation (NSF)/ ; 2029478//National Science Foundation (NSF)/ ; },
abstract = {Anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tract of herbivores. While their presence in mammals is well documented, evidence for their occurrence in non-mammalian hosts is currently sparse. Culture-independent surveys of AGF in tortoises identified a unique community, with three novel deep-branching genera representing >90% of sequences in most samples. Representatives of all genera were successfully isolated under strict anaerobic conditions. Transcriptomics-enabled phylogenomic and molecular dating analyses indicated an ancient, deep-branching position in the AGF tree for these genera, with an evolutionary divergence time estimate of 104-112 million years ago (Mya). Such estimates push the establishment of animal-Neocallimastigomycota symbiosis from the late to the early Cretaceous. Further, tortoise-associated isolates (T-AGF) exhibited limited capacity for plant polysaccharides metabolism and lacked genes encoding several carbohydrate-active enzyme (CAZyme) families. Finally, we demonstrate that the observed curtailed degradation capacities and reduced CAZyme repertoire is driven by the paucity of horizontal gene transfer (HGT) in T-AGF genomes, compared to their mammalian counterparts. This reduced capacity was reflected in an altered cellulosomal production capacity in T-AGF. Our findings provide insights into the phylogenetic diversity, ecological distribution, evolutionary history, evolution of fungal-host nutritional symbiosis, and dynamics of genes acquisition in Neocallimastigomycota.},
}
@article {pmid38546735,
year = {2024},
author = {Klose, SM and Legione, AR and Bushell, RN and Browning, GF and Vaz, PK},
title = {Unveiling genome plasticity and a novel phage in Mycoplasma felis: Genomic investigations of four feline isolates.},
journal = {Microbial genomics},
volume = {10},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001227},
pmid = {38546735},
issn = {2057-5858},
mesh = {Cats ; Animals ; Horses ; Australia ; Genomics ; *Mycoplasma/genetics ; *Felis ; *Bacteriophages ; },
abstract = {Mycoplasma felis has been isolated from diseased cats and horses, but to date only a single fully assembled genome of this species, of an isolate from a horse, has been characterized. This study aimed to characterize and compare the completely assembled genomes of four clinical isolates of M. felis from three domestic cats, assembled with the aid of short- and long-read sequencing methods. The completed genomes encoded a median of 759 ORFs (range 743-777) and had a median average nucleotide identity of 98.2 % with the genome of the available equid origin reference strain. Comparative genomic analysis revealed the occurrence of multiple horizontal gene transfer events and significant genome reassortment. This had resulted in the acquisition or loss of numerous genes within the Australian felid isolate genomes, encoding putative proteins involved in DNA transfer, metabolism, DNA replication, host cell interaction and restriction modification systems. Additionally, a novel mycoplasma phage was detected in one Australian felid M. felis isolate by genomic analysis and visualized using cryo-transmission electron microscopy. This study has highlighted the complex genomic dynamics in different host environments. Furthermore, the sequences obtained in this work will enable the development of new diagnostic tools, and identification of future infection control and treatment options for the respiratory disease complex in cats.},
}
@article {pmid38543613,
year = {2024},
author = {Mei, L and Song, Y and Liu, X and Li, K and Guo, X and Liu, L and Liu, Y and Kozlakidis, Z and Cheong, IH and Wang, D and Wei, Q},
title = {Characterization and Implications of IncP-2A Plasmid pMAS152 Harboring Multidrug Resistance Genes in Extensively Drug-Resistant Pseudomonas aeruginosa.},
journal = {Microorganisms},
volume = {12},
number = {3},
pages = {},
pmid = {38543613},
issn = {2076-2607},
support = {2022YFC2602200//National Key Research and Development Program of China/ ; Project No. National Pathogen Resource Center-NPRC-32//National Science and Technology Infrastructure of China/ ; },
abstract = {Bacterial antimicrobial resistance (AMR) poses a significant global public health challenge. The escalation of AMR is primarily attributed to the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs), often facilitated by plasmids. This underscores the critical need for a comprehensive understanding of the resistance mechanisms and transmission dynamics of these plasmids. In this study, we utilized in vitro drug sensitivity testing, conjugation transfer assays, and whole-genome sequencing to investigate the resistance mechanism of an extensively drug-resistant (XDR) Pseudomonas aeruginosa clinical isolate, MAS152. We specifically focused on analyzing the drug-resistant plasmid pMAS152 it harbors and its potential for widespread dissemination. Bioinformatics analysis revealed that MAS152 carries a distinct IncpP-2A plasmid, pMAS152, characterized by a 44.8 kb multidrug resistance (MDR) region. This region houses a 16S rRNA methyltransferase (16S-RMTase) gene, rmtB, conferring high-level resistance to aminoglycoside antibiotics. Notably, this region also contains an extended-spectrum β-Lactamase (ESBL) gene, blaPER-1, and an efflux pump operon, tmexCD-oprJ, which mediate resistance to β-Lactams and quinolone antibiotics, respectively. Such a combination of ARGs, unprecedented in reported plasmids, could significantly undermine the effectiveness of first-line antibiotics in treating P. aeruginosa infections. Investigation into the genetic environment of the MDR region suggests that Tn2 and IS91 elements may be instrumental in the horizontal transfer of rmtB. Additionally, a complex Class I integron with an ISCR1 structure, along with TnAs1, seems to facilitate the horizontal transfer of blaPER-1. The conjugation transfer assay, coupled with the annotation of conjugation-related genes and phylogenetic analysis, indicates that the plasmid pMAS152 functions as a conjugative plasmid, with other genus Pseudomonas species as potential hosts. Our findings provide vital insights into the resistance mechanisms and transmission potential of the XDR P. aeruginosa isolate MAS152, underlining the urgent need for novel strategies to combat the spread of AMR. This study highlights the complex interplay of genetic elements contributing to antibiotic resistance and underscores the importance of continuous surveillance of emerging ARGs in clinical isolates.},
}
@article {pmid38543545,
year = {2024},
author = {Skwor, T and Jones, DC and Cahak, C and Newton, RJ},
title = {First Report and Characterization of a Plasmid-Encoded blaSFO-1 in a Multi-Drug-Resistant Aeromonas hydrophila Clinical Isolate.},
journal = {Microorganisms},
volume = {12},
number = {3},
pages = {},
pmid = {38543545},
issn = {2076-2607},
abstract = {Antibiotic resistance remains one of the most pressing public health issues facing the world today. At the forefront of this battle lies the ever-increasing identification of extended-spectrum beta-lactamases and carbapenemases within human pathogens, conferring resistance towards broad-spectrum and last-resort antimicrobials. This study was prompted due to the identification of a pathogenic Aeromonas hydrophila isolate (strain MAH-4) collected from abdominal fluid, which presented a robust resistance pattern against second-, third-, and fourth-generation cephalosporins, ertapenem, ciprofloxacin, gentamicin, levofloxacin and moxifloxacin, and beta lactam/beta-lactamase inhibitor combinations. Whole genome sequencing was performed and identified a 328 kb plasmid (pMAH4) encoding 10 antibiotic resistance genes, including blaSFO-1, blaTEM-1, and blaOXA-1 of A. hydrophia MAH-4. This is the first report of beta-lactamase SFO-1 within a clinical strain of Aeromonas. Due to the remarkable sequence identity of pMAH4 to plasmids associated with Enterobacterales genera like Klebsiella and the extensive capabilities of Aeromonas for horizontal gene transfer, our identification of a clinical isolate encoding SFO-1 on a plasmid suggests antibiotic resistance gene mobility between Enterobacterales and non-Enterobacterales species.},
}
@article {pmid38542054,
year = {2024},
author = {Barathan, M and Ng, SL and Lokanathan, Y and Ng, MH and Law, JX},
title = {Unseen Weapons: Bacterial Extracellular Vesicles and the Spread of Antibiotic Resistance in Aquatic Environments.},
journal = {International journal of molecular sciences},
volume = {25},
number = {6},
pages = {},
doi = {10.3390/ijms25063080},
pmid = {38542054},
issn = {1422-0067},
support = {DIP-2023-011//National University of Malaysia/ ; FF-2021-518//Faculty of Medicine, Universiti Kebangsaan Malaysia/ ; },
abstract = {This paper sheds light on the alarming issue of antibiotic resistance (ABR) in aquatic environments, exploring its detrimental effects on ecosystems and public health. It examines the multifaceted role of antibiotic use in aquaculture, agricultural runoff, and industrial waste in fostering the development and dissemination of resistant bacteria. The intricate interplay between various environmental factors, horizontal gene transfer, and bacterial extracellular vesicles (BEVs) in accelerating the spread of ABR is comprehensively discussed. Various BEVs carrying resistance genes like blaCTX-M, tetA, floR, and sul/I, as well as their contribution to the dominance of multidrug-resistant bacteria, are highlighted. The potential of BEVs as both a threat and a tool in combating ABR is explored, with promising strategies like targeted antimicrobial delivery systems and probiotic-derived EVs holding significant promise. This paper underscores the urgency of understanding the intricate interplay between BEVs and ABR in aquatic environments. By unraveling these unseen weapons, we pave the way for developing effective strategies to mitigate the spread of ABR, advocating for a multidisciplinary approach that includes stringent regulations, enhanced wastewater treatment, and the adoption of sustainable practices in aquaculture.},
}
@article {pmid38539090,
year = {2024},
author = {Kumar, G and Balakrishna, K and Mukhopadhyay, C and Kalwaje Eshwara, V},
title = {Comparison of integron mediated antimicrobial resistance in clinical isolates of Escherichia coli from urinary and bacteremic sources.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {102},
pmid = {38539090},
issn = {1471-2180},
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a global threat driven mainly by horizontal gene transfer (HGT) mechanisms through mobile genetic elements (MGEs) including integrons. The variable region (VR) of an integron can acquire or excise gene cassettes (GCs) that confer resistance to antibiotics based on the selection pressure. Escherichia coli plays a significant role in the genetic transfer of resistance determinants to other Gram-negative bacteria. Current study is aimed to detect and compare integron-mediated resistance in clinical isolates of E. coli. Unique isolates of E. coli from urine or blood cultures were studied for their antimicrobial resistance patterns and integrons were detected using polymerase chain reaction assays followed by Sanger sequencing of GCs.<br><br>RESULTS: During the study period, a total of 470 E. coli isolates were obtained, 361 (76.8%) from urinary and 109 (23.1%) from bacteremic sources. Class 1 integrons were detected in 66 (18.2%) and 26 (23.8%) isolates respectively. Urinary isolates of E. coli harbouring Class 1 integrons demonstrated significantly higher rates of resistance (p&#x2009;<&#x2009;0.05) for most antibiotics (12/16, 75%) compared to integron negative isolates. Although not statistically significant, similar differences were observed in bacteremic isolates. Among the urinary isolates, 27 (40.9%) had a VR, in which the most common GC array detected was DfrA17-AadA5 (n&#x2009;=&#x2009;14), followed by DfrA5 (n&#x2009;=&#x2009;4) and DfrA12 (n&#x2009;=&#x2009;3). Among bacteremic isolates, only 4 (15.3%) had a VR, all of which were carrying DfrA17. The detected GC array correlated with the respective isolates' phenotypic resistance patterns.<br><br>CONCLUSION: We found a strong correlation between integron positivity and trimethoprim resistance among E. coli from urinary sources. Although higher rates of resistance were observed in bacteremic isolates, they mostly carried empty integrons.},
}
@article {pmid38538528,
year = {2024},
author = {Chiquito-Contreras, CJ and Meza-Menchaca, T and Guzmán-López, O and Vásquez, EC and Ricaño-Rodríguez, J},
title = {Molecular Insights into Plant-Microbe Interactions: A Comprehensive Review of Key Mechanisms.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {16},
number = {1},
pages = {9},
doi = {10.31083/j.fbe1601009},
pmid = {38538528},
issn = {1945-0508},
abstract = {In most ecosystems, plants establish complex symbiotic relationships with organisms, such as bacteria and fungi, which significantly influence their health by promoting or inhibiting growth. These relationships involve biochemical exchanges at the cellular level that affect plant physiology and have evolutionary implications, such as species diversification, horizontal gene transfer, symbiosis and mutualism, environmental adaptation, and positive impacts on community structure and biodiversity. For these reasons, contemporary research, moving beyond observational studies, seeks to elucidate the molecular basis of these interactions; however, gaps in knowledge remain. This is particularly noticeable in understanding how plants distinguish between beneficial and antagonistic microorganisms. In light of the above, this literature review aims to address some of these gaps by exploring the key mechanisms in common interspecies relationships. Thus, our study presents novel insights into these evolutionary archetypes, focusing on the antibiosis process and microbial signaling, including chemotaxis and quorum sensing. Additionally, it examined the biochemical basis of endophytism, pre-mRNA splicing, and transcriptional plasticity, highlighting the roles of transcription factors and epigenetic regulation in the functions of the interacting organisms. These findings emphasize the importance of understanding these confluences in natural environments, which are crucial for future theoretical and practical applications, such as improving plant nutrition, protecting against pathogens, developing transgenic crops, sustainable agriculture, and researching disease mechanisms. It was concluded that because of the characteristics of the various biomolecules involved in these biological interactions, there are interconnected molecular networks in nature that give rise to different ecological scaffolds. These networks integrate a myriad of functionally organic units that belong to various kingdoms. This interweaving underscores the complexity and multidisciplinary integration required to understand plant-microbe interactions at the molecular level. Regarding the limitations inherent in this study, it is recognized that researchers face significant obstacles. These include technical difficulties in experimentation and fieldwork, as well as the arduous task of consolidating and summarizing findings for academic articles. Challenges range from understanding complex ecological and molecular dynamics to unbiased and objective interpretation of diverse and ever-changing literature.},
}
@article {pmid38536216,
year = {2024},
author = {Dechêne-Tempier, M and de Boisséson, C and Lucas, P and Bougeard, S and Libante, V and Marois-Créhan, C and Payot, S},
title = {Virulence genes, resistome and mobilome of Streptococcus suis strains isolated in France.},
journal = {Microbial genomics},
volume = {10},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001224},
pmid = {38536216},
issn = {2057-5858},
mesh = {Humans ; Animals ; Swine ; *Streptococcus suis ; Virulence ; France ; Virulence Factors ; DNA ; },
abstract = {Streptococcus suis is a leading cause of infection in pigs, causing extensive economic losses. In addition, it can also infect wild fauna, and can be responsible for severe infections in humans. Increasing antimicrobial resistance (AMR) has been described in S. suis worldwide and most of the AMR genes are carried by mobile genetic elements (MGEs). This contributes to their dissemination by horizontal gene transfer. A collection of 102 strains isolated from humans, pigs and wild boars in France was subjected to whole genome sequencing in order to: (i) study their genetic diversity, (ii) evaluate their content in virulence-associated genes, (iii) decipher the mechanisms responsible for their AMR and their association with MGEs, and (iv) study their ability to acquire extracellular DNA by natural transformation. Analysis by hierarchical clustering on principal components identified a few virulence-associated factors that distinguish invasive CC1 strains from the other strains. A plethora of AMR genes (n=217) was found in the genomes. Apart from the frequently reported erm(B) and tet(O) genes, more recently described AMR genes were identified [vga(F)/sprA, vat(D)]. Modifications in PBPs/MraY and GyrA/ParC were detected in the penicillin- and fluoroquinolone-resistant isolates respectively. New AMR gene-MGE associations were detected. The majority of the strains have the full set of genes required for competence, i.e for the acquisition of extracellular DNA (that could carry AMR genes) by natural transformation. Hence the risk of dissemination of these AMR genes should not be neglected.},
}
@article {pmid38534711,
year = {2024},
author = {Li, Q and Li, J and He, T and Ji, X and Wei, R and Yu, M and Wang, R},
title = {Sub-MIC Antibiotics Modulate Productions of Outer Membrane Vesicles in Tigecycline-Resistant Escherichia coli.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {3},
pages = {},
pmid = {38534711},
issn = {2079-6382},
support = {32102728//National Natural Science Foundation of China/ ; ZX(21)1224//Exploration and Disruptive Innovation Projects of Jiangsu Academy of Agricultural Sciences/ ; GJFP20230305//National Agricultural Product Quality and Safety Risk Assessment/ ; },
abstract = {Antimicrobial resistance (AMR) has been recognized as one of the most important crises affecting global human health in the 21st century. Tigecycline is one of the last resort antibiotics for treating severe infections caused by multi-drug resistant Enterobacteriaceae. However, the mobile resistance gene tet(X4), which could mediate high-level tigecycline resistance, was discovered in 2019. The outer membrane vesicle (OMV) has been recognized as a new route for horizontal gene transfer; antimicrobial resistant bacteria also have the ability to secret OMVs, while little is known about the impact of antibiotics on the secretion and characteristics of OMVs from tigecycline resistant bacteria till now. This study aimed to investigate the effects of antibiotics on the production and traits of a tigecycline resistant Escherichia coli strain of 47EC. The results showed that sub-inhibitory (1/2 MIC or 1/4 MIC) concentrations of gentamicin, meropenem, ceftazidime, chloramphenicol, tigecycline, ciprofloxacin, polymycin, rifaximin and mitomycin C could significantly increase the secretion of OMVs (0.713 ± 0.05~6.333 ± 0.15 mg/mL) from E. coli 47EC compared to the respective untreated control (0.709 ± 0.03 mg/mL). In addition, the particle sizes of OMVs were generally larger, and the zeta potential were lower in the antibiotics-treated groups than those of the antibiotic-free group. The copy numbers of the tigecycline resistance gene of tet(X4) in the OMVs of most antimicrobial-treated groups were higher than that of the control group. Moreover, transcriptome analysis on ciprofloxacin-treated E. coli 47EC indicated that the SOS response and prophage activation might participate in the ciprofloxacin-induced OMV formation. In conclusion, the clinical application of antibiotics in treating bacterial infections, especially multi-drug resistant bacteria, might lead to the increased secretion of bacterial OMVs and the enrichment of antimicrobial-resistant genes in the OMVs.},
}
@article {pmid38534448,
year = {2024},
author = {Duwor, S and Brites, D and Mäser, P},
title = {Phylogenetic Analysis of Pyruvate-Ferredoxin Oxidoreductase, a Redox Enzyme Involved in the Pharmacological Activation of Nitro-Based Prodrugs in Bacteria and Protozoa.},
journal = {Biology},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/biology13030178},
pmid = {38534448},
issn = {2079-7737},
abstract = {The present frontrunners in the chemotherapy of infections caused by protozoa are nitro-based prodrugs that are selectively activated by PFOR-mediated redox reactions. This study seeks to analyze the distribution of PFOR in selected protozoa and bacteria by applying comparative genomics to test the hypothesis that PFOR in eukaryotes was acquired through horizontal gene transfer (HGT) from bacteria. Furthermore, to identify other putatively acquired genes, proteome-wide and gene enrichment analyses were used. A plausible explanation for the patchy occurrence of PFOR in protozoa is based on the hypothesis that bacteria are potential sources of genes that enhance the adaptation of protozoa in hostile environments. Comparative genomics of Entamoeba histolytica and the putative gene donor, Desulfovibrio vulgaris, identified eleven candidate genes for HGT involved in intermediary metabolism. If these results can be reproduced in other PFOR-possessing protozoa, it would provide more validated evidence to support the horizontal transfer of pfor from bacteria.},
}
@article {pmid38533399,
year = {2024},
author = {Peng, D and Wang, Z and Tian, J and Wang, W and Guo, S and Dai, X and Yin, H and Li, L},
title = {Phyllosphere bacterial community dynamics in response to bacterial wildfire disease: succession and interaction patterns.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1331443},
pmid = {38533399},
issn = {1664-462X},
abstract = {Plants interact with complex microbial communities in which microorganisms play different roles in plant development and health. While certain microorganisms may cause disease, others promote nutrient uptake and resistance to stresses through a variety of mechanisms. Developing plant protection measures requires a deeper comprehension of the factors that influence multitrophic interactions and the organization of phyllospheric communities. High-throughput sequencing was used in this work to investigate the effects of climate variables and bacterial wildfire disease on the bacterial community's composition and assembly in the phyllosphere of tobacco (Nicotiana tabacum L.). The samples from June (M1), July (M2), August (M3), and September (M4) formed statistically separate clusters. The assembly of the whole bacterial population was mostly influenced by stochastic processes. PICRUSt2 predictions revealed genes enriched in the M3, a period when the plant wildfire disease index reached climax, were associated with the development of the wildfire disease (secretion of virulence factor), the enhanced metabolic capacity and environmental adaption. The M3 and M4 microbial communities have more intricate molecular ecological networks (MENs), bursting with interconnections within a densely networked bacterial population. The relative abundances of plant-beneficial and antagonistic microbes Clostridiales, Bacillales, Lactobacillales, and Sphingobacteriales, showed significant decrease in severally diseased sample (M3) compared to the pre-diseased samples (M1/M2). Following the results of MENs, we further test if the correlating bacterial pairs within the MEN have the possibility to share functional genes and we have unraveled 139 entries of such horizontal gene transfer (HGT) events, highlighting the significance of HGT in shaping the adaptive traits of plant-associated bacteria across the MENs, particularly in relation to host colonization and pathogenicity.},
}
@article {pmid38530969,
year = {2024},
author = {Nasser, F and Gaudreau, A and Lubega, S and Zaker, A and Xia, X and Mer, AS and D'Costa, VM},
title = {Characterization of the diversity of type IV secretion system-encoding plasmids in Acinetobacter.},
journal = {Emerging microbes &amp; infections},
volume = {13},
number = {1},
pages = {2320929},
doi = {10.1080/22221751.2024.2320929},
pmid = {38530969},
issn = {2222-1751},
abstract = {The multi-drug resistant pathogen Acinetobacter baumannii has gained global attention as an important clinical challenge. Owing to its ability to survive on surfaces, its capacity for horizontal gene transfer, and its resistance to front-line antibiotics, A. baumannii has established itself as a successful pathogen. Bacterial conjugation is a central mechanism for pathogen evolution. The epidemic multidrug-resistant A. baumannii ACICU harbours a plasmid encoding a Type IV Secretion System (T4SS) with homology to the E. coli F-plasmid, and plasmids with homologous gene clusters have been identified in several A. baumannii sequence types. However the genetic and host strain diversity, global distribution, and functional ability of this group of plasmids is not fully understood. Using systematic analysis, we show that pACICU2 belongs to a group of almost 120 T4SS-encoding plasmids within four different species of Acinetobacter and one strain of Klebsiella pneumoniae from human and environmental origin, and globally distributed across 20 countries spanning 4 continents. Genetic diversity was observed both outside and within the T4SS-encoding cluster, and 47% of plasmids harboured resistance determinants, with two plasmids harbouring eleven. Conjugation studies with an extensively drug-resistant (XDR) strain showed that the XDR plasmid could be successfully transferred to a more divergent A. baumanii, and transconjugants exhibited the resistance phenotype of the plasmid. Collectively, this demonstrates that these T4SS-encoding plasmids are globally distributed and more widespread among Acinetobacter than previously thought, and that they represent an important potential reservoir for future clinical concern.},
}
@article {pmid38529905,
year = {2024},
author = {Crowley, C and Selvaraj, A and Hariharan, A and Healy, CM and Moran, GP},
title = {Fusobacterium nucleatum subsp. polymorphum recovered from malignant and potentially malignant oral disease exhibit heterogeneity in adhesion phenotypes and adhesin gene copy number, shaped by inter-subspecies horizontal gene transfer and recombination-derived mosaicism.},
journal = {Microbial genomics},
volume = {10},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001217},
pmid = {38529905},
issn = {2057-5858},
mesh = {Humans ; *Mosaicism ; Phylogeny ; *Gene Transfer, Horizontal ; Fusobacterium/genetics ; Phenotype ; Gene Dosage ; },
abstract = {Fusobacterium nucleatum is an anaerobic commensal of the oral cavity associated with periodontitis and extra-oral diseases, including colorectal cancer. Previous studies have shown an increased relative abundance of this bacterium associated with oral dysplasia or within oral tumours. Using direct culture, we found that 75 % of Fusobacterium species isolated from malignant or potentially malignant oral mucosa were F. nucleatum subsp. polymorphum. Whole genome sequencing and pangenome analysis with Panaroo was carried out on 76 F. nucleatum subsp. polymorphum genomes. F. nucleatum subsp. polymorphum was shown to possesses a relatively small core genome of 1604 genes in a pangenome of 7363 genes. Phylogenetic analysis based on the core genome shows the isolates can be separated into three main clades with no obvious genotypic associations with disease. Isolates recovered from healthy and diseased sites in the same patient are generally highly related. A large repertoire of adhesins belonging to the type V secretion system (TVSS) could be identified with major variation in repertoire and copy number between strains. Analysis of intergenic recombination using fastGEAR showed that adhesin complement is shaped by horizontal gene transfer and recombination. Recombination events at TVSS adhesin genes were not only common between lineages of subspecies polymorphum, but also between different subspecies of F. nucleatum. Strains of subspecies polymorphum with low copy numbers of TVSS adhesin encoding genes tended to have the weakest adhesion to oral keratinocytes. This study highlights the genetic heterogeneity of F. nucleatum subsp. polymorphum and provides a new framework for defining virulence in this organism.},
}
@article {pmid38527381,
year = {2024},
author = {Ferilli, F and Lione, G and Gonthier, P and Turina, M and Forgia, M},
title = {First detection of mycoviruses in Gnomoniopsis castaneae suggests a putative horizontal gene transfer event between negative-sense and double-strand RNA viruses.},
journal = {Virology},
volume = {594},
number = {},
pages = {110057},
doi = {10.1016/j.virol.2024.110057},
pmid = {38527381},
issn = {1096-0341},
abstract = {Gnomoniopsis castaneae is an ascomycetous fungus mainly known as a major pathogen of chestnut causing nut rots, although it is often found as an endophyte in chestnut tissues. To date, no virus has been reported as associated with to this fungus. Here, a collection of G. castaneae isolates from several European countries was screened to detect mycoviruses infecting the fungus: for the first time we report the identification and prevalence of mitovirus Gnomoniopsis castaneae mitovirus 1 (GcMV1) and the chrysovirus Gnomoniopsis castaneae chrysovirus 1 (GcCV1). Interestingly, we provide evidence supporting a putative horizontal gene transfer between members of the phyla Negarnaviricota and Duplornaviricota: a small putative protein of unknown function encoded on the RNA3 of GcCV1 (Chrysoviridae) has homologs in the genome of viruses of the family Mymonaviridae.},
}
@article {pmid38521802,
year = {2024},
author = {Asad, A and Jahan, I and Munni, MA and Begum, R and Mukta, MA and Saif, K and Faruque, SN and Hayat, S and Islam, Z},
title = {Multidrug-resistant conjugative plasmid carrying mphA confers increased antimicrobial resistance in Shigella.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {6947},
pmid = {38521802},
issn = {2045-2322},
support = {NIH FIC TW010540/TW/FIC NIH HHS/United States ; K43TW011447/TW/FIC NIH HHS/United States ; },
mesh = {Child ; Humans ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Dysentery, Bacillary/drug therapy/epidemiology ; Macrolides/pharmacology/therapeutic use ; Drug Resistance, Bacterial/genetics ; *Shigella ; Azithromycin/pharmacology/therapeutic use ; Ciprofloxacin/pharmacology/therapeutic use ; Ceftriaxone/pharmacology ; Microbial Sensitivity Tests ; Protein Synthesis Inhibitors/pharmacology ; Plasmids/genetics ; },
abstract = {Shigellosis remains a common gastrointestinal disease mostly in children < 5 years of age in developing countries. Azithromycin (AZM), a macrolide, is currently the first-line treatment for shigellosis in Bangladesh; ciprofloxacin (CIP) and ceftriaxone (CRO) are also used frequently. We aimed to evaluate the current epidemiology of antimicrobial resistance (AMR) and mechanism(s) of increasing macrolide resistance in Shigella in Bangladesh. A total of 2407 clinical isolates of Shigella from 2009 to 2016 were studied. Over the study period, Shigella sonnei was gradually increasing and become predominant (55%) over Shigella flexneri (36%) by 2016. We used CLSI-guided epidemiological cut-off value (ECV) for AZM in Shigella to set resistance breakpoints (zone-diameter ≤ 15 mm for S. flexneri and ≤ 11 mm for S. sonnei). Between 2009 and 2016, AZM resistance increased from 22% to approximately 60%, CIP resistance increased by 40%, and CRO resistance increased from zero to 15%. The mphA gene was the key macrolide resistance factor in Shigella; a 63MDa conjugative middle-range plasmid was harboring AZM and CRO resistance factors. Our findings show that, especially after 2014, there has been a rapid increase in resistance to the three most effective antibiotics. The rapid spread of macrolide (AZM) resistance genes among Shigella are driven by horizontal gene transfer rather than direct lineage.},
}
@article {pmid38521276,
year = {2024},
author = {Liu, Q and Peng, Y and Liao, J and Liu, X and Peng, J and Wang, JH and Shao, Z},
title = {Broad-spectrum hydrocarbon-degrading microbes in the global ocean metagenomes.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {171746},
doi = {10.1016/j.scitotenv.2024.171746},
pmid = {38521276},
issn = {1879-1026},
abstract = {Understanding the diversity and functions of hydrocarbon-degrading microorganisms in marine environments is crucial for both advancing knowledge of biogeochemical processes and improving bioremediation methods. In this study, we leveraged nearly 20,000 metagenome-assembled genomes (MAGs), recovered from a wide array of marine samples across the global oceans, to map the diversity of aerobic hydrocarbon-degrading microorganisms. A broad bacterial diversity was uncovered, with a notable preference for degrading aliphatic hydrocarbons over aromatic ones, primarily within Proteobacteria and Actinobacteriota. Three types of broad-spectrum hydrocarbon-degrading bacteria were identified for their ability to degrade various hydrocarbons and possession of multiple copies of hydrocarbon biodegradation genes. These bacteria demonstrate extensive metabolic versatility, aiding their survival and adaptability in diverse environmental conditions. Evidence of gene duplication and horizontal gene transfer in these microbes suggests a potential enhancement in the diversity of hydrocarbon-degrading bacteria. Positive correlations were observed between the abundances of hydrocarbon-degrading genes and environmental parameters such as temperature (-5 to 35 °C) and salinity (20 to 42 PSU). Overall, our findings offer valuable insights into marine hydrocarbon-degrading microorganisms and suggest considerations for selecting microbial strains for oil pollution remediation.},
}
@article {pmid38519541,
year = {2024},
author = {Baker, BA and Gutiérrez-Preciado, A and Rodríguez Del Río, &#xc1; and McCarthy, CGP and López-García, P and Huerta-Cepas, J and Susko, E and Roger, AJ and Eme, L and Moreira, D},
title = {Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {38519541},
issn = {2058-5276},
support = {787904//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 803151//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
abstract = {Extremely halophilic archaea (Haloarchaea, Nanohaloarchaeota, Methanonatronarchaeia and Halarchaeoplasmatales) thrive in saturating salt concentrations where they must maintain osmotic equilibrium with their environment. The evolutionary history of adaptations enabling salt tolerance remains poorly understood, in particular because the phylogeny of several lineages is conflicting. Here we present a resolved phylogeny of extremely halophilic archaea obtained using improved taxon sampling and state-of-the-art phylogenetic approaches designed to cope with the strong compositional biases of their proteomes. We describe two uncultured lineages, Afararchaeaceae and Asbonarchaeaceae, which break the long branches at the base of Haloarchaea and Nanohaloarchaeota, respectively. We obtained 13 metagenome-assembled genomes (MAGs) of these archaea from metagenomes of hypersaline aquatic systems of the Danakil Depression (Ethiopia). Our phylogenomic analyses including these taxa show that at least four independent adaptations to extreme halophily occurred during archaeal evolution. Gene-tree/species-tree reconciliation suggests that gene duplication and horizontal gene transfer played an important role in this process, for example, by spreading key genes (such as those encoding potassium transporters) across extremely halophilic lineages.},
}
@article {pmid38518756,
year = {2024},
author = {Gàlvez-Morante, A and Guéguen, L and Natsidis, P and Telford, MJ and Richter, DJ},
title = {Dollo parsimony overestimates ancestral gene content reconstructions.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae062},
pmid = {38518756},
issn = {1759-6653},
abstract = {Ancestral reconstruction is a widely-used technique that has been applied to understand the evolutionary history of gain and loss of gene families. Ancestral gene content can be reconstructed via different phylogenetic methods, but many current and previous studies employ Dollo parsimony. We hypothesize that Dollo parsimony is not appropriate for ancestral gene content reconstruction inferences based on sequence homology, as Dollo parsimony is derived from the assumption that a complex character cannot be regained. This premise does not accurately model molecular sequence evolution, in which false orthology can result from sequence convergence or lateral gene transfer. The aim of this study is to test Dollo parsimony's suitability for ancestral gene content reconstruction and to compare its inferences with a maximum likelihood-based approach which allows a gene family to be gained more than once within a tree. We first compared the performance of the two approaches on a series of artificial datasets each of 5,000 genes that were simulated according to a spectrum of evolutionary rates without gene gain or loss, so that inferred deviations from the true gene count would arise only from errors in orthology inference and ancestral reconstruction. Next, we reconstructed protein domain evolution on a phylogeny representing known eukaryotic diversity. We observed that Dollo parsimony produced numerous ancestral gene content overestimations, especially at nodes closer to the root of the tree. These observations led us to the conclusion that, confirming our hypothesis, Dollo parsimony is not an appropriate method for ancestral reconstruction studies based on sequence homology.},
}
@article {pmid38517978,
year = {2024},
author = {Sheinman, M and Arndt, PF and Massip, F},
title = {Modeling the mosaic structure of bacterial genomes to infer their evolutionary history.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {13},
pages = {e2313367121},
doi = {10.1073/pnas.2313367121},
pmid = {38517978},
issn = {1091-6490},
abstract = {The chronology and phylogeny of bacterial evolution are difficult to reconstruct due to a scarce fossil record. The analysis of bacterial genomes remains challenging because of large sequence divergence, the plasticity of bacterial genomes due to frequent gene loss, horizontal gene transfer, and differences in selective pressure from one locus to another. Therefore, taking advantage of the rich and rapidly accumulating genomic data requires accurate modeling of genome evolution. An important technical consideration is that loci with high effective mutation rates may diverge beyond the detection limit of the alignment algorithms used, biasing the genome-wide divergence estimates toward smaller divergences. In this article, we propose a novel method to gain insight into bacterial evolution based on statistical properties of genome comparisons. We find that the length distribution of sequence matches is shaped by the effective mutation rates of different loci, by the horizontal transfers, and by the aligner sensitivity. Based on these inputs, we build a model and show that it accounts for the empirically observed distributions, taking the Enterobacteriaceae family as an example. Our method allows to distinguish segments of vertical and horizontal origins and to estimate the time divergence and exchange rate between any pair of taxa from genome-wide alignments. Based on the estimated time divergences, we construct a time-calibrated phylogenetic tree to demonstrate the accuracy of the method.},
}
@article {pmid38511257,
year = {2024},
author = {Fogg, PCM},
title = {Gene transfer agents: The ambiguous role of selfless viruses in genetic exchange and bacterial evolution.},
journal = {Molecular microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mmi.15251},
pmid = {38511257},
issn = {1365-2958},
support = {BB/V016288/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 109363/Z/15/A/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Gene transfer agents (GTAs) are genetic elements derived from ancestral bacteriophages that have become domesticated by the host. GTAs are present in diverse prokaryotic organisms, where they can facilitate horizontal gene transfer under certain conditions. Unlike typical bacteriophages, GTAs do not exhibit any preference for the replication or transfer of the genes encoding them; instead, they exhibit a remarkable capacity to package chromosomal, and sometimes extrachromosomal, DNA into virus-like capsids and disseminate it to neighboring cells. Because GTAs resemble defective prophages, identification of novel GTAs is not trivial. The detection of candidates relies on the genetic similarity to known GTAs, which has been fruitful in α-proteobacterial lineages but challenging in more distant bacteria. Here we consider several fundamental questions: What is the true prevalence of GTAs in prokaryote genomes? Given there are high costs for GTA production, what advantage do GTAs provide to the bacterial host to justify their maintenance? How is the bacterial chromosome recognized and processed for inclusion in GTA particles? This article highlights the challenges in comprehensively understanding GTAs' prevalence, function and DNA packaging method. Going forward, broad study of atypical GTAs and use of ecologically relevant conditions are required to uncover their true impact on bacterial chromosome evolution.},
}
@article {pmid38510031,
year = {2024},
author = {Liu, X and Zhao, H and Wong, A},
title = {Accounting for the health risk of probiotics.},
journal = {Heliyon},
volume = {10},
number = {6},
pages = {e27908},
pmid = {38510031},
issn = {2405-8440},
abstract = {Probiotics have long been associated with a myriad of health benefits, so much so that their adverse effects whether mild or severe, are often neglected or overshadowed by the enormous volume of articles describing their beneficial effects in the current literature. Recent evidence has demonstrated several health risks of probiotics that warrant serious reconsideration of their applications and further investigations. This review aims to highlight studies that report on how probiotics might cause opportunistic systemic and local infections, detrimental immunological effects, metabolic disturbance, allergic reactions, and facilitating the spread of antimicrobial resistance. To offer a recent account of the literature, articles within the last five years were prioritized. The narration of these evidence was based on the nature of the studies in the following order of preference: clinical studies or human samples, in vivo or animal models, in situ, in vitro and/or in silico. We hope that this review will inform consumers, food scientists, and medical practitioners, on the health risks, while also encouraging research that will focus on and clarify the adverse effects of probiotics.},
}
@article {pmid38507447,
year = {2024},
author = {Kehlet-Delgado, H and Montoya, AP and Jensen, KT and Wendlandt, CE and Dexheimer, C and Roberts, M and Torres Martínez, L and Friesen, ML and Griffitts, JS and Porter, SS},
title = {The evolutionary genomics of adaptation to stress in wild rhizobium bacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {13},
pages = {e2311127121},
doi = {10.1073/pnas.2311127121},
pmid = {38507447},
issn = {1091-6490},
support = {IOS-1755454//National Science Foundation (NSF)/ ; DEB-1943239//National Science Foundation (NSF)/ ; },
mesh = {Humans ; *Rhizobium/genetics ; Nickel ; *Metals, Heavy/toxicity ; Genomics ; Soil ; },
abstract = {Microbiota comprise the bulk of life's diversity, yet we know little about how populations of microbes accumulate adaptive diversity across natural landscapes. Adaptation to stressful soil conditions in plants provides seminal examples of adaptation in response to natural selection via allelic substitution. For microbes symbiotic with plants however, horizontal gene transfer allows for adaptation via gene gain and loss, which could generate fundamentally different evolutionary dynamics. We use comparative genomics and genetics to elucidate the evolutionary mechanisms of adaptation to physiologically stressful serpentine soils in rhizobial bacteria in western North American grasslands. In vitro experiments demonstrate that the presence of a locus of major effect, the nre operon, is necessary and sufficient to confer adaptation to nickel, a heavy metal enriched to toxic levels in serpentine soil, and a major axis of environmental soil chemistry variation. We find discordance between inferred evolutionary histories of the core genome and nreAXY genes, which often reside in putative genomic islands. This suggests that the evolutionary history of this adaptive variant is marked by frequent losses, and/or gains via horizontal acquisition across divergent rhizobium clades. However, different nre alleles confer distinct levels of nickel resistance, suggesting allelic substitution could also play a role in rhizobium adaptation to serpentine soil. These results illustrate that the interplay between evolution via gene gain and loss and evolution via allelic substitution may underlie adaptation in wild soil microbiota. Both processes are important to consider for understanding adaptive diversity in microbes and improving stress-adapted microbial inocula for human use.},
}
@article {pmid38506281,
year = {2024},
author = {Adeyelu, OO and Essien, EN and Adebote, V and Ajayi, A and Essiet, UU and Adeleye, AI and Smith, SI},
title = {Antimicrobial resistance genetic determinants and susceptibility profile of Pseudomonas aeruginosa isolated from clinical samples in a tertiary hospital in Ogun State, Nigeria.},
journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene},
volume = {},
number = {},
pages = {},
doi = {10.1093/trstmh/trae012},
pmid = {38506281},
issn = {1878-3503},
abstract = {BACKGROUND: Genetic determinants are known to promote antibiotic resistance through horizontal gene transfer.<br><br>METHODS: We molecularly characterized integrons, plasmid replicon types and metallo-&#x3b2;-lactamase-encoding genes of 38 Pseudomonas aeruginosa strains isolated from clinical samples.<br><br>RESULTS: The P. aeruginosa isolates displayed high resistance (97.4%) to &#x3b2;-lactams. Seventeen (44.74%) of them possessed plasmids. Of the 17 isolates that possessed plasmids, 11 (64.7%) of them harboured IncFIA plasmid replicon type, while 6 (35.3%), 5 (29.4%) and 5 (29.4%) were of the IncFIB, IncF and IncW types, respectively. The intI1 gene was detected in 19 (50%) of the isolates. The blaNDM-A, blaNDM-B and blaVIM genes were detected in 14 (35.9%), 4 (10.3%) and 5 (12.8%) of the isolates, respectively.<br><br>CONCLUSIONS: High resistance to &#x3b2;-lactams was observed among P. aeruginosa strains of clinical origin in this study. They possessed transmissible genetic elements indicating the potential for continuous dissemination, thus continuous surveillance is advocated.},
}
@article {pmid38504610,
year = {2024},
author = {Tekle, YI and Tefera, H},
title = {A Small Genome Amidst the Giants: Evidence of Genome Reduction in a Small Tubulinid Free-Living Amoeba.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae058},
pmid = {38504610},
issn = {1759-6653},
abstract = {This study investigates the genomic characteristics of Echinamoeba silvestris, a small-sized amoeba within the Tubulinea clade of the Amoebozoa supergroup. Despite Tubulinea's significance in various fields, genomic data for this clade have been scarce. E. silvestris presents the smallest free-living amoeba genome within Tubulinea and Amoebozoa to date. Comparative analysis reveals intriguing parallels with parasitic lineages in terms of genome size and predicted gene numbers, emphasizing the need to understand the consequences of reduced genomes in free-living amoebae. Functional categorization of predicted genes in E. silvestris shows similar percentages of ortholog groups to other amoebae in various categories, but a distinctive feature is the extensive gene contraction in orphan (ORFan) genes and those involved in biological processes. Notably, among the few genes that underwent expansion, none are related to cellular components, suggesting adaptive processes that streamline biological processes and cellular components for efficiency and energy conservation. Additionally, our investigation into non-coding and repetitive elements sheds light on the evolution of genome size in amoebae, with E. silvestris distinguished by low percentage of repetitive elements. Furthermore, the analysis reveals that E. silvestris has the lowest mean number of introns per gene among the species studied, providing further support for its observed compact genome. Overall, this research underscores the diversity within Tubulinea, highlights knowledge gaps in Amoebozoa genomics, and positions E. silvestris as a valuable addition to genomic datasets, prompting further exploration of complexities in Amoebozoa diversity and genome evolution.},
}
@article {pmid38498548,
year = {2024},
author = {Bernabeu, M and Manzano-Morales, S and Gabaldón, T},
title = {On the impact of incomplete taxon sampling on the relative timing of gene transfer events.},
journal = {PLoS biology},
volume = {22},
number = {3},
pages = {e3002460},
pmid = {38498548},
issn = {1545-7885},
mesh = {Phylogeny ; *Gene Flow ; *Biological Evolution ; Gene Transfer, Horizontal ; },
abstract = {A recent study questioned the use of branch length methods to assess the relative timing of horizontal gene transfers because of the effects of so-called "ghost" lineages. This Formal Comment discusses key considerations regarding the potential effect of missing lineages when assessing relative timing of evolutionary events.},
}
@article {pmid38497640,
year = {2024},
author = {Wang, P and Du, X and Zhao, Y and Wang, W and Cai, T and Tang, K and Wang, X},
title = {Combining CRISPR/Cas9 and natural excision for the precise and complete removal of mobile genetic elements in bacteria.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0009524},
doi = {10.1128/aem.00095-24},
pmid = {38497640},
issn = {1098-5336},
abstract = {Horizontal gene transfer, facilitated by mobile genetic elements (MGEs), is an adaptive evolutionary process that contributes to the evolution of bacterial populations and infectious diseases. A variety of MGEs not only can integrate into the bacterial genome but also can survive or even replicate like plasmids in the cytoplasm, thus requiring precise and complete removal for studying their strategies in benefiting host cells. Existing methods for MGE removal, such as homologous recombination-based deletion and excisionase-based methods, have limitations in effectively eliminating certain MGEs. To overcome these limitations, we developed the Cas9-NE method, which combines the CRISPR/Cas9 system with the natural excision of MGEs. In this approach, a specialized single guide RNA (sgRNA) element is designed with a 20-nucleotide region that pairs with the MGE sequence. This sgRNA is expressed from a plasmid that also carries the Cas9 gene. By utilizing the Cas9-NE method, both the integrative and circular forms of MGEs can be precisely and completely eliminated through Cas9 cleavage, generating MGE-removed cells. We have successfully applied the Cas9-NE method to remove four representative MGEs, including plasmids, prophages, and genomic islands, from Vibrio strains. This new approach not only enables various investigations on MGEs but also has significant implications for the rapid generation of strains for commercial purposes.IMPORTANCEMobile genetic elements (MGEs) are of utmost importance for bacterial adaptation and pathogenicity, existing in various forms and multiple copies within bacterial cells. Integrated MGEs play dual roles in bacterial hosts, enhancing the fitness of the host by delivering cargo genes and potentially modifying the bacterial genome through the integration/excision process. This process can lead to alterations in promoters or coding sequences or even gene disruptions at integration sites, influencing the physiological functions of host bacteria. Here, we developed a new approach called Cas9-NE, allowing them to maintain the natural sequence changes associated with MGE excision. Cas9-NE allows the one-step removal of integrated and circular MGEs, addressing the challenge of eliminating various MGE forms efficiently. This approach simplifies MGE elimination in bacteria, expediting research on MGEs.},
}
@article {pmid38494146,
year = {2024},
author = {Xu, H and Tan, C and Li, C and Li, J and Han, Y and Tang, Y and Lei, C and Wang, H},
title = {ESBL- E. coli extracellular vesicles mediate bacterial resistance to β-lactam and mediate horizontal transfer of blaCTX-M-55.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107145},
doi = {10.1016/j.ijantimicag.2024.107145},
pmid = {38494146},
issn = {1872-7913},
abstract = {Extracellular vesicles (EVs) have become the focus of research as an emerging method of horizontal gene transfer. In recent years, studies on the association between EVs and the spread of bacterial resistance have emerged, but there is a lack of research on the role of EVs secreted by ESBL-producing E. coli in the spread of β-lactam resistance. Therefore, in this study, the role of EVs secreted by ESBL-E. coli in the transmission of β-lactam resistance in E. coli was evaluated. The results showed that ESBL-EVs were protective against β-lactam antibiotic-susceptible bacteria, and this protective effect was dependent on the integrity of the EVs and showed dose- and time-dependent effects. At the same time, ESBL-EVs can also mediate the horizontal transmission of blaCTX-M-55, and EVs-mediated gene transfer is selective, preferring to transfer in more closely related species. In this study, we demonstrated the important role of EVs in the transmission of β-lactam resistance in chicken ESBL-E. coli, and evaluated the risk of EVs-mediated horizontal gene transfer, which provided a theoretical basis for elucidating the mechanism of EVs-mediated resistance transmission.},
}
@article {pmid38493856,
year = {2024},
author = {You, Z and Wang, C and Yang, X and Liu, Z and Guan, Y and Mu, J and Shi, H and Zhao, Z},
title = {Effects of eutrophication on the horizontal transfer of antibiotic resistance genes in microalgal-bacterial symbiotic systems.},
journal = {Environmental research},
volume = {251},
number = {Pt 2},
pages = {118692},
doi = {10.1016/j.envres.2024.118692},
pmid = {38493856},
issn = {1096-0953},
abstract = {Overloading of nutrients such as nitrogen causes eutrophication of freshwater bodies. The spread of antibiotic resistance genes (ARGs) poses a threat to ecosystems. However, studies on the enrichment and spread of ARGs from increased nitrogen loading in algal-bacterial symbiotic systems are limited. In this study, the transfer of extracellular kanamycin resistance (KR) genes from large (RP4) small (pEASY-T1) plasmids into the intracellular and extracellular DNA (iDNA, eDNA) of the inter-algal environment of Chlorella pyrenoidosa was investigated, along with the community structure of free-living (FL) and particle-attached (PA) bacteria under different nitrogen source concentrations (0-2.5 g/L KNO3). The results showed that KR gene abundance in the eDNA adsorbed on solid particles (D-eDNA) increased initially and then decreased with increasing nitrogen concentration, while the opposite was true for the rest of the free eDNA (E-eDNA). Medium nitrogen concentrations promoted the transfer of extracellular KR genes into the iDNA attached to algal microorganisms (A-iDNA), eDNA attached to algae (B-eDNA), and the iDNA of free microorganisms (C-iDNA); high nitrogen contributed to the transfer of KR genes into C-iDNA. The highest percentage of KR genes was found in B-eDNA with RP4 plasmid treatment (66.2%) and in C-iDNA with pEASY-T1 plasmid treatment (86.88%). In addition, dissolved oxygen (DO) significantly affected the bacterial PA and FL community compositions. Nephelometric turbidity units (NTU) reflected the abundance of ARGs in algae. Proteobacteria, Cyanobacteria, Bacteroidota, and Actinobacteriota were the main potential hosts of ARGs. These findings provide new insights into the distribution and dispersal of ARGs in the phytoplankton inter-algal environment.},
}
@article {pmid38486809,
year = {2024},
author = {Novikova, PV and Bhanu Busi, S and Probst, AJ and May, P and Wilmes, P},
title = {Functional prediction of proteins from the human gut archaeome.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycad014},
pmid = {38486809},
issn = {2730-6151},
abstract = {The human gastrointestinal tract contains diverse microbial communities, including archaea. Among them, Methanobrevibacter smithii represents a highly active and clinically relevant methanogenic archaeon, being involved in gastrointestinal disorders, such as inflammatory bowel disease and obesity. Herein, we present an integrated approach using sequence and structure information to improve the annotation of M. smithii proteins using advanced protein structure prediction and annotation tools, such as AlphaFold2, trRosetta, ProFunc, and DeepFri. Of an initial set of 873 481 archaeal proteins, we found 707 754 proteins exclusively present in the human gut. Having analysed archaeal proteins together with 87 282 994 bacterial proteins, we identified unique archaeal proteins and archaeal-bacterial homologs. We then predicted and characterized functional domains and structures of 73 unique and homologous archaeal protein clusters linked the human gut and M. smithii. We refined annotations based on the predicted structures, extending existing sequence similarity-based annotations. We identified gut-specific archaeal proteins that may be involved in defense mechanisms, virulence, adhesion, and the degradation of toxic substances. Interestingly, we identified potential glycosyltransferases that could be associated with N-linked and O-glycosylation. Additionally, we found preliminary evidence for interdomain horizontal gene transfer between Clostridia species and M. smithii, which includes sporulation Stage V proteins AE and AD. Our study broadens the understanding of archaeal biology, particularly M. smithii, and highlights the importance of considering both sequence and structure for the prediction of protein function.},
}
@article {pmid38485028,
year = {2024},
author = {Liu, H and Zhang, Z and Li, X and Zhou, T and Wang, Z and Li, J and Li, Y and Wang, Q},
title = {Temperature-phased anaerobic sludge digestion effectively removes antibiotic resistance genes in a full-scale wastewater treatment plant.},
journal = {The Science of the total environment},
volume = {924},
number = {},
pages = {171555},
doi = {10.1016/j.scitotenv.2024.171555},
pmid = {38485028},
issn = {1879-1026},
abstract = {Sludge is a major by-product and the final reservoir of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs). Temperature-phased anaerobic digestion (TPAD), consisting of thermophilic anaerobic digestion (AD) (55 °C) and mesophilic AD processes (37 °C), has been implemented in WWTPs for sludge reduction while improving the biomethane production. However, the impact of TPAD on the ARGs' fate is still undiscovered in lab-scale experiments and full-scale WWTPs. This study, for the first time, investigated the fate of ARGs during the TPAD process across three seasons in a full-size WWTP. Ten typical ARGs and one integrase gene of class 1 integron (intI1) involving ARGs horizontal gene transfer were examined in sludge before and after each step of the TPAD process. TPAD reduced aac(6')-Ib-cr, blaTEM, drfA1, sul1, sul2, ermb, mefA, tetA, tetB and tetX by 87.3-100.0 %. TPAD reduced the overall average absolute abundance of targeted ARGs and intI1 by 92.39 % and 92.50 %, respectively. The abundance of targeted ARGs in sludge was higher in winter than in summer and autumn before and after TPAD. During the TPAD processes, thermophilic AD played a major role in the removal of ARGs, contributing to >60 % removal of ARGs, while the subsequent mesophilic AD contributed to a further 31 % removal of ARGs. The microbial community analysis revealed that thermophilic AD reduced the absolute abundance of ARGs hosts, antibiotic resistant bacteria. In addition, thermophilic AD reduced the abundance of the intI1, while the intI1 did not reproduce during the mesophilic AD, also contributing to a decline in the absolute abundance of ARGs in TPAD. This study demonstrates that TPAD can effectively reduce the abundance of ARGs in sludge, which will suppress the transmission of ARGs from sludge into the natural environment and deliver environmental and health benefits to our society.},
}
@article {pmid38478693,
year = {2024},
author = {Keith, M and Park de la Torriente, A and Chalka, A and Vallejo-Trujillo, A and McAteer, SP and Paterson, GK and Low, AS and Gally, DL},
title = {Predictive phage therapy for Escherichia coli urinary tract infections: Cocktail selection for therapy based on machine learning models.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {12},
pages = {e2313574121},
doi = {10.1073/pnas.2313574121},
pmid = {38478693},
issn = {1091-6490},
support = {BBS/E/D/20002173//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Humans ; Animals ; Escherichia coli/genetics ; *Phage Therapy ; *Escherichia coli Infections/microbiology ; *Bacteriophages/genetics ; Anti-Bacterial Agents/pharmacology ; *Urinary Tract Infections/drug therapy ; },
abstract = {This study supports the development of predictive bacteriophage (phage) therapy: the concept of phage cocktail selection to treat a bacterial infection based on machine learning (ML) models. For this purpose, ML models were trained on thousands of measured interactions between a panel of phage and sequenced bacterial isolates. The concept was applied to Escherichia coli associated with urinary tract infections. This is an important common infection in humans and companion animals from which multidrug-resistant (MDR) bloodstream infections can originate. The global threat of MDR infection has reinvigorated international efforts into alternatives to antibiotics including phage therapy. E. coli exhibit extensive genome-level variation due to horizontal gene transfer via phage and plasmids. Associated with this, phage selection for E. coli is difficult as individual isolates can exhibit considerable variation in phage susceptibility due to differences in factors important to phage infection including phage receptor profiles and resistance mechanisms. The activity of 31 phage was measured on 314 isolates with growth curves in artificial urine. Random Forest models were built for each phage from bacterial genome features, and the more generalist phage, acting on over 20% of the bacterial population, exhibited F1 scores of >0.6 and could be used to predict phage cocktails effective against previously untested strains. The study demonstrates the potential of predictive ML models which integrate bacterial genomics with phage activity datasets allowing their use on data derived from direct sequencing of clinical samples to inform rapid and effective phage therapy.},
}
@article {pmid38477539,
year = {2024},
author = {Shang, Y and Zhang, Y and Wang, R and Peng, Y and Ding, B and Liu, Y and Li, C and Feng, L and Liu, H and Yang, C and Tang, Y},
title = {Deciphering the molecular and functional basis of TMexCD1: the plasmid-encoded efflux pump of resistance-nodulation-division superfamily.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {e0167823},
doi = {10.1128/aac.01678-23},
pmid = {38477539},
issn = {1098-6596},
abstract = {Horizontal gene transfer has been demonstrated to be an important driver for the emergency of multidrug-resistant pathogens. Recently, a transferable gene cluster tmexCD1-toprJ1 of the resistance-nodulation-division (RND) superfamily was identified in the plasmids of animal-derived Klebsiella pneumoniae strains, with a higher efflux capacity for various drugs than the Escherichia coli AcrAB-TolC homolog system. In this study, we focused on the differences in the inner membrane pump of these two systems and identified some key residues that contribute to the robust efflux activity of the TMexCD1 system. With the aid of homologous modeling and molecular docking, eight residues from the proximal binding pocket (PBP) and nine from the distal binding pocket (DBP) were selected and subjected to site-directed mutagenesis. Several of them, such as S134, I139, D181, and A290, were shown to be important for substrate binding in the DBP region, and all residues in PBP and DBP showed certain substrate preferences. Apart from the conservative switch loop (L613-623[TMexD1]) previously identified in the E. coli AcrB (EcAcrB), a relatively unconservative loop (L665-675[TMexD1]) at the bottom of PBP was proposed as a critical element for the robust activity of TMexD1, due to variations at sites E669, G670, N673, and S674 compared to EcAcrAB, and the significantly altered efflux activity due to their mutations. The conservation and flexibility of these key factors can contribute to the evolution of the RND efflux pumps and thus serve as potential targets for developing inhibitors to block the widespread of the TMexCD1 system.},
}
@article {pmid38471323,
year = {2024},
author = {Li, J and Liao, Q and Wang, Y and Wang, X and Liu, J and Zha, R and He, JZ and Zhang, M and Zhang, W},
title = {Involvement of functional metabolism promotes the enrichment of antibiotic resistome in drinking water: Based on the PICRUSt2 functional prediction.},
journal = {Journal of environmental management},
volume = {356},
number = {},
pages = {120544},
doi = {10.1016/j.jenvman.2024.120544},
pmid = {38471323},
issn = {1095-8630},
abstract = {Biofilters are the important source and sink of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARB) in the drinking water. Current studies generally ascribed the prevalence of BAR in biofilter from the perspective of gene behavior, i.e. horizontal gene transfer (HGT), little attentions have been paid on the ARGs carrier- ARB. In this study, we proposed the hypothesis that ARB participating in pollutant metabolism processes and becoming dominant is an important way for the enrichment of ARGs. To verify this, the antibiotic resistome and bacterial functional metabolic pathways of a sand filter was profiled using heterotrophic bacterial plate counting method (HPC), high-throughput qPCR, Illumina Hiseq sequencing and PICRUSt2 functional prediction. The results illustrated a significant leakage of ARB in the effluent of the sand filter with an average absolute abundance of approximately 10[2]-10[3] CFU/mL. Further contribution analysis revealed that the dominant genera, such as Acinetobacter spp., Aeromonas spp., Elizabethkingia spp., and Bacillus spp., were primary ARGs hosts, conferring resistance to multiple antibiotics including sulfamethoxazole, tetracycline and β-lactams. Notably, these ARGs hosts were involved in nitrogen metabolism, including extracellular nitrate/nitrite transport and nitrite reduction, which are crucial in nitrification and denitrification in biofilters. For example, Acinetobacter spp., the dominant bacteria in the filter (relative abundance 69.97 %), contributed the majority of ARGs and 53.79 % of nitrite reduction function. That is, ARB can predominate by participating in the nitrogen metabolism pathways, facilitating the enrichment of ARGs. These findings provide insights into the stable presence of ARGs in biofilters from a functional metabolism perspective, offering a significant supplementary to the mechanisms of the emergence, maintenance, and transmission of BARin drinking water.},
}
@article {pmid38470054,
year = {2024},
author = {Beck, C and Krusche, J and Notaro, A and Walter, A and Kränkel, L and Vollert, A and Stemmler, R and Wittmann, J and Schaller, M and Slavetinsky, C and Mayer, C and De Castro, C and Peschel, A},
title = {Wall teichoic acid substitution with glucose governs phage susceptibility of Staphylococcus epidermidis.},
journal = {mBio},
volume = {},
number = {},
pages = {e0199023},
doi = {10.1128/mbio.01990-23},
pmid = {38470054},
issn = {2150-7511},
abstract = {The species- and clone-specific susceptibility of Staphylococcus cells for bacteriophages is governed by the structures and glycosylation patterns of wall teichoic acid (WTA) glycopolymers. The glycosylation-dependent phage-WTA interactions in the opportunistic pathogen Staphylococcus epidermidis and in other coagulase-negative staphylococci (CoNS) have remained unknown. We report a new S. epidermidis WTA glycosyltransferase TagE whose deletion confers resistance to siphoviruses such as ΦE72 but enables binding of otherwise unbound podoviruses. S. epidermidis glycerolphosphate WTA was found to be modified with glucose in a tagE-dependent manner. TagE is encoded together with the enzymes PgcA and GtaB providing uridine diphosphate-activated glucose. ΦE72 transduced several other CoNS species encoding TagE homologs, suggesting that WTA glycosylation via TagE is a frequent trait among CoNS that permits interspecies horizontal gene transfer. Our study unravels a crucial mechanism of phage-Staphylococcus interaction and horizontal gene transfer, and it will help in the design of anti-staphylococcal phage therapies.IMPORTANCEPhages are highly specific for certain bacterial hosts, and some can transduce DNA even across species boundaries. How phages recognize cognate host cells remains incompletely understood. Phages infecting members of the genus Staphylococcus bind to wall teichoic acid (WTA) glycopolymers with highly variable structures and glycosylation patterns. How WTA is glycosylated in the opportunistic pathogen Staphylococcus epidermidis and in other coagulase-negative staphylococci (CoNS) species has remained unknown. We describe that S. epidermidis glycosylates its WTA backbone with glucose, and we identify a cluster of three genes responsible for glucose activation and transfer to WTA. Their inactivation strongly alters phage susceptibility patterns, yielding resistance to siphoviruses but susceptibility to podoviruses. Many different CoNS species with related glycosylation genes can exchange DNA via siphovirus ΦE72, suggesting that glucose-modified WTA is crucial for interspecies horizontal gene transfer. Our finding will help to develop antibacterial phage therapies and unravel routes of genetic exchange.},
}
@article {pmid38466360,
year = {2024},
author = {Kim, YH and Lee, DH and Seo, HS and Eun, SH and Lee, DS and Choi, YK and Lee, SH and Kim, TY},
title = {Genome-based taxonomic identification and safety assessment of an Enterococcus strain isolated from a homemade dairy product.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {38466360},
issn = {1618-1905},
abstract = {The aim of this study was to explore the taxonomic identification and evaluate the safety of a bacterium, Enterococcus lactis IDCC 2105, isolated from homemade cheese in Korea, using whole genome sequence (WGS) analysis. It sought to identify the species level of this Enter