@article {pmid39611587,
year = {2024},
author = {Sayid, R and van den Hurk, AWM and Rothschild-Rodriguez, D and Herrema, H and de Jonge, PA and Nobrega, FL},
title = {Characteristics of phage-plasmids and their impact on microbial communities.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20240014},
pmid = {39611587},
issn = {1744-1358},
support = {AUF 5188//Amsterdam University Fund/ ; PhD fellowship//Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers (ACS)/ ; //Bowel Research UK (BRUK)/ ; Aspasia premium (015.017.050)//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; BB/T008768/1//Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Black Futures Research Studentship//University of Southampton (University of Southampton UK)/ ; },
abstract = {Bacteria host various foreign genetic elements, most notably plasmids and bacteriophages (or phages). Historically, these two classes were seen as separate, but recent research has shown considerable interplay between them. Phage-plasmids (P-Ps) exhibit characteristics of both phages and plasmids, allowing them to exist extrachromosomally within bacterial hosts as plasmids, but also to infect and lyse bacteria as phages. This dual functionality enables P-Ps to utilize the modes of transmission of both phage and plasmids, facilitating the rapid dissemination of genetic material, including antibiotic resistance and virulence genes, throughout bacterial populations. Additionally, P-Ps have been found to encode toxin-antitoxin and CRISPR-Cas adaptive immune systems, which enhance bacterial survival under stress and provide immunity against other foreign genetic elements. Despite a growing body of literature on P-Ps, large gaps remain in our understanding of their ecological roles and environmental prevalence. This review aims to synthesise existing knowledge and identify research gaps on the impacts of P-Ps on microbial communities.},
}

@article {pmid39611041,
year = {2024},
author = {Liu, L and Lian, ZH and Lv, AP and Salam, N and Zhang, JC and Li, MM and Sun, WM and Tan, S and Luo, ZH and Gao, L and Yuan, Y and Ming, YZ and OuYang, YT and Li, YX and Liu, ZT and Hu, CJ and Chen, Y and Hua, ZS and Shu, WS and Hedlund, BP and Li, WJ and Jiao, JY},
title = {Insights into chemoautotrophic traits of a prevalent bacterial phylum CSP1-3, herein Sysuimicrobiota.},
journal = {National science review},
volume = {11},
number = {11},
pages = {nwae378},
pmid = {39611041},
issn = {2053-714X},
abstract = {Candidate bacterial phylum CSP1-3 has not been cultivated and is poorly understood. Here, we analyzed 112 CSP1-3 metagenome-assembled genomes and showed they are likely facultative anaerobes, with 3 of 5 families encoding autotrophy through the reductive glycine pathway (RGP), Wood-Ljungdahl pathway (WLP) or Calvin-Benson-Bassham (CBB), with hydrogen or sulfide as electron donors. Chemoautotrophic enrichments from hot spring sediments and fluorescence in situ hybridization revealed enrichment of six CSP1-3 genera, and both transcribed genes and DNA-stable isotope probing were consistent with proposed chemoautotrophic metabolisms. Ancestral state reconstructions showed that the ancestors of phylum CSP1-3 may have been acetogens that were autotrophic via the RGP, whereas the WLP and CBB were acquired by horizontal gene transfer. Our results reveal that CSP1-3 is a widely distributed phylum with the potential to contribute to the cycling of carbon, sulfur and nitrogen. The name Sysuimicrobiota phy. nov. is proposed.},
}

@article {pmid39606649,
year = {2024},
author = {Qing, Y and Zou, Z and Jiang, G and Qin, L and Liu, K and Liu, Z},
title = {A global perspective on the abundance, diversity and mobility of antibiotic resistance genes in Escherichia coli.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1442159},
pmid = {39606649},
issn = {2297-1769},
abstract = {INTRODUCTION: Escherichia coli (E. coli), a ubiquitous opportunistic pathogen, poses a growing threat to human health due to the increasing prevalence of antibiotic resistance. However, a comprehensive understanding of the global distribution, diversity, and transmission of antibiotic resistance genes (ARGs) in E. coli remains lacking, hindering effective strategies to combat resistance.

METHODS: In this study, we analyzed 94,762 E. coli genome sequences obtained from the NCBI database using advanced bioinformatics tools. ARGs were identified by comparing sequences against a custom ARG database using BLAST. Mobile genetic element (MGE)-associated ARGs were identified by matching with ISfinder databases. Global distribution of ARGs was analyzed by clustering mobile ARG sequences with 99% genetic similarity.

RESULTS: Our analysis revealed that 50.51% of the E. coli genome sequences contained ARGs, totaling 301,317 identified ARG sequences. These ARGs were categorized into 12 major classes and 229 subtypes. Notably, ARGs associated with multi-drug resistance (MDR), β-lactams, macrolide-lincosamide-streptogramins (MLS), tetracyclines, and aminoglycosides were particularly abundant, with the subtypes mdtK, macB, and ampC being especially prevalent. Additionally, significant differences in ARG abundance and diversity were observed across countries, with higher diversity found in high-income nations. Furthermore, 9.28% of the ARG sequences were linked to MGEs, accounting for 98.25% of all ARG subtypes. Notably, 4.20% of mobile ARGs were identified in over 20 countries, with β-lactam and aminoglycoside ARGs being the most widespread.

DISCUSSION: This study provides a comprehensive overview of the global distribution and transmission of ARGs in E. coli. The high abundance of MDR and β-lactam-related ARGs, along with their widespread transmission across countries, highlights the urgent need for global surveillance and control measures. Furthermore, the strong association between ARGs and MGEs underscores the role of horizontal gene transfer in the spread of resistance. The observed variations in ARG diversity between countries suggest that socioeconomic factors, such as healthcare infrastructure and antibiotic usage patterns, significantly influence ARG prevalence. These findings are crucial for informing global strategies to mitigate the spread of antibiotic resistance and improve public health outcomes.},
}

@article {pmid39606646,
year = {2024},
author = {Wang, Z and Sun, M and Guo, S and Wang, Y and Meng, L and Shi, J and Geng, C and Han, D and Fu, X and Xue, J and Ma, H and Liu, K},
title = {Detection of drug resistance in Escherichia coli from calves with diarrhea in the Tongliao region: an analysis of multidrug-resistant strains.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1466690},
pmid = {39606646},
issn = {2297-1769},
abstract = {INTRODUCTION: Escherichia coli is a major pathogen responsible for calf diarrhea, which has been exacerbated by the irrational and unscientific use of antimicrobial drugs, leading to significant drug resistance.

METHODS: This study focused on the isolation and identification of E. coli from calf diarrhea samples in the Tongliao area of China. Isolation was conducted using selective media, Gram staining, and 16S rRNA sequencing. The minimum inhibitory concentration (MIC) of E. coli was determined through the microbroth dilution method. Additionally, the presence of antibiotic-resistant genes was detected, and multidrug-resistant strains were selected for whole-genome sequencing (WGS).

RESULTS: The results revealed that all 40 isolated strains of E. coli exhibited resistance to sulfadiazine sodium, enrofloxacin, and ciprofloxacin, with 90% of the strains being susceptible to polymyxin B. Notably, strains 11, 23, and 24 demonstrated severe resistance. The detection rates of the antibiotic resistance genes TEM-1, TEM-206, strA, strB, qacH, and blaCTX were 100%, indicating a high prevalence of these genes. Moreover, the majority of strains carried antibiotic resistance genes consistent with their resistance phenotypes. WGS of strains 11, 23, and 24 revealed genome sizes of 4,897,185 bp, 4,920,234 bp, and 4,912,320 bp, respectively. These strains carried two, one, and two plasmids, respectively. The prediction of antibiotic resistance genes showed a substantial number of these genes within the genomes, with strain 24 harboring the highest number, totaling 77 subspecies containing 88 antibiotic resistance genes.

DISCUSSION: In conclusion, all 40 isolated strains of E. coli from calf diarrhea in this study were multidrug-resistant, exhibiting a broad distribution of antibiotic resistance genes and mobile components. This poses a significant risk of horizontal gene transfer, highlighting the critical situation of antibiotic resistance in this region.},
}

@article {pmid39423563,
year = {2024},
author = {Gomberg, AF and Grossman, AD},
title = {It's complicated: relationships between integrative and conjugative elements and their bacterial hosts.},
journal = {Current opinion in microbiology},
volume = {82},
number = {},
pages = {102556},
doi = {10.1016/j.mib.2024.102556},
pmid = {39423563},
issn = {1879-0364},
support = {R35 GM148343/GM/NIGMS NIH HHS/United States ; },
mesh = {*Conjugation, Genetic ; *Bacteria/genetics/metabolism ; *DNA Transposable Elements/genetics ; Chromosomes, Bacterial/genetics ; Gene Transfer, Horizontal ; },
abstract = {Integrative and conjugative elements (ICEs) are typically found integrated in a bacterial host chromosome. They can excise, replicate, and transfer from cell to cell. Many contain genes that confer phenotypes to host cells, including antibiotic resistances, specialized metabolisms, phage defense, and symbiosis or pathogenesis determinants. Recent studies revealed that at least three ICEs (ICEclc, Tn916, and TnSmu1) cause growth arrest or death of host cells upon element activation. This review highlights the complex interactions between ICEs and their hosts, including the recent examples of the significant costs to host cells. We contrast two examples of killing, ICEclc and Tn916, in which killing, respectively, benefits or impairs conjugation and emphasize the importance of understanding the impacts of ICE-host relationships on conjugation. ICEs are typically only active in a small fraction of cells in a population, and we discuss how phenotypes normally occurring in a small subset of host cells can be uncovered.},
}

*Conjugation, Genetic
*Bacteria/genetics/metabolism
*DNA Transposable Elements/genetics
Chromosomes, Bacterial/genetics
Gene Transfer, Horizontal

@article {pmid39515144,
year = {2024},
author = {Luo, Y and Xu, T and Li, B and Liu, F and Wu, B and Dobson, PS and Yin, H and Chen, Z and Qiu, Y and Huang, X},
title = {The effects of small plastic particles on antibiotic resistance gene transfer revealed by single cell and community level analysis.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136271},
doi = {10.1016/j.jhazmat.2024.136271},
pmid = {39515144},
issn = {1873-3336},
mesh = {*Escherichia coli/drug effects/genetics ; *Polystyrenes/toxicity/chemistry ; *Particle Size ; Microplastics/toxicity ; Gene Transfer, Horizontal ; Sewage/microbiology ; Single-Cell Analysis ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics/drug effects ; Plastics/toxicity ; Anti-Bacterial Agents/pharmacology/toxicity ; },
abstract = {Small plastic particles with sizes comparable to bacterial cells, widely exist in environment. However, their effects on antibiotic resistance gene (ARG) dissemination remain unclear. Using polystyrene (PS) particles (0.2 µm, 2 µm, 5 µm, 10 µm, 15 µm, 20 µm) as models, conjugative transfer of ARGs between the donor E. coli and different recipients (E. coli or sludge bacterial community) was investigated. Compared to the pure strain, the sludge bacterial community exposed to PS particles showed higher transfer frequencies (1.67 to 14.31 times the blank control). The transfer frequencies first decreased and then increased with particle size, and plastics similar in size to bacteria (e.g., 2 µm) appear to be a transitional zone with minimal impact on ARG transmission. Furthermore, using microfluidics, in-situ observation at single cell level found that 2 µm plastics can act as barriers between donor and recipient bacteria inhibiting growth, but conjugation events mostly occurred around them. Conversely, nanoplastics (e.g., 0.2 µm) and larger microplastics (e.g., 20 µm) significantly promote conjugation, mainly due to increased reactive oxygen species production and cell membrane permeability, or facilitating bacterial adhesion and biofilm formation, respectively. This study aids in assessing environmental risks of small plastic particles on ARG dissemination.},
}

*Escherichia coli/drug effects/genetics
*Polystyrenes/toxicity/chemistry
*Particle Size
Microplastics/toxicity
Gene Transfer, Horizontal
Sewage/microbiology
Single-Cell Analysis
Drug Resistance, Microbial/genetics
Drug Resistance, Bacterial/genetics/drug effects
Plastics/toxicity
Anti-Bacterial Agents/pharmacology/toxicity

@article {pmid39454331,
year = {2024},
author = {Wang, Y and Ren, Z and Wu, Y and Li, Y and Han, S},
title = {Antibiotic resistance genes transfer risk: Contributions from soil erosion and sedimentation activities, agricultural cycles, and soil chemical contamination.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136227},
doi = {10.1016/j.jhazmat.2024.136227},
pmid = {39454331},
issn = {1873-3336},
mesh = {*Agriculture ; *Soil Pollutants/toxicity/analysis ; *Drug Resistance, Microbial/genetics ; *Soil/chemistry ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/toxicity ; Soil Microbiology ; Geologic Sediments/chemistry ; },
abstract = {The transfer of antibiotic resistance genes (ARGs) pose environmental risks that are influenced by soil activity and pollution. Soil erosion and sedimentation accelerate degradation and migration, thereby affecting soil distribution and contamination. This study quantified the vertical and horizontal transfer capabilities of ARGs and simulated soil environments under various scenarios, such as erosion, agricultural cycles, and chemical pollution. The results showed that slope, runoff, and sediment volume significantly affected soil erosion and ARG transfer risks. The response of environmental factors to the transfer risk of ARGs is as follows: the promotion effect of soil deposition (average: 21.41 %) is significantly greater than the inhibitory effect of soil erosion (average: -11.31 %); the planting period (average: -64.654) is greater than the harvest period (average: -56.225); the response to soil chemical pollution is: the impact of phosphate fertilizer residues, antibiotics, and pesticide pollution is more significant. This study constructed a vertical and horizontal transfer system of ARGs in soil erosion and sedimentation environments and proposed a response analysis method for the impact of factors, such as soil erosion and sedimentation activities, agricultural cycles, and soil chemical pollution, on ARGs transfer capabilities.},
}

*Agriculture
*Soil Pollutants/toxicity/analysis
*Drug Resistance, Microbial/genetics
*Soil/chemistry
Gene Transfer, Horizontal
Anti-Bacterial Agents/toxicity
Soil Microbiology
Geologic Sediments/chemistry

@article {pmid39423639,
year = {2024},
author = {Xu, Y and Li, H and Ding, Y and Zhang, D and Liu, W},
title = {How nanoscale plastics facilitate the evolution of antibiotic resistance?.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136157},
doi = {10.1016/j.jhazmat.2024.136157},
pmid = {39423639},
issn = {1873-3336},
mesh = {*Serratia marcescens/drug effects/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Plastics/chemistry ; Gene Transfer, Horizontal ; Nanoparticles/chemistry ; Drug Resistance, Microbial/genetics ; },
abstract = {The plastic can enhance the proliferation of antibiotic resistance genes (ARGs), however, the effect of nanoplastics (NPLs) on bacterial antibiotic resistance has not been clearly explained. Herein, we explored the effects and mechanisms of NPLs of different sizes (200 and 600 nm) on the evolution of antibiotic resistance in Serratia marcescens. The results indicated that the evolution of bacterial antibiotic resistance could be promoted under NPLs exposure, which the median of relative abundance of ARGs was 1.11-1.46 times compared to the treatment without NPLs. Transcriptomic analysis showed that the larger size of NPLs mainly increased the permeability of bacterial cell membranes to efflux antibiotics, thus potentiating antibiotic resistance. While, the smaller NPLs is more than that, its enhanced the expression of antibiotic resistance by modulating bacterial metabolic processes. The genome SNP analysis found that the NPLs could cause the genetic mutation occurrence to alter the membrane transport and metabolism processes, and it increased at a size of 200 nm more than at 600 nm NPLs. Importantly, we demonstrated that the horizontal transfer of ARGs was augmented due to the NPLs could dock to bacterial surface proteins and pull their movement to contact with other bacteria (binding energy of membrane proteins: -8.54 kcal/mol), especially the smaller size. It suggests that NPLs will also contribute to the proliferation of ARGs in the environment. This study provides data for understanding the risk of bacterial resistance.},
}

*Serratia marcescens/drug effects/genetics/metabolism
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Plastics/chemistry
Gene Transfer, Horizontal
Nanoparticles/chemistry
Drug Resistance, Microbial/genetics

@article {pmid39305593,
year = {2024},
author = {Shen, Y and Zhang, B and Yao, Y and Wang, H and Chen, Z and Hao, A and Guo, P},
title = {Insights into the interactions of plant-associated bacteria and their role in the transfer of antibiotic resistance genes from soil to plant.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135881},
doi = {10.1016/j.jhazmat.2024.135881},
pmid = {39305593},
issn = {1873-3336},
mesh = {*Soil Microbiology ; *Rhizosphere ; *Bacteria/genetics/metabolism/classification ; *Plant Roots/microbiology ; Plants/microbiology ; Microbiota ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Plant Shoots/microbiology/growth & development ; Gene Transfer, Horizontal ; },
abstract = {This study discussed the role of plant-associated microbiome in regulating ARG transfer in soil-plant systems. Results showed that target ARGs in plants were mainly derived from rhizosphere soil. Cooperative interactions among bacteria in rhizosphere soil, plant-roots, plant-shoots, and soil-roots-shoots systems occurred during ARG transfer. The number of modules and keystone taxa identified as positively correlated with ARG transfer in rhizosphere soil, roots, and shoots was 3 and 49, 3 and 41, 2 and 5, respectively. Among these modules, module 3 in roots was significantly positively correlated with module 3 in rhizosphere soils and module 2 in shoots, indicating that module 3 in roots played central hub roles in ARG transfer from rhizosphere soil to roost and shoots. This may be because module 3 in roots increased cell motility and xenobiotics biodegradation and metabolism. These keystone taxa mainly belonged to Proteobacteria that can carry ARGs to transfer in soil-plant systems, especially Clostridium-sensu_stricito and Pseudomonas in rhizosphere soil carried ARGs into the shoot. Additionally, they promoted ARG transfer by increasing plant biomass, net photosynthetic rate and water use efficiency. The findings helped reveal the mechanism of plant-associated bacterial interactions and provided understanding for potential risks of ARG transfer from soil to plants.},
}

*Soil Microbiology
*Rhizosphere
*Bacteria/genetics/metabolism/classification
*Plant Roots/microbiology
Plants/microbiology
Microbiota
Genes, Bacterial
Drug Resistance, Microbial/genetics
Plant Shoots/microbiology/growth & development
Gene Transfer, Horizontal

@article {pmid39605964,
year = {2024},
author = {Jia, J and Liu, Q and Zhao, E and Li, X and Xiong, X and Wu, C},
title = {Biofilm formation on microplastics and interactions with antibiotics, antibiotic resistance genes and pathogens in aquatic environment.},
journal = {Eco-Environment & Health},
volume = {3},
number = {4},
pages = {516-528},
pmid = {39605964},
issn = {2772-9850},
abstract = {Microplastics (MPs) in aquatic environments easily support biofilm development, which can interact with other environmental pollutants and act as harbors for microorganisms. Recently, numerous studies have investigated the fate and behavior of MP biofilms in aquatic environments, highlighting their roles in the spread of pathogens and antibiotic resistance genes (ARGs) to aquatic organisms and new habitats. The prevalence and effects of MP biofilms in aquatic environments have been extensively investigated in recent decades, and their behaviors in aquatic environments need to be synthesized systematically with updated information. This review aims to reveal the development of MP biofilm and its interactions with antibiotics, ARGs, and pathogens in aquatic environments. Recent research has shown that the adsorption capabilities of MPs to antibiotics are enhanced after the biofilm formation, and the adsorption of biofilms to antibiotics is biased towards chemisorption. ARGs and microorganisms, especially pathogens, are selectively enriched in biofilms and significantly different from those in surrounding waters. MP biofilm promotes the propagation of ARGs through horizontal gene transfer (HGT) and vertical gene transfer (VGT) and induces the emergence of antibiotic-resistant pathogens, resulting in increased threats to aquatic ecosystems and human health. Some future research needs and strategies in this review are also proposed to better understand the antibiotic resistance induced by MP biofilms in aquatic environments.},
}

@article {pmid39605872,
year = {2024},
author = {Kettlewell, R and Jones, C and Felton, TW and Lagator, M and Gifford, DR},
title = {Insights into durability against resistance from the antibiotic nitrofurantoin.},
journal = {npj antimicrobials and resistance},
volume = {2},
number = {1},
pages = {41},
pmid = {39605872},
issn = {2731-8745},
abstract = {Nitrofurantoin has shown exceptional durability against resistance over 70 years of use. This longevity stems from factors such as rapid achievement of therapeutic concentrations, multiple physiological targets against bacteria, low risk of horizontal gene transfer, and the need to acquire multiple mutations to achieve resistance. These combined features limit resistance emergence and spread of nitrofurantoin resistance. We propose nitrofurantoin as an exemplar for developing other durable treatments.},
}

@article {pmid39602248,
year = {2024},
author = {Dai, L and Wu, Z and Sahin, O and Zhao, S and Yu, EW and Zhang, Q},
title = {Mutation-based mechanism and evolution of the potent multidrug efflux pump RE-CmeABC in Campylobacter.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {51},
pages = {e2415823121},
doi = {10.1073/pnas.2415823121},
pmid = {39602248},
issn = {1091-6490},
support = {R01AI140669//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {*Campylobacter jejuni/genetics/metabolism ; *Evolution, Molecular ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacterial Proteins/genetics/metabolism ; *Mutation ; *Membrane Transport Proteins/genetics/metabolism ; Campylobacter/genetics/metabolism ; Humans ; Campylobacter Infections/microbiology ; Promoter Regions, Genetic ; Amino Acid Substitution ; },
abstract = {The resistance-nodulation-cell division (RND) superfamily of multidrug efflux systems are important players in mediating antibiotic resistance in gram-negative pathogens. Campylobacter jejuni, a major enteric pathogen, utilizes an RND-type transporter system, CmeABC, as the primary mechanism for extrusion of various antibiotics. Recently, a functionally potent variant of CmeABC (named RE-CmeABC) emerged in clinical Campylobacter isolates, conferring enhanced resistance to multiple antibiotic classes. Despite the clinical importance of RE-CmeABC, the molecular mechanisms for its functional gain and its evolutionary trajectory remain unknown. Here, we demonstrated that amino acid substitutions in RE-CmeB (inner membrane transporter), but not in RE-CmeA (periplasmic protein) and RE-CmeC (outer membrane protein), in conjunction with a nucleotide mutation in the promoter region of the efflux operon, are responsible for the functional gain of the multidrug efflux system. We also showed that RE-cmeABC is emerging globally and distributed in genetically diverse C. jejuni strains, suggesting its possible spread by horizontal gene transfer. Notably, many of RE-cmeABC harboring isolates were associated with the human host including strains from large disease outbreaks, indicating the clinical relevance and significance of RE-CmeABC. Evolutionary analysis indicated that RE-cmeB likely originated from Campylobacter coli, but its expansion mainly occurred in C. jejuni, possibly driven by antibiotic selection pressure. Additionally, RE-cmeB, but not RE-cmeA and RE-cmeC, experienced a selective sweep and was progressing to be fixed during evolution. Together, these results identify a mutation-based mechanism for functional gain in RE-CmeABC and reveal the key role of RE-CmeB in facilitating Campylobacter adaptation to antibiotic selection.},
}

*Campylobacter jejuni/genetics/metabolism
*Evolution, Molecular
*Drug Resistance, Multiple, Bacterial/genetics
*Anti-Bacterial Agents/pharmacology
*Bacterial Proteins/genetics/metabolism
*Mutation
*Membrane Transport Proteins/genetics/metabolism
Campylobacter/genetics/metabolism
Humans
Campylobacter Infections/microbiology
Promoter Regions, Genetic
Amino Acid Substitution

@article {pmid39599864,
year = {2024},
author = {Richards, VA and Ferrell, BD and Polson, SW and Wommack, KE and Fuhrmann, JJ},
title = {Soybean Bradyrhizobium spp. Spontaneously Produce Abundant and Diverse Temperate Phages in Culture.},
journal = {Viruses},
volume = {16},
number = {11},
pages = {},
pmid = {39599864},
issn = {1999-4915},
support = {1736030//National Science Foundation/ ; },
mesh = {*Bradyrhizobium/virology ; *Glycine max/virology/microbiology ; *Bacteriophages/isolation & purification/genetics/classification/physiology/ultrastructure ; Lysogeny ; Genome, Viral ; Symbiosis ; Microscopy, Electron, Transmission ; },
abstract = {Soybean bradyrhizobia (Bradyrhizobium spp.) are symbiotic root-nodulating bacteria that fix atmospheric nitrogen for the host plant. The University of Delaware Bradyrhizobium Culture Collection (UDBCC; 353 accessions) was created to study the diversity and ecology of soybean bradyrhizobia. Some UDBCC accessions produce temperate (lysogenic) bacteriophages spontaneously under routine culture conditions without chemical or other apparent inducing agents. Spontaneous phage production may promote horizontal gene transfer and shape bacterial genomes and associated phenotypes. A diverse subset (n = 98) of the UDBCC was examined for spontaneously produced virus-like particles (VLPs) using epifluorescent microscopy, with a majority (69%) producing detectable VLPs (>1 × 10[7] mL[-1]) in laboratory culture. Phages from the higher-producing accessions (>2.0 × 10[8] VLP mL[-1]; n = 44) were examined using transmission electron microscopy. Diverse morphologies were observed, including various tail types and lengths, capsid sizes and shapes, and the presence of collars or baseplates. In many instances, putative extracellular vesicles of a size similar to virions were also observed. Three of the four species examined (B. japonicum, B. elkanii, and B. diazoefficiens) produced apparently tailless phages. All species except B. ottawaense also produced siphovirus-like phages, while all but B. diazoefficiens additionally produced podovirus-like phages. Myovirus-like phages were restricted to B. japonicum and B. elkanii. At least three strains were polylysogens, producing up to three distinct morphotypes. These observations suggest spontaneously produced phages may play a significant role in the ecology and evolution of soybean bradyrhizobia.},
}

*Bradyrhizobium/virology
*Glycine max/virology/microbiology
*Bacteriophages/isolation & purification/genetics/classification/physiology/ultrastructure
Lysogeny
Genome, Viral
Symbiosis
Microscopy, Electron, Transmission

@article {pmid39599778,
year = {2024},
author = {Yoxsimer, AM and Offenberg, EG and Katzer, AW and Bell, MA and Massengill, RL and Kingsley, DM},
title = {Genomic Sequence of the Threespine Stickleback Iridovirus (TSIV) from Wild Gasterosteus aculeatus in Stormy Lake, Alaska.},
journal = {Viruses},
volume = {16},
number = {11},
pages = {},
pmid = {39599778},
issn = {1999-4915},
support = {Investigator/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; *Phylogeny ; Alaska ; *Smegmamorpha/virology ; *Genome, Viral ; *Fish Diseases/virology ; *Open Reading Frames ; *Iridovirus/genetics/classification/isolation & purification ; *Lakes/virology ; DNA Virus Infections/veterinary/virology ; Genomics/methods ; DNA, Viral/genetics ; },
abstract = {The threespine stickleback iridovirus (TSIV), a double-stranded DNA virus, was the first megalocytivirus detected in wild North American fishes. We report a second occurrence of TSIV in threespine stickleback (Gasterosteus aculeatus) from Stormy Lake, Alaska, and assemble a nearly complete genome of TSIV. The 115-kilobase TSIV genome contains 94 open reading frames (ORFs), with 91 that share homology with other known iridoviruses. We identify three ORFs that likely originate from recent lateral gene transfers from a eukaryotic host and one ORF with homology to B22 poxvirus proteins that likely originated from a lateral gene transfer between viruses. Phylogenetic analysis of 24 iridovirus core genes and pairwise sequence identity analysis support TSIV as a divergent sister taxon to other megalocytiviruses and a candidate for a novel species designation. Screening of stickleback collected from Stormy Lake before and after a 2012 rotenone treatment to eliminate invasive fish shows 100% positivity for TSIV in the two years before treatment (95% confidence interval: 89-100% prevalence) and 0% positivity for TSIV in 2024 after treatment (95% confidence interval: 0 to 3.7% prevalence), suggesting that the rotenone treatment and subsequent crash and reestablishment of the stickleback population is associated with loss of TSIV.},
}

Animals
*Phylogeny
Alaska
*Smegmamorpha/virology
*Genome, Viral
*Fish Diseases/virology
*Open Reading Frames
*Iridovirus/genetics/classification/isolation & purification
*Lakes/virology
DNA Virus Infections/veterinary/virology
Genomics/methods
DNA, Viral/genetics

@article {pmid39597557,
year = {2024},
author = {Shah, Y and Kafaie, S},
title = {Evaluating Sequence Alignment Tools for Antimicrobial Resistance Gene Detection in Assembly Graphs.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
pmid = {39597557},
issn = {2076-2607},
abstract = {Antimicrobial resistance (AMR) is an escalating global health threat, often driven by the horizontal gene transfer (HGT) of resistance genes. Detecting AMR genes and understanding their genomic context within bacterial populations is crucial for mitigating the spread of resistance. In this study, we evaluate the performance of three sequence alignment tools-Bandage, SPAligner, and GraphAligner-in identifying AMR gene sequences from assembly and de Bruijn graphs, which are commonly used in microbial genome assembly. Efficiently identifying these genes allows for the detection of neighboring genetic elements and possible HGT events, contributing to a deeper understanding of AMR dissemination. We compare the performance of the tools both qualitatively and quantitatively, analyzing the precision, computational efficiency, and accuracy in detecting AMR-related sequences. Our analysis reveals that Bandage offers the most precise and efficient identification of AMR gene sequences, followed by GraphAligner and SPAligner. The comparison includes evaluating the similarity of paths returned by each tool and measuring output accuracy using a modified edit distance metric. These results highlight Bandage's potential for contributing to the accurate identification and study of AMR genes in bacterial populations, offering important insights into resistance mechanisms and potential targets for mitigating AMR spread.},
}

@article {pmid39597512,
year = {2024},
author = {Banerji, A and Brinkman, NE and Davis, B and Franklin, A and Jahne, M and Keely, SP},
title = {Food Webs and Feedbacks: The Untold Ecological Relevance of Antimicrobial Resistance as Seen in Harmful Algal Blooms.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
pmid = {39597512},
issn = {2076-2607},
abstract = {Antimicrobial resistance (AMR) has long been framed as an epidemiological and public health concern. Its impacts on the environment are unclear. Yet, the basis for AMR is altered cell physiology. Just as this affects how microbes interact with antimicrobials, it can also affect how they interact with their own species, other species, and their non-living environment. Moreover, if the microbes are globally notorious for causing landscape-level environmental issues, then these effects could alter biodiversity and ecosystem function on a grand scale. To investigate these possibilities, we compiled peer-reviewed literature from the past 20 years regarding AMR in toxic freshwater cyanobacterial harmful algal blooms (HABs). We examined it for evidence of AMR affecting HAB frequency, severity, or persistence. Although no study within our scope was explicitly designed to address the question, multiple studies reported AMR-associated changes in HAB-forming cyanobacteria (and co-occurring microbes) that pertained directly to HAB timing, toxicity, and phase, as well as to the dynamics of HAB-afflicted aquatic food webs. These findings highlight the potential for AMR to have far-reaching environmental impacts (including the loss of biodiversity and ecosystem function) and bring into focus the importance of confronting complex interrelated issues such as AMR and HABs in concert, with interdisciplinary tools and perspectives.},
}

@article {pmid39516559,
year = {2024},
author = {Ares-Arroyo, M and Nucci, A and Rocha, EPC},
title = {Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids.},
journal = {Nature microbiology},
volume = {9},
number = {12},
pages = {3240-3253},
pmid = {39516559},
issn = {2058-5276},
mesh = {*Plasmids/genetics ; *Escherichia coli/genetics ; *Conjugation, Genetic ; *Klebsiella pneumoniae/genetics ; *Acinetobacter baumannii/genetics/classification ; Computational Biology/methods ; Gene Transfer, Horizontal ; Replication Origin/genetics ; DNA, Bacterial/genetics/chemistry ; },
abstract = {Conjugative plasmids are important drivers of bacterial evolution. Most plasmids lack genes for conjugation and characterized origins of transfer (oriT), which has hampered our understanding of plasmid mobility. Here we used bioinformatic analyses to characterize occurrences of known oriT families across 38,057 plasmids, confirming that most conjugative and mobilizable plasmids lack identifiable oriTs. Recognizable oriT sequences tend to be intergenic, upstream of relaxase genes and specifically associated with relaxase types. We used these criteria to develop a computational method to search for and identify 21 additional families of oriT-containing sequences in plasmids from the pathogens Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii. Sequence analyses found 3,072 occurrences of these oriT-containing sequences across 2,976 plasmids, many of which encoded antimicrobial resistance genes. Six candidate oriT-containing sequences were validated experimentally and were shown to facilitate conjugation in E. coli. These findings expand our understanding of plasmid mobility.},
}

*Plasmids/genetics
*Escherichia coli/genetics
*Conjugation, Genetic
*Klebsiella pneumoniae/genetics
*Acinetobacter baumannii/genetics/classification
Computational Biology/methods
Gene Transfer, Horizontal
Replication Origin/genetics
DNA, Bacterial/genetics/chemistry

@article {pmid39596782,
year = {2024},
author = {Mendoza-Guido, B and Barrantes, K and Rodríguez, C and Rojas-Jimenez, K and Arias-Andres, M},
title = {The Impact of Urban Pollution on Plasmid-Mediated Resistance Acquisition in Enterobacteria from a Tropical River.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/antibiotics13111089},
pmid = {39596782},
issn = {2079-6382},
support = {C1455, C2650, C3509//Vicerrectoría de Investigación of the Universidad de Costa Rica/ ; SIA 0483-21//Universidad Nacional, Costa Rica/ ; Proyecto Plasmidoma//Consejo Nacional de Rectores (CONARE), Costa Rica/ ; },
abstract = {Background: The exposure of environmental bacteria to contaminants in aquatic ecosystems accelerates the dissemination of antibiotic-resistance genes (ARGs) through horizontal gene transfer (HGT). Methods: In this study, we sampled three locations along a contamination gradient of a polluted river, focusing on isolating Enterobacteria from the surface waters to investigate the relationship between urban pollution and antibiotic resistance. The genomes of 15 isolates (5 per site) were sequenced to identify plasmid-borne ARGs and their association with resistance phenotypes. Results: Isolates from the site with the highest contamination (Site 3) showeda larger number of ARGs, plasmids, and resistance phenotypes. Notably, one of the isolates analyzed, E. coli A231-12, exhibited phenotypic resistance to seven antibiotics, presumably conferred by a single plasmid carrying 12 ARGs. Comparative analysis of this plasmid revealed its close evolutionary relationship with another IncH plasmid hosted by Salmonella enterica, underscoring its high ARG burden in the aquatic environment. Other plasmids identified in our isolates carried sul and dfrA genes, conferring resistance to trimethoprim/sulfamethoxazole, a commonly prescribed antibiotic combination in clinical settings. Conclusions: These results highlight the critical need to expand research on the link between pollution and plasmid-mediated antimicrobial resistance in aquatic ecosystems, which can act as reservoirs of ARGs.},
}

@article {pmid39596781,
year = {2024},
author = {Ifedinezi, OV and Nnaji, ND and Anumudu, CK and Ekwueme, CT and Uhegwu, CC and Ihenetu, FC and Obioha, P and Simon, BO and Ezechukwu, PS and Onyeaka, H},
title = {Environmental Antimicrobial Resistance: Implications for Food Safety and Public Health.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/antibiotics13111087},
pmid = {39596781},
issn = {2079-6382},
abstract = {Antimicrobial resistance (AMR) is a serious global health issue, aggravated by antibiotic overuse and misuse in human medicine, animal care, and agriculture. This study looks at the different mechanisms that drive AMR, such as environmental contamination, horizontal gene transfer, and selective pressure, as well as the severe implications of AMR for human and animal health. This study demonstrates the need for concerted efforts across the scientific, healthcare, agricultural, and policy sectors to control the emergence of AMR. Some crucial strategies discussed include developing antimicrobial stewardship (AMS) programs, encouraging targeted narrow-spectrum antibiotic use, and emphasizing the significance of strict regulatory frameworks and surveillance systems, like the Global Antimicrobial Resistance and Use Surveillance System (GLASS) and the Access, Watch, and Reserve (AWaRe) classification. This study also emphasizes the need for national and international action plans in combating AMR and promotes the One Health strategy, which unifies environmental, animal, and human health. This study concludes that preventing the spread of AMR and maintaining the effectiveness of antibiotics for future generations requires a comprehensive, multidisciplinary, and internationally coordinated strategy.},
}

@article {pmid39596258,
year = {2024},
author = {Dec, M and Nowak, T and Webster, J and Wódz, K},
title = {Serotypes, Antimicrobial Susceptibility, and Potential Mechanisms of Resistance Gene Transfer in Erysipelothrix rhusiopathiae Strains from Waterfowl in Poland.},
journal = {International journal of molecular sciences},
volume = {25},
number = {22},
pages = {},
doi = {10.3390/ijms252212192},
pmid = {39596258},
issn = {1422-0067},
mesh = {Animals ; Poland ; *Erysipelothrix/genetics ; *Serogroup ; *Anti-Bacterial Agents/pharmacology ; *Geese/microbiology ; Ducks/microbiology ; Microbial Sensitivity Tests ; Erysipelothrix Infections/microbiology/genetics ; Multilocus Sequence Typing ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {Erysipelas is a significant problem in the waterfowl farming in Poland, and information on the characteristics of the Erysipelothrix rhusiopathiae strains causing this disease is limited. In this study, we determined the serotypes, antimicrobial susceptibility, and potential mechanisms of resistance gene transfer in E. rhusiopathiae isolates (n = 60) from domestic geese and ducks. We also developed a multiplex PCR for the detection of resistance genes. The antimicrobial susceptibility of the isolates was assessed using the broth microdilution method. Resistance genes, integrative conjugative element (ICE)-specific genes, phage-specific genes, and serotype determinants were detected by PCR. Multilocus sequence typing (MLST) was performed for selected resistant strains. The comparative analyses included 260 E. rhusiopathiae strains whose whole genome sequences (WGSs) are publicly available. E. rhusiopathiae isolates represented 7 serotypes, among which serotypes 5 (38.3%) and 1b (28.3%) were the most common. All strains were susceptible to β-lactams, and the vast majority of them were resistant to tetracycline (85%) and enrofloxacin (80%). The percentages of isolates resistant to other antimicrobials used ranged from 3.3% to 16.7%. Ten isolates (16.7%) were found to be multidrug resistant (MDR). The genotypic resistance profiles of the E. rhusiopathiae strains corresponded to their phenotypic resistance, and the amplification patterns obtained using the 10-plex PCR developed in this study were fully consistent with the results of single PCRs. The most prevalent resistance gene was tetM. In enrofloxacin-resistant strains, nonsynonymous mutations in the gyrA and parC genes were identified. The presence of ICE-specific genes was confirmed in resistant strains, and in MDR isolates of serotype 8 that represented sequence type (ST) 113, prophage DNA (Javan630-like) linked to the lsaE gene was additionally detected. The results indicate that β-lactam antibiotics should be the first choice for the treatment of waterfowl erysipelas in Poland. ICEs, including a transposon from the Tn916/Tn1545 family, and bacteriophages are most likely responsible for the transfer of resistance genes in E. rhusiopathiae.},
}

Animals
Poland
*Erysipelothrix/genetics
*Serogroup
*Anti-Bacterial Agents/pharmacology
*Geese/microbiology
Ducks/microbiology
Microbial Sensitivity Tests
Erysipelothrix Infections/microbiology/genetics
Multilocus Sequence Typing
Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal
Drug Resistance, Multiple, Bacterial/genetics

@article {pmid39592962,
year = {2024},
author = {Mane, A and Sanderson, H and White, AP and Zaheer, R and Beiko, R and Chauve, C},
title = {Plaseval: a framework for comparing and evaluating plasmid detection tools.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {365},
pmid = {39592962},
issn = {1471-2105},
mesh = {*Plasmids/genetics/metabolism ; Software ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active research area. Plasmid binning aims at detecting, in a draft genome assembly, groups (bins) of contigs likely to originate from the same plasmid. Several methods for plasmid binning have been developed recently, such as PlasBin-flow, HyAsP, gplas, MOB-suite, and plasmidSPAdes. This motivates the problem of evaluating the performances of plasmid binning methods, either against a given ground truth or between them.

RESULTS: We describe PlasEval, a novel method aimed at comparing the results of plasmid binning tools. PlasEval computes a dissimilarity measure between two sets of plasmid bins, that can originate either from two plasmid binning tools, or from a plasmid binning tool and a ground truth set of plasmid bins. The PlasEval dissimilarity accounts for the contig content of plasmid bins, the length of contigs and is repeat-aware. Moreover, the dissimilarity score computed by PlasEval is broken down into several parts, that allows to understand qualitative differences between the compared sets of plasmid bins. We illustrate the use of PlasEval by benchmarking four recently developed plasmid binning tools-PlasBin-flow, HyAsP, gplas, and MOB-recon-on a data set of 53 E. coli bacterial genomes.

CONCLUSION: Analysis of the results of plasmid binning methods using PlasEval shows that their behaviour varies significantly. PlasEval can be used to decide which specific plasmid binning method should be used for a specific dataset. The disagreement between different methods also suggests that the problem of plasmid binning on short-read contigs requires further research. We believe that PlasEval can prove to be an effective tool in this regard. PlasEval is publicly available at https://github.com/acme92/PlasEval.},
}

*Plasmids/genetics/metabolism
Software
Genome, Bacterial
Sequence Analysis, DNA/methods

@article {pmid39592922,
year = {2024},
author = {Das, VA and Gautam, B and Yadav, PK and Varadwaj, PK and Wadhwa, G and Singh, S},
title = {Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {1127},
pmid = {39592922},
issn = {1471-2229},
mesh = {*Bacillus/genetics/physiology ; *Malus/microbiology/genetics ; *Genome, Bacterial ; Genetic Fitness ; Genomics/methods ; Genomic Islands ; Computational Biology/methods ; },
abstract = {A comparative genomic analysis approach provides valuable information about genetic variations and evolutionary relationships among microorganisms, aiding not only in the identification of functional genes responsible for traits such as pathogenicity, antibiotic resistance, and metabolic capabilities but also in enhancing our understanding of microbial genomic diversity and their ecological roles, such as supporting plant growth promotion, thereby enabling the development of sustainable strategies for agriculture. We used two strains from different Bacillus species, Bacillus velezensis AK-0 and Bacillus atrophaeus CNY01, which have previously been reported to have PGP activity in apple, and performed comparative genomic analysis to understand their evolutionary process and obtain a mechanistic understanding of their plant growth-promoting activity. We identified genomic features such as mobile genetic elements (MGEs) that encode key proteins involved in the survival, adaptation and growth of these bacterial strains. The presence of genomic islands and intact prophage DNA in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 suggests that horizontal gene transfer has contributed to their diversification and acquisition of adaptive traits, enhancing their evolutionary advantage. We also identified novel DNA motifs that are associated with key physiological processes and metabolic pathways.},
}

*Bacillus/genetics/physiology
*Malus/microbiology/genetics
*Genome, Bacterial
Genetic Fitness
Genomics/methods
Genomic Islands
Computational Biology/methods

@article {pmid39591316,
year = {2024},
author = {Jafari Jozani, R and Khallawi, MFHA and Trott, D and Petrovski, K and Low, WY and Hemmatzadeh, F},
title = {Unravelling Antimicrobial Resistance in Mycoplasma hyopneumoniae: Genetic Mechanisms and Future Directions.},
journal = {Veterinary sciences},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/vetsci11110542},
pmid = {39591316},
issn = {2306-7381},
support = {2021/0025//Australian Pork (APL)/ ; },
abstract = {Antimicrobial resistance (AMR) in Mycoplasma hyopneumoniae, the causative agent of Enzootic Pneumonia in swine, poses a significant challenge to the swine industry. This review focuses on the genetic foundations of AMR in M. hyopneumoniae, highlighting the complexity of resistance mechanisms, including mutations, horizontal gene transfer, and adaptive evolutionary processes. Techniques such as Whole Genome Sequencing (WGS) and multiple-locus variable number tandem repeats analysis (MLVA) have provided insights into the genetic diversity and resistance mechanisms of M. hyopneumoniae. The study underscores the role of selective pressures from antimicrobial use in driving genomic variations that enhance resistance. Additionally, bioinformatic tools utilizing machine learning algorithms, such as CARD and PATRIC, can predict resistance traits, with PATRIC predicting 7 to 12 AMR genes and CARD predicting 0 to 3 AMR genes in 24 whole genome sequences available on NCBI. The review advocates for a multidisciplinary approach integrating genomic, phenotypic, and bioinformatics data to combat AMR effectively. It also elaborates on the need for refining genotyping methods, enhancing resistance prediction accuracy, and developing standardized antimicrobial susceptibility testing procedures specific to M. hyopneumoniae as a fastidious microorganism. By leveraging contemporary genomic technologies and bioinformatics resources, the scientific community can better manage AMR in M. hyopneumoniae, ultimately safeguarding animal health and agricultural productivity. This comprehensive understanding of AMR mechanisms will be beneficial in the adaptation of more effective treatment and management strategies for Enzootic Pneumonia in swine.},
}

@article {pmid39590772,
year = {2024},
author = {Cui, H and Lu, J and Ding, W and Zhang, W},
title = {Genomic Features and Antimicrobial Activity of Phaeobacter inhibens Strains from Marine Biofilms.},
journal = {Marine drugs},
volume = {22},
number = {11},
pages = {},
pmid = {39590772},
issn = {1660-3397},
mesh = {*Biofilms/drug effects ; *Rhodobacteraceae/genetics ; *Phylogeny ; *Genome, Bacterial ; *Anti-Bacterial Agents/pharmacology ; *Tropolone/pharmacology/analogs & derivatives ; Multigene Family ; Aquatic Organisms ; Vibrio/genetics/drug effects ; Genomics/methods ; Animals ; },
abstract = {Members of the genus Phaeobacter are widely distributed in the marine environment and are known for their ability to produce tropodithietic acid (TDA). Studies investigating the genomic and metabolic features of Phaeobacter strains from marine biofilms are sparse. Here, we analyze the complete genomes of 18 Phaeobacter strains isolated from biofilms on subtidal stones, with the aim of determining their potential to synthesize secondary metabolites. Based on whole-genome comparison and average nucleotide identity calculation, the isolated bacteria are classified as novel strains of Phaeobacter inhibens. Further analysis reveals a total of 153 biosynthetic gene clusters, which are assigned to 32 gene cluster families with low similarity to previously published ones. Complete TDA clusters are identified in 14 of the 18 strains, while in the other 4 strains the TDA clusters are rather incomplete and scattered across different chromosome and plasmid locations. Phylogenetic analysis suggests that their presence or absence may be potentially attributed to horizontal gene transfer. High-performance liquid chromatography-mass spectrometry analysis demonstrates the production of TDA in all the examined strains. Furthermore, the Phaeobacter strains have strong antibacterial activity against the pathogenic strain Vibrio owensii ems001, which is associated with acute hepatopancreatic necrosis in South American white shrimp. Altogether, this study ameliorates our knowledge of marine biofilm-associated Phaeobacter and offers new avenues for exploiting marine antimicrobial agents.},
}

*Biofilms/drug effects
*Rhodobacteraceae/genetics
*Phylogeny
*Genome, Bacterial
*Anti-Bacterial Agents/pharmacology
*Tropolone/pharmacology/analogs & derivatives
Multigene Family
Aquatic Organisms
Vibrio/genetics/drug effects
Genomics/methods
Animals

@article {pmid39589125,
year = {2024},
author = {Zhang, Z and Tong, M and Ding, W and Liu, S and Jong, M-C and Radwan, AA and Cai, Z and Zhou, J},
title = {Changes in the diversity and functionality of viruses that can bleach healthy coral.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0081624},
doi = {10.1128/msphere.00816-24},
pmid = {39589125},
issn = {2379-5042},
abstract = {UNLABELLED: Coral microbiomes play a crucial role in maintaining the health and functionality of holobionts. Disruption in the equilibrium of holobionts, including bacteria, fungi, and archaea, can result in the bleaching of coral. However, little is known about the viruses that can infect holobionts in coral, especially bacteriophages. Here, we employed a combination of amplicon and metagenomic analyses on Acropora muricata and Galaxea astreata to investigate the diversity and functionality of viruses in healthy and bleached corals. Analysis showed that the alpha diversity of holobionts (bacteria, eukaryotes, zooxanthellae, and lysogenic and lytic viruses) was higher in bleached corals than that in healthy corals. Meanwhile, bleached corals exhibited a relatively higher abundance of specific viral classes, including Revtraviricetes, Arfiviricetes, Faserviricetes, Caudoviricetes, Herviviricetes, and Tectiliviricetes; moreover, we found that the expression levels of functional genes involved in carbon and sulfur metabolism were enriched. An increase in Vibrio abundance has been reported as a notable factor in coral bleaching; our analysis also revealed an increased abundance of Vibrio in bleached coral. Finally, bleached corals contained a higher abundance of Vibrio phages and encoded more virulence factor genes to increase the competitiveness of Vibrio after coral bleaching. In conclusion, we attempted to understand the causes of coral bleaching from the perspective of phage-bacteria-coral tripartite interaction.

IMPORTANCE: Viruses, especially bacteriophages, outnumber other microorganisms by approximately 10-fold and represent the most abundant members of coral holobionts. Corals represent a model system for the study of symbiosis, the influence of viruses on organisms inhabiting healthy coral reef, the role of rapid horizontal gene transfer, and the expression of auxiliary metabolic genes. However, the least studied component of coral holobiont are viruses. Therefore, there is a critical need to investigate the viral community of viruses, and their functionality, in healthy and bleached coral. Here, we compared the composition and functionality of viruses in healthy and bleached corals and found that viruses may participate in the induction of coral bleaching by enhancing the expression of virulence genes and other auxiliary metabolic functions.},
}

@article {pmid39587099,
year = {2024},
author = {Sheikh, S and Fu, CJ and Brown, MW and Baldauf, SL},
title = {The Acrasis kona genome and developmental transcriptomes reveal deep origins of eukaryotic multicellular pathways.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10197},
pmid = {39587099},
issn = {2041-1723},
support = {VR 2017-04351//Vetenskapsrådet (Swedish Research Council)/ ; 2100888//National Science Foundation (NSF)/ ; },
mesh = {*Transcriptome ; *Dictyostelium/genetics/growth & development ; Genome, Protozoan ; Amoeba/genetics ; Phylogeny ; Gene Transfer, Horizontal ; Protozoan Proteins/genetics/metabolism ; Proteome/metabolism/genetics ; Genome ; },
abstract = {Acrasids are amoebae with the capacity to form multicellular fruiting bodies in a process known as aggregative multicellularity (AGM). This makes acrasids the only known example of multicellularity among the earliest branches of eukaryotes (the former Excavata). Here, we report the Acrasis kona genome sequence plus transcriptomes from pre-, mid- and post-developmental stages. The genome is rich in novelty and genes with strong signatures of horizontal transfer, and multigene families encode nearly half of the amoeba's predicted proteome. Development in A. kona appears molecularly simple relative to the AGM model, Dictyostelium discoideum. However, the acrasid also differs from the dictyostelid in that it does not appear to be starving during development. Instead, developing A. kona appears to be very metabolically active, does not induce autophagy and does not up-regulate its proteasomal genes. Together, these observations strongly suggest that starvation is not essential for AGM development. Nonetheless, development in the two amoebae appears to employ remarkably similar pathways for signaling, motility and, potentially, construction of an extracellular matrix surrounding the developing cell mass. Much of this similarity is also shared with animal development, suggesting that much of the basic tool kit for multicellular development arose early in eukaryote evolution.},
}

*Transcriptome
*Dictyostelium/genetics/growth & development
Genome, Protozoan
Amoeba/genetics
Phylogeny
Gene Transfer, Horizontal
Protozoan Proteins/genetics/metabolism
Proteome/metabolism/genetics
Genome

@article {pmid39581358,
year = {2024},
author = {Fischer, K and Valentin Jordbræk, S and Olsen, S and Bockwoldt, M and Schwacke, R and Usadel, B and Krause, K},
title = {Taken to extremes: Loss of plastid rpl32 in Streptophyta and Cuscuta's unconventional solution for its replacement.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108243},
doi = {10.1016/j.ympev.2024.108243},
pmid = {39581358},
issn = {1095-9513},
abstract = {The evolution of plant genomes is riddled with exchanges of genetic material within one plant (endosymbiotic gene transfer/EGT) and between unrelated plants (horizontal gene transfer/HGT). These exchanges have left their marks on plant genomes. Parasitic plants with their special evolutionary niche provide ample examples for these processes because they are under a reduced evolutionary pressure to maintain autotrophy and thus to conserve their plastid genomes. On the other hand, the close physical connections with different hosts enabled them to acquire genetic material from other plants. Based on an analysis of an extensive dataset including the parasite Cuscuta campestris and other parasitic plant species, we identified a unique evolutionary history of rpl32 genes coding for an essential plastid ribosomal subunit in Cuscuta. Our analysis suggests that the gene was most likely sequestered by HGT from a member of the Oxalidales order serving as host to an ancestor of the Cuscuta subgenus Grammica. Oxalidales had suffered an ancestral EGT of rpl32 predating the evolution of the genus Cuscuta. The HGT subsequently relieved the plastid rpl32 from its evolutionary constraint and led to its loss from the plastid genome. The HGT-based acquisition in Cuscuta is supported by a high sequence similarity of the mature L32 protein between species of the subgenus Grammica and representatives of the Oxalidales, and by a surprisingly conserved transit peptide, whose functionality in Cuscuta was experimentally verified. The findings are discussed in view of an overall pattern of EGT events for plastid ribosomal subunits in Streptophyta.},
}

@article {pmid39581254,
year = {2024},
author = {Xu, F and Xiang, Q and Xu, ML and Carter, LJ and Du, WC and Zhu, CW and Ai, FX and Yin, Y and Ji, R and Guo, HY},
title = {Elevated CO2 alters antibiotic resistome in soil amended with sulfamethazine via chemical-organic fertilization.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120416},
doi = {10.1016/j.envres.2024.120416},
pmid = {39581254},
issn = {1096-0953},
abstract = {Rising antimicrobial resistance (AMR) is an enormous challenge for global healthcare systems. The effects of elevated CO2 (eCO2) on AMR are poorly characterized. Using a free-air CO2 enrichment system and high-throughput qPCR arrays, we investigated the response of soil antibiotic resistome and bacterial communities to eCO2 (ambient + 200 ppm) in soils amended with sulfamethazine (SMZ) at 0.1 and 1 mg kg[-1] via chemical-organic fertilizer (COL, COH). Results showed that under ambient condition, COH significantly enhanced the diversity of high-risk antibiotic resistance genes (ARGs), relative abundance of low risk ARGs, unassessed ARGs and total ARGs compared to COL. Nevertheless, eCO2 mitigated the effects of COH, with no significant difference found between COL and COH on the above high risk, low risk, unassessed and total ARGs. Meanwhile, eCO2 decreased the relative abundance of spcN, ermA, olec, oprD, sulA-olP, tetB, tetT and vanXD in COL, and alleviated the enrichment of pikR2, ampC, lunC, oprD and pncA caused by the application of SMZ at 1 mg kg[-1]. Correlation and network analysis illustrated that changes of certain bacteria biomarkers and horizontal gene transfer of integrase gene were associated with the altered response of ARGs abundance to eCO2. This study adds knowledge of the potential risk of antibiotic resistance in agricultural exposure scenarios under increasing CO2 concentration.},
}

@article {pmid39581077,
year = {2024},
author = {Guernier-Cambert, V and Trachsel, J and Atkinson, B and Oladeinde, A and Anderson, CL and Bearson, SMD and Monson, MS and Looft, T},
title = {Tetracycline resistance gene transfer from Escherichia coli donors to Salmonella Heidelberg in chickens is impacted by the genetic context of donors.},
journal = {Veterinary microbiology},
volume = {299},
number = {},
pages = {110294},
doi = {10.1016/j.vetmic.2024.110294},
pmid = {39581077},
issn = {1873-2542},
abstract = {Chicken ceca are a rich source of bacteria, including zoonotic pathogens such as Salmonella enterica. The microbiota includes strains/species carrying antimicrobial resistance genes and horizontal transfer of resistance determinants between species may increase the risk to public health and farming systems. Possible sources of these antimicrobial resistance donors - the eggshell carrying bacteria from the hen vertically transmitted to the offspring, or the barn environment where chicks are hatched and raised - has been little explored. In this study, we used Salmonella enterica serovar Heidelberg to evaluate if layer chicks raised in different environments (using combinations of sterilized or non-sterile eggs placed in sterilized isolation chambers or non-sterile rooms) acquired transferable tetracycline resistance genes from surrounding bacteria, especially Escherichia coli. Two-day old chicks were challenged with an antibiotic-susceptible S. Heidelberg strain SH2813nal[R] and Salmonella recovered from the cecum of birds at different timepoints to test the in vivo acquisition of tetracycline resistance. Tetracycline-resistant E. coli isolates recovered from birds from the in vivo experiment were used to test the in vitro transfer of tetracycline resistance genes from E. coli to Salmonella. Even though Salmonella SH2813nal[R] colonized the 2-day old chicks after oral challenge, tetracycline-resistant Salmonella transconjugants were not recovered, as previously observed. In vitro experiments provided similar results. We discuss several hypotheses that might explain the absence of transconjugants in vitro and in vivo, despite the presence of diverse plasmids in the recovered E. coli. The factors that can inhibit/promote antimicrobial resistance transfers to Salmonella for different plasmid types need further exploration.},
}

@article {pmid39577948,
year = {2024},
author = {Sheng, H and Zhao, L and Suo, J and Yang, Q and Cao, C and Chen, J and Cui, G and Fan, Y and Ma, Y and Huo, S and Wu, X and Yang, T and Cui, X and Chen, S and Cui, S and Yang, B},
title = {Niche-specific evolution and gene exchange of Salmonella in retail pork and chicken.},
journal = {Food research international (Ottawa, Ont.)},
volume = {197},
number = {Pt 2},
pages = {115299},
doi = {10.1016/j.foodres.2024.115299},
pmid = {39577948},
issn = {1873-7145},
mesh = {Animals ; *Chickens/microbiology ; *Salmonella/genetics ; Swine ; *Food Microbiology ; China ; *Pork Meat/microbiology ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Meat/microbiology ; Drug Resistance, Bacterial/genetics ; Genetic Variation ; Red Meat/microbiology ; },
abstract = {Salmonella exhibits extensive genetic diversity, facilitated by horizontal gene transfer occurring within and between species, playing a pivotal role in this diversification. Nevertheless, most studies focus on clinical and farm animal isolates, and research on the pangenome dynamics of Salmonella isolates from retail stage of the animal food supply chain is limited. Here, we investigated the genomes of 950 Salmonella isolates recovered from retail chicken and pork meats in seven provinces and one municipality of China in 2018. We observed a strong correlation between Salmonella sublineage diversity and the accessory genome with meat type, revealing reduced diversity associated with increased resistance. Importantly, genes associated with antibiotic, biocide, and heavy metal resistance were unevenly distributed in Salmonella from retail chicken and pork. Pork Salmonella isolates showed a higher prevalence of copper and silver resistance genes, while chicken Salmonella isolates displayed a significant predominance of genetic determinants associated with cephalosporin and ciprofloxacin resistance. Moreover, co-occurrence patterns of resistance determinants and their interaction with mobile genetic elements also correlated with meat type. In summary, our findings shed light on how Salmonella achieves their ecological niche success driven by evolution and gene changes in the retail stage of the animal food supply chain.},
}

Animals
*Chickens/microbiology
*Salmonella/genetics
Swine
*Food Microbiology
China
*Pork Meat/microbiology
Anti-Bacterial Agents/pharmacology
Gene Transfer, Horizontal
Meat/microbiology
Drug Resistance, Bacterial/genetics
Genetic Variation
Red Meat/microbiology

@article {pmid39577842,
year = {2024},
author = {Whangsuk, W and Dulyayangkul, P and Loprasert, S and Dubbs, JM and Vattanaviboon, P and Mongkolsuk, S},
title = {Re-sensitization of imipenem-resistant Pseudomonas aeruginosa and restoration of cephalosporins susceptibility in Enterobacteriaceae by recombinant Esterase B.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovae118},
pmid = {39577842},
issn = {1472-765X},
abstract = {Sphingobium sp. SM42 Esterase B (EstB) is an enzyme with a dual function in degrading dibutyl phthalate (DBP) and catalyzing the cleavage of the C-S bond in C3-sidechains of the dihydrothiazine ring of cephalosporins, generating more active β-lactam derivatives. Global prokaryotic genome analysis revealed the existence of a gene identical to estB in Pseudomonas aeruginosa strain PS1 suggesting a horizontal gene transfer event involving estB. To investigate the effect of ectopic expression of EstB in the periplasm of Pseudomonas aeruginosa and several Enterobacteriaceae on antibiotic susceptibility levels, plasmid, pEstB, carrying a recombinant EstB fused with the signal peptide from Escherichia coli outer membrane protein A (OmpA) for periplasmic localization was constructed. The expression of EstB in the periplasm of P. aeruginosa and the Enterobacteriaceae: E. coli, Klebsiella pneumoniae, and Salmonella enterica serovar Typhi, increased susceptibility to carbapenems and cephalosporins. EstB reversed the imipenem resistance of P. aeruginosa ΔmexS and restored the changes in susceptibility to cephalosporins conferred by the downregulation of the outer membrane proteins, OmpK35 and OmpK36, in K. pneumoniae ΔramR-ompK36 to wild-type level. The introduction of EstB to the periplasmic space of Gram-negative bacteria can increase carbapenem and cephalosporin susceptibility.},
}

@article {pmid39577583,
year = {2024},
author = {Yu, K and He, B and Xiong, J and Kan, P and Sheng, H and Zhi, S and Zhu, DZ and Yao, Z},
title = {Deciphering basic and key traits of bio-pollutants in a long-term reclaimed water headwater urban stream.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177696},
doi = {10.1016/j.scitotenv.2024.177696},
pmid = {39577583},
issn = {1879-1026},
abstract = {Reclaimed water has been recognized as a stable water resource for ecological replenishment in riverine environment. However, information about the bio-pollutants spatial and temporal distributions and the associated risk in this environment remains insufficient. Herein, the bio-pollutant profile in a long-term reclaimed water headwater urban stream, including antibiotic resistance genes (ARGs), mobile genetic elements and pathogens, were revealed by metagenomics. Notably, the temporal variation in bio-pollutant levels exceeded spatial fluctuations, possibly due to the varied rainfall intensity. Specially, multidrug resistance genes and Acinetobacter baumannii (A. baumannii) were the dominant ARGs and pathogens, respectively, exhibiting higher abundance in the dry season, especially in the downstream of the receiving point, where the bio-risk also peaked. A. baumannii and Ralstonia solanacearum were found to be the main plasmids contributors inducing the horizontal gene transfer process in this stream. Overall, A. baumannii contributed over 50 % bio-risk values in most samples, indicating that it was the "overlord" in this headwater urban stream. This study revealed characteristics of bio-pollutants in a typical long-term reclaimed water headwater urban stream, highlighting the superiority of A. baumannii in bio-pollutants, which should be a key consideration in the bio-pollutants surveillance for reclaimed waters.},
}

@article {pmid39575186,
year = {2024},
author = {Verma, T and Hendiani, S and Carbajo, C and Andersen, SB and Hammarlund, EU and Burmølle, M and Sand, KK},
title = {Recurrence and propagation of past functions through mineral facilitated horizontal gene transfer.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1449094},
pmid = {39575186},
issn = {1664-302X},
abstract = {Horizontal gene transfer is one of the most important drivers of bacterial evolution. Transformation by uptake of extracellular DNA is traditionally not considered to be an effective mode of gene acquisition, simply because extracellular DNA is degraded in a matter of days when it is suspended in e.g. seawater. Recently the age span of stored DNA was increased to at least 2 Ma. Here, we show that Acinetobacter baylyi can incorporate 60 bp DNA fragments adsorbed to common sedimentary minerals and that the transformation frequencies scale with mineral surface properties. Our work highlights that ancient environmental DNA can fuel the evolution of contemporary bacteria. In contrast to heritable stochastic mutations, the processes by which bacteria acquire new genomic material during times of increased stress and needs, indicate a non-random mechanism that may propel evolution in a non-stochastic manner.},
}

@article {pmid39572773,
year = {2024},
author = {Hoffmann, L},
title = {Finding the sweet spot in the deep ocean.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1544},
pmid = {39572773},
issn = {2399-3642},
abstract = {‘Candidatus Endonucleobacter’ infects the nuclei of deep-sea mussels but it was unknown how they can prevent apoptosis of the host. A new study by Porras and colleagues, published in Nature Microbiology, suggests that the bacterium upregulates host-derived apoptosis inhibitors and genes for digesting sugars, lipids and amino acids acquired through horizontal gene transfer from the mussels.},
}

@article {pmid39571737,
year = {2024},
author = {Jing, T and Yang, J and Pan, J and Liu, X and Yang, X and Farhan, M and Su, H and Ma, X and Zhang, S},
title = {A near-complete genome reveals the population evolution of the cotton-melon aphid Aphis gossypii.},
journal = {Insect biochemistry and molecular biology},
volume = {},
number = {},
pages = {104215},
doi = {10.1016/j.ibmb.2024.104215},
pmid = {39571737},
issn = {1879-0240},
abstract = {The cotton-melon aphid Aphis gossypii Glover is a severe pest worldwide. Interhaplotype genomic variation can be used as a starting point to analyze the adaptability of Ap. gossypii. In this study, we utilized long-read PacBio HiFi sequencing and HiC scaffolding techniques to assemble a near telomere-to-telomere gap-free genome assembly of Hap4. The assembly had two gaps totaling 321.24 Mb. We characterized five telomeric repetitive regions (GGTTA)n, including the four found at the 3' end of the chromosomes, and obtained new structural information about the telomeres. Due to the improved sequencing technology, we also identified more than 55.03 Mb of repetitive DNA in the genome assembly of Hap4, which contributed significantly to the increase in genome size compared to that of Hap1 and Hap3. Most of the additional repetitive DNA content was located on the X chromosome, and the tandem repeat sequence occupied 16.8% of the X chromosome length. The Hap4 assembly showed that the X chromosome exhibited a greater abundance of AT-rich satDNA arrays (11 satDNA arrays longer than 100 kb) than that observed in the autosomes (A1 and A2 harboured 3 and 1 satDNA arrays). We detected presence-absence variations, insertions, and deletions events between Hap1, Hap3, and Hap4 Ap. gossypii, which had significant effects on gene expression. Additionally, we identified a male-specific glyceraldehyde-3-phosphate dehydrogenase of fungal origin in all strains of Ap. gossypii. This comprehensive genome assembly provides valuable insights into the structural characteristics of highly repetitive regions and allows comparative genomic analyses that facilitate our understanding of Ap. gossypii's adaptation and diversification.},
}

@article {pmid39571576,
year = {2024},
author = {Denoeud, F and Godfroy, O and Cruaud, C and Heesch, S and Nehr, Z and Tadrent, N and Couloux, A and Brillet-Guéguen, L and Delage, L and Mckeown, D and Motomura, T and Sussfeld, D and Fan, X and Mazéas, L and Terrapon, N and Barrera-Redondo, J and Petroll, R and Reynes, L and Choi, SW and Jo, J and Uthanumallian, K and Bogaert, K and Duc, C and Ratchinski, P and Lipinska, A and Noel, B and Murphy, EA and Lohr, M and Khatei, A and Hamon-Giraud, P and Vieira, C and Avia, K and Akerfors, SS and Akita, S and Badis, Y and Barbeyron, T and Belcour, A and Berrabah, W and Blanquart, S and Bouguerba-Collin, A and Bringloe, T and Cattolico, RA and Cormier, A and Cruz de Carvalho, H and Dallet, R and De Clerck, O and Debit, A and Denis, E and Destombe, C and Dinatale, E and Dittami, S and Drula, E and Faugeron, S and Got, J and Graf, L and Groisillier, A and Guillemin, ML and Harms, L and Hatchett, WJ and Henrissat, B and Hoarau, G and Jollivet, C and Jueterbock, A and Kayal, E and Knoll, AH and Kogame, K and Le Bars, A and Leblanc, C and Le Gall, L and Ley, R and Liu, X and LoDuca, ST and Lopez, PJ and Lopez, P and Manirakiza, E and Massau, K and Mauger, S and Mest, L and Michel, G and Monteiro, C and Nagasato, C and Nègre, D and Pelletier, E and Phillips, N and Potin, P and Rensing, SA and Rousselot, E and Rousvoal, S and Schroeder, D and Scornet, D and Siegel, A and Tirichine, L and Tonon, T and Valentin, K and Verbruggen, H and Weinberger, F and Wheeler, G and Kawai, H and Peters, AF and Yoon, HS and Hervé, C and Ye, N and Bapteste, E and Valero, M and Markov, GV and Corre, E and Coelho, SM and Wincker, P and Aury, JM and Cock, JM},
title = {Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.10.049},
pmid = {39571576},
issn = {1097-4172},
abstract = {Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, and are under considerable threat from climate change. In this study, analysis of multiple genomes has provided insights across the entire evolutionary history of this lineage, from initial emergence, through later diversification of the brown algal orders, down to microevolutionary events at the genus level. Emergence of the brown algal lineage was associated with a marked gain of new orthologous gene families, enhanced protein domain rearrangement, increased horizontal gene transfer events, and the acquisition of novel signaling molecules and key metabolic pathways, the latter notably related to biosynthesis of the alginate-based extracellular matrix, and halogen and phlorotannin biosynthesis. We show that brown algal genome diversification is tightly linked to phenotypic divergence, including changes in life cycle strategy and zoid flagellar structure. The study also showed that integration of large viral genomes has had a significant impact on brown algal genome content throughout the emergence of the lineage.},
}

@article {pmid39568508,
year = {2024},
author = {Mukherjee, K and Moroz, LL},
title = {Evolution of g-type lysozymes in metazoa: insights into immunity and digestive adaptations.},
journal = {Frontiers in cell and developmental biology},
volume = {12},
number = {},
pages = {1487920},
pmid = {39568508},
issn = {2296-634X},
abstract = {Exploring the evolutionary dynamics of lysozymes is critical for advancing our knowledge of adaptations in immune and digestive systems. Here, we characterize the distribution of a unique class of lysozymes known as g-type, which hydrolyze key components of bacterial cell walls. Notably, ctenophores, and choanoflagellates (the sister group of Metazoa), lack g-type lysozymes. We reveal a mosaic distribution of these genes, particularly within lophotrochozoans/spiralians, suggesting the horizontal gene transfer events from predatory myxobacteria played a role in their acquisition, enabling specialized dietary and defensive adaptations. We further identify two major groups of g-type lysozymes based on their widespread distribution in gastropods. Despite their sequence diversity, these lysozymes maintain conserved structural integrity that is crucial for enzymatic activity, underscoring independent evolutionary pathways where g-type lysozymes have developed functionalities typically associated with different lysozyme types in other species. Specifically, using Aplysia californica as a reference species, we identified three distinct g-type lysozyme genes: two are expressed in organs linked to both feeding and defense, and the third exhibits broader distribution, likely associated with immune functions. These findings advance our understanding of the evolutionary dynamics shaping the recruitment and mosaic functional diversification of these enzymes across metazoans, offering new insights into ecological physiology and physiological evolution as emerging fields.},
}

@article {pmid39565221,
year = {2024},
author = {Molano, LG and Hirsch, P and Hannig, M and Müller, R and Keller, A},
title = {The PLSDB 2025 update: enhanced annotations and improved functionality for comprehensive plasmid research.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae1095},
pmid = {39565221},
issn = {1362-4962},
support = {//European Commission/ ; 466168626//DFG/ ; },
abstract = {Plasmids are extrachromosomal DNA molecules in bacteria and archaea, playing critical roles in horizontal gene transfer, antibiotic resistance, and pathogenicity. Since its first release in 2018, our database on plasmids, PLSDB, has significantly grown and enhanced its content and scope. From 34 513 records contained in the 2021 version, PLSDB now hosts 72 360 entries. Designed to provide life scientists with convenient access to extensive plasmid data and to support computer scientists by offering curated datasets for artificial intelligence (AI) development, this latest update brings more comprehensive and accurate information for plasmid research, with interactive visualization options. We enriched PLSDB by refining the identification and classification of plasmid host ecosystems and host diseases. Additionally, we incorporated annotations for new functional structures, including protein-coding genes and biosynthetic gene clusters. Further, we enhanced existing annotations, such as antimicrobial resistance genes and mobility typing. To accommodate these improvements and to host the increase plasmid sets, the webserver architecture and underlying data structures of PLSDB have been re-reconstructed, resulting in decreased response times and enhanced visualization of features while ensuring that users have access to a more efficient and user-friendly interface. The latest release of PLSDB is freely accessible at https://www.ccb.uni-saarland.de/plsdb2025.},
}

@article {pmid39565095,
year = {2024},
author = {Bulka, O and Mahadevan, R and Edwards, EA},
title = {Pangenomic insights into Dehalobacter evolution and acquisition of functional genes for bioremediation.},
journal = {Microbial genomics},
volume = {10},
number = {11},
pages = {},
pmid = {39565095},
issn = {2057-5858},
mesh = {*Biodegradation, Environmental ; *Phylogeny ; *Genome, Bacterial ; Evolution, Molecular ; Bacterial Proteins/genetics/metabolism ; Genomics ; Gene Transfer, Horizontal ; Metagenome ; },
abstract = {Dehalobacter is a genus of organohalide-respiring bacteria that is recognized for its fastidious growth using reductive dehalogenases (RDases). In the SC05 culture, however, a Dehalobacter population also mineralizes dichloromethane (DCM) produced by chloroform dechlorination using the mec cassette, just downstream of its active RDase. A closed genome of this DCM-mineralizing lineage has previously evaded assembly. Here, we present the genomes of two novel Dehalobacter strains, each of which was assembled from the metagenome of a distinct subculture from SC05. A pangenomic analysis of the Dehalobacter genus, including RDase synteny and phylogenomics, reveals at least five species of Dehalobacter based on average nucleotide identity, RDase and core gene synteny, as well as differential functional genes. An integration hotspot is also pinpointed in the Dehalobacter genome, in which many recombinase islands have accumulated. This nested recombinase island encodes the active RDase and mec cassette in both SC05 Dehalobacter genomes, indicating the transfer of key functional genes between species of Dehalobacter. Horizontal gene transfer between these two novel Dehalobacter strains has implications for the evolutionary history within the SC05 subcultures and of the Dehalobacter genus as a whole, especially regarding adaptation to anthropogenic chemicals.},
}

*Biodegradation, Environmental
*Phylogeny
*Genome, Bacterial
Evolution, Molecular
Bacterial Proteins/genetics/metabolism
Genomics
Gene Transfer, Horizontal
Metagenome

@article {pmid39564482,
year = {2024},
author = {Huang, CJ and Wu, TL and Wu, YL and Wang, RS and Lin, YC},
title = {Comparative genomic analysis uncovered phylogenetic diversity, evolution of virulence factors, and horizontal gene transfer events in tomato bacterial spot Xanthomonas euvesicatoria.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1487917},
pmid = {39564482},
issn = {1664-302X},
abstract = {INTRODUCTION: Bacterial spot, caused by diverse xanthomonads classified into four lineages within three species, poses a significant threat to global pepper and tomato production. In Taiwan, tomato bacterial spot xanthomonads phylogenetically related to an atypical Xanthomonas euvesicatoria pv. perforans (Xep) strain NI1 from Nigeria were found.

METHODS: To investigate the genetic structure of Taiwanese Xep strains and determine the phylogenetic position of the atypical strains, we completed high-quality, gap-free, circularized genomes of seven Taiwanese Xep strains and performed comparative genomic analyses with genomes of X. euvesicatoria pathovars. Average nucleotide identity, core genome analysis, and phylogenomic analysis were conducted.

RESULTS: Three sequenced strains were identified as typical Xep, while four clustered with the atypical strain NI1, forming a distinct genomovar within X. euvesicatoria, proposed as X. euvesicatoria genomovar taiwanensis (Xet). This new lineage likely originated in Taiwan and spread to Nigeria through global seed trade. At the genomovar level, chromosomes remained conserved among Taiwanese strains, while plasmids likely contributed to bacterial virulence, avirulence, and field fitness. Gap-free genomes revealed associations between the evolution of type III effectors, horizontal gene transfer events, plasmid diversity, and recombination.

DISCUSSION: This study highlights the critical roles of horizontal gene transfer and plasmids in shaping the genetic makeup, evolution, and environmental adaptation of plant pathogenic xanthomonads. The identification of a new genomovar, X. euvesicatoria genomovar taiwanensis, provides insights into the diversity and global spread of bacterial spot pathogens through seed trade.},
}

@article {pmid39562586,
year = {2024},
author = {Goh, YX and Anupoju, SMB and Nguyen, A and Zhang, H and Ponder, M and Krometis, LA and Pruden, A and Liao, J},
title = {Evidence of horizontal gene transfer and environmental selection impacting antibiotic resistance evolution in soil-dwelling Listeria.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10034},
pmid = {39562586},
issn = {2041-1723},
mesh = {*Gene Transfer, Horizontal ; *Soil Microbiology ; *Listeria/genetics/drug effects ; *Phylogeny ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Genome, Bacterial/genetics ; Evolution, Molecular ; Selection, Genetic ; },
abstract = {Soil is an important reservoir of antibiotic resistance genes (ARGs) and understanding how corresponding environmental changes influence their emergence, evolution, and spread is crucial. The soil-dwelling bacterial genus Listeria, including L. monocytogenes, the causative agent of listeriosis, serves as a key model for establishing this understanding. Here, we characterize ARGs in 594 genomes representing 19 Listeria species that we previously isolated from soils in natural environments across the United States. Among the five putatively functional ARGs identified, lin, which confers resistance to lincomycin, is the most prevalent, followed by mprF, sul, fosX, and norB. ARGs are predominantly found in Listeria sensu stricto species, with those more closely related to L. monocytogenes tending to harbor more ARGs. Notably, phylogenetic and recombination analyses provide evidence of recent horizontal gene transfer (HGT) in all five ARGs within and/or across species, likely mediated by transformation rather than conjugation and transduction. In addition, the richness and genetic divergence of ARGs are associated with environmental conditions, particularly soil properties (e.g., aluminum and magnesium) and surrounding land use patterns (e.g., forest coverage). Collectively, our data suggest that recent HGT and environmental selection play a vital role in the acquisition and diversification of bacterial ARGs in natural environments.},
}

*Gene Transfer, Horizontal
*Soil Microbiology
*Listeria/genetics/drug effects
*Phylogeny
*Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial/genetics
Genes, Bacterial
Genome, Bacterial/genetics
Evolution, Molecular
Selection, Genetic

@article {pmid39555914,
year = {2024},
author = {Ulrich, NJ and Miller, SR},
title = {Integration of horizontally acquired light-harvesting genes into an ancestral regulatory network in the cyanobacterium Acaryochloris marina MBIC11017.},
journal = {mBio},
volume = {},
number = {},
pages = {e0242324},
doi = {10.1128/mbio.02423-24},
pmid = {39555914},
issn = {2150-7511},
abstract = {The acquisition of new capabilities by horizontal gene transfer (HGT) shapes the distribution of traits during microbial diversification. In the Chlorophyll (Chl) d-producing cyanobacterium Acaryochloris marina, the genes involved in the production and disassembly of the light-harvesting phycobiliprotein phycocyanin (PC) were lost in the A. marina common ancestor but then subsequently regained via HGT in A. marina strain MBIC11017. However, it remains unknown how the HGT-acquired PC genes in MBIC11017 have been reintegrated into its existing regulatory network after tens of millions of years since their loss. Here, we investigated potential mechanisms of regulatory assimilation of PC genes by comparing the transcriptomes of A. marina strain MBIC11017 and a PC-lacking close relative under both low irradiance far-red light and high irradiance white light. We found that PC assembly and degradation processes have been re-assimilated into a conserved ancestral response to high light. Further, we identified putative regulatory elements that were likely co-transferred with PC genes and could be recognized by A. marina's pre-existing light response machinery. This study offers insights into how HGT-acquired genes can be reintegrated into an existing transcriptional regulatory network that has evolved in their absence.IMPORTANCEHorizontal gene transfer, the asymmetric movement of genetic information between donor and recipient organisms, is an important mechanism for acquiring new traits. In order for newly acquired gene content to be retained, it must be integrated into the genetic repertoire and regulatory networks of the recipient cell. In a strain of the Chlorophyll d-producing cyanobacterium Acaryochloris marina, the recent reacquisition of the genes required to produce the light-harvesting pigment phycocyanin offers a rare opportunity to understand the mechanisms underlying the regulatory assimilation of an acquired complex trait in bacteria. The significance in our research is in characterizing how an ancestrally lost, complex trait can be reintegrated into a conserved regulatory network, even after millions of years.},
}

@article {pmid39552541,
year = {2024},
author = {Singh, CK and Sodhi, KK},
title = {Targeting bioinformatics tools to study the dissemination and spread of antibiotic resistant genes in the environment and clinical settings.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/1040841X.2024.2429603},
pmid = {39552541},
issn = {1549-7828},
abstract = {Antibiotic resistance has expanded as a result of the careless use of antibiotics in the medical field, the food industry, agriculture, and other industries. By means of genetic recombination between commensal and pathogenic bacteria, the microbes obtain antibiotic resistance genes (ARGs). In bacteria, horizontal gene transfer (HGT) is the main mechanism for acquiring ARGs. With the development of high-throughput sequencing, ARG sequence analysis is now feasible and widely available. Preventing the spread of AMR in the environment requires the implementation of ARGs mapping. The metagenomic technique, in particular, has helped in identifying antibiotic resistance within microbial communities. Due to the exponential growth of experimental and clinical data, significant investments in computer capacity, and advancements in algorithmic techniques, the application of machine learning (ML) algorithms to the problem of AMR has attracted increasing attention over the past five years. The review article sheds a light on the application of bioinformatics for the antibiotic resistance monitoring. The most advanced tool currently being employed to catalog the resistome of various habitats are metagenomics and metatranscriptomics. The future lies in the hands of artificial intelligence (AI) and machine learning (ML) methods, to predict and optimize the interaction of antibiotic-resistant compounds with target proteins.},
}

@article {pmid39551215,
year = {2024},
author = {Bierge, P and Sánchez-Osuna, M and Duarte, B and Gómez-Sánchez, I and Espasa, M and Freitas, AR and Peixe, L and Gasch, O and Pich, OQ and Novais, C},
title = {Diverse genomic and epidemiological landscapes of redundant pbp5 genes in Enterococcus spp.: Insights into plasmid mobilization, ampicillin susceptibility, and environmental interactions.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {177562},
doi = {10.1016/j.scitotenv.2024.177562},
pmid = {39551215},
issn = {1879-1026},
abstract = {Genetic redundancy in bacteria plays a crucial role in enhancing adaptability and accelerating evolution in response to selective pressures, particularly those associated with rapid environmental changes. Aminopenicillins like ampicillin are important therapeutic options for Enterococcus infections in both humans and animals, with resistance mostly associated with pbp5 gene mutations or overexpression. While the occurrence of redundant pbp5 genes has been occasionally reported, the advantages for the host bacteria have not been explored in detail. During a whole-genome sequencing project of Enterococcus faecium from bacteremic patients, we identified an ST592 strain (Efm57) with redundant pbp5 genes. This presented an opportunity to investigate the prevalence and implications of multiple pbp5 acquisitions in diverse Enterococcus species across various sources, geographical regions, and timeframes. The analysis of 618 complete Enterococcus genomes from public databases revealed that 3.2 % harbored redundant pbp5 genes, located on chromosomes or plasmids across different species from diverse epidemiological backgrounds. The proteins encoded by these genes showed homologies ranging from 51.1 % to 97.5 % compared to native copies. Phylogenetic analysis grouped redundant PBP5 amino acid sequences into three distinct clades, with insertion sequences (mostly IS6-like) facilitating their recent spread to diverse plasmids with varying genetic backbones. The presence of multiple antibiotic resistance genes on pbp5-plasmids, including those conferring resistance to linezolid, underscores their involvement in co-selection and recombination events with other clinically-relevant antibiotics. Conjugation experiments confirmed the transferability of a specific 24 kb pbp5-plasmid from the Efm57 strain. This plasmid was associated with higher minimum inhibitory concentrations of ampicillin and conferred bacteria growth advantages at 22 °C. In conclusion, the widespread distribution of redundant pbp5 genes among Enterococcus spp. highlights the complex interplay between genetic mobility, environmental factors, and multidrug resistance in overlapping ecosystems emphasizing the importance of understanding these dynamics to mitigate antibiotic resistance spread within the One Health framework.},
}

@article {pmid39550371,
year = {2024},
author = {Yang, JX and Peng, Y and Yu, QY and Yang, JJ and Zhang, YH and Zhang, HY and Adams, CA and Willing, CE and Wang, C and Li, QS and Han, XG and Gao, C},
title = {Gene horizontal transfers and functional diversity negatively correlated with bacterial taxonomic diversity along a nitrogen gradient.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {128},
pmid = {39550371},
issn = {2055-5008},
mesh = {*Gene Transfer, Horizontal ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Nitrogen/metabolism ; *Phylogeny ; *Biodiversity ; Metagenome ; DNA, Bacterial/genetics ; Soil Microbiology ; },
abstract = {Horizontal gene transfer (HGT) mediated diversification is a critical force driving evolutionary and ecological processes. However, how HGT might relate to anthropogenic activity such as nitrogen addition, and its subsequent effect on functional diversity and cooccurrence networks remain unknown. Here we approach this knowledge gap by blending bacterial 16S rRNA gene amplicon and shotgun metagenomes from a platform of cessation of nitrogen additions and continuous nitrogen additions. We found that bacterial HGT events, functional genes, and virus diversities increased whereas bacterial taxonomic diversity decreased by nitrogen additions, resulting in a counterintuitive strong negative association between bacterial taxonomic and functional diversities. Nitrogen additions, especially the ceased one, complexified the cooccurrence network by increasing the contribution of vitamin B12 auxotrophic Acidobacteria, indicating cross-feeding. These findings advance our perceptions of the causes and consequences of the diversification process in community ecology.},
}

*Gene Transfer, Horizontal
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
*Nitrogen/metabolism
*Phylogeny
*Biodiversity
Metagenome
DNA, Bacterial/genetics
Soil Microbiology

@article {pmid39549700,
year = {2024},
author = {Siozios, S and Nadal-Jimenez, P and Azagi, T and Sprong, H and Frost, CL and Parratt, SR and Taylor, G and Brettell, L and Liew, KC and Croft, L and King, KC and Brockhurst, MA and Hypša, V and Novakova, E and Darby, AC and Hurst, GDD},
title = {Genome dynamics across the evolutionary transition to endosymbiosis.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.10.044},
pmid = {39549700},
issn = {1879-0445},
abstract = {Endosymbiosis-where a microbe lives and replicates within a host-is an important contributor to organismal function that has accelerated evolutionary innovations and catalyzed the evolution of complex life. The evolutionary processes associated with transitions to endosymbiosis, however, are poorly understood. Here, we leverage the wide diversity of host-associated lifestyles of the genus Arsenophonus to reveal the complex evolutionary processes that occur during the transition to a vertically transmitted endosymbiotic lifestyle from strains maintained solely by horizontal (infectious) transmission. We compared the genomes of 38 strains spanning diverse lifestyles from horizontally transmitted pathogens to obligate interdependent endosymbionts. Among culturable strains, we observed those with vertical transmission had larger genome sizes than closely related horizontally transmitting counterparts, consistent with evolutionary innovation and the rapid gain of new functions. Increased genome size was a consequence of prophage and plasmid acquisition, including a cargo of type III effectors, alongside the concomitant loss of CRISPR-Cas genome defense systems, enabling mobile genetic element expansion. Persistent endosymbiosis was also associated with loss of type VI secretion, which we hypothesize to be a consequence of reduced microbe-microbe competition. Thereafter, the transition to endosymbiosis with strict vertical inheritance was associated with the expected relaxation of purifying selection, gene pseudogenization, metabolic degradation, and genome reduction. We argue that reduced phage predation in endosymbiotic niches drives the loss of genome defense systems driving rapid genome expansion upon the adoption of endosymbiosis and vertical transmission. This remodeling enables rapid horizontal gene transfer-mediated evolutionary innovation and precedes the reductive evolution traditionally associated with adaptation to endosymbiosis.},
}

@article {pmid39366703,
year = {2024},
author = {Gomez-Simmonds, A and Annavajhala, MK and Seeram, D and Hokunson, TW and Park, H and Uhlemann, AC},
title = {Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of bla KPC.},
journal = {Genome research},
volume = {34},
number = {11},
pages = {1895-1907},
doi = {10.1101/gr.279355.124},
pmid = {39366703},
issn = {1549-5469},
support = {K23 AI137316/AI/NIAID NIH HHS/United States ; R01 AI175414/AI/NIAID NIH HHS/United States ; },
mesh = {*Plasmids/genetics ; *beta-Lactamases/genetics ; Humans ; *Gene Transfer, Horizontal ; *Bacterial Proteins/genetics ; *Carbapenems/pharmacology ; New York City/epidemiology ; Carbapenem-Resistant Enterobacteriaceae/genetics ; Enterobacteriaceae Infections/microbiology/epidemiology/transmission ; Klebsiella pneumoniae/genetics/drug effects ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Molecular Epidemiology ; Multilocus Sequence Typing ; },
abstract = {Transmission of carbapenem-resistant Enterobacterales (CRE) in hospitals has been shown to occur through complex, multifarious networks driven by both clonal spread and horizontal transfer mediated by plasmids and other mobile genetic elements. We performed nanopore long-read sequencing on CRE isolates from a large urban hospital system to determine the overall contribution of plasmids to CRE transmission and identify specific plasmids implicated in the spread of bla KPC (the Klebsiella pneumoniae carbapenemase [KPC] gene). Six hundred and five CRE isolates collected between 2009 and 2018 first underwent Illumina sequencing for genome-wide genotyping; 435 bla KPC-positive isolates were then successfully nanopore sequenced to generate hybrid assemblies including circularized bla KPC-harboring plasmids. Phylogenetic analysis and Mash clustering were used to define putative clonal and plasmid transmission clusters, respectively. Overall, CRE isolates belonged to 96 multilocus sequence types (STs) encoding bla KPC on 447 plasmids which formed 54 plasmid clusters. We found evidence for clonal transmission in 66% of CRE isolates, over half of which belonged to four clades comprising K. pneumoniae ST258. Plasmid-mediated acquisition of bla KPC occurred in 23%-27% of isolates. While most plasmid clusters were small, several plasmids were identified in multiple different species and STs, including a highly promiscuous IncN plasmid and an IncF plasmid putatively spreading bla KPC from ST258 to other clones. Overall, this points to both the continued dominance of K. pneumoniae ST258 and the dissemination of bla KPC across clones and species by diverse plasmid backbones. These findings support integrating long-read sequencing into genomic surveillance approaches to detect the hitherto silent spread of carbapenem resistance driven by mobile plasmids.},
}

*Plasmids/genetics
*beta-Lactamases/genetics
Humans
*Gene Transfer, Horizontal
*Bacterial Proteins/genetics
*Carbapenems/pharmacology
New York City/epidemiology
Carbapenem-Resistant Enterobacteriaceae/genetics
Enterobacteriaceae Infections/microbiology/epidemiology/transmission
Klebsiella pneumoniae/genetics/drug effects
Phylogeny
Anti-Bacterial Agents/pharmacology
Molecular Epidemiology
Multilocus Sequence Typing

@article {pmid39141706,
year = {2024},
author = {Souque, C and González Ojeda, I and Baym, M},
title = {From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance.},
journal = {Annual review of microbiology},
volume = {78},
number = {1},
pages = {361-382},
doi = {10.1146/annurev-micro-041522-102707},
pmid = {39141706},
issn = {1545-3251},
support = {T32 GM008313/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; *Evolution, Molecular ; *Drug Resistance, Bacterial/genetics ; Bacterial Infections/microbiology/drug therapy ; },
abstract = {Tackling the challenge created by antibiotic resistance requires understanding the mechanisms behind its evolution. Like any evolutionary process, the evolution of antimicrobial resistance (AMR) is driven by the underlying variation in a bacterial population and the selective pressures acting upon it. Importantly, both selection and variation will depend on the scale at which resistance evolution is considered (from evolution within a single patient to the host population level). While laboratory experiments have generated fundamental insights into the mechanisms underlying antibiotic resistance evolution, the technological advances in whole genome sequencing now allow us to probe antibiotic resistance evolution beyond the lab and directly record it in individual patients and host populations. Here we review the evolutionary forces driving antibiotic resistance at each of these scales, highlight gaps in our current understanding of AMR evolution, and discuss future steps toward evolution-guided interventions.},
}

Humans
*Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects
*Evolution, Molecular
*Drug Resistance, Bacterial/genetics
Bacterial Infections/microbiology/drug therapy

@article {pmid39545400,
year = {2024},
author = {Stern, DB and Raborn, RT and Lovett, SP and Boise, NR and Carasquilla, L and Enke, S and Radune, D and Woodruff, DL and Wahl, K and Rosovitz, MJ},
title = {Novel toxin biosynthetic gene cluster in harmful algal bloom-causing Heteroscytonema crispum: Insights into the origins of paralytic shellfish toxins.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae248},
pmid = {39545400},
issn = {1759-6653},
abstract = {Caused by both eukaryotic dinoflagellates and prokaryotic cyanobacteria, harmful algal blooms (HABs) are events of severe ecological, economic, and public health consequence, and their incidence has become more common of late. Despite coordinated research efforts to identify and characterize the genomes of HAB-causing organisms, the genomic basis and evolutionary origins of paralytic shellfish toxins (PSTs) produced by HABs remain at best incomplete. The PST saxitoxin has an especially complex genomic architecture and enigmatic phylogenetic distribution, spanning dinoflagellates and multiple cyanobacterial genera. Using filtration and extraction techniques to target the desired cyanobacteria from non-axenic culture, coupled with a combination of short and long read sequencing, we generated a reference-quality hybrid genome assembly for Heteroscytonema crispum UTEX LB 1556, a freshwater, PST-producing cyanobacterium thought to have the largest known genome in its phylum. We report a complete, novel biosynthetic gene cluster for the PST saxitoxin. Leveraging this biosynthetic gene cluster, we find support for the hypothesis that PST production has appeared in divergent Cyanobacteria lineages through widespread and repeated horizontal gene transfer. This work demonstrates the utility of long-read sequencing and metagenomic assembly toward advancing our understanding of PST biosynthetic gene cluster diversity and suggests a mechanism for the origin of PST biosynthetic genes.},
}

@article {pmid39542384,
year = {2024},
author = {Wang, J and Wu, Y and Zhu, L and Guo, K and Gao, S and Dong, Y},
title = {Genomic evolution and patterns of horizontal gene transfer in Papilio.},
journal = {Genomics},
volume = {116},
number = {6},
pages = {110956},
doi = {10.1016/j.ygeno.2024.110956},
pmid = {39542384},
issn = {1089-8646},
abstract = {The Papilio genus, known for its ecological and phenotypic diversity, is a valuable model for evolutionary studies. This study conducted a comparative genomic analysis of 11 Papilio species, revealing species-specific gene family expansions, including the UDP-glucosyltransferase 2 gene associated with insect detoxification, particularly expanding in Papilio polyxenes. Our analysis also revealed 199 horizontal gene transfer (HGT) acquired genes from 76 microbial species, with Pseudomonadota and Bacillota as common HGT donors across these genomes. Furthermore, we examined the evolutionary patterns of nine ABC transporter subfamilies, uncovering potential links between gene family evolution and environmental adaptation. This study provides new insights into evolutionary relationships and genomic adaptations within the Papilio genus, contributing to broader butterfly evolutionary research.},
}

@article {pmid39542270,
year = {2024},
author = {Yuan, S and Jin, G and Cui, R and Wang, X and Wang, M and Chen, Z},
title = {Transmission and control strategies of antimicrobial resistance from the environment to the clinic: A holistic review.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177461},
doi = {10.1016/j.scitotenv.2024.177461},
pmid = {39542270},
issn = {1879-1026},
abstract = {The environment serves as a significant reservoir of antimicrobial resistance (AMR) microbes and genes and is increasingly recognized as key source of clinical AMR. Modern human activities impose an additional burden on environmental AMR, promoting its transmission to clinical setting and posing a serious threat to human health and welfare. Therefore, a comprehensive review of AMR transmission from the environment to the clinic, along with proposed effective control strategies, is crucial. This review systematically summarized current research on the transmission of environmental AMR to clinical settings. Furthermore, the transmission pathways, horizontal gene transfer (HGT) mechanisms, as well as the influential drivers including triple planetary crisis that may facilitate AMR transfer from environmental species to clinical pathogens are highlighted. In response to the growing trend of AMR transmission, we propose insightful mitigation strategies under the One Health framework, integrating advanced surveillance and tracking technologies, interdisciplinary knowledge, multisectoral interventions, alongside multiple antimicrobial use and stewardship approaches to tacking development and spread of AMR.},
}

@article {pmid39541852,
year = {2024},
author = {Wang, Q and Wang, M and Yang, Q and Feng, L and Zhang, H and Wang, R and Wang, R},
title = {The role of bacteriophages in facilitating the horizontal transfer of antibiotic resistance genes in municipal wastewater treatment plants.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122776},
doi = {10.1016/j.watres.2024.122776},
pmid = {39541852},
issn = {1879-2448},
abstract = {Bacteriophages play integral roles in the ecosystem; however, their precise involvement in horizontal gene transfer and the spread of antibiotic resistance genes (ARGs) are not fully understood. In this study, a coculture system involving consortia of bacteriophages and multidrug-resistant bacteria from an aerobic tank in a municipal wastewater treatment plant (WWTP) was established to investigate the functions of bacteriophages in ARG transfer and spread. The results of the cocultivation of the MRB and bacteriophage consortia indicated that the bacterial community remained stable throughout the whole process, but the addition of bacteriophages significantly increased ARG abundance, especially in bacteriophage DNA. Nine out of the 11 identified ARGs significantly increased, indicating that more bacteriophage particles carried ARGs in the system after cocultivation. In addition, 686 plasmids were detected during cocultivation, of which only 3.36 % were identified as conjugative plasmids, which is significantly lower than the proportion found among previously published plasmids (25.2 %, totaling 14,029 plasmids). Our findings revealed that bacteriophages may play important roles in the horizontal transfer of ARGs through both bacteriophage-mediated conduction and an increase in extracellular ARGs; however, conjugative transfer may not be the main mechanism by which multidrug-resistant bacteria acquire and spread ARGs. Unlike in most previous reports, a coculture system of diverse bacteria and bacteriophages was established in this study to assess bacteriophage functions in ARG transfer and dissemination in the environment, overcoming the limitations associated with the isolation of bacteria and bacteriophages, as well as the specificity of bacteriophage hosts.},
}

@article {pmid39541851,
year = {2024},
author = {Wang, F and Huang, W and Chen, J and Luo, Y and Cao, J and Fang, F and Liu, X and Wu, Y and Luo, J},
title = {Non-antibiotic disinfectant synchronously interferes methane production and antibiotic resistance genes propagation during sludge anaerobic digestion: Activation of microbial adaptation and reconfiguration of bacteria-archaea synergies.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122773},
doi = {10.1016/j.watres.2024.122773},
pmid = {39541851},
issn = {1879-2448},
abstract = {Waste activated sludge (WAS) presents both resource recovery potential and pollution risks, making its efficient treatment challenging. Anaerobic digestion is broadly recognized as a green and sustainable approach to WAS treatment, whose efficiency is easily impacted by the exogeneous pollutants in WAS. However, the impact of polyhexamethylene guanidine (PHMG), as a widely-used non-antibiotic disinfectant, on WAS digestion under semi-continuous flow conditions remains unclear. In this study, CH4 production decreased from 16.1 mL/g volatile suspended solids (VSS) in the control to 13.2 mL/g VSS and 0.3 mL/g VSS under low and high PHMG exposure, respectively, while PHMG increased the number of antibiotic resistance gene (ARG) copies per bacterium by 4.6-12.7 %. Molecular docking analysis revealed that PHMG could spontaneously bind to and disintegrate WAS (binding energy:2.35 and -9.62 kcal/mol), increasing the likelihood of microbial exposure to PHMG. This led to an increase in bacterial abundance and a reduction in archaeal populations, resulting in bacterial dominance in ecological niches. The network topology index in PHMG-treated reactors was consistently lower than in the control, with a higher proportion of negatively correlated links, indicating a more antagonistic relationship between bacteria and archaea. Consequently, PHMG significantly interfered with key genes involved in CH4 biosynthesis (e.g., mch and mtd). Interestingly, methanogenic activity and archaeal chemotaxis (e.g., rfk and cheA) partially recovered under low PHMG exposure due to archaeal adaptation through quorum sensing and two-component systems. However, this adaptation process also contributed to the propagation of ARGs through horizontal gene transfer, facilitated by the enhancement of mobile genetic elements and ARGs hosts. These findings confirm the ecological risks of PHMG and highlight the need for effective WAS disposal strategies.},
}

@article {pmid39306135,
year = {2024},
author = {Wang, B and Farhan, MHR and Yuan, L and Sui, Y and Chu, J and Yang, X and Li, Y and Huang, L and Cheng, G},
title = {Transfer dynamics of antimicrobial resistance among gram-negative bacteria.},
journal = {The Science of the total environment},
volume = {954},
number = {},
pages = {176347},
doi = {10.1016/j.scitotenv.2024.176347},
pmid = {39306135},
issn = {1879-1026},
mesh = {*Gram-Negative Bacteria/drug effects ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Bacteriophages/physiology ; Plasmids/genetics ; },
abstract = {Antimicrobial resistance (AMR) in gram-negative bacteria (GNBs) is a significant global health concern, exacerbated by mobile genetic elements (MGEs). This review examines the transfer of antibiotic resistance genes (ARGs) within and between different species of GNB facilitated by MGEs, focusing on the roles of plasmids and phages. The impact of non-antibiotic chemicals, environmental factors affecting ARG transfer frequency, and underlying molecular mechanisms of bacterial resistance evolution are also discussed. Additionally, the study critically assesses the impact of fitness costs and compensatory evolution driven by MGEs in host organisms, shedding light on the transfer frequency of ARGs and host evolution within ecosystems. Overall, this comprehensive review highlights the factors and mechanisms influencing ARG movement among diverse GNB species and underscores the importance of implementing holistic One-Health strategies to effectively address the escalating public health challenges associated with AMR.},
}

*Gram-Negative Bacteria/drug effects
*Drug Resistance, Bacterial/genetics
*Anti-Bacterial Agents/pharmacology
Gene Transfer, Horizontal
Interspersed Repetitive Sequences
Bacteriophages/physiology
Plasmids/genetics

@article {pmid39540883,
year = {2024},
author = {Garcia, LE and Sanchez-Puerta, MV},
title = {Mitochondrial Splicing Efficiency Is Lower in Holoparasites Than in Free-Living Plants.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcae120},
pmid = {39540883},
issn = {1471-9053},
abstract = {Mitochondria play a crucial role in eukaryotic organisms, housing their own genome with genes vital for oxidative phosphorylation. Coordination between nuclear and mitochondrial genomes is pivotal for organelle gene expression. Splicing, editing and processing of mitochondrial transcripts are regulated by nuclear-encoded factors. Splicing efficiency (SEf) of the many group II introns present in plant mitochondrial genes is critical for mitochondrial function since a splicing defect or splicing deficiency can severely impact plant growth and development. This study investigates SEf in free-living and holoparasitic plants, focusing on 25 group II introns from 15 angiosperm species. Our comparative analyses reveal distinctive splicing patterns with holoparasites exhibiting significantly lower SEf, potentially linked to their unique evolutionary trajectory. Given the preponderance of horizontal gene transfer (HGT) in parasitic plants, we investigated the effect of HGT on SEf, such as the presence of foreign introns or foreign nuclear-encoded splicing factors. Contrary to expectations, the SEf reductions do not correlate with HGT events, suggesting that other factors are at play, such as the loss of photosynthesis or the transition to a holoparasitic lifestyle. The findings of this study broaden our understanding of the molecular evolution in parasitic plants and shed light on the multifaceted factors influencing organelle gene expression.},
}

@article {pmid39535289,
year = {2024},
author = {Vanhout, Z and Abdellati, S and Gestels, Z and De Baetselier, I and de Block, T and Vanbaelen, T and Manoharan-Basil, SS and Kenyon, C},
title = {Macrolide resistance is pervasive in oral streptococci in the Belgian general population: a cross-sectional survey.},
journal = {Journal of medical microbiology},
volume = {73},
number = {11},
pages = {},
doi = {10.1099/jmm.0.001932},
pmid = {39535289},
issn = {1473-5644},
mesh = {Humans ; Belgium/epidemiology ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; Child ; Cross-Sectional Studies ; *Macrolides/pharmacology ; *Drug Resistance, Bacterial ; Female ; Adult ; Male ; *Streptococcal Infections/microbiology/epidemiology ; Child, Preschool ; *Streptococcus/drug effects/genetics/isolation & purification ; Mouth/microbiology ; Azithromycin/pharmacology ; Middle Aged ; Adolescent ; Young Adult ; Parents ; Prevalence ; Infant ; },
abstract = {Background. Commensal streptococci are common inhabitants of the oral microbiome and regulate its structure and function in beneficial ways for human health. They can, however, also be opportunistic pathogens and act as a reservoir of resistance genes that can be passed on to other bacteria, including pathogens. Little is known about the prevalence of these commensals in parents and their children and their antimicrobial susceptibilities in the Belgian general population.Gap Statement. The macrolide susceptibility of commensal oral Streptococci in Belgium is unknown.Methods. We assessed the prevalence and azithromycin susceptibility of commensal streptococcal species in the parents (n=38) and children (n=50) of 35 families in Belgium.Results. The most frequently detected taxonomic grouping was Streptococcus mitis/oralis, which was detected in 78/181 (43.1%) of the children's isolates and 66/128 (51.6%) of the parents' isolates. Of the 311 isolates collected in this study, 282 isolates (90.7%) had an azithromycin MIC value greater than the breakpoint of 0.25 mg l[-1] and 146 isolates (46.9%) had azithromycin MICs greater than 2 mg l[-1]. There was no difference in the azithromycin MIC distribution of all streptococcal isolates between children and parents. All individuals were colonized by streptococci with azithromycin MICs greater than 0.25 mg l[-1], and 87.5% of individuals had streptococci with MICs greater than 2 mg l[-1].Interpretation. The most prevalent species identified in both age groups was S. mitis/oralis. All individuals harboured streptococci with macrolide resistance. This highlights the need for additional antimicrobial stewardship initiatives to reduce the consumption of macrolides in the general population.},
}

Humans
Belgium/epidemiology
*Anti-Bacterial Agents/pharmacology
*Microbial Sensitivity Tests
Child
Cross-Sectional Studies
*Macrolides/pharmacology
*Drug Resistance, Bacterial
Female
Adult
Male
*Streptococcal Infections/microbiology/epidemiology
Child, Preschool
*Streptococcus/drug effects/genetics/isolation & purification
Mouth/microbiology
Azithromycin/pharmacology
Middle Aged
Adolescent
Young Adult
Parents
Prevalence
Infant

@article {pmid39527185,
year = {2024},
author = {Kim, K and Islam, MM and Bang, S and Kim, J and Lee, CY and Lee, JC and Shin, M},
title = {H-NS is a Transcriptional Repressor of the CRISPR-Cas System in Acinetobacter baumannii ATCC 19606.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {39527185},
issn = {1976-3794},
support = {2022R1A2C2010683//Ministry of Science and ICT, South Korea/ ; },
abstract = {Acinetobacter baumannii is a multidrug-resistant opportunistic pathogen primarily associated with hospital-acquired infections. The bacterium can gain multidrug resistance through several mechanisms, including horizontal gene transfer. A CRISPR-Cas system including several Cas genes could restrict the horizontal gene transfer. However, the molecular mechanism of CRISPR- Cas transcriptional regulation remains unclear. We identified a type I-F CRISPR-Cas system in A. baumannii ATCC 19606[T] standard strain based on sequence analysis. We focused on the transcriptional regulation of Cas3, a key protein of the CRISPR-Cas system. We performed a DNA affinity chromatography-pulldown assay to identify transcriptional regulators of the Cas3 promoter. We identified several putative transcriptional factors, such as H-NS, integration host factor, and HU, that can bind to the promoter region of Cas3. We characterized AbH-NS using size exclusion chromatography and cross-linking experiments and demonstrated that the Cas3 promoter can be regulated by AbH-NS in a concentration-dependent manner via an in vitro transcription assay. CRISPR-Cas expression levels in wild-type and hns mutant strains in the early stationary phase were examined by qPCR and β-galactosidase assay. We found that H-NS can act as a repressor of Cas3. Our transformation efficiency results indicated that the hns mutation decreased the transformation efficiency, while the Cas3 mutation increased it. We report the existence and characterization of the CRISPR-Cas system in A. baumannii 19606[T] and demonstrate that AbH-NS is a transcriptional repressor of CRISPR-Cas-related genes in A. baumannii.},
}

@article {pmid39526401,
year = {2024},
author = {Jiang, Y and Wang, Y and Che, L and Yang, S and Zhang, X and Lin, Y and Shi, Y and Zou, N and Wang, S and Zhang, Y and Zhao, Z and Li, SC},
title = {GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae1007},
pmid = {39526401},
issn = {1362-4962},
support = {20220814183301001//Shenzhen Science and Technology Program/ ; },
abstract = {Metagenomic studies have revealed the critical roles of complex microbial interactions, including horizontal gene transfer (HGT) and functional redundancy (FR), in shaping the gut microbiome's functional capacity and resilience. However, the lack of comprehensive data integration and systematic analysis approaches has limited the in-depth exploration of HGT and FR dynamics across large-scale gut microbiome datasets. To address this gap, we present GutMetaNet (https://gutmetanet.deepomics.org/), a first-of-its-kind database integrating extensive human gut microbiome data with comprehensive HGT and FR analyses. GutMetaNet contains 21 567 human gut metagenome samples with whole-genome shotgun sequencing data related to various health conditions. Through systematic analysis, we have characterized the taxonomic profiles and FR profiles, and identified 14 636 HGT events using a shared reference genome database across the collected samples. These HGT events have been curated into 8049 clusters, which are annotated with categorized mobile genetic elements, including transposons, prophages, integrative mobilizable elements, genomic islands, integrative conjugative elements and group II introns. Additionally, GutMetaNet incorporates automated analyses and visualizations for the HGT events and FR, serving as an efficient platform for in-depth exploration of the interactions among gut microbiome taxa and their implications for human health.},
}

@article {pmid39521804,
year = {2024},
author = {Jerlström-Hultqvist, J and Gallot-Lavallée, L and Salas-Leiva, DE and Curtis, BA and Záhonová, K and Čepička, I and Stairs, CW and Pipaliya, S and Dacks, JB and Archibald, JM and Roger, AJ},
title = {A unique symbiosome in an anaerobic single-celled eukaryote.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9726},
pmid = {39521804},
issn = {2041-1723},
support = {12188//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 5782//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 12188//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 12188//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; RES0043758//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; RES0046091//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; FRN-142349//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; },
mesh = {*Symbiosis ; Anaerobiosis ; In Situ Hybridization, Fluorescence ; Eukaryota/genetics/metabolism ; Phylogeny ; Gene Transfer, Horizontal ; Microscopy, Electron, Scanning ; },
abstract = {Symbiotic relationships between eukaryotes and prokaryotes played pivotal roles in the evolution of life and drove the emergence of specialized symbiotic structures in animals, plants and fungi. The host-evolved symbiotic structures of microbial eukaryotes - the vast majority of such hosts in nature - remain largely unstudied. Here we describe highly structured symbiosomes within three free-living anaerobic protists (Anaeramoeba spp.). We dissect this symbiosis using complete genome sequencing and transcriptomics of host and symbiont cells coupled with fluorescence in situ hybridization, and 3D reconstruction using focused-ion-beam scanning electron microscopy. The emergence of the symbiosome is underpinned by expansion of gene families encoding regulators of membrane trafficking and phagosomal maturation and extensive bacteria-to-eukaryote lateral transfer. The symbionts reside deep within a symbiosomal membrane network that enables metabolic syntrophy by precisely positioning sulfate-reducing bacteria alongside host hydrogenosomes. Importantly, the symbionts maintain connections to the Anaeramoeba plasma membrane, blurring traditional boundaries between ecto- and endosymbiosis.},
}

*Symbiosis
Anaerobiosis
In Situ Hybridization, Fluorescence
Eukaryota/genetics/metabolism
Phylogeny
Gene Transfer, Horizontal
Microscopy, Electron, Scanning

@article {pmid39518977,
year = {2024},
author = {Traglia, GM and Pasteran, F and Moheb, S and Akhtar, U and Gonzalez, S and Maldonado, C and Furtado, N and Mohamed, A and Escalante, J and Tuttobene, MR and Quillen, A and Fontan, C and Albornoz, E and Corso, A and Bonomo, RA and Rao, GG and Tolmasky, ME and Ramirez, MS},
title = {Insights into Acinetobacter baumannii AMA205's Unprecedented Antibiotic Resistance.},
journal = {International journal of molecular sciences},
volume = {25},
number = {21},
pages = {},
pmid = {39518977},
issn = {1422-0067},
support = {SC3GM125556 to MSR, R01AI100560, R01AI063517, R01AI072219 to RAB, and 2R15 AI047115 to MET/GF/NIH HHS/United States ; },
mesh = {*Acinetobacter baumannii/genetics/drug effects ; Humans ; *beta-Lactamases/genetics/metabolism ; *Acinetobacter Infections/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology ; COVID-19/virology ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; SARS-CoV-2/drug effects/genetics ; Genome, Bacterial ; Argentina ; Virulence Factors/genetics ; },
abstract = {The rise of antibiotic-resistant bacteria in clinical settings has become a significant global concern. Among these bacteria, Acinetobacter baumannii stands out due to its remarkable ability to acquire resistance genes and persist in hospital environments, leading to some of the most challenging infections. Horizontal gene transfer (HGT) plays a crucial role in the evolution of this pathogen. The A. baumannii AMA205 strain, belonging to sequence type ST79, was isolated from a COVID-19 patient in Argentina in 2021. This strain's antimicrobial resistance profile is notable as it harbors multiple resistance genes, some of which had not been previously described in this species. The AmpC family β-lactamase blaCMY-6, commonly found in Enterobacterales, had never been detected in A. baumannii before. Furthermore, this is the first ST79 strain known to carry the carbapenemase blaNDM-1 gene. Other acquired resistance genes include the carbapenemase blaOXA-23, further complicating treatment. Susceptibility testing revealed high resistance to most antibiotic families, including cefiderocol, with significant contributions from blaCMY-6 and blaNDM-1 genes to the cephalosporin and carbapenem resistance profiles. The A. baumannii AMA205 genome also contains genetic traits coding for 111 potential virulence factors, such as the iron-uptake system and biofilm-associated proteins. This study underscores A. baumannii's ability to acquire multiple resistance genes and highlights the need for alternative therapies and effective antimicrobial stewardship to control the spread of these highly resistant strains.},
}

*Acinetobacter baumannii/genetics/drug effects
Humans
*beta-Lactamases/genetics/metabolism
*Acinetobacter Infections/microbiology/drug therapy
*Anti-Bacterial Agents/pharmacology
COVID-19/virology
Bacterial Proteins/genetics/metabolism
Drug Resistance, Multiple, Bacterial/genetics
Microbial Sensitivity Tests
Gene Transfer, Horizontal
SARS-CoV-2/drug effects/genetics
Genome, Bacterial
Argentina
Virulence Factors/genetics

@article {pmid39511299,
year = {2024},
author = {Hu, Y and Duan, G and Yan, H and Guo, Y and Chang, J and Zhou, M and Yan, S and Li, W and Ruan, C and Gao, S},
title = {Discovery of the first Tn630 member and the closest homolog of IS630 from viruses.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {27081},
pmid = {39511299},
issn = {2045-2322},
support = {2024-KF-03//the Open Project of Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources/ ; },
mesh = {*DNA Transposable Elements/genetics ; Phylogeny ; Viruses/genetics ; Bacteria/genetics/virology ; Animals ; Host Specificity/genetics ; },
abstract = {IS630/Tc1/mariner (ITm) represents the most widely distributed superfamily of DNA transposons in nature. Currently, bioinformatics research on ITm members primarily involves collecting data of existing and emerging members and organizing them into new groups or families. In the present study, our survey revealed that Tc1 and IS630 members have a broad host range, spanning across all six biological kingdoms (bacteria, fungi, plantae, animalia, archaea and protista) and viruses. The primary discoveries include the first Tn630 member-Tn630-NC1 and the closest homolog of IS630 from viruses-Tc1-C#1. By incorporating our discoveries into existing knowledge, we proposed a model to elucidate the formation of composite transposons. Organization of Tc1 and IS630 members into groups across biological kingdoms facilitates data collection for future research, particularly on their horizontal transfer between different kingdoms. The formation of composite transposons may result from asymmetric of terminal inverted repeats. IS630 should be merged with Tc1 into a single family IS630/Tc1. Furthermore, IS630 and its homologs constitute a valuable resource for studying horizontal gene transfer between gut bacteria and phages, opening up new avenues for research in this field.},
}

*DNA Transposable Elements/genetics
Phylogeny
Viruses/genetics
Bacteria/genetics/virology
Animals
Host Specificity/genetics

@article {pmid39510298,
year = {2024},
author = {Song, J and Huang, Z and Gao, Y and Wang, W and Guo, G and Duan, Y and Zhou, S and Tang, Z},
title = {Metagenomic insight into the enrichment of antibiotic resistance genes in activated sludge upon exposure to nanoplastics.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {363},
number = {Pt 2},
pages = {125260},
doi = {10.1016/j.envpol.2024.125260},
pmid = {39510298},
issn = {1873-6424},
abstract = {Activated sludge is an important reservoir for the co-occurring emerging contaminants including nanoplastics (NPs) and antibiotic resistance genes (ARGs). However, the impacts and potential mechanisms of NPs on the fate of ARGs in activated sludge are not fully understood. Herein, we used metagenomic approach to investigate the responses of ARGs, host bacteria, mobile genetic elements (MGEs), and functional genes to polystyrene (PS) NPs at environmentally relevant (0.5 mg/L) and high stress concentrations (50 mg/L) in activated sludge. The results showed that 0.5 and 50 mg/L PS NPs increased the relative abundance of ARGs in the activated sludge by 58.68% and 46.52%, respectively (p < 0.05). Host tracking analysis elucidated that the hosts of ARGs were significantly enriched by PS NPs (p < 0.05), with Proteobacteria being the predominant host bacteria. Additionally, the occurrence of new ARGs hosts and the enrichment of MGEs and functional genes (i.e., genes related to SOS response, cell membrane permeability, and secretion system, etc.) indicated that PS NPs promoted horizontal gene transfer (HGT) of ARGs. Finally, path modeling analysis revealed that the proliferation of ARGs caused by PS NPs was primarily attributed to the enhancement of HGT and the enrichment of host bacteria. Our findings contribute to a comprehensive understanding of the spread risk of ARGs in activated sludge under NPs pollution.},
}

@article {pmid39510271,
year = {2024},
author = {Xiong, J and Hu, S and Xu, Z and Li, C and Li, Z and Li, S and Ma, Y and Ren, X and Huang, B and Pan, X},
title = {Different paths, same destination: Bisphenol A and its substitute induce the conjugative transfer of antibiotic resistance genes.},
journal = {Chemosphere},
volume = {368},
number = {},
pages = {143625},
doi = {10.1016/j.chemosphere.2024.143625},
pmid = {39510271},
issn = {1879-1298},
abstract = {Antibiotic resistance genes are primarily spread through horizontal gene transfer in aquatic environments. Bisphenols, which are widely used in industry, are pervasive contaminants in such environments. This study investigated how environmentally relevant concentrations of bisphenol A and its substitute (bisphenol S, Bisphenol AP and Bisphenol AF) affect the spread of antibiotic resistance genes among Escherichia coli. As a result, bisphenol A and its three substitutes were found to promote the RP4 plasmid-mediated conjugative transfer of antibiotic resistance genes with different promotive efficiency. Particularly, bisphenol A and bisphenol S were found to induce more than double the incidence of conjugation at 0.1 nmol/L concentration. They therefore were selected as model compounds to investigate the involved mechanisms. Surprisingly, both slightly inhibited bacterial activity, but there was no significant increase in cell death. Bisphenols exposure changed the polymeric substances excreted by the bacteria, increased the permeability of their cell membranes, induced the secretion of antioxidant enzymes and generated reactive oxygen species. They also affected the expression of genes related to conjugative transfer by upregulating replication and DNA transfer genes and downregulating global regulatory genes. It should be noted that gene expression levels were higher in the BPS-exposed group than in the BPA-exposed group. The synthesis of bacterial metabolites and functional components was also significantly affected by bisphenols exposure. This research has helped to clarify the potential health risks of bisphenol contamination of aquatic environments.},
}

@article {pmid39508585,
year = {2024},
author = {Androsiuk, L and Maane, S and Tal, S},
title = {CRISPR spacers acquired from plasmids primarily target backbone genes, making them valuable for predicting potential hosts and host range.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0010424},
doi = {10.1128/spectrum.00104-24},
pmid = {39508585},
issn = {2165-0497},
abstract = {In recent years, there has been a surge in metagenomic studies focused on identifying plasmids in environmental samples. Although these studies have unearthed numerous novel plasmids, enriching our understanding of their environmental roles, a significant gap remains: the scarcity of information regarding the bacterial hosts of these newly discovered plasmids. Furthermore, even when plasmids are identified within bacterial isolates, the reported host is typically limited to the original isolate, with no insights into alternative hosts or the plasmid's potential host range. Given that plasmids depend on hosts for their existence, investigating plasmids without the knowledge of potential hosts offers only a partial perspective. This study introduces a method for identifying potential hosts and host ranges for plasmids through alignment with CRISPR spacers. To validate the method, we compared the PLSDB plasmids database with the CRISPR spacers database, yielding host predictions for 46% of the plasmids. When compared with reported hosts, our predictions achieved 84% concordance at the family level and 99% concordance at the phylum level. Moreover, the method frequently identified multiple potential hosts for a plasmid, thereby enabling predictions of alternative hosts and the host range. Notably, we found that CRISPR spacers predominantly target plasmid backbone genes while sparing functional genes, such as those linked to antibiotic resistance, aligning with our hypothesis that CRISPR spacers are acquired from plasmid-specific regions rather than insertion elements from diverse sources. Finally, we illustrate the network of connections among different bacterial taxa through plasmids, revealing potential pathways for horizontal gene transfer.IMPORTANCEPlasmids are notorious for their role in distributing antibiotic resistance genes, but they may also carry and distribute other environmentally important genes. Since plasmids are not free-living entities and rely on host bacteria for survival and propagation, predicting their hosts is essential. This study presents a method for predicting potential hosts for plasmids and offers insights into the potential paths for spreading functional genes between different bacteria. Understanding plasmid-host relationships is crucial for comprehending the ecological and clinical impact of plasmids and implications for various biological processes.},
}

@article {pmid39506544,
year = {2024},
author = {Choufa, C and Gascht, P and Leblond, H and Gauthier, A and Vos, M and Bontemps, C and Leblond, P},
title = {Conjugation mediates large-scale chromosomal transfer in Streptomyces driving diversification of antibiotic biosynthetic gene clusters.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msae236},
pmid = {39506544},
issn = {1537-1719},
abstract = {Streptomyces are ubiquitous soil dwelling bacteria with large, linear genomes that are of special importance as a source of metabolites used in human and veterinary medicine, agronomy and industry. Conjugative elements (Actinomycetes Integrative and Conjugative Elements, AICEs) are the main drivers of Streptomyces Horizontal Gene Transfer. AICE transfer has long been known to be accompanied by mobilization of chromosomal DNA. However, the magnitude of DNA transfer, or the localization of acquired DNA across their linear chromosome, has remained undetermined. We here show that conjugative crossings in sympatric strains of Streptomyces result in the large-scale, genome-wide distributed replacement of up to one third of the recipient chromosome, a phenomenon for which we propose the name 'Streptomyces Chromosomal Transfer' (SCT). Such chromosome blending results in the acquisition, loss and hybridization of Specialized Metabolite Biosynthetic Gene Clusters, leading to a novel metabolic arsenal in exconjugant offspring. Harnessing conjugation-mediated SMBGC diversification holds great promise in the discovery of new bioactive compounds including antibiotics.},
}

@article {pmid39504695,
year = {2024},
author = {Liu, M and Su, X and Yuan, J and Yang, X and Chen, Y and Xu, Q and Huang, X and Xu, J and He, Y},
title = {Unravelling the processes involved in biodegradation of chlorinated organic pollutant: From microbial community to isolated organohalide degraders.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122730},
doi = {10.1016/j.watres.2024.122730},
pmid = {39504695},
issn = {1879-2448},
abstract = {Hundreds of studies have demonstrated the bioremediation of chlorinated organic pollutants (COPs) in flooded environments. However, the role of specific functional strains in degrading COPs under complex media such as wetlands is still unclear. Here, we focused on the microbial characteristics of COP-polluted sediments, identified the bacteria responsible for degradation and conducted a genomic analysis of these bacteria. Four strains were obtained and identified as Petrimonas sulfuriphila PET, Robertmurraya sp. CYTO, Hungatella sp. CloS1 and Enterococcus avium PseS3, respectively. They were capable of degrading a typical COP, γ-hexachlorocyclohexane (γ-HCH). The residual γ-HCH concentrations were 58.8 % (PET), 45.6 % (CYTO), 60.2 % (CloS1), and 69.3 % (PseS3) of its initial value, respectively. Strain PET, CYTO and CloS1 could degrade γ-HCH to its dehalogenation product chlorobenzene. Each strain harbors genes annotated to the pathway of halogenated organic matter degradation (e.g. 2-haloacid dehalogenase) and cobalamin biosynthesis, which are involved in the degradation of COPs. Comparative genomic analysis of the four strains and other classical organohalide-respiring bacteria (e.g. Dehalococcoides mccartyi and Sulfurospirillum multivorans DSM 12446) showed that they share orthologous clusters related to the cobalamin biosynthetic process (GO:0009236). VB12 was also detected in the culture systems of the four strains, further highlighting the importance of cobalamin in COPs degradation. In the genome of the four strains, some genes were annotated to the halogenated organic matter degradation and cobalamin biosynthesis pathway within horizontal gene transfer (HGT) regions. This further indicated that microorganisms carrying these genes can adapt faster to pollution stress through HGT. Together, these findings revealed the co-evolution mechanism of functional strains and may provide novel insights into improved bioremediation strategies for COP-polluted complex media based on generalist organochlorine-degrading bacteria.},
}

@article {pmid39503503,
year = {2024},
author = {Werner Lass, S and Smith, BE and Camphire, S and Eutsey, RA and Prentice, JA and Yerneni, SS and Arun, A and Bridges, AA and Rosch, JW and Conway, JF and Campbell, P and Hiller, NL},
title = {Pneumococcal extracellular vesicles mediate horizontal gene transfer via the transformation machinery.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0072724},
doi = {10.1128/msphere.00727-24},
pmid = {39503503},
issn = {2379-5042},
abstract = {Bacterial cells secrete extracellular vesicles (EVs), the function of which is a matter of intense investigation. Here, we show that the EVs secreted by the human pathogen Streptococcus pneumoniae (pneumococcus) are associated with bacterial DNA on their surface and can deliver this DNA to the transformation machinery of competent cells. These findings suggest that EVs contribute to gene transfer in Gram-positive bacteria and, in doing so, may promote the spread of drug resistance genes in the population.IMPORTANCEThis work extends our understanding of horizontal gene transfer and the roles of extracellular vesicles in pneumococcus. This bacterium serves as the model for transformation, a process by which bacteria can take up naked DNA from the environment. Here, we show that extracellular vesicles secreted by the pneumococcus have DNA on their surface and that this DNA can be imported by the transformation machinery, facilitating gene transfer. Understanding EV-mediated gene transfer may provide new avenues to manage the spread of antibiotic drug resistance.},
}

@article {pmid39500921,
year = {2024},
author = {Stewart, RD and Oluwalana-Sanusi, AE and Munzeiwa, WA and Magoswana, L and Chaukura, N},
title = {Profiling the bacterial microbiome diversity and assessing the potential to detect antimicrobial resistance bacteria in wastewater in Kimberley, South Africa.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {26867},
pmid = {39500921},
issn = {2045-2322},
mesh = {*Wastewater/microbiology ; South Africa ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/classification/isolation & purification/drug effects ; RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; Phylogeny ; },
abstract = {Wastewater treatment plants (WWTPs) are hotspots for pathogens, and can facilitate horizontal gene transfer, potentially releasing harmful genetic material and antimicrobial resistance genes into the environment. Little information exists on the composition and behavior of microbes in WWTPs, especially in developing countries. This study used environmental DNA (eDNA) techniques to examine the microbiome load of wastewater from WWTPs. The DNA was isolated from wastewater samples collected from the treatment trains of three WWTPs in Kimberley, South Africa, and the microbial diversity and composition was compared through 16 S rRNA gene sequencing. The microbes detected were of the Kingdom Bacteria, and of these, 48.27% were successfully identified to genus level. The majority of reads from the combined bacterial data fall within the class Gammaproteobacteria, which is known to adversely impact ecological and human health. Arcobacteraceae constituted 19% of the bacterial reads, which is expected as this family is widespread in aquatic environments. Interestingly, the most abundant bacterial group was Bacteroides, which contain a variety of antibiotic-resistant members. Overall, various antibiotic-resistant taxa were detected in the wastewater, indicating a concerning level of antibiotic resistance within the bacterial community. Therefore, eDNA analysis can be a valuable tool in monitoring and assessing the bacterial microbiome in wastewater, thus providing important information for the optimization and improvement of wastewater treatment systems and mitigate public health risks.},
}

*Wastewater/microbiology
South Africa
*Microbiota/genetics
*Drug Resistance, Bacterial/genetics
*Bacteria/genetics/classification/isolation & purification/drug effects
RNA, Ribosomal, 16S/genetics
Anti-Bacterial Agents/pharmacology
Phylogeny

@article {pmid39500447,
year = {2024},
author = {Fagunwa, OE and Ashiru-Oredope, D and Gilmore, BF and Doherty, S and Oyama, LB and Huws, SA},
title = {Climate change as a challenge for pharmaceutical storage and tackling antimicrobial resistance.},
journal = {The Science of the total environment},
volume = {956},
number = {},
pages = {177367},
doi = {10.1016/j.scitotenv.2024.177367},
pmid = {39500447},
issn = {1879-1026},
abstract = {The rise of antimicrobial resistance (AMR) remains a pressing global health challenge. Infections that were once easily treatable with first-line antimicrobials are becoming increasingly difficult to manage. This shift directly threatens the wellness of humans, animals, plants, and the environment. While the AMR crisis can be attributed to a myriad of factors, including lack of infection prevention and control measures, over-prescription of antimicrobials, patient non-compliance, and the misuse of antimicrobials, one aspect that has garnered less attention is the role of storage conditions of these medicines. The way medications, particularly antimicrobials, are transported and stored until the point of use can influence their efficacy and, subsequently, may impact the development of resistant microbial strains. This review delves deeper into the often-overlooked domain of climate change (CC) and antimicrobial storage practices and the potential effects. Inappropriate storage conditions, such as exposure to extreme temperatures, humidity or light, can degrade the potency of antimicrobials. When these compromised medicines are administered to patients or animals alike, they may not effectively eradicate the targeted pathogens, leading to partial survival of the pathogens. These surviving pathogens, having been exposed to sub-lethal doses, are more likely to evolve and develop resistance mechanisms. The review discusses the mechanism underlying this and underscores the implications of antimicrobial storage practices in relation to two of the most pressing global health challenges: AMR and CC. The review also presents specific case studies and highlights the importance of monitoring storage practices and supply chain surveillance. Furthermore, the importance of deploying genomic tools to understand the potential impact of storage conditions on the development of AMR is discussed, and antimicrobial storage highlighted as a crucial part of comprehensive strategies in the fight against AMR.},
}

@article {pmid39481552,
year = {2024},
author = {Zhao, X and Qiao, Q and Qin, X and Zhao, P and Li, X and Xie, J and Zhai, F and Li, Y},
title = {Viral community and antibiotic resistance genes carried by virus in soil microbial fuel cells.},
journal = {The Science of the total environment},
volume = {955},
number = {},
pages = {177260},
doi = {10.1016/j.scitotenv.2024.177260},
pmid = {39481552},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Bioelectric Energy Sources ; *Drug Resistance, Microbial/genetics ; Soil/chemistry ; Gene Transfer, Horizontal ; Viruses/genetics ; },
abstract = {Soil microbial fuel cells (MFCs) can control the horizontal transfer of antibiotic resistance genes (ARGs) by reducing the abundance of mobile genetic elements. However, little is known about the effect of soil MFCs on the horizontal transfer pathway of ARGs transduced by viruses. In this study, the average abundance of ARGs in soil MFCs was 11 % lower than that in the open-circuit control. Lower virus abundance in soil MFCs suggested less detriment of microbial communities. The structure of the viral community was respectively shifted by the introduction of electrodes and the stimulation of biocurrent, especially for the top three viral genera Oslovirus, Tequatrovirus and Incheonvrus in soil. The ARGs aac(6)-I, cat chloramphenicol acetyltransferase, qnrA and vanY were found as the highest health risk (Rank I), and their total abundance showed the lowest in MFCs, with a decrease of 91-99 % compared to the controls. As the main carrier of ARGs, the abundance of Caudoviricetes showed a significant positive correlation with ARGs. Viral integrase was identified respectively coexisting with arnA and vanR (Rank III) in the same contig, which might aggravate their horizontal transfer. Proteobacteria was the main host of viruses carrying ARGs, which exhibited the lowest abundance in the soil MFC. The genus Pseudomonas was the host of viruses carrying ARGs, whose amount reduced by soil MFCs. This study provides an insight into the bioelectrochemical control of ARGs horizontal transfer.},
}

*Soil Microbiology
*Bioelectric Energy Sources
*Drug Resistance, Microbial/genetics
Soil/chemistry
Gene Transfer, Horizontal
Viruses/genetics

@article {pmid39441990,
year = {2024},
author = {Uppal, S and Waterworth, SC and Nick, A and Vogel, H and Flórez, LV and Kaltenpoth, M and Kwan, JC},
title = {Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39441990},
issn = {1751-7370},
support = {ERC CoG 819585//European Research Council through an ERC Consolidator/ ; 1845890//National Science Foundation/ ; },
mesh = {Animals ; *Symbiosis ; *Coleoptera/microbiology ; *Burkholderia/genetics/metabolism/classification/physiology ; Phylogeny ; Metagenomics ; Genome, Bacterial ; Gene Transfer, Horizontal ; },
abstract = {Microbial symbionts associate with multicellular organisms on a continuum from facultative associations to mutual codependency. In the oldest intracellular symbioses there is exclusive vertical symbiont transmission, and co-diversification of symbiotic partners over millions of years. Such symbionts often undergo genome reduction due to low effective population sizes, frequent population bottlenecks, and reduced purifying selection. Here, we describe multiple independent acquisition events of closely related defensive symbionts followed by genome erosion in a group of Lagriinae beetles. Previous work in Lagria villosa revealed the dominant genome-eroded symbiont of the genus Burkholderia produces the antifungal compound lagriamide, protecting the beetle's eggs and larvae from antagonistic fungi. Here, we use metagenomics to assemble 11 additional genomes of lagriamide-producing symbionts from 7 different host species within Lagriinae from 5 countries, to unravel the evolutionary history of this symbiotic relationship. In each host, we detected one dominant genome-eroded Burkholderia symbiont encoding the lagriamide biosynthetic gene cluster. However, we did not find evidence for host-symbiont co-diversification or for monophyly of the lagriamide-producing symbionts. Instead, our analyses support a single ancestral acquisition of the gene cluster followed by at least four independent symbiont acquisitions and subsequent genome erosion in each lineage. By contrast, a clade of plant-associated relatives retained large genomes but secondarily lost the lagriamide gene cluster. Our results, therefore, reveal a dynamic evolutionary history with multiple independent symbiont acquisitions characterized by a high degree of specificity and highlight the importance of the specialized metabolite lagriamide for the establishment and maintenance of this defensive symbiosis.},
}

Animals
*Symbiosis
*Coleoptera/microbiology
*Burkholderia/genetics/metabolism/classification/physiology
Phylogeny
Metagenomics
Genome, Bacterial
Gene Transfer, Horizontal

@article {pmid39404074,
year = {2024},
author = {Mateo-Cáceres, V and Redrejo-Rodríguez, M},
title = {Pipolins are bimodular platforms that maintain a reservoir of defense systems exchangeable with various bacterial genetic mobile elements.},
journal = {Nucleic acids research},
volume = {52},
number = {20},
pages = {12498-12516},
pmid = {39404074},
issn = {1362-4962},
support = {PID2021-123403NB-I00//ERDF/ ; SI3/PJI/2021-00271//Comunidad de Madrid/ ; SFPI/2023-00603//UAM/ ; },
mesh = {*Interspersed Repetitive Sequences/genetics ; *Genomic Islands ; *Integrases/genetics/metabolism ; Bacteria/genetics/classification ; Plasmids/genetics ; Genome, Bacterial/genetics ; Phylogeny ; Bacterial Proteins/genetics ; Gammaproteobacteria/genetics ; Gene Transfer, Horizontal ; },
abstract = {Defense genes gather in diverse types of genomic islands in bacteria and provide immunity against viruses and other genetic mobile elements. Here, we disclose pipolins, previously found in diverse bacterial phyla and encoding a primer-independent PolB, as a new category of widespread defense islands. The analysis of the occurrence and structure of pipolins revealed that they are commonly integrative elements flanked by direct repeats in Gammaproteobacteria genomes, mainly Escherichia, Vibrio or Aeromonas, often taking up known mobile elements integration hotspots. Remarkably, integrase dynamics correlates with alternative integration spots and enables diverse lifestyles, from integrative to mobilizable and plasmid pipolins, such as in members of the genera Limosilactobacillus, Pseudosulfitobacter or Staphylococcus. Pipolins harbor a minimal core and a large cargo module enriched for defense factors. In addition, analysis of the weighted gene repertoire relatedness revealed that many of these defense factors are actively exchanged with other mobile elements. These findings indicate pipolins and, potentially other defense islands, act as orthogonal reservoirs of defense genes, potentially transferable to immune autonomous MGEs, suggesting complementary exchange mechanisms for defense genes in bacterial populations.},
}

*Interspersed Repetitive Sequences/genetics
*Genomic Islands
*Integrases/genetics/metabolism
Bacteria/genetics/classification
Plasmids/genetics
Genome, Bacterial/genetics
Phylogeny
Bacterial Proteins/genetics
Gammaproteobacteria/genetics
Gene Transfer, Horizontal

@article {pmid39500253,
year = {2024},
author = {Zhang, G and Ren, R and Yan, X and Zhang, H and Zhu, Y},
title = {Effects of microplastics on dissipation of oxytetracycline and its relevant resistance genes in soil without and with Serratia marcescens: Comparison between biodegradable and conventional microplastics.},
journal = {Ecotoxicology and environmental safety},
volume = {287},
number = {},
pages = {117235},
doi = {10.1016/j.ecoenv.2024.117235},
pmid = {39500253},
issn = {1090-2414},
abstract = {The biodegradable (polybutylene adipate terephthalate: PBAT) and conventional (polyethylene: PE) microplastics (MPs) at 0.5 %, 1 %, and 2 % dosages (w/w) were added into soils with and without Serratia marcescens ZY01 (ZY01, a tet-host strain) to understand their different effects on the dissipation of oxytetracycline (OTC) and tet. The results showed that the dosages of PBAT MP exhibited different inhibition degrees of OTC biodegradation in soils regardless of ZY01, while the dosages of PE MP did not change the enhancement degree of OTC biodegradation in soils without ZY01. These differences were due to the higher adsorption capacity of OTC on PBAT MP and the stronger toxicity of PBAT MP to microorganisms. Besides soil organic matter, pH and total phosphorus were important factors regulating specific tet-host bacteria in soils with MPs (e.g., the nitrogen-cycling bacteria Steroidobacter and Nitrospira) and MPs + ZY01 (e.g., the phosphorus-cycling bacteria Saccharimonadales and Haliangium), respectively. Regardless of ZY01, a stronger selective harboring of tet-host bacteria in PE MP treatments than PBAT MP treatments was observed at the MP dosage of 1 % (w/w), while the opposite trend was true at the MP dosages of 0.5 % and 2 % (w/w). Some specific genera belonging to Actinobacteriota strongly associated with the class 1 integron-integrase gene (intI1), playing a critical role in the horizontal gene transfer of tet in soils especially for the co-existence of MPs and ZY01. This study will be helpful for understanding on how biodegradable and conventional MPs as hotspots affect the environmental behavior of antibiotics and ARGs in soil.},
}

@article {pmid39499398,
year = {2024},
author = {Fu, J and Zhang, P and Yin, X and Zhu, L and Zong, G and Zhong, C and Cao, G},
title = {A scientific research training programme for teaching biomedical students to identify the horizontal transfer of antibiotic resistance genes.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {39499398},
issn = {1874-9356},
support = {SDYAL2022135//the Course Construction Project of Shandong Province/ ; },
abstract = {Worldwide prevalence of multi-antibiotic resistant bacteria is rapidly increasing, and the education of undergraduates and graduates about antibiotic resistance and its associated horizontal gene transfer is critical in the general effort to confront the spread of antibiotic resistance. In this study, a deeper understanding of antibiotic resistance and horizontal gene transfer was achieved by biomedical undergraduate students through a scientific research programme. The enthusiasm of students to participate in the training programme was very high, and results revealed that each student could identify the antibiotic resistance integrative and conjugative element from the Stenotrophomonas maltophilia MER1 genome. Each student could also draw the phylogenetic relationship of the antibiotic resistance integrative and conjugative element. In addition, students proved the horizontal transfer of antibiotic resistance genes from S. maltophilia MER1 to Escherichia coli strain 25DN through conjugation and PCR assays. Each group of students was able to obtain the expected results, indicating that the outcome of the scientific research programme was highly reproducible. This programme improved the theoretical knowledge about antibiotic resistance and horizontal gene transfer and the research skills of biomedical sciences students. Through this programme, students learned that antibiotic resistance genes can be horizontally transferred among different bacteria, laying a solid foundation for students to value the importance of the appropriate use of antibiotics in their future work and life.},
}

@article {pmid39498151,
year = {2024},
author = {Dias, YJM and Dezordi, FZ and Wallau, GDL},
title = {EEfinder, a general purpose tool for identification of bacterial and viral endogenized elements in eukaryotic genomes.},
journal = {Computational and structural biotechnology journal},
volume = {23},
number = {},
pages = {3662-3668},
pmid = {39498151},
issn = {2001-0370},
abstract = {Horizontal gene transfer is a phenomenon of genetic material transmission between species with no parental relationship. It has been characterized among several major branches of life, including among prokaryotes, viruses and eukaryotes. The characterization of endogenous elements derived from viruses or bacteria provides a snapshot of past host-pathogen interactions and coevolution as well as reference information to remove false positive results from metagenomic studies. Currently there is a lack of general purpose standardized tools for endogenous elements screening which limits reproducibility and hinder comparative analysis between studies. Here we describe EEfinder, a new general purpose tool for identification and classification of endogenous elements derived from viruses or bacteria found in eukaryotic genomes. The tool was developed to include six common steps performed in this type of analysis: data cleaning, similarity search through sequence alignment, filtering candidate elements, taxonomy assignment, merging of truncated elements and flanks extraction. We evaluated the sensitivity of EEfinder to identify endogenous elements through comparative analysis using data from the literature and showed that EEfinder automatically detected 97 % of the EVEs compared to published results obtained by manual curation and detected an almost exact full integration of a Wolbachia genome described using wet-lab experiments. Therefore, EEfinder can effectively and systematically identify endogenous elements with bacterial/viral origin integrated in eukaryotic genomes. EEfinder is publicly available on https://github.com/WallauBioinfo/EEfinder.},
}

@article {pmid39245329,
year = {2024},
author = {Zhang, F and Li, Z and Liu, X and Li, Z and Lei, Z and Zhao, J and Zhang, Y and Wu, Y and Yang, X and Lu, B},
title = {In-host intra- and inter-species transfer of blaKPC-2 and blaNDM-1 in Serratia marcescens and its local and global epidemiology.},
journal = {International journal of antimicrobial agents},
volume = {64},
number = {5},
pages = {107327},
doi = {10.1016/j.ijantimicag.2024.107327},
pmid = {39245329},
issn = {1872-7913},
mesh = {*Serratia marcescens/genetics/drug effects/isolation & purification ; *beta-Lactamases/genetics ; Humans ; *Serratia Infections/microbiology/epidemiology ; *Gene Transfer, Horizontal ; *Plasmids/genetics ; *Whole Genome Sequencing ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Phylogeny ; Providencia/genetics/drug effects ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {OBJECTIVES: The aim of this study was to investigate interspecies transfer of resistance gene blaNDM-1 and intraspecies transfer of resistance gene blaKPC-2 in Serratia marcescens, and explore the epidemical and evolutionary characteristics of carbapenemase-producing S. marcescens (CPSM) regionally and globally.

METHODS: Interspecies and intraspecies transfer of blaKPC-2- or blaNDM-1 were identified by antimicrobial susceptibility testing, plasmid conjugation and curing, discovery of transposable units (TUs), outer membrane vesicles (OMVs), qPCR, whole-genome sequencing (WGS) and bioinformatic analysis. The genomic evolution of CPSM strains was explored by cgSNP and maximum-likelihood phylogenetic tree.

RESULTS: CPSM S50079 strain, co-carrying blaKPC-2 and blaNDM-1 on one plasmid, was isolated from the blood of a patient with acute pancreatitis and could generate TUs carrying either blaKPC-2 or blaNDM-1. The interspecies transfer of blaNDM-1-carrying plasmid from Providencia rettgeri P50213, producing the identical blaNDM-1-carrying TUs, to S. marcescens S50079K, an S50079 variant via plasmid curing, was identified through blaNDM-1-harbouring plasmid conjugation and OMVs transfer. Moreover, the intraspecies transfer of blaKPC-2, mediated by IS26 from plasmid to chromosome in S50079, was also identified. In another patient, who underwent lung transplantation, interspecies transfer of blaNDM-1 carried by IncX3 plasmid was identified among S. marcescens and Citrobacter freundii as well as Enterobacter hormaechei via plasmid transfer. Furthermore, 11 CPSM from 349 non-repetitive S. marcescens strains were identified in the same hospital, and clonal dissemination, with carbapenemase evolution from blaKPC-2 to both blaKPC-2 and blaNDM-1, was found in the 8 CPSM across 4 years. Finally, the analysis of 236 global CPSM from 835 non-repetitive S. marcescens genomes, retrieved from the NCBI database, revealed long-term spread and evolution worldwide, and would cause the convergence of more carbapenemase genes.

CONCLUSIONS: Interspecies transfer of resistance gene blaNDM-1 and intraspecies transfer of resistance gene blaKPC-2 in CPSM were identified. Nosocomial and global dissemination of CPSM were revealed and more urgent surveillance was acquired.},
}

*Serratia marcescens/genetics/drug effects/isolation & purification
*beta-Lactamases/genetics
Humans
*Serratia Infections/microbiology/epidemiology
*Gene Transfer, Horizontal
*Plasmids/genetics
*Whole Genome Sequencing
Microbial Sensitivity Tests
Anti-Bacterial Agents/pharmacology
Bacterial Proteins/genetics
Phylogeny
Providencia/genetics/drug effects
Drug Resistance, Multiple, Bacterial/genetics

@article {pmid39498132,
year = {2024},
author = {Abe, K and Yahara, H and Nakao, R and Yamaguchi, T and Akeda, Y},
title = {A simple and cost-effective transformation system for Porphyromonas gingivalis via natural competence.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1476171},
pmid = {39498132},
issn = {1664-302X},
abstract = {Porphyromonas gingivalis is a major oral bacterial pathogen responsible for severe periodontal diseases. Numerous studies have used genetic approaches to elucidate the molecular mechanisms underlying its pathogenicity. Typically, electroporation and conjugation are utilized for mutagenesis of P. gingivalis; however, these techniques require specialized equipment such as high-voltage electroporators, conjugative plasmids and donor strains. In this study, we present a simple, cost-effective transformation method for P. gingivalis without any special equipment by exploiting its natural DNA competence. P. gingivalis ATCC 33277 was grown to the early-exponential phase and mixed with a donor DNA cassette. This mixture was then spotted onto a BHI-HM blood-agar plate and incubated for one day to promote colony biofilm formation. The resulting colony biofilm was suspended in a liquid medium and spread onto antibiotic-containing agar plates. Transformants appeared within 4 to 5 days, achieving a maximum efficiency of 7.7 × 10[6] CFU/μg. Although we optimized the transformation conditions using a representative strain ATCC 33277, but the method was also effective for other P. gingivalis strains, W83 and TDC60. Additionally, we discovered that deletion of PGN_0421 or PGN_0519, encoding putative ComEA and ComEC, abolished competency, indicating that these gene products are essential for the natural competence.},
}

@article {pmid39497365,
year = {2024},
author = {Qu, S and Zhang, Y and Weng, L and Shan, X and Cheng, P and Li, Q and Li, L},
title = {The role of bacterial extracellular vesicles in promoting antibiotic resistance.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/1040841X.2024.2423159},
pmid = {39497365},
issn = {1549-7828},
abstract = {The burgeoning proliferation of infections attributed to multidrug-resistant (MDR) bacterial pathogens is profoundly undermining conventional chemotherapeutic modalities, portending a grave menace to global public health. The propagation of drug resistance among bacteria is fundamentally facilitated by bacterial interactions, with extracellular vesicles (EVs) assuming a critical role in interbacterial communication. Here, we briefly delineate the methodologies for isolation, extraction, and characterization of EVs from both Gram-negative and Gram-positive bacterial origins. We further investigate assorted methodologies to augment EV production, embracing physical stimulation, chemical elicitation, and genetic engineering. Moreover, we expound on the pivotal involvement of EVs in the facilitation of bacterial drug resistance proliferation and anticipate future trajectories of research and application potential. This overview of EV-mediated novel mechanisms of horizontal gene transfer implicated in antibiotic resistance among bacteria aims to obstruct the transmission conduits of bacterial drug resistance and thus fortify public health integrity.},
}

@article {pmid39494898,
year = {2024},
author = {Priya, S and Rossbach, S and Eng, T and Lin, H-H and Andeer, PF and Mortimer, JC and Northen, TR and Mukhopadhyay, A},
title = {Assessing horizontal gene transfer in the rhizosphere of Brachypodium distachyon using fabricated ecosystems (EcoFABs).},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0150524},
doi = {10.1128/aem.01505-24},
pmid = {39494898},
issn = {1098-5336},
abstract = {Horizontal gene transfer (HGT) is a major process by which genes are transferred between microbes in the rhizosphere. However, examining HGT remains challenging due to the complexity of mimicking conditions within the rhizosphere. Fabricated ecosystems (EcoFABs) have been used to investigate several complex processes in plant-associated environments. Here we show that EcoFABs are efficient tools to examine and measure HGT frequency in the rhizosphere. We provide the first demonstration of gene transfer via a triparental conjugation system in the Brachypodium distachyon rhizosphere in an EcoFAB using Pseudomonas putida KT2440 as both donor and recipient bacterial strain with the donor containing a mobilizable and non-self-transmissible plasmid. We observed that the frequency of plasmid transfer in the rhizosphere is potentially dependent on the plant developmental stage and the composition and amount of root exudates. The frequency of plasmid transfer also increased with higher numbers of donor cells. We demonstrate the transfer of plasmid from P. putida to another B. distachyon root colonizer, Burkholderia sp. OAS925, showing HGT within a rhizosphere microbial community. Environmental stresses also influenced the rate and efficiency of HGT in the rhizosphere between different species and genera. This study provides a robust workflow to evaluate transfer of engineered plasmids in the rhizosphere when such plasmids are potentially introduced in a field or other plant-associated environments.IMPORTANCEWe report the use of EcoFABs to investigate the HGT process in a rhizosphere environment. It highlights the potential of EcoFABs in recapitulating the dynamic rhizosphere conditions as well as their versatility in studying plant-microbe interactions. This study also emphasizes the importance of studying the parameters impacting the HGT frequency. Several factors such as plant developmental stages, nutrient conditions, number of donor cells, and environmental stresses influence gene transfer within the rhizosphere microbial community. This study paves the way for future investigations into understanding the fate and movement of engineered plasmids in a field environment.},
}

@article {pmid39494882,
year = {2024},
author = {Oke, MT and Martz, K and Mocăniță, M and Knezevic, S and D'Costa, VM},
title = {Analysis of Acinetobacter P-type type IV secretion system-encoding plasmid diversity uncovers extensive secretion system conservation and diverse antibiotic resistance determinants.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {e0103824},
doi = {10.1128/aac.01038-24},
pmid = {39494882},
issn = {1098-6596},
abstract = {Acinetobacter baumannii is globally recognized as a multi-drug-resistant pathogen of critical concern due to its capacity for horizontal gene transfer and resistance to antibiotics. Phylogenetically diverse Acinetobacter species mediate human infection, including many considered as important emerging pathogens. While globally recognized as a pathogen of concern, pathogenesis mechanisms are poorly understood. P-type type IV secretion systems (T4SSs) represent important drivers of pathogen evolution, responsible for horizontal gene transfer and secretion of proteins that mediate host-pathogen interactions, contributing to pathogen survival, antibiotic resistance, virulence, and biofilm formation. Genes encoding a P-type T4SS were previously identified on plasmids harboring the carbapenemase gene blaNDM-1 in several clinically problematic Acinetobacter; however, their prevalence among the genus, geographical distribution, the conservation of T4SS proteins, and full capacity for resistance genes remain unclear. Using systematic analyses, we show that these plasmids belong to a group of 53 P-type T4SS-encoding plasmids in 20 established Acinetobacter species, the majority of clinical relevance, including diverse A. baumannii sequence types and one strain of Providencia rettgeri. The strains were globally distributed in 14 countries spanning five continents, and the conjugative operon's T4SS proteins were highly conserved in most plasmids. A high proportion of plasmids harbored resistance genes, with 17 different genes spanning seven drug classes. Collectively, this demonstrates that P-type T4SS-encoding plasmids are more widespread among the Acinetobacter genus than previously anticipated, including strains of both clinical and environmental importance. This research provides insight into the spread of resistance genes among Acinetobacter and highlights a group of plasmids of importance for future surveillance.},
}

@article {pmid39493848,
year = {2024},
author = {Yang, Y and Zhang, H and Zhao, R and Qiu, X and Ye, J and Lu, W and Li, Q and Wu, G},
title = {Distribution diversity and expression regulation of class 1 integron promoters in clinical isolates of Morganella morganii.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1459162},
pmid = {39493848},
issn = {1664-302X},
abstract = {BACKGROUND: Morganella morganii is an emerging nosocomial opportunistic pathogen with increasing multidrug resistance. Antibiotic resistance, driven primarily by the horizontal transfer of resistance genes, has become a global health crisis. Integrons, mobile genetic elements, are now understood to facilitate the transfer of these genes, contributing to the rapid proliferation of resistant strains. Understanding the regulatory role of integrons in drug resistance gene expression is crucial for developing novel strategies to combat this pressing public health issue.

OBJECTIVE: To investigate the distribution of promoter types in the variable regions of class 1 integrons isolated from clinical isolates of M. morganii and their regulatory role in the expression of downstream drug resistance gene cassettes.

METHODS: Ninety seven clinical isolates of M. morganii were screened for the presence of class 1 integrons (intI1) using polymerase chain reaction (PCR). Gene cassettes within the variable regions of positive isolates were characterized, and the gene cassette promoter Pc variants and downstream auxiliary promoter P2 were identified. Enterobacterial repetitive intergenic consensus (ERIC)-PCR was employed for homology analysis. Recombinant plasmids containing different variable region promoters and gene cassettes were constructed to evaluate drug resistance genes and integrase (intI1) expression levels using reverse transcription-quantitative PCR (RT-qPCR) and antimicrobial susceptibility testing.

RESULTS: Of the clinical isolates, 28.9% (n = 28/97) were positive for class 1 integrons. 24.7% (n = 24/97) of these isolates carried gene cassettes encoding resistance to aminoglycosides and trimethoprim. Three Pc promoter types (PcH1, PcS, and PcW) were identified, while all P2 promoters were inactive with a 14-base pair spacing between the -35 and -10 regions. ERIC-PCR analysis classified the integron-positive strains into 6 genotypes, with high consistency in promoter types and gene cassettes within each genotype. RT-qPCR and antimicrobial susceptibility testing demonstrated that strong promoters significantly enhanced the expression of downstream drug resistance gene cassettes compared to weak promoters. Additionally, RT-qPCR revealed a negative correlation between intI1 expression and Pc promoter strength.

CONCLUSION: Class 1 integrons are prevalent in M. morganii. The promoter types within these integrons are diverse, and promoter strength is closely linked to downstream gene cassette expression. Integron-positive strains exhibit high homology, suggesting horizontal gene transfer and dissemination in clinical settings.},
}

@article {pmid39492387,
year = {2023},
author = {Duan, Z and Zhu, Y and Xia, H and Huang, K and Peng, L},
title = {A novel strategy for eliminating antibiotic resistance genes during fertilization of dewatered sludge by earthworms: Vermicomposting practice using Chinese herbal residues derived from Lianhua Qingwen as a bulking material.},
journal = {Journal of environmental management},
volume = {349},
number = {},
pages = {119444},
doi = {10.1016/j.jenvman.2023.119444},
pmid = {39492387},
issn = {1095-8630},
abstract = {Vermicomposting is a sustainable sludge recycling technology that utilizes an eco-friendly composting using earthworms and microorganisms. However, a high abundance of antibiotic resistance genes (ARGs) remains in dewatered sludge that is not satisfactorily eliminated by vermicomposting. Chinese herbs have played a major role in curing many diseases in East Asia, leading to a large amount of Chinese herbal residues (CHRs) are difficult to dispose of. The present study investigated the feasibility of CHRs on the ARGs reduction in dewatered sludge during vermicomposting. The CHRs derived from Lianhua Qingwen were added separately to sludge with weight ratios of 0%, 10%, 30%, and 50%; sludge was then vermicomposted for 30 days. The results showed that co-vermicomposting of sludge and CHRs is a feasible strategy. The CHR treatments significantly (P < 0.05) decreased antibiotic concentration and bacterial population by 23.64%-49.68% and 42.58%-93.07%, respectively, compared to counterpart. Compared to the control, the CHR addition lowered the absolute abundances of macrolide, tetracycline, and sulfonamide ARGs by 42.69%-85.15%, 22.03%-75.24%, and 23.59%-90.66%, respectively. In addition, sludge containing 30% CHRs showed significant (P < 0.05) elimination of intⅠ-1 and tnpA-4 genes with abundance reductions of 71.40% and 52.33%, respectively, relative to the control. This study suggests that the CHRs can effectively reduce ARGs content in sludge by decreasing the bacterial population and horizontal gene transfer capacity during vermicomposting.},
}

@article {pmid39491810,
year = {2024},
author = {Pereira, AB and Marano, M and Bathala, R and Zaragoza, RA and Neira, A and Samano, A and Owoyemi, A and Casola, C},
title = {Orphan genes are not a distinct biological entity.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e2400146},
doi = {10.1002/bies.202400146},
pmid = {39491810},
issn = {1521-1878},
support = {//Texas A&M AgriLife Research/ ; 1019860//USDA National Institute of Food and Agriculture/ ; //Texas A&M Forest Service/ ; },
abstract = {The genome sequencing revolution has revealed that all species possess a large number of unique genes critical for trait variation, adaptation, and evolutionary innovation. One widely used approach to identify such genes consists of detecting protein-coding sequences with no homology in other genomes, termed orphan genes. These genes have been extensively studied, under the assumption that they represent valid proxies for species-specific genes. Here, we critically evaluate taxonomic, phylogenetic, and sequence evolution evidence showing that orphan genes belong to a range of evolutionary ages and thus cannot be assigned to a single lineage. Furthermore, we show that the processes generating orphan genes are substantially more diverse than generally thought and include horizontal gene transfer, transposable element domestication, and overprinting. Thus, orphan genes represent a heterogeneous collection of genes rather than a single biological entity, making them unsuitable as a subject for meaningful investigation of gene evolution and phenotypic innovation.},
}

@article {pmid39491220,
year = {2023},
author = {Anantharajah, A and Goormaghtigh, F and Mantu, EN and Güler, B and Bearzatto, B and Momal, A and Werion, A and Hantson, P and Kabamba-Mukadi, B and Van Bambeke, F and Rodriguez-Villalobos, H and Verroken, A},
title = {Long-term ICU outbreak of carbapenamase-producing organisms associated with contaminated sink drains.},
journal = {The Journal of hospital infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhin.2023.10.010},
pmid = {39491220},
issn = {1532-2939},
abstract = {BACKGROUND: Between 2018 and 2022, a Belgian tertiary care hospital faced a growing issue with acquiring carbapenemase-producing organisms (CPO), mainly VIM-producing P. aeruginosa (PA-VIM) and NDM-producing Enterobacterales (CPE-NDM) among hospitalized patients in the adult intensive care unit (ICU). We report the investigation of this ICU long-term CPO outbreak involving multiple species and a persistent environmental reservoir.

METHODS: Active case finding, environmental sampling, whole genome sequencing (WGS) analysis of patient and environmental strains and implemented control strategies were described in this study.

FINDINGS: From 2018 to 2022, 37 patients became colonised or infected with PA-VIM and/ or CPE-NDM during their ICU stay. WGS confirmed the epidemiological link between clinical and environmental strains collected from the sink drains with clonal strains dissemination and horizontal gene transfer mediated by plasmid conjugation and/or transposon jumps. Environmental disinfection by quaternary ammonium-based disinfectant and replacement of contaminated equipment failed to eradicate environmental sources. Interestingly, efflux pumps genes conferring resistance to quaternary ammonium compounds were widespread in the isolates. As removing sinks was not feasible, a combination of a foaming product degrading the biofilm and foaming disinfectant based on peracetic acid and hydrogen peroxide has been evaluated and has so far prevented re-colonisation of the proximal sink drain by CPO.

CONCLUSION: The persistence in the hospital environment of antibiotic-and-disinfectant resistant bacteria with the ability to transfer mobile genetic elements poses a serious threat on ICU patients with a risk of shifting towards an endemicity scenario. Innovative strategies are needed to address persistent environmental reservoirs and prevent CPO transmission.},
}

@article {pmid39487157,
year = {2024},
author = {Wardi, M and Lemkhente, Z and Alla, AA and Slimani, N and Abali, M and Idaghdour, Y and Belmouden, A},
title = {Resistome analysis of wastewater treatment plants in Agadir city, Morocco, using a metagenomics approach.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {26328},
pmid = {39487157},
issn = {2045-2322},
mesh = {*Wastewater/microbiology ; Morocco ; *Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; Water Purification/methods ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; },
abstract = {Water scarcity has evolved into a pressing global issue, significantly impacting numerous regions worldwide. The use of treated wastewater stands out as a promising solution to this problem. However, the proliferation of various contaminants, primarily Antimicrobial Resistance Genes (ARGs), poses a significant challenge to its safe and sustainable use. In this study, we assessed the composition and abundance of 373 ARGs, corresponding to 31 different classes of antibiotics, in six wastewater treatment plants (WWTP) in Agadir city of Morocco. Influent and effluent samples were collected during the months of February and July in 2020, in addition to samples from the Atlantic Ocean. In total, 223 ARGs were uncovered, highlighting in particular resistance to aminoglycoside, macrolide lincosamide, beta-lactamase, chloramphenicol, sulfonamide, tetracycline, and other antibiotics. The mechanisms of action of these ARGs were mainly antibiotic inactivation, antibiotic target alteration, efflux pump and cellular protection. Mobile genetic elements (MGEs) were detected at high levels their co-occurrence with ARGs highlights their involvement in the acquisition and transmission of ARGs in microbial communities through horizontal gene transfer. While many wastewater treatment methods effectively reduce a large proportion of gene material and pathogens, a substantial fraction of ARGs and other contaminants persist in treated wastewater. This persistence poses potential risks to both human health and the environment, warranting the need of more effective treatment strategies.},
}

*Wastewater/microbiology
Morocco
*Metagenomics/methods
Anti-Bacterial Agents/pharmacology
Water Purification/methods
Bacteria/genetics/drug effects
Genes, Bacterial
Drug Resistance, Bacterial/genetics

@article {pmid39488185,
year = {2024},
author = {Guo, J and Jin, X and Zhou, Y and Gao, B and Li, Y and Zhou, Y},
title = {Microplastic and antibiotics in waters: Interactions and environmental risks.},
journal = {Journal of environmental management},
volume = {371},
number = {},
pages = {123125},
doi = {10.1016/j.jenvman.2024.123125},
pmid = {39488185},
issn = {1095-8630},
abstract = {Antibiotics (ATs) are ubiquitously detected in natural waters worldwide, and their tendency to co-migrate with microplastics (MPs) post-adsorption leads to heightened environmental risk. Research on the adsorption of ATs on MPs and their subsequent effects on the environmental risks is gaining significant attention globally. This adsorption process predominantly occurs through hydrophobic forces, hydrogen bonds, and electrostatic interactions and is influenced by various environmental factors. The interaction between MPs and ATs exhibited varying degrees of efficiency across different pH levels and ionic strengths. Furthermore, this paper outlines the environmental risks associated with the co-presence of MPs and ATs in aquatic environments, emphasizing the potential effect of MPs on the distribution of antibiotic resistance genes (ARGs) and related environmental risks. The potential hazards posed by MPs and ATs in aquatic systems warrant serious consideration. Future research should concentrate on the adsorption of ATs/ARGs on MPs under real environmental conditions, horizontal gene transfer on MPs, as well as biofilm formation and agglomeration behavior on MPs that needs to be emphasized.},
}

@article {pmid39488061,
year = {2024},
author = {Zhao, Y and Zhang, J and Zheng, Y and Shi, J and Hu, Z and Xie, H and Guo, Z and Liang, S and Wu, H},
title = {Overlooked dissemination risks of antimicrobial resistance through green tide proliferation.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122714},
doi = {10.1016/j.watres.2024.122714},
pmid = {39488061},
issn = {1879-2448},
abstract = {Green tides, particularly those induced by Enteromorpha, pose significant environmental challenges, exacerbated by climate change, coastal eutrophication, and other anthropogenic impacts. More concerningly, these blooms may influence the spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) within ecosystems. However, the manner in which Enteromorpha blooms affect the distribution and spread of antimicrobial resistance (AMR) remains uncertain. This study investigated ARG profiles, dynamic composition, and associated health risks within the Enteromorpha phycosphere and surrounding seawater in typical bays (Jiaozhou, Aoshan, and Lingshan) in the South Yellow Sea. The Enteromorpha phycosphere exhibited significantly higher ARG abundance (p < 0.05) but lower diversity compared to the surrounding seawater. Source-tracking and metagenomic analyses revealed that the phycosphere was the main contributor to the resistome of surrounding seawater. Moreover, resistant pathogens, especially ESKAPE pathogens, with horizontal gene transfer (HGT) potential, were more abundant in the phycosphere than in the surrounding seawater. The phycosphere released high-risk ARGs to the surrounding seawater during Enteromorpha blooms, posing serious health and ecological AMR risks in marine environments. This study highlights the significant role of Enteromorpha blooms in ARG spread and associated risks, urging a reassessment of AMR burden from a public health perspective.},
}

@article {pmid39486342,
year = {2024},
author = {Dai, S and Han, Z and Liu, S and Wang, Y and Zhang, Y and Yang, M},
title = {Bacterial hosts and horizontal transfer characteristics of clinically important tet(X)-variant genes in municipal wastewater treatment plants using epicPCR-directed cultivation strategy.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122658},
doi = {10.1016/j.watres.2024.122658},
pmid = {39486342},
issn = {1879-2448},
abstract = {Mobile tet(X)-variant genes confer resistance to a wide range of tetracyclines, including the antibiotic of last-resort, tigecycline, raising significant concerns regarding their potential spread cross-environmental dissemination. However, the bacterial hosts and environmental spread of these genes remain poorly understood. Herein, a retrospective study unveiled the prevalence of tet(X)-variant genes (ranging from tet(X3) to tet(X6)) in activated sludge samples from five municipal wastewater treatment plants (WWTPs) from 2013 to 2021. Among these variants, tet(X4) exhibited the highest detection frequency (100 %) and abundance [(2.48 ± 3.07) × 10[7] copies/g dry weight] with an increasing trend. An epicPCR-directed cultivation strategy was proposed to facilitate the targeted isolation of tet(X4)-carrying bacterial hosts in activated sludge. This strategy involves the identification of bacterial host profiles using epicPCR and subsequent selective isolating target bacteria. Enterobacteriaceae emerged as the primary bacterial host for tet(X4), alongside previously unreported genera like Providencia, Advenella, and Moheibacter. Subsequent selective isolation of the most abundant Enterobacteriaceae based on the epicPCR-informed host spectrum yielded 39 tet(X4)-carrying Escherichia coli strains from the WWTP. Whole genome sequencing of tet(X4)-positive strains revealed that plasmid-mediated horizontal gene transfer is the primary mechanism driving tet(X4) dissemination. Plasmids including IncFIA(HI1)/IncHI1A/IncHI1B(R27) and IncX1, commonly reported in various clinical and animal settings, were identified as the predominant carriers of tet(X4). E. coli strains harbouring tet(X4) in the WWTP showed substantial genetic similarity to strains from hospital and animal sources, underscoring concerns about the potential risk of across diverse sectors. This study provided the first glimpse of the presence of mobile tet(X)-variants in WWTPs, and highlighted the promise of the epicPCR-directed cultivation strategy for exploring bacterial hosts of clinically important ARGs in different habitats from a One Health perspective.},
}

@article {pmid39260133,
year = {2024},
author = {Xu, Q and Xie, M and Yang, X and Liu, X and Ye, L and Chen, K and Chan, EW and Chen, S},
title = {Conjugative transmission of virulence plasmid in Klebsiella pneumoniae mediated by a novel IncN-like plasmid.},
journal = {Microbiological research},
volume = {289},
number = {},
pages = {127896},
doi = {10.1016/j.micres.2024.127896},
pmid = {39260133},
issn = {1618-0623},
mesh = {*Klebsiella pneumoniae/genetics/pathogenicity ; *Plasmids/genetics ; Animals ; *Klebsiella Infections/microbiology/transmission ; Virulence/genetics ; *Conjugation, Genetic ; Mice ; *Virulence Factors/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Interleukin-1beta/genetics ; Phagocytosis ; Disease Models, Animal ; Macrophages/microbiology ; Female ; Humans ; Type IV Secretion Systems/genetics ; },
abstract = {Klebsiella pneumoniae (Kp) is increasingly recognized as a reservoir for a range of antibiotic resistance genes and a pathogen that frequently causes severe infections in both hospital and community settings. In this study, we have identified a novel mechanism of conjugative transfer of a non-conjugative virulence plasmid through the formation of a fusion plasmid between the virulence plasmid and a novel 59,162 bp IncN- plasmid. This plasmid was found to be a multidrug-resistance (MDR) plasmid and carried a T4SS cluster, which greatly facilitated the efficient horizontal transfer of the fusion plasmid between Kp strains. The fused virulence plasmid conferred the resistance of serum killing and macrophage phagocytosis to the transconjugants. Importantly, this plasmid was shown to be essential for Kp virulence in a mouse model. Mechanistic analysis revealed that the virulence factors encoded by this virulence plasmid contributed to resistance to in vivo clearance and induced a high level of proinflammatory cytokine IL-1β, which acts as an inducer for more neutrophil recruitment. The transmission of the fusion plasmid in Kp has the potential to convert it into both MDR and hypervirulent Kp, accelerating its evolution, and posing a serious threat to human health. The findings of this study provide new insights into the rapid evolution of MDR and hypervirulent Kp in recent years.},
}

*Klebsiella pneumoniae/genetics/pathogenicity
*Plasmids/genetics
Animals
*Klebsiella Infections/microbiology/transmission
Virulence/genetics
*Conjugation, Genetic
Mice
*Virulence Factors/genetics
*Drug Resistance, Multiple, Bacterial/genetics
Gene Transfer, Horizontal
Interleukin-1beta/genetics
Phagocytosis
Disease Models, Animal
Macrophages/microbiology
Female
Humans
Type IV Secretion Systems/genetics

@article {pmid39484419,
year = {2024},
author = {Dalia, TN and Machouri, M and Lacrouts, C and Fauconnet, Y and Guerois, R and Andreani, J and Radicella, JP and Dalia, AB},
title = {DprA recruits ComM to facilitate recombination during natural transformation in Gram-negative bacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.21.619469},
pmid = {39484419},
issn = {2692-8205},
abstract = {UNLABELLED: Natural transformation (NT) represents one of the major modes of horizontal gene transfer in bacterial species. During NT, cells can take up free DNA from the environment and integrate it into their genome by homologous recombination. While NT has been studied for >90 years, the molecular details underlying this recombination remain poorly understood. Recent work has demonstrated that ComM is an NT-specific hexameric helicase that promotes recombinational branch migration in Gram-negative bacteria. How ComM is loaded onto the post-synaptic recombination intermediate during NT, however, remains unclear. Another NT-specific recombination mediator protein that is ubiquitously conserved in both Gram-positive and Gram-negative bacteria is DprA. Here, we uncover that DprA homologs in Gram-negative species contain a C-terminal winged helix domain that is predicted to interact with ComM by AlphaFold. Using Helicobacter pylori and Vibrio cholerae as model systems, we demonstrate that ComM directly interacts with the DprA winged-helix domain, and that this interaction is critical for DprA to recruit ComM to the recombination site to promote branch migration during NT. These results advance our molecular understanding of recombination during this conserved mode of horizontal gene transfer. Furthermore, they demonstrate how structural modeling can help uncover unexpected interactions between well-studied proteins to provide deep mechanistic insight into the molecular coordination required for their activity.

SIGNIFICANCE STATEMENT: Bacteria can acquire novel traits like antibiotic resistance and virulence through horizontal gene transfer by natural transformation. During this process, cells take up free DNA from the environment and integrate it into their genome by homologous recombination. Many of the molecular details underlying this process, however, remain incompletely understood. In this study, we identify a new protein-protein interaction between ComM and DprA, two factors that promote homologous recombination during natural transformation in Gram-negative species. Through a combination of bioinformatics, structural modeling, cell biological assays, and complementary genetic approaches, we demonstrate that this interaction is required for DprA to recruit ComM to the site of homologous recombination.},
}

@article {pmid39481662,
year = {2024},
author = {Liu, W and Wang, Z and Huang, Y and Liu, Y and Li, R and Wang, M and Zhang, H and Meng, C and Xiao, X},
title = {Acetylshikonin reduces the spread of antibiotic resistance via plasmid conjugation.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107370},
doi = {10.1016/j.ijantimicag.2024.107370},
pmid = {39481662},
issn = {1872-7913},
abstract = {The plasmid-mediated conjugative transfer of antibiotic resistance genes (ARGs) stands out as the primary driver behind the dissemination of antimicrobial resistance (AMR). Developing effective inhibitors that target conjugative transfer represents an efficient strategy for addressing the issue of AMR. Here, we studied the effect of acetylshikonin (ASK), a botanical derivative, on plasmid conjugation. The conjugative transfer of RP4-7 plasmid inter and intra species was notably reduced by ASK. The conjugation process of IncI2 and IncX4 plasmids harboring the mobile colistin resistance gene (mcr-1), IncX4 and IncX3 plasmids containing the carbapenem resistance gene (blaNDM-5), and IncFI and IncFII plasmids possessing the tetracycline resistance gene [tet(X4)] were also reduced by ASK. Importantly, the conjugative transfer frequency of mcr-1 positive IncI2 plasmid in mouse peritoneal conjugation model and gut conjugation model was reduced by ASK. The mechanism investigation showed that ASK disrupt the functionality of the bacterial cell membrane. Furthermore, the proton motive force (PMF) was dissipated. In addition, ASK blocked the electron transmission in bacteria's electron transport chain (ETC) through disturbing the quinone interaction, resulting in an insufficient energy supply for conjugation. Collectively, ASK is a potential conjugative transfer inhibitor, providing novel strategies to prevent the spread of AMR.},
}

@article {pmid39481609,
year = {2024},
author = {Tang, B and Hu, X and Wu, B and Zhao, G and Yue, M},
title = {Global Antimicrobial Resistance Threats: Insights from the Resurgence of Whooping Cough.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106337},
doi = {10.1016/j.jinf.2024.106337},
pmid = {39481609},
issn = {1532-2742},
}

@article {pmid39476778,
year = {2024},
author = {Li, J and Sun, Y and Zhang, Q and Liu, S and Liu, P and Zhang, XX},
title = {Unveiling the potential role of virus-encoded polyphosphate kinases in enhancing phosphorus removal in activated sludge systems.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122678},
doi = {10.1016/j.watres.2024.122678},
pmid = {39476778},
issn = {1879-2448},
abstract = {While microbial phosphate removal in activated sludge (AS) systems has been extensively studied, the role of viruses in this process remains largely unexplored. In this study, we identified 149 viral auxiliary metabolic genes associated with phosphorus cycling from 2,510 viral contigs (VCs) derived from AS systems. Notably, polyphosphate kinase 1 (ppk1) and polyphosphate kinase 2 (ppk2) genes, which are primarily responsible for phosphate removal, were found in five unclassified VCs. These genes exhibited conserved protein structures and active catalytic sites, indicating a pivotal role of viruses in enhancing phosphorus removal. Phylogenetic analysis demonstrated a close relationship between viral ppk genes and their bacterial counterparts, suggesting the occurrence of horizontal gene transfer. Furthermore, experimental assays validated that viral ppk genes enhanced host phosphate removal capabilities. VCs carrying ppk genes were observed across diverse ecological and geographical contexts, suggesting their potential to bolster host functions in varied environmental and nutrient settings, spanning natural and engineered systems. These findings uncover a previously underappreciated mechanism by which viruses enhance phosphate removal in wastewater treatment plants. Overall, our study highlights the potential for leveraging virus-encoded genes to improve the efficiency of biological phosphorus removal processes, offering new insights into the microbial ecology of AS systems and the role of viruses in biogeochemical cycling.},
}

@article {pmid39475308,
year = {2024},
author = {Schrago, CG and Mello, B},
title = {Challenges in Assembling the Dated Tree of Life.},
journal = {Genome biology and evolution},
volume = {16},
number = {10},
pages = {},
pmid = {39475308},
issn = {1759-6653},
mesh = {*Phylogeny ; Evolution, Molecular ; Gene Transfer, Horizontal ; },
abstract = {The assembly of a comprehensive and dated Tree of Life (ToL) remains one of the most formidable challenges in evolutionary biology. The complexity of life's history, involving both vertical and horizontal transmission of genetic information, defies its representation by a simple bifurcating phylogeny. With the advent of genome and metagenome sequencing, vast amounts of data have become available. However, employing this information for phylogeny and divergence time inference has introduced significant theoretical and computational hurdles. This perspective addresses some key methodological challenges in assembling the dated ToL, namely, the identification and classification of homologous genes, accounting for gene tree-species tree mismatch due to population-level processes along with duplication, loss, and horizontal gene transfer, and the accurate dating of evolutionary events. Ultimately, the success of this endeavor requires new approaches that integrate knowledge databases with optimized phylogenetic algorithms capable of managing complex evolutionary models.},
}

*Phylogeny
Evolution, Molecular
Gene Transfer, Horizontal

@article {pmid39474943,
year = {2024},
author = {Sharma, P and Kishore, A and Singh, M},
title = {Single-use polyethylene terephthalate bottle-derived nanoplastics propagate antibiotic resistance in bacteria via transformation and outer membrane vesicle secretion.},
journal = {Nanoscale},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4nr02613f},
pmid = {39474943},
issn = {2040-3372},
abstract = {Plastic pollution arising from single-use plastic bottles (SUPBs) and containers leads to the formation of micro/nanoplastics (NPs). These NPs raise concerns due to their potential toxicity and interactions with microorganisms. In various environments, including our digestive system, both microorganisms and plastics coexist. The interactions between these NPs and microorganisms can have far-reaching consequences, potentially affecting the ecosystems and human health. Therefore, understanding these interactions is crucial for addressing the challenges posed by plastic pollution. This study investigated the role of NPs in propagating antibiotic resistance (AR), specifically through outer membrane vesicles (OMVs), which is a mechanism that has not been fully explored to date in terms of NPs' effects. To explore this, NPs were synthesized using polyethylene terephthalate (PET) SUPBs, mimicking the natural chemical composition of environmental nanoplastics, unlike previous studies, which used pure PET, polystyrene (PS) or other pure plastic materials. The resulting PET bottle-derived nanoplastics (PBNPs), which exhibited diverse shapes and sizes (50-850 nm), were found to facilitate horizontal gene transfer (HGT) through transformation and outer membrane vesicles (OMVs), enabling the transport of plasmids among bacteria. In transformation, PBNPs physically carried plasmids across the bacterial membrane. In another scenario, PBNPs induced oxidative stress and bacterial surface damage, which led to the upregulation of stress response-associated genes and the escalation of OMV secretion in E. coli. This novel pathway highlights how PBNPs contribute to AR gene dissemination, potentially exacerbating the global antibiotic resistance crisis. Furthermore, PBNPs mediate cross-species gene transfer from E. coli to Lactobacillus acidophilus, underscoring their impact on diverse microorganisms, including those in the human gut. Our findings suggest that nanoplastics may be an unrecognized contributor to the rising tide of antibiotic resistance, with significant consequences for human health and the environment. Molecular analyses revealed the upregulated expression of genes associated with stress response and OMV secretion, offering deeper insights into the biological mechanisms affected by PBNPs. This study offers crucial insights into the interactions of NPs and microorganisms for developing strategies to address the ecological and health implications of nanoplastic contamination.},
}

@article {pmid39472795,
year = {2024},
author = {Andriyanov, P and Zhurilov, P and Menshikova, A and Tutrina, A and Yashin, I and Kashina, D},
title = {Large-scale genomic analysis of Elizabethkingia anophelis.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1015},
pmid = {39472795},
issn = {1471-2164},
mesh = {*Flavobacteriaceae/genetics ; *Genome, Bacterial ; *Phylogeny ; *Genomics/methods ; Gene Transfer, Horizontal ; Humans ; Flavobacteriaceae Infections/microbiology ; Animals ; Drug Resistance, Bacterial/genetics ; },
abstract = {The recent emergence of Elizabethkingia anophelis as a human pathogen is a major concern for global public health. This organism has the potential to cause severe infections and has inherent antimicrobial resistance. The potential for widespread outbreaks and rapid global spread highlights the critical importance of understanding the biology and transmission dynamics of this infectious agent. We performed a large-scale analysis of available 540 E. anophelis, including one novel strain isolated from raw milk and sequenced in this study. Pan-genome analysis revealed an open and diverse pan-genome in this species, characterized by the presence of many accessory genes. This suggests that the species has a high level of adaptability and can thrive in a variety of environments. Phylogenetic analysis has also revealed a complex population structure, with limited source-lineage correlation. We identified diverse antimicrobial resistance factors, including core-genome and accessory ones often associated with mobile genetic elements within specific lineages. Mobilome analysis revealed a dynamic landscape primarily composed of genetic islands, integrative and conjugative elements, prophage elements, and small portion of plasmids emphasizing a complex mechanism of horizontal gene transfer. Our study underscores the adaptability of E. anophelis, characterized by a diverse range of antimicrobial resistance genes, putative virulence factors, and genes enhancing fitness. This adaptability is also supported by the organism's ability to acquire genetic material through horizontal gene transfer, primarily facilitated by mobile genetic elements such as integrative and conjugative elements (ICEs). The potential for rapid evolution of this emerging pathogen poses a significant challenge to public health efforts.},
}

*Flavobacteriaceae/genetics
*Genome, Bacterial
*Phylogeny
*Genomics/methods
Gene Transfer, Horizontal
Humans
Flavobacteriaceae Infections/microbiology
Animals
Drug Resistance, Bacterial/genetics

@article {pmid39471530,
year = {2024},
author = {Qi, H and Lv, J and Liao, J and Jin, J and Ren, Y and Tao, Y and Wang, D and Alvarez, PJJ and Yu, P},
title = {Metagenomic insights into microalgae-bacterium-virus interactions and viral functions in phycosphere facing environmental fluctuations.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122676},
doi = {10.1016/j.watres.2024.122676},
pmid = {39471530},
issn = {1879-2448},
abstract = {Despite the ecological and biotechnological significance of microalgae-bacterium symbionts, the response of host-virus interactions to external environmental fluctuations and the role of viruses in phycosphere remain largely unexplored. Herein, we employed algal-bacterial granular sludge (ABGS) with varying light intensity and organic carbon loading to investigate the mechanisms of microalgae-bacterium-virus symbionts in response to environmental fluctuations. Metagenomics revealed that enhanced light intensity decreased the diversity of microalgae, so did the diversity of symbiotic bacteria and viruses. As carbon sources decreased, bacteria prompted horizontal gene transfer in phycosphere by 12.76 %-157.40 %, increased the proportion of oligotrophs as keystone species (0.00 % vs 14.29 %) as well as viruses using oligotrophs as hosts (18.52 % vs 25.00 %). Furthermore, virus-carried auxiliary metabolic genes (AMGs) and biosynthetic gene clusters (BGCs) encoding vitamin B12 synthesis (e.g., cobS), antioxidation (e.g., queC), and microbial aggregation (e.g., cysE). Additionally, phylogenetic and similarity analysis further revealed the evolutionary origin and potential horizontal transfer of the AMGs and BGCs, which could potentially enhance the adaptability of bacteria and eukaryotic microalgae. Overall, our research demonstrates that environmental fluctuations have cascading effects on the microalgae-bacteria-virus interactions, and emphasizes the important role of viruses in maintaining the stability of the phycosphere symbiotic community.},
}

@article {pmid39470278,
year = {2024},
author = {Scherff, N and Rothgänger, J and Weniger, T and Mellmann, A and Harmsen, D},
title = {Real-time plasmid transmission detection pipeline.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0210024},
doi = {10.1128/spectrum.02100-24},
pmid = {39470278},
issn = {2165-0497},
abstract = {UNLABELLED: The spread of antimicrobial resistance among bacteria by horizontal plasmid transmissions poses a major challenge for clinical microbiology. Here, we evaluate a new real-time plasmid transmission detection pipeline implemented in the SeqSphere[+] (Ridom GmbH, Münster, Germany) software. Within the pipeline, a local Mash plasmid database is created, and Mash searches with a distance threshold of 0.001 are used to trigger plasmid transmission early warning alerts (EWAs). Clonal transmissions are detected using core-genome multi-locus sequence typing allelic differences. The tools MOB-suite, NCBI AMRFinderPlus, CGE MobileElementFinder, pyGenomeViz, and MUMmer, integrated in SeqSphere+, are used to characterize plasmids and for visual pairwise plasmid comparisons, respectively. We evaluated the pipeline using published hybrid assemblies (Oxford Nanopore Technology/Illumina) of a surveillance and outbreak data set with plasmid transmissions. To emulate prospective usage, samples were imported in chronological order of sampling date. Different combinations of the user-adjustable parameters sketch size (1,000 vs 10,000) and plasmid size correction were tested, and discrepancies between resulting clusters were analyzed with Quast. When using a sketch size of 1,000 with size correction turned on, the SeqSphere[+] pipeline agreed with the published data and produced the same clonal and carbapenemase-carrying plasmid clusters. EWAs were in the correct chronological order. In summary, the developed pipeline presented here is suitable for integration into clinical microbiology settings with limited bioinformatics knowledge due to its automated analyses and alert system, which are combined with the GUI-based SeqSphere[+] platform. Thus, with its integrated sample database, (near) real-time plasmid transmission detection is within reach in bacterial routine-diagnostic settings when long-read sequencing is employed.

IMPORTANCE: Plasmid-mediated spread of antimicrobial resistance is a major challenge for clinical microbiology, and monitoring of potential plasmid transmissions is essential to combat further dissemination. Whole-genome sequencing is often used to surveil nosocomial transmissions but usually limited to the detection of clonal transmissions (based on chromosomal markers). Recent advances in long-read sequencing technologies enable full reconstruction of plasmids and the detection of very similar plasmids, but so far, easy-to-use bioinformatic tools for this purpose have been missing. Here, we present an evaluation of an innovative real-time plasmid transmission detection pipeline. It is integrated into the GUI-based SeqSphere[+] software, which already offers core-genome multi-locus sequence typing-based pathogen outbreak detection. It requires very limited bioinformatics knowledge, and its database, automated analyses, and alert system make it well suited for prospective clinical application.},
}

@article {pmid39467614,
year = {2024},
author = {Gobbo, A and Fraiture, MA and Van Poelvoorde, L and De Keersmaecker, SCJ and Garcia-Graells, C and Van Hoorde, K and Verhaegen, B and Huwaert, A and Maloux, H and Hutse, V and Ceyssens, PJ and Roosens, N},
title = {Strategy to develop and validate digital droplet PCR methods for global antimicrobial resistance wastewater surveillance.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {96},
number = {11},
pages = {e11145},
doi = {10.1002/wer.11145},
pmid = {39467614},
issn = {1554-7531},
support = {//Sciensano (contract NAP-AMR)/ ; },
mesh = {*Wastewater/microbiology ; Real-Time Polymerase Chain Reaction/methods ; Environmental Monitoring/methods ; Polymerase Chain Reaction/methods ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; },
abstract = {According to World Health Organization (WHO), antimicrobial resistance (AMR) is currently one of the world's top 10 health threats, causing infections to become difficult or impossible to treat, increasing the risk of disease spread, severe illness, disability, and death. Accurate surveillance is a key component in the fight against AMR. Wastewater is progressively becoming a new player in AMR surveillance, with the promise of a cost-effective real-time tracking of global AMR profiles in specific regions. One of the most useful analytical methods for wastewater surveillance is currently based on real-time PCR (qPCR) and digital droplet PCR (ddPCR) technologies. As stated in the EU Wastewater Treatment Directive proposal, methodological standardization, including a workflow for method development and validation, will play a crucial role in global monitoring of AMR in wastewater. However, according to our knowledge, there are currently no qPCR and ddPCR methods for AMR surveillance available that have been validated according to international standard performance criteria. Therefore, this study proposes a workflow for the development and validation of PCR-based methods for a harmonized and global AMR surveillance, including the construction of specific sequence databases and microbial collections for an efficient method development and method specificity evaluation. Following this strategy, we have developed and validated four duplex ddPCR methods responding to international standard performance criteria, focusing on seven AMR genes (ARG's), including extended spectrum beta-lactam (blaCTX-M), carbapenem (blaKPC-2/3), tetracycline (tet(M)), erythromycin (erm(B)), vancomycin (vanA), sulfonamide (sul2), and aminoglycoside (aac(3)-IV), as well as one indicator of antibiotic (multi-) resistance and horizontal gene transfer, named the class I integron (intl1). The performance of these ddPCR methods was successfully assessed for their specificity, as no false-positive and false-negative results were observed. These ddPCR methods were also considered to be highly sensitive as showing a limit of detection below 25 copies of the targets. In addition, their applicability was confirmed using 14 wastewater samples collected from two Belgian water resource recovery facilities. The proposed study represents therefore a step forward to reinforce method harmonization in the context of the global AMR surveillance in wastewater. PRACTITIONER POINTS: In the context of wastewater surveillance, no PCR-based methods for global AMR monitoring are currently validated according to international standards. Consequently, we propose a workflow to develop and validate PCR-based methods for a harmonized and global AMR surveillance. This workflow resulted here in four duplex ddPCR methods targeting seven ARGs and one general indicator for mobilizable resistance genes. The applicability of these validated ddPCR methods was confirmed on 14 wastewater samples from two Belgian water resource recovery facilities.},
}

*Wastewater/microbiology
Real-Time Polymerase Chain Reaction/methods
Environmental Monitoring/methods
Polymerase Chain Reaction/methods
Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial

@article {pmid39459963,
year = {2024},
author = {Pu, F and Zhang, N and Pang, J and Zeng, N and Baloch, FB and Li, Z and Li, B},
title = {Deciphering the Genetic Architecture of Staphylococcus warneri Prophage vB_G30_01: A Comprehensive Molecular Analysis.},
journal = {Viruses},
volume = {16},
number = {10},
pages = {},
pmid = {39459963},
issn = {1999-4915},
support = {31271818//National Natural Science Foundation of China/ ; 2023-01//International Cooperation Project of Universities in Liaoning Province/ ; 2022030673-JH5/104//Liaoning Province Rural Science and Technology Special Action Project/ ; 22-319-2-13//Shenyang Science and Technology Project/ ; 202108857002//China Scholarship Council/ ; },
mesh = {*Genome, Viral ; *Staphylococcus/virology/genetics ; *Prophages/genetics/physiology ; *Phylogeny ; *Host Specificity ; *Open Reading Frames ; *Staphylococcus Phages/genetics/classification/physiology/ultrastructure ; *Lysogeny ; DNA, Viral/genetics ; Genomics/methods ; },
abstract = {The current knowledge of Staphylococcus warneri phages is limited, with few genomes sequenced and characterized. In this study, a prophage, vB_G30_01, isolated from Staphylococcus warneri G30 was characterized and evaluated for its lysogenic host range. The phage was studied using transmission electron microscopy and a host range. The phage genome was sequenced and characterized in depth, including phylogenetic and taxonomic analyses. The linear dsDNA genome of vB_G30_01 contains 67 predicted open reading frames (ORFs), classifying it within Bronfenbrennervirinae. With a total of 10 ORFs involved in DNA replication-related and transcriptional regulator functions, vB_G30_01 may play a role in the genetics and transcription of a host. Additionally, vB_G30_01 possesses a complete set of genes related to host lysogeny and lysis, implying that vB_G30_01 may influence the survival and adaptation of its host. Furthermore, a comparative genomic analysis reveals that vB_G30_01 shares high genomic similarity with other Staphylococcus phages and is relatively closely related to those of Exiguobacterium and Bacillus, which, in combination with the cross-infection assay, suggests possible cross-species infection capabilities. This study enhances the understanding of Staphylococcus warneri prophages, providing insights into phage-host interactions and potential horizontal gene transfer.},
}

*Genome, Viral
*Staphylococcus/virology/genetics
*Prophages/genetics/physiology
*Phylogeny
*Host Specificity
*Open Reading Frames
*Staphylococcus Phages/genetics/classification/physiology/ultrastructure
*Lysogeny
DNA, Viral/genetics
Genomics/methods