@article {pmid42667951,
year = {2026},
author = {Kofler, R and Saadain, S and Pinhasi, R},
title = {Genomic time-series data may reveal the true magnitude of horizontal exchange between species.},
journal = {Current opinion in insect science},
volume = {78},
number = {},
pages = {101608},
doi = {10.1016/j.cois.2026.101608},
pmid = {42667951},
issn = {2214-5753},
mesh = {Animals ; *Gene Transfer, Horizontal ; *DNA Transposable Elements ; Genomics ; *Insecta/genetics ; },
abstract = {Species largely evolve in isolation, with little exchange of genetic material between them. Occasionally, however, mechanisms like horizontal transfer disrupt this isolation and transfer genetic information between species. Transposable elements (TEs), short DNA sequences that can multiply within genomes, are frequently involved in such exchanges. The frequency of horizontal transposon transfer (HTT) between species remains a fundamental open question in biology, as classical sequence comparison approaches may substantially underestimate the true extent of HTT. In this review, we highlight that genomic time-series (GTS), that is, genomes of specimens sampled across different years in the past, enable an alternative approach that may provide a more unbiased estimate of the true magnitude of HTT between species. Analysis of GTS in fruit flies suggests that HTT may be rampant, with 12 events found over the past 200 years. Species may thus exchange genetic material far more frequently than previously thought. We discuss the pros and cons of different approaches for detecting HTT, show how GTS can be generated for diverse species, and highlight various strategies for identifying HTT events. GTS may generally constitute a valuable resource for addressing a broad range of evolutionary questions.},
}

Animals
*Gene Transfer, Horizontal
*DNA Transposable Elements
Genomics
*Insecta/genetics

@article {pmid42834358,
year = {2026},
author = {Marchi, A and Wenne, M and Varga, V and Bengtsson-Palme, J},
title = {On the hunt for candidate genes involved in host-adaptation in Pseudomonas aeruginosa using comparative genomics.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42834358},
issn = {1471-2164},
support = {KAW 2020.0239//Knut och Alice Wallenbergs Stiftelse/ ; 2020-03629//Vetenskapsrådet/ ; FFL21-0174//Stiftelsen för Strategisk Forskning/ ; },
mesh = {*Pseudomonas aeruginosa/genetics/physiology/isolation & purification ; *Genomics/methods ; Humans ; Virulence Factors/genetics ; *Host Adaptation/genetics ; Genome, Bacterial ; Bacterial Proteins/genetics ; Multigene Family ; Gene Transfer, Horizontal ; Pseudomonas Infections/microbiology ; *Host-Pathogen Interactions/genetics ; },
abstract = {BACKGROUND: Pseudomonas aeruginosa is an opportunistic pathogen responsible for causing severe hospital-acquired infections, largely due to its adaptability, diverse range of virulence factors and drug resistance mechanisms. Despite extensive research, a substantial portion of the genome of P. aeruginosa remains functionally uncharacterized. The aim of this study was to identify candidate host-adaptation genes, including potential virulence factors, among these numerous uncharacterized genes.

RESULTS: We performed a comparative genomic analysis of P. aeruginosa strains isolated from human clinical sources versus those from natural environments to identify clusters of homologous proteins significantly enriched with sequences from bacteria isolated from humans. Our analysis revealed that approximately 3% of all protein clusters showed significant enrichment in sequences from human isolates. Functional characterization of 45 selected clusters with particularly large enrichment of human isolates showed that these clusters contained genes with roles primarily related to host interaction and horizontal gene transfer. Notably, twelve of the 45 selected clusters consisted of genes with unknown function, suggesting the existence of potentially novel virulence factors or genes involved in the infection process within human-derived isolates.

CONCLUSIONS: Our findings highlight specific uncharacterized protein clusters as promising targets for future investigation. The identification of both known virulence-associated functions and uncharacterized proteins among human-enriched clusters demonstrates the ability of our comparative genomics approach to detect established as well as potentially novel candidate host-adaptation genes. These findings further suggest that this strategy may be broadly applicable to the study of other opportunistic pathogens.},
}

*Pseudomonas aeruginosa/genetics/physiology/isolation & purification
*Genomics/methods
Humans
Virulence Factors/genetics
*Host Adaptation/genetics
Genome, Bacterial
Bacterial Proteins/genetics
Multigene Family
Gene Transfer, Horizontal
Pseudomonas Infections/microbiology
*Host-Pathogen Interactions/genetics

@article {pmid42835138,
year = {2026},
author = {Aguirre-Carvajal, K and Munteanu, CR and Armijos-Jaramillo, V},
title = {A machine learning framework for interpreting phylogenetic tree patterns in interkingdom horizontal gene transfer.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1891949},
pmid = {42835138},
issn = {2673-7647},
abstract = {INTRODUCTION: Horizontal gene transfer (HGT), the movement of genetic material between unrelated organisms, is widely recognized as an important driver of genome evolution in bacteria. In eukaryotes, however, the evolutionary impact of HGT remains debated. The identification of interkingdom HGT (iHGT) is especially challenging due to the lack of gold standard methods. While automated approaches for iHGT candidate detection exist, the interpretation of phylogenetic tree topologies into biologically meaningful evolutionary patterns has traditionally depended on expert manual inspection, a process that is subjective, difficult to reproduce, and not scalable to large datasets.

METHODS: We present a computational framework that formalizes phylogenetic tree interpretation as a supervised machine-learning problem. We define five recurrent phylogenetic patterns (iHGT, NoHGT, Limited donor evidence, Multiple major clades, and Patchy phylogeny) and developed a feature-extraction pipeline that captures taxonomic composition and phylogenetic topology through six biologically interpretable descriptors derived from unrooted gene trees. Several machine-learning algorithms were evaluated using repeated stratified cross-validation, and model interpretability was assessed through permutation importance, SHAP analysis, rule-based baselines, and feature ablation. Performance was further validated on simulated datasets, real biological iHGT candidates, and an independently annotated external dataset.

RESULTS: A Random Forest (RF) classifier achieved the best performance (AUC-ROC = 0.98; accuracy = 0.89). Topological distance and lineage-distribution features were identified as the strongest contributors to classification performance. Feature ablation and rule-based baseline comparisons demonstrated that model performance cannot be explained solely by explicit annotation rules and benefits from combining clade-composition and topology-based information. The RF classifier showed low misclassification rates on simulated and real biological datasets (7.8% and 10.43%, respectively), showed substantial agreement (69.4%) with an independently annotated external dataset, and consistently outperformed AVP (Alienness vs. Predictor), Alien Index, and HGT Index across all evaluated metrics.

CONCLUSION: These results support the use of machine learning for the automated, reproducible, and scalable classification of expert-defined phylogenetic patterns. The framework also highlights that some topologies commonly interpreted as evidence of iHGT may reflect alternative evolutionary processes, emphasizing the need for cautious and context-aware inference.},
}

@article {pmid42836310,
year = {2026},
author = {Haldar, A and Yosef, I and Goren, MG and Globus, R and Yakunina, M and Mahata, T and Qimron, U},
title = {Adaptation-coupled CRISPRi identifies antibiotic-sensitizing genes leading to a novel plasmid selection marker.},
journal = {Nucleic acids research},
volume = {54},
number = {18},
pages = {},
pmid = {42836310},
issn = {1362-4962},
support = {101248381//H2020 European Research Council/ ; 818878//H2020 European Research Council/ ; //ERC/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology ; Escherichia coli/genetics/drug effects ; *Plasmids/genetics ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; *CRISPR-Cas Systems ; DNA Gyrase/genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Salmonella/genetics/drug effects ; Shigella/genetics/drug effects ; },
abstract = {Antibiotic resistance through horizontal gene transfer is a major challenge in microbiology and medicine. We describe a CRISPR-based screening system that couples spacer adaptation with gene repression to identify bacterial genes that sensitize bacteria to antibiotics. We used this screening system in Escherichia coli, on seven different antibiotics to select spacers that conferred resistance to them. The screen identified both known and previously unrecognized genes that modulate antibiotic susceptibility. We defined this collection of genes that sensitize bacteria to antibiotics as the 'sensitasome'. Among the identified targets were the essential genes gyrA and gyrB, whose repression increased resistance to multiple antibiotics. Some sensitization genes exhibited a clear trade-off: their repression conferred resistance to certain antibiotics while increasing susceptibility to others. Sensitasome-targeting spacers were also effective in Shigella and Salmonella, indicating that the resistance mechanism is conserved across species. Finally, we repurposed a selected spacer as a CRISPR-based antibiotic selection marker using the compact Cas12m effector. Together, these findings establish adaptation-coupled CRISPRi as a simple platform for discovering antibiotic sensitization genes and provide an environmentally safer alternative to conventional antibiotic resistance markers.},
}

*Anti-Bacterial Agents/pharmacology
Escherichia coli/genetics/drug effects
*Plasmids/genetics
*Genes, Bacterial
*Drug Resistance, Bacterial/genetics
*CRISPR-Cas Systems
DNA Gyrase/genetics
*Clustered Regularly Interspaced Short Palindromic Repeats
Salmonella/genetics/drug effects
Shigella/genetics/drug effects

@article {pmid42836481,
year = {2026},
author = {Xie, L and Wang, L and Ma, L and Wang, J and Wu, D and Lin, A and Wang, L and Ye, M and Li, X and Zhang, T and Zhu, D},
title = {Microplastic-driven carbon availability differentiates phage-host interactions in shaping soil resistome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag258},
pmid = {42836481},
issn = {1751-7370},
abstract = {The growing prevalence of microplastics (MPs) in agroecosystem has raised significant concerns regarding their ability in facilitating the dissemination of antibiotic resistance genes (ARGs). Biodegradable and nondegradable MPs exhibited inherently different degradation rates, resulting in divergent carbon bioavailability that might trigger distinct microbial response and ARG profiles. Here, by integrating multi-omics (metagenomics, virome and metatranscriptomics) with experimental validation, we explored how microbial responses to MPs impacted ARG dissemination in a long-term field experiment. We showed that both biodegradable and nondegradable MPs significantly increased ARG abundance and transcriptional activity, differing in the drive mechanisms. Biodegradable MPs triggered bacterial oxidative stress and SOS response, increasing mobile genetic elements abundance and horizontal gene transfer of ARGs. Accordingly, increasing proportion of lysogenic phages and intensified phage-host interactions might promote ARG transduction through lysogenic conversion. In contrast, nondegradable MPs increased recalcitrant carbon, which enriched bacteria harboring genes for complex compound degradation. ARG-carrying bacteria within these taxa gained fitness advantages, facilitating their enrichment and ARG proliferation. Concurrently, phages infecting ARG-carrying bacteria encoded more auxiliary metabolic genes in complex carbohydrate metabolism, thereby enhancing host competitiveness and promoting ARG spread. In vitro validation experiments confirmed that lysogenic phages facilitated transduction of ARGs under biodegradable MPs, while phage-encoded auxiliary metabolic genes conferred growth advantages on ARG-carrying bacteria utilizing recalcitrant carbon source, consistent with conditions induced by nondegradable MPs. Our findings clarify how phages differentially impacted ARG profiles under biodegradable and nondegradable MPs, underscoring the importance of considering phage-mediated processes in assessing the risks of MPs and ARG dissemination.},
}

@article {pmid42836822,
year = {2026},
author = {Malaluan, RPP and Dy, RLV},
title = {Acquisition of novel arrays via horizontal gene transfer rewires CRISPR-mediated defense in Pseudomonas aeruginosa.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0033926},
doi = {10.1128/jb.00339-26},
pmid = {42836822},
issn = {1098-5530},
abstract = {UNLABELLED: Clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) systems form the adaptive immunity of prokaryotes, conferring sequence-specific protection against genetic parasites. Here, we functionally characterized the type I-F CRISPR-Cas system of Pseudomonas aeruginosa ATCC 10145 (PA10145), which led us to discover the existence of an isolated CRISPR array unique to this system. Its core CRISPR-Cas system is composed of a cas operon flanked by two divergently organized arrays: CRISPR2 and CRISPR1. Meanwhile, the isolated CRISPR array, CRISPR3, was found ~1.3 million bp away from cas. The cas and three CRISPR arrays together function toward adaptive immunity, eliminating plasmids engineered with protospacer targets. If plasmids possessed an intact protospacer adjacent motif (PAM), hyperactive adaptation was stimulated in all CRISPR arrays of PA10145, whereas minimal to no adaptation was observed when the PAM was mutated. Spacer acquisition via interference-driven adaptation proceeds through strand-biased priming in PA10145. Interestingly, the isolated CRISPR3 and cas-adjacent CRISPR2 have nearly identical leader sequences, with only 3 bp mismatches. Of the 1,196 P. aeruginosa genomes analyzed, all 281 isolated arrays only occur as type I-F with similarly matching leaders to CRISPR2. Integrative conjugative elements and prophages only associate with CRISPR2 and CRISPR3, suggesting that isolated arrays might have originated from recombination events involving CRISPR2 as facilitated by these highly transmissible mobile genetic elements. Tracing evolutionary trajectories of the isolated CRISPR3 relative to cas-adjacent arrays revealed that CRISPR3 is horizontally transferred across P. aeruginosa genomes. Taken together, these results implicate the role of horizontally acquired isolated arrays in CRISPR-mediated pan-immunity as gateways to mobilize genetic memories.

IMPORTANCE: Clustered regularly interspaced short palindromic repeat (CRISPR) arrays are typically located adjacent to cas genes, constituting the adaptive immune system. However, a substantial subset of CRISPR arrays, called isolated arrays, is found distantly located from their cognate cas operons. Despite their prevalence, the functional significance and evolutionary implications of isolated arrays have remained poorly understood. Here, we show that isolated arrays are active components of type I-F CRISPR-Cas systems in Pseudomonas aeruginosa. These arrays are continuously updated through hyperactive strand-biased primed adaptation and are transferred horizontally across P. aeruginosa, acting as conduits of immunological memory and proponents of CRISPR-mediated pan-immunity. We posit that bacterial populations mobilize these isolated arrays to maintain transferable memory in the pangenome while remaining compatible with ongoing horizontal gene transfer.},
}

@article {pmid42838283,
year = {2026},
author = {Kitagawa, H and Nakano, S and Tadera, K and Koide, S and Otake, S and Sugawara, Y and Akeda, Y and Ohnishi, M and Sugai, M and Ohge, H},
title = {Phylogenetically Distinct CC128-Related Group A Streptococcus dysgalactiae subsp. equisimilis Lineages Identified in Bacteremia Cases in Japan.},
journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy},
volume = {},
number = {},
pages = {103099},
doi = {10.1016/j.jiac.2026.103099},
pmid = {42838283},
issn = {1437-7780},
abstract = {Streptococcus dysgalactiae subsp. equisimilis (SDSE) expressing the Lancefield group A antigen is an uncommon variant that is thought to have acquired the group A carbohydrate synthesis genes through horizontal gene transfer from Streptococcus pyogenes. Its prevalence and genomic characteristics remain incompletely understood. We retrospectively investigated 48 SDSE isolates recovered from blood cultures at a tertiary care hospital in Japan, between 2010 and 2023. Lancefield grouping was performed for all isolates, and whole-genome sequencing and phylogenetic analyses were performed for the two group A SDSE isolates. Among the 48 isolates, 44 (91.7%) were group G, two (4.2%) were group A, and two (4.2%) were group C. The two group A isolates, HUSD042 and HUSD047, belonged to clonal complex 128 (CC128); HUSD042 belonged to sequence type 177 (ST177), a single-locus variant of ST128, and HUSD047 belonged to ST128. Both isolates carried the emm subtype stG485.0. Comparative genomic analysis revealed a hybrid gac/gcc carbohydrate synthesis locus, in which the central region corresponding to the group C SDSE gccF-gccK region was replaced by an S. pyogenes-derived gacF-gacL region, consistent with a previously described invasive ST128-related group A SDSE lineage. Bayesian phylogenetic analysis showed that HUSD042 clustered within a clade predominantly composed of Japanese isolates, whereas HUSD047 clustered within a clade composed mainly of isolates from the United States. These findings demonstrate the presence of phylogenetically distinct CC128-related group A SDSE lineages in Japan and highlight the genomic diversity of this rare variant. Continued genomic surveillance with broader geographic sampling and detailed epidemiological information is warranted to clarify its evolution and geographic distribution.},
}

@article {pmid42838473,
year = {2026},
author = {Artuso, I and Salaris, S and Cenere, G and Losasso, C and Scaltriti, E and Bracchi, C and Bolzoni, L and Lucarelli, C and Garcia-Fernandez, A and Di Giampietro, G and De Marchis, ML and Villa, L and Barco, L},
title = {Genomic evidence of lac operon acquisition in Salmonella Strathcona clinical isolates in Italy.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {145},
number = {},
pages = {106040},
doi = {10.1016/j.meegid.2026.106040},
pmid = {42838473},
issn = {1567-7257},
abstract = {We report six lactose-fermenting Salmonella Strathcona isolates carrying a lac operon on an IncHI2/IncHI2A plasmid. Whole-genome sequencing revealed intact lacI-lacZ-lacY and truncated lacA genes. These isolates represent the first detection of lactose-fermenting S. Strathcona, highlighting a risk of diagnostic errors due to reliance on lactose fermentation-based phenotypic identification.},
}

@article {pmid41865193,
year = {2026},
author = {Mathkor, DM and Aldairi, AF and Faidah, H and Babalghith, AO and Johargy, AK and Ahmad, F and Haque, S and Bantun, F},
title = {The role of breastfeeding in modulating antimicrobial resistance in neonates: a systematic review.},
journal = {Pediatric research},
volume = {100},
number = {2},
pages = {652-665},
pmid = {41865193},
issn = {1530-0447},
mesh = {Humans ; *Breast Feeding ; Infant, Newborn ; *Milk, Human/microbiology ; *Gastrointestinal Microbiome ; Female ; Anti-Bacterial Agents/therapeutic use ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; },
abstract = {Antimicrobial resistance (AMR) is a growing health concern in neonates. Breastfeeding potentially plays a pivotal role in modulating neonatal gut microbiota, thereby influencing the acquisition and transmission of AMR genes (ARGs). This systematic review evaluates the links between breastfeeding and the origin of neonatal gut microbiota and AMR. Selection of pertinent studies published between 2015 and 2025 focusing on major outcome measures of neonatal AMR and ARG transfer was performed on scholarly databases. Following quality assessment, 22 studies met the inclusion criteria for further consideration. Evidence consistently demonstrates that breast milk is an active contributor to the microbial and genetic landscape of the neonatal gut microbiome. Further, studies implicated breast milk as a source of ARG transfer in neonates. Other reports indicated that exclusive breastfeeding and human milk-associated bioactive compounds promoted the colonization of beneficial commensals, limited colonization of multidrug-resistant species, and suppressed horizontal transfer of ARGs. Interestingly, maternal factors, such as maternal antibiotic history, lifestyle, and overall health status, appeared to influence the links between breast milk and transmission and impact of ARGs in neonates. In conclusion, while breastfeeding-based strategies are important to neonatal AMR mitigation, further mechanistic studies are required to establish causal pathways. IMPACT: Breastfeeding has an active role in altering neonatal gut microbiota and influences antimicrobial resistance (AMR) acquisition. This review synthesizes evidence from 2015-2025 indicating that breastfeeding is both a source of antimicrobial resistance genes (ARGs) and contains bioactive components that suppress ARG transmission and promote beneficial colonization. Maternal factors, such as antibiotic exposure, lifestyle, and overall health, potently influence these links. Mechanistic comprehension of the links between breastfeeding, neonatal microbiome, and AMR acquisition may allow identification of prevention strategies against neonatal infections. The analyses underscore the need for longitudinal, mechanistic studies to determine causal relationships and long-term effects of breastfeeding on neonatal AMR.},
}

Humans
*Breast Feeding
Infant, Newborn
*Milk, Human/microbiology
*Gastrointestinal Microbiome
Female
Anti-Bacterial Agents/therapeutic use
*Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal

@article {pmid42824066,
year = {2026},
author = {Dahal, SP and Munang'andu, HM and Solberg, A and Sørum, H},
title = {The R plasmid pRAS2 in the fish pathogen Aeromonas salmonicida is a global mediator of antibiotic resistance in aquaculture and can be used by pRAS3 for mobilization.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1872994},
pmid = {42824066},
issn = {1664-302X},
abstract = {Horizontal gene transfer (HGT) mediated by conjugative plasmids is a major driver of antimicrobial resistance (AMR) dissemination in aquatic environments. In Aeromonas salmonicida, plasmid-mediated HGT is largely driven by the pRAS plasmid family. Here we present genomic and experimental characterization of pRAS2 from A. salmonicida strain 1682/92 and demonstrate its role in helper-dependent mobilization of the co-resident pRAS3. Whole genome sequencing (WGS) divided the pRAS2 backbone into three modules. Module A encodes replication, maintenance and inheritance stability functions, including transposase, resolvase, partitioning and antitoxin-associated genes. Module B encodes a canonical type IV secretion system (T4SS) conjugation module containing virB2-virB6, virB8-virB11 and virD4 with virB2 and virB5 forming the transfer pilus. Module C encodes the resistance determinants sul2, aph(6)-Id, neo and Tet 31. Modules A and B were organized as in plasmids of Vibrio alginolyticus, Edwardsiella piscicida and Piscirickettsia salmonis, indicating that pRAS2 shares a conserved backbone with plasmids of other aquatic bacteria, including fish pathogens isolated on different continents. Module C was the most variable region: sul2 and aph(6)-Id were shared with pEIB202 of E. piscicida, whereas the tetracycline resistance determinant remained the same, being Tet 31 in pRAS2 as well as in pEIB202, p3PS10 and p3PS11, but absent from pVb1978 (Vibrio alginolyticus), pVIM-20710 (Enterobacter hormaechei) and p4PS9. The pRAS3 plasmids of strains 1682/92 and 2131/90, used as donors in conjugation experiments with an Escherichia coli DH5α recipient, carried the same mobilization-associated (MOB) genes and the tetracycline resistance determinant Tet C. Transfer of pRAS3 occurred only from strain 1682/92, which carried both pRAS2 and pRAS3; no transconjugant colonies were recovered from strain 2131/90, which carried pRAS3 alone. WGS showed an identical organization of the MOB, tetA(C) and tetR(C) genes in the 1682/92 donor and its transconjugant, providing experimental evidence that pRAS2 functions as a conjugative helper plasmid mediating mobilization of pRAS3. Conjugation trials performed with these strains between 1993 and 1995 further show that pRAS2 is self-transmissible, transferring autonomously at a frequency approximately three orders of magnitude higher than that of its co-mobilization of pRAS3. This demonstrates plasmid-plasmid cooperation within the pRAS plasmid family as a mechanism supporting the spread of AMR genes in aquatic bacterial communities.},
}

@article {pmid42825581,
year = {2026},
author = {Fang, C and Zhou, Z and Li, J and Zhang, X and Xia, J and Liu, S and Zhao, Y and Xu, X and Shang, S and Zhou, M},
title = {Genomic characterization of carbapenem-resistant organisms from pediatric patients with hematological malignancies and genomic comparison of infection versus intestinal colonizing strains.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0171926},
doi = {10.1128/spectrum.01719-26},
pmid = {42825581},
issn = {2165-0497},
abstract = {UNLABELLED: This study aimed to characterize the species distribution, sequence types, and antimicrobial resistance mechanisms of carbapenem-resistant organisms (CROs) in pediatric patients with hematological malignancies, and to clarify the genomic relationship between clinical infectious CROs and intestinal colonizing CROs. Non-duplicate infectious CRO strains and paired intestinal colonizing CROs were collected from 2020 to 2024. Whole-genome sequencing and bioinformatics analyses were performed to identify bacterial species, multilocus sequence types, resistance genes, mobile genetic elements, and genomic relatedness. Seven CRO species were identified, dominated by Pseudomonas aeruginosa, Klebsiella pneumoniae, and Enterobacter hormaechei. A total of 34 carbapenem resistance-associated genes were detected, with efflux pump overexpression and antibiotic inactivation as the main mechanisms. Three patients carried both infectious and intestinal CROs. Two pairs showed nearly identical genomes (average nucleotide identity >99.99%), confirming infections originated from intestinal colonization. One pair belonged to different species but shared an identical KPC-2 gene located on the same Tn7247-like transposon, indicating potential horizontal gene transfer. Diverse CROs and corresponding resistance mechanisms are prevalent in pediatric patients with hematological malignancies. This study identifies the dominant CRO species and key resistance mechanisms in this high-risk population, supporting the gastrointestinal tract as a potential reservoir for CROs, and indicating the likelihood of horizontal transmission of carbapenemase genes. These findings underscore the necessity of intensive surveillance and strict infection control measures to curb the dissemination of CROs in vulnerable pediatric populations.

IMPORTANCE: Carbapenem-resistant organisms (CROs) cause life-threatening infections in pediatric patients with hematological malignancies, who are highly vulnerable due to chemotherapy-induced immunosuppression. This study characterized CRO species, resistance mechanisms, and genomic links between infectious and intestinal colonizing strains in this population. We confirmed that intestinal colonization is an important source of subsequent CRO infections and identified interspecies horizontal transfer of the carbapenemase gene KPC-2 via a Tn7247-like transposon. These findings highlight the critical need for enhanced intestinal CRO screening and strict infection control measures to protect this vulnerable pediatric group.},
}

@article {pmid42826078,
year = {2026},
author = {Abubakar, TM and Mohd Zain, NA},
title = {Wastewater surveillance of tetracycline resistance genes: a global bibliometric and trend analysis.},
journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering},
volume = {},
number = {},
pages = {1-26},
doi = {10.1080/10934529.2026.2740561},
pmid = {42826078},
issn = {1532-4117},
abstract = {Tetracycline resistance genes (TRGs) in wastewater pose environmental and public health risks through antimicrobial resistance dissemination. However, the global development of wastewater surveillance for TRG monitoring remains insufficiently characterized. Scopus-indexed TRG wastewater surveillance research (2001-2025) was analyzed using bibliometric methods, yielding 700 articles after screening. Data were cleaned using biblioMagika[®] and OpenRefine, with VOSviewer used for keyword co-occurrence analysis. Temporal trends were assessed using the Mann-Kendall test, Sen's slope estimator, and Hamed-Rao correction for serial autocorrelation. Publication output increased significantly (τ = 0.891, P = 1.15 × 10[-9]; Sen's slope ≈ 3.84 publications/year) and remained significant after autocorrelation correction (N/N* ≈ 3.16, P = 6.16 × 10[-4]). China and the United States led publication output (370 and 99 publications, respectively), while publication volume was not significantly associated with normalized citation impact (r = 0.163, P = 0.436). Environmental science and microbiology dominated. Six thematic clusters centered on antibiotic resistance genes, horizontal gene transfer, metagenomics, and wastewater treatment. TRG wastewater surveillance research is expanding rapidly, highlighting the need for international collaboration, methodological standardization, and capacity building within a One Health framework.},
}

@article {pmid42826521,
year = {2026},
author = {Cancino-Muñoz, I and González-Rubio, JM and Coscollá, M and González-Camacho, F},
title = {Genomic and phenotypic characterization of a novel recombinant Legionella pneumophila lineage associated with long-term persistence in a building water system and recurrent legionellosis outbreaks.},
journal = {Water research},
volume = {308},
number = {Pt C},
pages = {127035},
doi = {10.1016/j.watres.2026.127035},
pmid = {42826521},
issn = {1879-2448},
abstract = {Understanding Legionella pneumophila microevolution within building water systems is crucial for effective long-term water safety plans. We investigated an exceptional 20-year contamination case within a closed, state-managed residential facility where routine engineering controls, including hyperchlorination and thermal shocks, systematically failed. Integrating genomic surveillance, transcriptomics, 3D biofilm characterisation and cell infection models, we show this persistence was driven by the in situ emergence of a novel recombinant strain (ST3043), which achieved over 80% dominance. Phylodynamic modelling revealed that this recombination event, involving the acquisition of a 225-kb fragment that rewired a cyclic-di-GMP hub, occurred at the time of the building's commissioning. This proves that the infrastructure acted as an evolutionary sieve. Importantly, while the ancestral parental lineages remained confined to minor environmental niches, ST3043 underwent sharp phenotypic divergence. Biofilm architectural characterisation revealed that, whereas parental strains produced thin, compact layers (∼24 µm), ST3043 developed a complex 3D matrix featuring a non-adherent, loose fraction (∼90 µm), which occupied 95% of the total biofilm space. Viability assays showed that cells within this dispersal compartment had high metabolic activity and acted as an efficient seeding source in the liquid phase. Furthermore, detached ST3043 cells displayed optimised fitness, with robust intracellular replication inside human macrophage and epithelial models, compared to impaired parental cells. This combination of enhanced environmental persistence, efficient dispersal and intracellular fitness may have contributed to the predominance of ST3043 among clinical isolates linked to the facility, with its high environmental abundance likely increasing the opportunity for human exposure. Overall, localised, infrastructure-driven recombination may contribute to the emergence and persistence of successful clones by combining environmental dominance with traits that may facilitate infection, thereby exposing specific vulnerabilities.},
}

@article {pmid42828074,
year = {2026},
author = {Oktem Okullu, S and Akcelik-Deveci, S and Buyukcolak-Cebeci, Y and Gokduman, SN and Sele, G},
title = {Bacterial extracellular vesicles as central mediators of microbiota-host communication.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1910885},
pmid = {42828074},
issn = {1664-302X},
abstract = {Bacterial extracellular vesicles (BEVs) are nanoscale, lipid bilayer-enclosed structures released by both Gram-negative and Gram-positive bacteria that act as active mediators of microbial and host-microbe communication rather than simple byproducts of membrane turnover. By packaging proteins, nucleic acids, lipids, and metabolites, BEVs participate in quorum sensing, biofilm regulation, horizontal gene transfer, and immune modulation, with functional outcomes that depend strongly on microbial origin and environmental context: pathogen-derived BEVs frequently promote inflammation and tissue damage, whereas commensal- and probiotic-derived BEVs are more often linked to epithelial protection and immune regulation. These properties have positioned BEVs as promising translational tools for biomarker discovery, vaccine development, and engineered drug delivery. However, vesicle heterogeneity, inconsistent isolation and purification methods, and an incomplete understanding of in vivo behavior continue to limit reproducibility and slow clinical translation. Here, we synthesize current evidence on BEV biogenesis, cargo selection, and biological function, and outline the methodological and translational challenges that must be addressed to establish BEVs as a validated interface between microbial activity and host physiology.},
}

@article {pmid42833337,
year = {2026},
author = {Yang, Y and Chen, W and Wang, J and Gao, X and Wang, G and Zou, L and Li, S and Li, G and Yuan, J},
title = {Oxygen availability shapes microbial community composition and function to determine antibiotic resistance genes and expression during composting: A pilot-scale study.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129287},
doi = {10.1016/j.envpol.2026.129287},
pmid = {42833337},
issn = {1873-6424},
abstract = {Temperature was considered the primary factor reducing antibiotic resistance genes (ARGs) during composting, with oxygen availability serving as the fundamental driver of temperature differences. However, how different oxygen levels shaped the composition and function of microbial communities, and subsequently affected ARGs and resistance expression during composting, remained unclear. Here, a pilot-scale long-term thermophilic aerobic and mesophilic facultative composting were constructed with metagenomics and stress (Oxygen/Antibiotic) plate screening to reveal the resistance potential and direct risk. The ratios of aerobic, facultative, and anaerobic bacteria were 1:0.94:0.75 in aerobic composting, and 1:0.96:0.99 in facultative composting. Metabolic functions were significantly enriched in aerobic composting, promoting temperature rise (peak 54 °C). In facultative composting, functions related to horizontal gene transfer and transcription/translation were enriched. Compared with mesophilic facultative composting, aerobic composting significantly reduced ARGs abundance (from 4.80 to 3.59 CPC) and mobility (from 3.66 to 2.27 CPC). ARGs hosts in aerobic composting were widely distributed, predominantly among aerobic microorganisms, while ARGs hosts in facultative composting were more concentrated, mostly among facultative anaerobes. The relative abundance of culturable antibiotic-resistant bacteria (25.00% vs. 15.88%) and active antibiotic-resistant pathogens (44.04% vs. 6.68%) were significantly higher in facultative composting than in aerobic composting. This study revealed the pathway by which oxygen shaped the composition and function of microorganisms with different oxygen requirements, thereby influencing compost antibiotic resistance, providing a theoretical basis for the safe application of manure to agricultural fields.},
}

@article {pmid42833977,
year = {2026},
author = {Li, W and Sun, J and Wu, Q and Kwok, LY and Dong, G and Sun, Z},
title = {Corrigendum to "Global genomics of Lactococcus lactis: horizontal gene transfer and intergenic variation drive multiple domestication and dairy adaptation" [J. Adv. Res. 83 (2026) 25-36].},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.09.016},
pmid = {42833977},
issn = {2090-1224},
}

@article {pmid42834255,
year = {2026},
author = {Morgado, SM and da Fonseca, EL and Vicente, ACP},
title = {Vibrio repeats (VXRs) play a role in horizontal dissemination of sedentary chromosomal integron-associated antibiotic resistance genes across Vibrio species.},
journal = {Functional & integrative genomics},
volume = {26},
number = {1},
pages = {},
pmid = {42834255},
issn = {1438-7948},
support = {SEI-260003/019688/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; },
mesh = {*Integrons/genetics ; *Vibrio/genetics/drug effects/classification ; *Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Phylogeny ; Chromosomes, Bacterial/genetics ; Genome, Bacterial ; },
abstract = {Sedentary chromosomal integrons (SCIs) are large integrons that harbor extensive arrays of gene cassettes and constitute major reservoirs of bacterial genetic diversity. In Vibrio, SCI cassettes are flanked by species-associated attC repeats, here referred to as Vibrio species repeats (VXRs). Although SCIs have been proposed as ancestral sources of antibiotic resistance genes (ARGs), the extent to which SCI-associated ARGs are exchanged among Vibrio species remains poorly understood. To investigate the dynamics of SCI-associated ARGs, we analyzed 37,812 genomes representing 181 Vibrio species. Using VXR mapping, comparative phylogenetics, and genome screening, we identified 8,679 putative ARG cassettes distributed across 8,517 genomes from 11 species. Despite the diversity of VXRs identified in SCIs, ARG cassettes were predominantly associated with a small subset of related VXRs shared among phylogenetically distant species, suggesting horizontal transfer of ARG-associated cassettes across the genus. Comparative analyses further suggested that members of the Cholera clade may act as potential sources of SCI-associated ARG dissemination. Five major ARG families were identified within SCIs, including catB, qnrVC, blaCARB, dfrA, and vatF, some of which displayed phylogenetic patterns consistent with interspecies transfer. Functional characterization of a SCI-associated qnrVC4 cassette from Vibrio mimicus confirmed its ability to confer reduced susceptibility to ciprofloxacin in a heterologous host. Together, our findings indicate that a conserved subset of VXR backbones, mainly from the Cholera clade, plays a role in ARG dissemination across Vibrio species, highlighting SCIs as active reservoirs contributing to the emergence and spread of antimicrobial resistance.},
}

*Integrons/genetics
*Vibrio/genetics/drug effects/classification
*Gene Transfer, Horizontal
*Drug Resistance, Bacterial/genetics
Phylogeny
Chromosomes, Bacterial/genetics
Genome, Bacterial

@article {pmid42821600,
year = {2026},
author = {Ma, J and Dong, S and Zhou, Y and Song, CP and Huang, J},
title = {Horizontal gene transfer as a driving force in plant terrestrialization and adaptive evolution.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiag733},
pmid = {42821600},
issn = {1532-2548},
abstract = {Horizontal gene transfer (HGT) has been considered as a pivotal source of genetic innovation during early plant evolution. This review synthesizes evidence that genes acquired from microbes (e.g., bacteria and fungi) by plants facilitated critical adaptations in their terrestrialization. These include stress tolerance, phytohormone signaling, cell wall biosynthesis, and defense against pathogens and herbivores. The integration of foreign genes, often following post-transfer domestication such as intron gain, underscores a dynamic evolutionary process in land plants. Furthermore, bidirectional HGT events between plants and other organisms reveal a complex "web of life". Ultimately, HGT is a fundamental and continuous force that has shaped plant evolution, particularly during plant colonization of land.},
}

@article {pmid42822935,
year = {2026},
author = {Zhang, J and Chen, J and Wang, C and Wang, P and Feng, B and Zhang, B and Zhang, S and Fu, J},
title = {Sulfate addition enhanced antibiotic resistance in lake sediments by enriching resistant bacteria and promoting the potential of horizontal gene transfer.},
journal = {Journal of environmental sciences (China)},
volume = {169},
number = {},
pages = {405-416},
doi = {10.1016/j.jes.2026.04.061},
pmid = {42822935},
issn = {1001-0742},
mesh = {*Lakes/microbiology/chemistry ; *Sulfates/analysis ; *Geologic Sediments/microbiology/chemistry ; *Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; Genes, Bacterial ; },
abstract = {Lake sediments represent a typical reservoir of antibiotic resistance genes (ARGs), an emerging contaminant. As a key nutrient for sediment microorganisms, elevated sulfate levels can profoundly influence sulfur cycling and related microbial processes. However, the impact of sulfate loads on the profiles of ARGs in lake sediments remains poorly understood. This study utilized a microcosm experiment to examine how sulfate addition at various concentrations (200, 400, and 600 mg/kg dry weight) affects the sediment resistome, via metagenomic analysis. Sulfate addition significantly increased sediment sulfides and the relative abundance of sulfate-reducing genes (SRGs). Notably, the high sulfate treatment (600 mg/kg) resulted in a significant rise in the relative abundance of ARGs, virulence factor genes (VFGs), and mobile genetic elements (MGEs), indicating an increased potential for resistance dissemination under high sulfate loading. The relative abundance of horizontal transfer related genes, including those mediating cell membrane permeability and type IV secretion system, was enhanced by sulfate addition, potentially promoting ARG dissemination. Linear regression identified strong positive relationships between the abundance of ARGs and abundances of both MGEs and VFGs. Sulfate addition enriched specific antibiotic-resistant bacteria (ARBs) carrying SRGs that were identified via network analysis. The genera Burkholderia, JACDDX01, and Hylemonella showed marked enrichment, with increases of 16.7 %, 13.2 %, and 94.6 %, respectively. Overall, the rise in ARG abundance under sulfate addition shows close links to specific ARBs and enhanced horizontal transfer. These findings have implications for understanding sulfate-driven changes in sediment resistome and assessing environmental risk in sulfate-enriched lake ecosystems.},
}

*Lakes/microbiology/chemistry
*Sulfates/analysis
*Geologic Sediments/microbiology/chemistry
*Gene Transfer, Horizontal
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
Bacteria/genetics/drug effects
Genes, Bacterial

@article {pmid42821447,
year = {2026},
author = {Castro-Delgado, ZL and Heredia, N and Merino-Mascorro, JA and Franco-Frías, E and Dávila-Aviña, JE and García, S},
title = {Survival, growth, and potential of horizontal gene transfer of antibiotic resistance genes of bovine Salmonella on the cantaloupe surface.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0107626},
doi = {10.1128/aem.01076-26},
pmid = {42821447},
issn = {1098-5336},
abstract = {Salmonella outbreaks are often linked to contaminated cantaloupes, and bacterial multiple antibiotic resistance is frequently observed. Research is needed to understand the growth and survival of Salmonella on cantaloupe surfaces, and the mechanisms of antibiotic resistance in that environment. This study investigated the growth, survival, and capacity for horizontal gene transfer of antibiotic resistance genes in Salmonella on the surface of cantaloupe. Bovine-derived Salmonella isolates were inoculated onto the surface of cantaloupe and incubated at 35°C under 65-75% humidity for 5 days. Each isolate was co-inoculated with donor E. coli CSH56 harboring helper plasmid RP4-8 and mobilizable plasmid pSC27, which carries kanamycin, neomycin, and ampicillin resistance genes. One hundred microliters of the Salmonella suspension (1 × 10[8] CFU/mL) and 100 µL of the E. coli suspension (1 × 10[7] CFU/mL) was applied to each cantaloupe (1:10 ratio). Salmonella survival and growth were monitored on Hektoen agar, transconjugants were enumerated on Hektoen agar with kanamycin, and donor E. coli were quantified on MacConkey agar. All Salmonella isolates survived and exhibited growth within the 5-day period, with increases ranging from 0.94 log10 CFU/mL to 3.43 log10 CFU/mL. Notably, all Salmonella isolates possess the capability to accept and integrate sequences derived from the pSC27 plasmid from E. coli into their chromosome, both in vitro and on cantaloupe. After conjugation, the count of Salmonella mutants carrying the plasmid was 2.79 log10 CFU/mL in vitro. The survival, growth, and horizontal gene transfer of Salmonella on the surface of cantaloupe pose significant risks to public health.IMPORTANCESalmonella, a leading cause of foodborne diseases, poses a global health threat, with multidrug resistance emerging as a severe problem. Cantaloupes have been implicated in salmonellosis outbreaks in multiple countries over the last three decades. We hypothesize that acquisition of antibiotic resistance genes from other bacteria may occur on the surface of the fruit. This study established that Salmonella can survive, proliferate, and acquire antibiotic resistance genes on cantaloupe surfaces. This observation underscores the potential risks on the growth and transfer of genes between pathogens such as Salmonella and E. coli in foods. This impact goes beyond disease production and contributes to the rapid escalation of antimicrobial resistance and transmission of virulence genes in foods and the environment, which is a significant threat to public health.},
}

@article {pmid42815131,
year = {2026},
author = {Mu, X and Bi, J and Yu, Q and Han, Q and Wang, X and Li, H},
title = {Urban parks as potential hotspots for pathogenic determinants: A One Health perspective on environmental-human transmission risks.},
journal = {Journal of environmental management},
volume = {418},
number = {},
pages = {131067},
doi = {10.1016/j.jenvman.2026.131067},
pmid = {42815131},
issn = {1095-8630},
abstract = {Urban parks are vital public spaces, yet their role as potential reservoirs and transmission pathways for pathogenic bacteria under the "One Health" framework remains poorly understood. We gathered paired soil, water, and human fecal samples from nine parks in Lanzhou, China. Metagenomic and 16S rRNA sequencing revealed abundant pathogenic bacteria, virulence factor (VF) genes, and pathogen-host interaction (PHI) genes. Pathogenic bacteria were significantly more abundant in water than in soil, and their presence was positively correlated with key environmental nutrients (TC, TN, TP, TS). Immune modulation and motility genes dominated the VF repertoire, while PHI genes primarily mediated virulence attenuation, maintenance, or enhancement. Crucially, the profile of these virulence genes was significantly shaped by the native bacterial community and mobile genetic elements (MGEs). Metagenomic binning provided direct genomic evidence that MGEs frequently co-localize with VF and PHI genes, demonstrating a high potential for horizontal gene transfer from park environments to humans. Our findings highlight urban parks as significant environmental reservoirs for pathogenic determinants and delineate the ecological and genetic drivers of their dissemination, providing a critical basis for targeted environmental management and public health protection.},
}

@article {pmid42816497,
year = {2026},
author = {Zhou, F and Pan, S and Ma, C and Sun, W and Ye, Y and Zhu, DZ and Xiong, J and Li, C and Zhang, J and Gan, J and Sun, X and Lu, D and Gan, H},
title = {Humic acid's sheltering effect paradoxically promotes antibiotic resistance gene dissemination during peroxymonosulfate water treatment.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42816497},
issn = {2041-1723},
support = {52070103//National Natural Science Foundation of China (National Science Foundation of China)/ ; LMS26E090008//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; },
mesh = {*Peroxides/pharmacology/chemistry ; Animals ; *Humic Substances/analysis ; *Water Purification/methods ; Caenorhabditis elegans/microbiology ; Gene Transfer, Horizontal/drug effects ; *Drug Resistance, Microbial/genetics ; Oxidative Stress/drug effects ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; Genes, Bacterial ; },
abstract = {Advanced oxidation processes (AOPs) utilizing peroxymonosulfate (PMS) are increasingly deployed for water disinfection, yet their impact on the dissemination of antibiotic resistance genes (ARGs) remains poorly understood. Here, we conducted field surveys in three aquaculture ponds in eastern China and employed a Transwell-based horizontal gene transfer (HRT) sorting assay, metagenomics, and transcriptomics to investigate the underlying mechanisms. We found that PMS-treated waters harbored significantly higher intracellular ARG burdens compared to untreated or chlorinated systems. Mechanistically, the ubiquitous humic acid (HA) acts as a selective radical scavenger, protecting bacteria from lethal oxidative damage while stimulating type IV pilus-mediated uptake of extracellular ARGs. This interaction redirects HGT from conjugation toward natural transformation. Crucially, this protective effect is oxidant-specific: HA effectively quenches PMS-derived radicals but provides no defense against direct electrophilic attack by chlorine. Furthermore, predation experiments using Caenorhabditis elegans demonstrate that this "sheltering effect" facilitates the accumulation of ARGs in nematodes, decoupling resistance acquisition from oxidative stress intensity. These findings highlight a critical risk pathway in which some water treatment chemicals can promote the spread of resistance, necessitating a reassessment of oxidant selection based on their specific chemical mechanisms.},
}

*Peroxides/pharmacology/chemistry
Animals
*Humic Substances/analysis
*Water Purification/methods
Caenorhabditis elegans/microbiology
Gene Transfer, Horizontal/drug effects
*Drug Resistance, Microbial/genetics
Oxidative Stress/drug effects
*Drug Resistance, Bacterial/genetics
Bacteria/genetics/drug effects
Genes, Bacterial

@article {pmid42818138,
year = {2026},
author = {Rodrigues, CM and Lucidarme, J and Exley, R and Clark, JL and Bai, X and Bayliss, C and Chand, M and Clark, SA and Cornelissen, CN and Derrick, JP and Green, LR and Groves, N and Gutierrez Vazquez, Y and Harrison, OB and Jolley, KA and McKeand, SA and Myers, R and Noinaj, N and Parfitt, KM and Ribeca, P and Borrow, R and Maiden, MC and Tang, CM},
title = {Emergence of short-lived meningococci causing focal epidemics can be associated with gene transfer from carriage-associated Neisseria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.17.752363},
pmid = {42818138},
issn = {2692-8205},
abstract = {UNLABELLED: In March 2026, an unusually large outbreak of invasive meningococcal disease (IMD) in Kent, UK, was linked to attendance at one nightclub over a single weekend. The outbreak organism was a Neisseria meningitidis variant belonging to the longstanding hyperinvasive genotype, cc41/44. Using genome analysis of six isolates from patients, alongside >48,000 meningococcal genomes, we investigated whether the outbreak variant had acquired traits potentially contributing to the highly invasive phenotype. The six isolates were capsular group B, sequence type (ST-)485, and essentially indistinguishable, consistent with the focal nature of the outbreak. Compared with their closest available relatives, we found changes mediated by phase variation, nucleotide variation, and horizontal gene transfer (HGT) involving adhesins, iron-acquisition systems (including Transferrin and Lactoferrin binding proteins, and FetA), and Type IV pili (Tfp), factors which affect bacteria-bacteria and bacteria-host interactions. These changes occurred in a ST-485 sub-lineage that expressed capsule at high levels and a PorA porin with a truncated surface-exposed epitope, both of which are predicted to reduce immune recognition. Donors for the HGT events were predominantly carriage-associated N. meningitidis and Neisseria cinerea . We show that meningococcal variants responsible for previous focal outbreaks have not been seen subsequently. We propose that focal outbreaks of IMD are caused by meningococcal variants that may have acquired traits from non- or less invasive organisms, but subsequently these variants disappear, as their highly invasive phenotype is inconsistent with sustained transmission. Ongoing disease surveillance alongside carriage studies are therefore essential to inform public health risk and manage epidemic IMD.

SIGNIFICANCE STATEMENT: Invasive meningococcal disease (IMD), comprising sepsis and/or meningitis, is a serious life-threatening infection. IMD is usually rare, but outbreaks occur, ranging from very large epidemics to small clusters, with cases occurring over days, weeks, or months. Following an unusually large, week-long, focal outbreak in Kent, UK, in 2026, affecting 21 individuals, we investigated outbreak-associated meningococcal characteristics, comparing outbreak variant genomes with their closest available relatives. We found changes in the outbreak variants, affecting bacteria-bacteria and bacteria-host cell interactions, and iron acquisition. These traits likely resulted in an unusually high invasive potential, likely at the cost of capacity for sustained transmission in asymptomatic carriage.},
}

@article {pmid42818523,
year = {2026},
author = {Chen, D and Wang, Y and Portik, DM and Nearing, J and Nickols, WA and Wilkinson, JE and Christiani, DC and Nguyen, LH and Franzosa, EA and Spengler, JD and Huttenhower, C and Thompson, KN},
title = {Microbial transmission and ecology of human and environmental microbial communities in childcare centers.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-10207669/v1},
pmid = {42818523},
issn = {2693-5015},
abstract = {Background Early-life microbial exposures profoundly impact lifelong health trajectories by shaping immune maturation and modulating disease risk, e.g. as described by the "hygiene hypothesis." Childcare facilities represent a critical yet understudied source of microbial exposures where preschool-aged children spend 7-10 hours daily during key developmental periods. This study presents the first multi-omic and multi-kingdom investigation of microbial transmission and community ecology across childcare environments, integrating microbiome samples from both high-touch and low-touch surfaces with children's nasal and oral microbiomes, using full-length 16S rRNA gene and internal transcribed spacer (ITS) amplicon sequencing paired with short-read (SR) and long-read (LR) metagenomic sequencing. This combination provides enhanced species-level taxonomic resolution and improved recovery of genomes and genomic elements compared to conventional short-read approaches. Results Our findings revealed distinct microbial signatures across environments, with human-associated microorganisms predominating in high-touch areas, while greater taxonomic diversity characterizes low-touch areas. Specifically, on high-touch surfaces, several bacterial and fungal species were shared between host and environmental communities, such as food-associated Lactococcus lactis and Streptococcus thermophilus , suggesting defined transmission routes via host shedding, environmental exposures, and food consumption. With improved genomic resolution and reconstruction from paired SR and LR metagenomics, we identified novel lateral gene transfer (LGT) events enriched for mobile elements, DNA-interacting domains, and adaptive elements such as antibiotic resistance and virulence factors. These methods also shed light on viral ecology, such as Caudoviricetes bacteriophages ubiquitous across host and environmental communities with phylogenetically-differentiated niche- and bacterial host-specific lineages. The positive relationship between the host prediction frequency and its community relative abundance suggested host abundance (availability)-driven phage-bacteria population dynamics. Conclusions This work highlights previously understudied components of early-life microbial exposures in childcare environments with enhanced resolution and provides methods for identifying potential pathogen reservoirs, tracking transmission routes, and developing targeted interventions.},
}

@article {pmid42808749,
year = {2026},
author = {Weng, J and Li, X and Yang, Z and Huang, H and Zhan, S},
title = {Comparative genomic analysis of the blaOXA-23-carrying plasmids.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0137426},
doi = {10.1128/spectrum.01374-26},
pmid = {42808749},
issn = {2165-0497},
abstract = {UNLABELLED: The global dissemination of the carbapenem resistance gene blaOXA-23 is partly facilitated by plasmids, yet a comprehensive characterization of these vectors is lacking. This study analyzed the blaOXA-23-carrying plasmids selected from the National Center for Biotechnology Information RefSeq database to elucidate their general characteristics and genomic diversity. The blaOXA-23-carrying plasmids were predominantly hosted by Acinetobacter baumannii (94.06%), and their sizes varied widely, from 8.22 to 336.05 kb. Replicon typing revealed that the majority belonged to the RP Rep family, specifically RP-T1 (62 plasmids) and RP-T2 (23 plasmids) types. A key finding of this analysis was the assignment of these two major plasmid groups to distinct plasmid taxonomic units (PTUs): all RP-T1 plasmids were classified as PTU-Pse5, whereas all RP-T2 plasmids were classified as PTU-Pse1. The blaOXA-23 gene of the plasmids was located within four kinds of composite transposons, with Tn2006 (33.67%), Tn2008 (32.67%), and Tn2009 (31.68%) being the predominant genetic contexts. Notably, the 62 plasmids of RP-T1 type (PTU-Pse5) and the 23 plasmids of RP-T2 type (PTU-Pse1), found predominantly in A. baumannii, carried genes encoding relaxases of the MOBF family, T4CPs of t4cp2, and type F T4SS, suggesting they are putatively conjugative. In addition, the 62 plasmids of RP-T1 type (PTU-Pse5) were identified in multiple countries within the data set, while the 23 plasmids of RP-T2 type (PTU-Pse1) were predominantly found in China. These findings provide a genomic view of blaOXA-23 plasmids, suggest their role in disseminating carbapenem resistance across species and regions, and offer a surveillance framework, highlighting key lineages for clinical intervention.

IMPORTANCE: The horizontal transfer of blaOXA-23 to Acinetobacter baumannii and other gram-negative pathogens has conferred high-level carbapenem resistance, posing significant therapeutic challenges in both hospital and community settings. Plasmids carrying conjugative transfer systems serve as key vehicles for the dissemination of blaOXA-23 among clinical isolates. In this study, we identified the plasmid lineages responsible for blaOXA-23 spread and categorized them into a limited number of groups. This finding underscores the considerable risk of horizontal gene transfer in propagating carbapenem resistance and provides a valuable framework for future surveillance efforts to track the transmission of these resistant plasmids. However, this study was based on current knowledge and available data. Given the ever-changing situation of antibiotic resistance, new plasmid variants or transfer mechanisms may emerge, potentially limiting the long‑term applicability and accuracy of our findings.},
}

@article {pmid42808883,
year = {2026},
author = {Tanabe, Y and Yamaguchi, H and Sano, T},
title = {Phylogenomic diversity and chromatic acclimation in phycoerythrin-containing Microcystis aeruginosa.},
journal = {Microbial genomics},
volume = {12},
number = {9},
pages = {},
pmid = {42808883},
issn = {2057-5858},
mesh = {*Phycoerythrin/genetics/metabolism ; *Microcystis/genetics/classification/metabolism ; *Phylogeny ; Genome, Bacterial ; Bacterial Proteins/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; },
abstract = {Microcystis aeruginosa is a bloom-forming cyanobacterium widely distributed in eutrophic freshwater systems. Most strains are blue-green due to the presence of the photosynthetic pigments phycocyanin and chlorophyll a. Less commonly, brownish strains have been reported, reflecting the presence of the red pigment phycoerythrin (PE). However, the genomic basis, phylogeny and evolutionary origin of PE pigmentation in M. aeruginosa remain poorly understood. Here, we characterized PE-containing M. aeruginosa strains, including six newly sequenced genomes. All genomes harboured putative PE synthesis and regulatory genes (the cpe cluster). Phylogenomic analysis further revealed that these PE-containing strains are distributed across three distinct phylogenetic groups. In contrast, the genomic organization of the cpe cluster was largely conserved. Spectroscopic analyses further indicated that strains belonging to different phylogenetic groups exhibit the same type of chromatic acclimation. Moreover, the phylogenetic relationships inferred for each PE gene were congruent and consistent with the whole-genome phylogeny. Our findings support a single origin of PE genes, with the observed distribution best explained by two independent horizontal transfer events rather than repeated gene loss during intraspecific diversification in M. aeruginosa.},
}

*Phycoerythrin/genetics/metabolism
*Microcystis/genetics/classification/metabolism
*Phylogeny
Genome, Bacterial
Bacterial Proteins/genetics
Evolution, Molecular
Gene Transfer, Horizontal

@article {pmid42810261,
year = {2026},
author = {Lin, Z and Huang, J and Chen, S and Liao, J and Shang, C and Xu, Y and Jia, R and Mai, H and Liu, Y and Lai, X and Chen, H and Chen, H and Guo, Z and Chen, J},
title = {Pollution duration drives divergent pathways of antibiotic and metal resistance gene dissemination in coastal mangrove sediments.},
journal = {Ecotoxicology and environmental safety},
volume = {324},
number = {},
pages = {120861},
doi = {10.1016/j.ecoenv.2026.120861},
pmid = {42810261},
issn = {1090-2414},
abstract = {Coastal mangrove sediments are critical reservoirs of antibiotic and heavy metal resistance genes (ARGs/HMRGs). Yet, how pollution history shapes their dissemination remains unclear. We elucidated this by comparing sedimentary resistomes across three distinct ecosystems: a pristine site (BH), a site under mid-term copper stress (BHCu), and a chronically multi-polluted site (FT). Chronic multi-pollution generated a persistent co-resistance reservoir, significantly enriching ARGs, HMRGs, mobile genetic elements (MGEs), and transferable ARG-MGE clusters. Bioavailable metal fractions cooperated with MGEs to promote horizontal gene transfer (HGT) and resistome dispersal, despite limited direct ARG-HMRG co-selection, and restructured communities toward MGE-rich, cross-resistant taxa. In contrast, the three-year Cu treatment increased bioavailable Cu and enriched stress-response genes, but showed little MGE enrichment and no significant ARG-HMRG networks; resistance spread depended mainly on vertical selection within tolerant specialist taxa. The pristine site maintained low, stochastic resistance, intrinsic regulation of ARGs/HMRGs, and suppressed MGE activity in a diverse, stable community. Multivariate analyses further showed that host-MGE and duration-metal interactions dominated resistome variation, with metal speciation providing a key mechanistic link. Pollution duration therefore governed resistome architecture: chronic exposure transformed mangroves into resistance hotspots via co-reservoir expansion and HGT-driven dispersal, whereas mid-term Cu stress caused transient disruption without sustained transfer capacity. This "pollution gradient-time scale" paradigm identifies duration as a fundamental but neglected parameter for forecasting environmental resistome risks.},
}

@article {pmid42810665,
year = {2026},
author = {Zhou, X and Chen, W and Zhao, K and Han, X and Fu, J and Chen, S and Yang, S and Yu, X and Zou, L},
title = {Thermophilic Parageobacillus toebii G12 suppresses ARG enrichment during chicken manure composting even with multidrug-resistant plasmid-harboring bacteria as a stressor.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125810},
doi = {10.1016/j.envres.2026.125810},
pmid = {42810665},
issn = {1096-0953},
abstract = {The enrichment of antibiotic resistance genes (ARGs) during composting poses a substantial risk to the safe utilization of chicken manure. However, the role of multidrug-resistant plasmid (MRP)-harboring bacteria in ARG dissemination and microbial succession during composting remains poorly understood. In this study, we investigated the regulatory effects of thermophilic Parageobacillus toebii G12 (G12) on ARG dynamics, as well as its performance under interference from MRP-harboring bacteria. Our results showed that G12 inoculation elevated compost temperature, extended the thermophilic phase, and accelerated maturation. It increased overall ARG removal to 60.9 % and 55.6 % in the conventional and MRP-contaminated systems, respectively, and reduced persistent ARG enrichment by 71.4 % and 66.3 %, respectively. Although MRP-associated stress shifted the suppression preference of G12 from protection-type to alteration/replacement-type persistent ARGs, the strain consistently suppressed efflux- and inactivation-type persistent ARGs. Moreover, G12 markedly reduced the coverage depth of MRPs after composting, thereby alleviating MRP-associated stress. Integrated analyses, including co-occurrence network, Mantel test, partial least squares path modeling, and metagenome-assembled genome approaches, revealed that G12 reshaped the microbial community by suppressing the dominant host Pseudomonadota, thereby reducing its efflux-type persistent ARGs, while directly diminishing integration/excision-type mobile genetic elements to curtail horizontal gene transfer potential. This study elucidates the core mechanisms by which G12 counteracts ARG enrichment and demonstrates its efficacy even under MRP-associated stress, providing a theoretical foundation for mitigating antimicrobial resistance risks in manure composting.},
}

@article {pmid42811538,
year = {2026},
author = {Meza-Padilla, I and Avrani, S and Müller, KM and Nissimov, JI},
title = {Reply to comment on "A jumbo cyanophage encodes the most comprehensive ribosomal protein set in the known virosphere" by LinXing Chen.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {42811538},
issn = {1751-7370},
}

@article {pmid42813775,
year = {2026},
author = {Bruna, RE and Selvaraj, AL and Bhowmik, S and Kendra, CG and Heister, R and Pontes, MH},
title = {Genomic and biochemical contexts determine the physiological role of a horizontally acquired gene.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0084526},
doi = {10.1128/msystems.00845-26},
pmid = {42813775},
issn = {2379-5077},
abstract = {The horizontally acquired mgtC gene from Salmonella enterica confers on this bacterium the abilities to survive episodes of magnesium (Mg[2+]) starvation and to replicate in mammalian macrophages. The former property allows bacteria to persist in the environment during Mg[2+] depletion, whereas the latter allows S. enterica to overcome self-limiting intestinal colonization and cause invasive systemic infection in susceptible mammalian hosts. Even though the biochemical function of MgtC is not completely understood, this protein is thought to function primarily by preventing the production of toxic levels of Mg[2+]-chelating adenosine triphosphate. In the current work, we investigated the physiological roles of mgtC homologs from an array of bacterial species by probing the processes controlled by this gene during replication in low-Mg[2+] medium and in macrophages. We determined that MgtC homologs that do not participate in Pi homeostasis during Mg[2+] starvation and do not promote intramacrophage replication in their resident species can partake in these processes when expressed in S. enterica. This indicates that the function of this protein is context dependent. Accordingly, we show that the physiological processes affected by S. enterica MgtC vary depending on whether the bacteria replicate in low-Mg[2+] medium or inside macrophages. While these results suggest that MgtC is a regulator, they also demonstrate that horizontally acquired genes can assume different roles, depending on the genome and the biochemical context into which they are inserted.IMPORTANCEThe mgtC gene encodes an inner membrane protein that has been horizontally acquired by multiple bacterial species, including several mammalian pathogens. In Salmonella enterica, MgtC promotes replication in mammalian macrophages and allows this bacterium to survive cytoplasmic magnesium (Mg[2+]) starvation. These phenotypes are thought to result from MgtC's inhibition of Pi metabolism and adenosine triphosphate (ATP) production, which prevents the accumulation of toxic levels of Mg[2+]-chelating ATP and disrupts other physiological processes that depend strictly on Mg[2+], such as ribosome assembly and translation. In the current study, we show that processes that are controlled by MgtC vary with the genetic and biochemical contexts in which this protein is expressed. While establishing a broader role for MgtC as a regulator, our findings illustrate how horizontally acquired regulatory genes can potentiate regulatory interactions, facilitating the evolution of new traits.},
}

@article {pmid42799925,
year = {2026},
author = {Torres, MM and Gervasio, JHD and Yépez, EAV and Santos, AS and Costa, GM and Zardo, ML and Cardinali-Rezende, J and de Araújo, WL and Gomez, JGC and da Silva, LF},
title = {Integrated genomic and experimental assessment of the biosafety of Paraburkholderia sacchari as a promising microbial chassis.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {10},
pages = {},
pmid = {42799925},
issn = {1573-0972},
mesh = {*Genome, Bacterial/genetics ; Phylogeny ; *Burkholderiaceae/genetics/pathogenicity/classification ; Genomics ; Virulence/genetics ; Virulence Factors/genetics ; Animals ; Gene Transfer, Horizontal ; Burkholderia/genetics/pathogenicity ; Containment of Biohazards ; },
abstract = {Paraburkholderia sacchari is an environmental member of the Burkholderiaceae with recognized biotechnological potential, yet its genomic diversity, biosafety profile, and evolutionary relationship to pathogenic Burkholderia species remain poorly understood. Here, we present a comprehensive genomic and phenotypic characterization of P. sacchari strain LMG 19,450[T] and compare it with three additional P. sacchari genomes and phylogenetically related Burkholderia species. A high-quality genome assembly confirmed its placement within the Paraburkholderia clade and species-level relatedness among P. sacchari strains despite detectable intraspecies genomic variability. Pangenome analysis revealed a large, conserved core genome and an extensive accessory gene repertoire, consistent with adaptation to plant-associated soil environments. Comparative analysis of virulence-associated genes showed a marked contrast between P. sacchari and pathogenic Burkholderia, with the former lacking most canonical pathogenicity determinants. Gene tree-species tree reconciliation further indicated a constrained horizontal gene transfer profile for virulence-associated gene families, while genes involved in transcriptional regulation displayed higher transfer propensity. Antimicrobial resistance profiling revealed a limited resistome dominated by efflux-associated homologs, consistent with broad phenotypic susceptibility. Notably, strain LMG 19,450[T] exhibited antibiotic susceptibility patterns comparable to those of the established microbial chassis Pseudomonas putida KT2440. Virulence assessment using the Galleria mellonella model demonstrated markedly attenuated pathogenicity relative to Burkholderia cepacia. Together, these findings support P. sacchari as an environmentally adapted bacterium with a favorable biosafety profile and highlight the value of integrating genomic and experimental approaches to evaluate emerging microbial chassis.},
}

*Genome, Bacterial/genetics
Phylogeny
*Burkholderiaceae/genetics/pathogenicity/classification
Genomics
Virulence/genetics
Virulence Factors/genetics
Animals
Gene Transfer, Horizontal
Burkholderia/genetics/pathogenicity
Containment of Biohazards

@article {pmid42801601,
year = {2026},
author = {Chikindas, ML and Xu, D and Popov, IV and Carneiro, KO and Elova, NA and Bekmurodova, GA and Amirsaidova, DA and Pepoyan, A and Miralimova, SM and Mitrokhin, OV and Sichel, LS and Tagg, J and Todorov, SD},
title = {Beyond Probiotics: Postbiotics for Healthy Aquaculture.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77737},
pmid = {42801601},
issn = {2198-3844},
support = {2023/05394-9//FAPESP/ ; UID/05937/2025//São Paulo, SP, Brazil, and Fundação para a Ciência e Tecnologia, Portugal/ ; 1819/2023//Agência USP de Cooperação 3Acadêmica Nacional e Internacional (AUCANI, USP International Cooperation Office)/ ; 32271568//National Natural Science Foundation of China/ ; },
abstract = {With a growing global population and strict restrictions on traditional antibiotics, sustainable fish health management is crucial for aquaculture. While live probiotics are popular alternatives, their real-world effectiveness remains highly controversial. Variable effectiveness results from complex interactions with different fish species, differences in fish gastrointestinal anatomy, and variations in environmental parameters such as salinity, pH, and temperature. Furthermore, live probiotics pose risks of ecological disturbance and horizontal gene transfer of antimicrobial resistance. This critical review assesses these limitations and proposes postbiotics, preparations of inanimate microorganisms and their metabolites, as a more stable, controlled, and biosafe formulation. Postbiotics offer significant advantages during industrial aquafeed production and storage. However, their practical implementation is currently hindered by vague terminology and legislative gaps. To overcome these obstacles, this review introduces an innovative modular analytical model utilizing specific chemical biomarkers (such as short-chain fatty acids, bacteriocins, and lipoteichoic acids). Implementing these matrix-matched, multi-module quality control panels to verify molecular safety, identity, and efficacy is critical to standardizing next-generation "precision postbiotics" for sustainable aquaculture development.},
}

@article {pmid42801657,
year = {2026},
author = {Huang, Y and Shen, R and Huang, X and Ji, GQ and Lan, JF and Ren, Q},
title = {Non-Coding Transcripts From Diversified Members of IgLec Family Protect Antiviral Effectors From Viral miRNA.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77981},
pmid = {42801657},
issn = {2198-3844},
support = {32674071//National Natural Science Foundation of China/ ; JSTJ-2024-167//Jiangsu Provincial Science and Technology Association Youth Talent Support Project/ ; //Startup Foundation for Introducing Talent of Nanjing University of Information Science and Technology/ ; },
abstract = {Immune gene families frequently produce numerous non-coding transcripts, yet their biological functions remain largely unexplored. Here, using the arthropod immunoglobulin domain-containing lectin (IgLec) family as a paradigm, we provide evidence that this complexity may reflect a critical defensive function for non-coding transcripts in antiviral immunity. IgLec is restricted to decapod infraorders (Brachyura and Astacidea), and a structurally related bacterial homolog suggests its origin may involve horizontal gene transfer. The IgLec family generates extraordinary transcript diversity through three mechanisms, multi-locus duplication, inter-locus recombination, and extensive alternative splicing, yielding both protein-coding and non-coding transcripts. Protein-coding IgLec variants restrict viral replication by inducing antimicrobial peptide expression. Upon white spot syndrome virus infection, non-coding transcripts (e.g., intron-retaining transcripts) are preferentially targeted by virus-encoded microRNA-N48, thereby protecting protein-coding isoforms from repression. Loss of these decoy transcripts compromises antiviral defense and increases host mortality. Collectively, these results reveal a decoy-based antiviral strategy in which non-coding transcripts safeguard immune effectors from pathogen subversion, uncovering an unrecognized layer of innate immunity.},
}

@article {pmid42622422,
year = {2026},
author = {Jiang, S and Yan, B and Liu, H and Sun, L and Chen, Y and Liu, L and Yu, Y},
title = {Strain-specific outer membrane vesicle-mediated transfer of a blaOXA-24-like plasmid in Acinetobacter baumannii restricts cross-species dissemination.},
journal = {mSphere},
volume = {11},
number = {9},
pages = {e0031126},
doi = {10.1128/msphere.00311-26},
pmid = {42622422},
issn = {2379-5042},
support = {2023YFC2307100//National Key Research and Development Program of China/ ; U22A20338//NSAF Joint Fund/ ; 82402677//National Natural Science Foundation of China/ ; 2022WJC055//2022 Hangzhou Biomedical and Health Industry Development Support Science and Technology Special Project/ ; },
mesh = {*Plasmids/genetics ; *Acinetobacter baumannii/genetics/drug effects/enzymology ; *beta-Lactamases/genetics ; *Gene Transfer, Horizontal ; Acinetobacter Infections/microbiology ; Acinetobacter/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Humans ; China ; Carbapenems/pharmacology ; Bacterial Proteins/genetics ; Microbial Sensitivity Tests ; Extrachromosomal DNA ; *Bacterial Outer Membrane ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {The rapid rise of multidrug-resistant Acinetobacter spp. poses a major global health threat. In Acinetobacter spp., carbapenem resistance is frequently mediated by OXA-type carbapenemases encoded by blaOXA genes, including blaOXA-24-like genes such as blaOXA-72. Outer membrane vesicles (OMVs) are nanoscale proteoliposomes secreted by Gram-negative bacteria that can facilitate plasmid transfer, yet the mechanisms limiting their dissemination remain unclear. Nationwide screening in China of 2,880 Acinetobacter clinical isolates identified 10 strains carrying blaOXA-24 and blaOXA-72 plasmids across three species (A. baumannii, A. pittii, and A. baylyi). Sequencing revealed nine distinct plasmids, most bearing a Rep_3/OrfX C-module backbone with blaOXA-pdif resistance modules (9/10). Among clinical strains, A2485 was identified as a high-OMV producer (2.74 ± 0.20-fold relative to ATCC 17978, P < 0.001). OMVs from A2485 transferred the blaOXA-72 plasmid to ATCC 17978 at 1.9 × 10[-7] transformants per CFU, exceeding direct supernatant transfer at 3.2 × 10[-8] transformants per CFU, and conferred resistance to meropenem, ceftazidime, and cefoperazone/sulbactam. Transfer was strictly donor-specific, with no transmission observed across 13 non-A. baumannii strains, and recipient strains failed to retransmit the plasmid, indicating a strong cross-species barrier and a non-reciprocal, donor-dependent process. Although all strains produced intact OMVs and encapsulated plasmid DNA, packaging efficiency varied considerably by host (~4.5-28.6 ng/μg). Strains with DNA loading (17978E/17978V: 28.62 and 23.98 ng/μg) equal to or exceeding that of donor A2485 (13.62 ng/μg) remained incapable of transfer. These findings demonstrate that dissemination is constrained by host-specific, post-packaging barriers rather than packaging efficiency, limiting resistance spread to specific lineages while enabling localized adaptation.IMPORTANCEAcinetobacter baumannii is a leading hospital-associated pathogen, and carbapenem resistance mediated by blaOXA-24-like genes poses a serious clinical challenge. Through nationwide screening of 2,880 clinical Acinetobacter isolates in China, we found that strains carrying blaOXA-24 and blaOXA-72 plasmids are relatively rare, occurring in only 10 isolates across three species. We provide the first evidence that outer membrane vesicle (OMV)-mediated plasmid transfer is subject to strict, host-specific barriers: the blaOXA-72 plasmid was successfully transferred among A. baumannii strains via OMVs, yet no transfer was observed to any of the 13 non-A. baumannii species tested. Transfer was also non-reciprocal-recipient strains that acquired the plasmid were unable to further disseminate it, whether via OMVs or supernatants. Critically, this restriction was not explained by DNA packaging efficiency, as strains with equal or greater plasmid loading than the donor remained incapable of transmission, pointing instead to post-packaging, donor-specific factors, such as membrane composition or vesicle biogenesis machinery. These findings clarify the sporadic distribution of blaOXA-24-like plasmids in China and challenge the conventional assumption that mobile genetic elements inherently carry broad dissemination potential, revealing that OMV-mediated resistance spread is constrained to specific bacterial lineages.},
}

*Plasmids/genetics
*Acinetobacter baumannii/genetics/drug effects/enzymology
*beta-Lactamases/genetics
*Gene Transfer, Horizontal
Acinetobacter Infections/microbiology
Acinetobacter/genetics/drug effects
Anti-Bacterial Agents/pharmacology
Humans
China
Carbapenems/pharmacology
Bacterial Proteins/genetics
Microbial Sensitivity Tests
Extrachromosomal DNA
*Bacterial Outer Membrane
Drug Resistance, Multiple, Bacterial/genetics

@article {pmid42795532,
year = {2026},
author = {Guo, Y and Bai, M and Liu, Y and Li, L and Ni, S and Ayra-Pardo, C and Yuan, W},
title = {CoFe2O4-Modified Biochar Is Associated with Microbial Community and Antibiotic Resistance Gene Profiles in Vertical Flow Constructed Wetlands Exposed to Oxytetracycline.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
pmid = {42795532},
issn = {2076-2607},
support = {241111320200, 262102321053, 252103810041//Henan Science and Technology Department/ ; 42407404//National Natural Science Foundation of China/ ; 2024.10667.CEECIND//Fundo Regional para a Ciência e Tecnologia/ ; },
abstract = {The widespread occurrence of antibiotics in aquatic environments has raised concern over the dissemination of antibiotic resistance genes (ARGs). Although vertical flow constructed wetlands (VFCWs) efficiently remove antibiotics from wastewater, the relationships between substrate configuration, microbial communities, and ARG abundance remain poorly understood. Here, five laboratory-scale VFCWs with different substrate configurations, including cobalt ferrite (CoFe2O4)-modified biochar and its composite with zeolite, were evaluated using synthetic domestic wastewater amended with oxytetracycline (OTC). CoFe2O4 modification increased the specific surface area and pore volume of biochar and altered its adsorption behavior. All VFCWs achieved high OTC removal (>97%), despite differences in OTC accumulation within the substrate. In contrast, ARG and mobile genetic element abundances and bacterial community profiles varied among reactors. Combined tetA and tetX abundance ranged from 2.55 × 10[2] to 1.90 × 10[5] copies g[-1], with the CoFe2O4-modified biochar-zeolite reactor showing the lowest mean ARG abundance. Exploratory co-occurrence analysis identified associations of Acinetobacter with tetA and Flavobacterium with tetA and tetX (nominal Spearman p < 0.05), although these correlations do not establish ARG host identity or horizontal gene transfer. Overall, the findings indicate that microbial ecological patterns associated with ARG abundance may differ among VFCWs even when antibiotic removal efficiencies are comparable.},
}

@article {pmid42795646,
year = {2026},
author = {Wu, Y and Feng, Y and Wu, B and Gao, Y and Xu, J},
title = {Effects of Chlorella pyrenoidosa Amendment on Tetracycline-Copper Dissipation, Soil Microbial Communities, and Tetracycline Resistance Genes.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
pmid = {42795646},
issn = {2076-2607},
support = {QNPY202104//Shenyang University of Technology Cultivation Fund/ ; 202563379//Science and Technology Commissioner Project of the Department of Science and Technology of Liaoning Province/ ; },
abstract = {Tetracycline (TC)-copper (Cu) co-contamination can impair soil functioning and intensify selection for antibiotic resistance. In a 49-day microcosm experiment, we evaluated the effects of Chlorella pyrenoidosa supplementation on soils treated with TC (0, 30, or 100 mg·kg[-1]) and Cu (0, 100, or 500 mg·kg[-1]). TC removal, extractable Cu, soil physicochemical properties, enzyme activities, tetracycline resistance genes (TRGs), and microbial community composition were assessed. In unamended contaminated microcosms, TC dissipation ranged from 22.7% to 43.5%, whereas C. pyrenoidosa amendment increased TC dissipation to 49.9-73.5%. The addition also reduced extractable Cu by 35.6-50.6%, partially restored dehydrogenase and catalase activities, and altered bacterial community structure. Metagenomic analysis showed that tetX was the predominant TRG detected and that algal supplementation was associated with lower total TRG signals and reduced relative abundances of several pollution-associated taxa, including Rhodanobacter. Correlation analyses revealed associations among TRGs, microbial taxa, and treatment conditions but did not establish direct host-gene relationships or horizontal gene transfer. Overall, C. pyrenoidosa application enhanced TC removal and Cu immobilization and was associated with reduced enrichment of the tetracycline resistome.},
}

@article {pmid42796731,
year = {2026},
author = {Stîngă, RI and Nadăş, GC},
title = {Biofilm Dynamics and Antimicrobial Resistance in Rabbit Odontogenic Infections: A One Health Perspective.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
pmid = {42796731},
issn = {2076-0817},
mesh = {Animals ; *Biofilms/drug effects/growth & development ; Rabbits ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/drug effects ; Humans ; },
abstract = {Rabbit odontogenic abscesses are among the most challenging chronic infections encountered in exotic animal medicine because of their polymicrobial etiology, biofilm-associated persistence, and poor response to conventional antimicrobial therapy. Biofilm formation plays a central role in disease pathogenesis by promoting bacterial adhesion, extracellular polymeric substance (EPS) production, quorum sensing (bacterial cell-to-cell communication), metabolic heterogeneity, and the persister-cell formation (transiently antibiotic-tolerant bacterial subpopulations), collectively reducing antimicrobial susceptibility and contributing to treatment failure and recurrence. In addition to biofilm-mediated tolerance, antimicrobial resistance (AMR) further complicates disease management through mechanisms including horizontal gene transfer, efflux pump activation, enzymatic antibiotic degradation, reduced membrane permeability, and target modification. This review summarizes current knowledge on the microbiology, biofilm dynamics, and resistance mechanisms associated with rabbit odontogenic infections while examining recent advances in molecular diagnostics, including culture-independent sequencing technologies, metagenomics, and advanced imaging approaches. Current and emerging anti-biofilm strategies, such as local antimicrobial delivery systems, enzymatic biofilm disruption, quorum-sensing inhibitors, bacteriophage therapy, antimicrobial peptides, photodynamic therapy, and nanotechnology-based approaches, are critically discussed in the context of their potential application in rabbits. Comparative evidence from human endodontic infections and other veterinary biofilm-associated diseases highlights the translational relevance of rabbit odontogenic abscesses as a naturally occurring model for chronic polymicrobial infections. Finally, key research gaps are identified, emphasizing the need for standardized experimental models, integrated multi-omics analyses, combining genomic, transcriptomic, proteomic, and metabolomic data, longitudinal clinical investigations, and evidence-based antimicrobial stewardship. By integrating microbiology, biofilm biology, antimicrobial resistance, and One Health concepts, this review provides a comprehensive framework to support future research and improve the diagnosis, treatment, and prevention of rabbit odontogenic infections.},
}

Animals
*Biofilms/drug effects/growth & development
Rabbits
*Drug Resistance, Bacterial
Anti-Bacterial Agents/pharmacology/therapeutic use
Bacteria/drug effects
Humans

@article {pmid42799311,
year = {2026},
author = {Pattis, I and Baschieri, A and Nelson, S and Bolton, A and Weaver, L},
title = {Linking Environmental Antimicrobial Resistance to Human Health: Pathways, Co-Selective Pressures and Attribution Gaps.},
journal = {Journal of the Royal Society of New Zealand},
volume = {56},
number = {5},
pages = {e70085},
pmid = {42799311},
issn = {1175-8899},
abstract = {Antimicrobial resistance (AMR) is recognised as a significant global health threat, yet research, surveillance and intervention strategies remain largely focused on clinical and veterinary settings, with limited attention to environmental reservoirs and transmission pathways. Growing global evidence, including from Aotearoa New Zealand (NZ), points to a clear link between dominant sources of AMR entering the environment (such as wastewater) and its dissemination in receiving environments. Once in these environments, a wide range of microorganisms, both environmental and introduced, interact in complex ways, with their associated resistomes contributing to potential human exposure pathways. However, clear attribution of environmental AMR contributions to human (and animal) health outcomes remains limited and represents a critical next step for research and surveillance. This viewpoint highlights global and regional evidence on environmental contributions to AMR transmission and dissemination, with emphasis on co-selective pressures including antibiotics, heavy metals, biocides and plastics that promote resistance selection, persistence and horizontal gene transfer. We identify key gaps in NZ, notably the lack of integrated, cross-sector monitoring, robust attribution approaches and quantitative assessment of risks to human health. We conclude that effective mitigation requires integrated cross-sector frameworks linking environmental surveillance, genomic data, microbial source attribution and quantitative risk assessment to inform targeted, risk-based interventions. These interventions need to be based on a deeper understanding of the interactions between environmental reservoirs, co-selective pressures and the key drivers and pathways of AMR, including broader environmental influences such as co-contaminants and climate change.},
}

@article {pmid42714431,
year = {2026},
author = {Belot, L and Payelleville, A and Jurėnas, D and Rocha, EPC and Van Melderen, L},
title = {Acquisition and erosion of toxin-antitoxin systems in bacterial chromosomes.},
journal = {Molecular biology and evolution},
volume = {43},
number = {9},
pages = {},
doi = {10.1093/molbev/msag230},
pmid = {42714431},
issn = {1537-1719},
support = {ADV X.1537.26F//FRFS-WELBIO/ ; //International Brachet Stiftung, the Université Libre de Bruxelles/ ; //FNRS-FRS/ ; //"Les Amis de l'Institut Pasteur à Bruxelles"/ ; //European Union's Horizon 2020/ ; 801505//Marie Skłodowska-Curie/ ; },
mesh = {*Toxin-Antitoxin Systems/genetics ; *Chromosomes, Bacterial/genetics ; *Photorhabdus/genetics ; Plasmids/genetics ; Evolution, Molecular ; Genome, Bacterial ; Bacterial Toxins/genetics ; Gene Transfer, Horizontal ; },
abstract = {Toxin-antitoxin systems are widespread in bacterial genomes. Yet, their integration, persistence, and impact on chromosome dynamics remain unclear. Here, we identified 80 type II toxin-antitoxin systems in the single chromosome of Photorhabdus laumondii TT01, 50 of which were experimentally validated. Comparative analysis across the Photorhabdus genus revealed a highly heterogeneous distribution, with toxin-antitoxin systems frequently clustering within discrete genomic regions, either alone or associated with cointegrate-forming transposases and integrases. Toxin-antitoxin systems rarely clustered with other putative defense systems and are preferentially associated with different types of recombinases, suggesting distinct pathways of acquisition for the two types of functions. Functional analyses showed that most validated toxin-antitoxin systems display addictive properties and stabilize plasmids. These addictive toxin-antitoxin systems are preferentially located in genomic regions characterized by high gene turnover, consistent with recent acquisition events. Despite their plasmid-stabilizing capacity, toxin-antitoxin systems do not promote long-term conservation of their immediate chromosomal neighborhoods. Instead, we observed frequent toxin-antitoxin loss, either through complete deletion or toxin pseudogenization, indicating relaxed selection for their persistence in bacterial lineages. We propose a stepwise model for toxin-antitoxin evolution in bacterial chromosomes: initial acquisition mediated by mobile genetic elements, preferential integration into permissive genomic regions, subsequent genetic streamlining of linked loci, and progressive gene loss. The short-lasting linkage between toxin-antitoxin systems and their genomic neighborhoods is consistent with the view that toxin-antitoxin modules can behave as autonomous, selfish genetic elements.},
}

*Toxin-Antitoxin Systems/genetics
*Chromosomes, Bacterial/genetics
*Photorhabdus/genetics
Plasmids/genetics
Evolution, Molecular
Genome, Bacterial
Bacterial Toxins/genetics
Gene Transfer, Horizontal

@article {pmid42795492,
year = {2026},
author = {Zhang, P and Ji, L and Yan, W and Chen, L and Dong, F},
title = {Genomic Dissection Reveals Polyphyletic Origins and Recombination-Driven Diversification of O/K Antigen Loci in Foodborne Vibrio parahaemolyticus O4:KUT Strains.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
pmid = {42795492},
issn = {2076-2607},
support = {2025JK094, 2026JKP-06,2026JKY031//Zhejiang Science and Technology Plan for Disease Prevention and Control/ ; 2026JKP-06//Disease Prevention and Control Innovation Team of Zhejiang Province/ ; },
abstract = {Vibrio parahaemolyticus is a leading cause of seafood-associated gastroenteritis worldwide. Traditional serotyping based on 13 O and 71 K antigens fails to classify many isolates, designated as K-untypable (KUT), whose genetic basis and evolutionary dynamics remain unclear. In this study, we conducted whole-genome sequencing of 47 O4:KUT strains from 40 clinical and 7 retail aquatic products (snail, river shrimp, Macrobrachium rosenbergii, etc.) to decipher the genomic diversity and structural variation in their O/K antigen loci. Phylogenomic analysis revealed a polyphyletic population structure spanning multiple sequence types, with O/K antigen loci classified into 13 distinct structural types comprising 149 biosynthetic genes. These clusters exhibited mosaic architectures and varied functional profiles. Notably, pervasive phylogenetic incongruence and robust recombination signals identified horizontal gene transfer as the primary mechanism driving O/K antigen loci diversification. Our findings reveal the evolutionary mechanisms of the foodborne O4:KUT serotype prevalent in local seafood and clinical samples from Huzhou, China, and provide a preliminary gene-signature framework that may inform the future development of molecular serotyping assays.},
}

@article {pmid42795514,
year = {2026},
author = {Hosseinpourlamardi, S and Labiba, S and Li, L and Dadvar, A and Guragain, M and Römling, U},
title = {Diverse Horizontally Transferred Cellulose Biosynthesis Gene Clusters in Escherichia coli Strains.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
pmid = {42795514},
issn = {2076-2607},
support = {2022-04865//Swedish Research Council/ ; },
abstract = {The phosphoethanolamine-modified exopolysaccharide cellulose synthesized by the type IIa cellulose biosynthesis nanomachine is a major extracellular matrix component of Escherichia coli. Here, we aim to investigate whether homologs of bcsABC genes of the core genome EcType 1 bcs cellulose biosynthesis gene cluster, which are diminished or abolished in high-virulence isolates, and entire clusters are mobilized on plasmids and occasionally manifested on E. coli chromosomes at alternative locations. While EcType BcsA2 and BcsA3 cellulose synthases are restricted to the genus Escherichia, the EcType BcsA4 cellulose synthase and associated bcs gene products are highly similar to Klebsiella pneumoniae counterparts. Cyclic di-GMP turnover proteins not previously recognized to post-translationally regulate cellulose biosynthesis on the chromosomal level are frequently co-localized with novel bcs genes. Thermotolerant meat-derived E. coli 730V1 uniquely harbors an EcType 4 bcs gene cluster of type Ib with a type IIb bcsG gene on a plasmid. Chemical, phenotypic and genetic evidence showed cellulose biosynthesis, cellulose-dependent cell aggregation and activation of biosynthesis by the second messenger cyclic di-GMP, an allosteric activator of the cellulose synthase. With gene duplication, horizontal gene transfer and recombination to contribute to the multiplication and diversification of bcs gene clusters in a number of different bacterial species, the extent and ecological role(s) of the multiplication, transfer and replacement of cellulose biosynthesis gene clusters, as well as in species other than E. coli, still need to be unraveled. Our data indicate, however, that although diversification and multiplication of bcs clusters is ongoing in the species E. coli, these events become rarely manifested in the population.},
}

@article {pmid42779942,
year = {2026},
author = {Hu, E and Gorman Durben, K and Budnik, B and H Arlow, D and F Oh, S and Nyerges, A},
title = {Firewalled synthetic commensal blocks horizontal gene transfer in the gut.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.17.752456},
pmid = {42779942},
issn = {2692-8205},
abstract = {Synthetic biology enables the rational reprogramming of microorganisms into living therapeutics and agents for bioremediation. However, such genetically modified organisms (GMOs) disseminate their synthetic genetic information into natural microbial communities through horizontal gene transfer (HGT), posing biosafety risks that limit clinical and environmental deployment. Reassigning sense codons to an alternative amino acid identity establishes a genetic firewall that simultaneously prevents incoming and outgoing gene flow, but reported implementations compromise fitness, precluding clinical and industrial use. Here, we overcome this limitation using genome design and laboratory evolution to create a high-fitness genetically firewalled Escherichia coli commensal. By directly altering the amino acid identity of TCA and TCG serine codons in the genetic code without an unassigned intermediate, we establish a robust genetic firewall that remains stable for thousands of generations. This firewalled commensal stably colonizes the mouse gastrointestinal tract for more than 100 days and blocks viral infections and HGT. As the long-term within-gut evolution of this firewalled organism identified adaptive mutations in genes responsible for carbon source utilization, we rationally redesigned the strain's genome to increase fitness. Together, this work establishes a genetically firewalled commensal for safer living therapeutics development and provides a strategy for designing high-fitness, virus- and gene-transfer-resistant organisms for clinical and environmental use.},
}

@article {pmid42780038,
year = {2026},
author = {Murray, I and Magar, RT and Piya, D and Selvakumar, H and Moriniere, L and Valappil, SK and Svab, M and Thongchol, J and Kazakov, A and Elisabeth, NH and Alayouni, M and Singh, PP and Muszyński, A and Azadi, P and Owen, SV and Zhang, J and Friedman, SD and Arkin, AP and Deutschbauer, AM and Roux, S and Mutalik, VK},
title = {Genome-wide characterization of host factors involved in single-stranded RNA and DNA phage infection pathways.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42780038},
issn = {2692-8205},
abstract = {Single stranded RNA (ssRNA) and single stranded DNA (ssDNA) bacteriophages represent a key component of the global virome, yet the host genetic networks supporting their infection cycles remain poorly understood. Here, we present a comprehensive, genome-wide mapping of the genetic landscape regulating infection cycles for F pilus-dependent ssRNA and ssDNA phages in Escherichia coli. Genetic screens across ssRNA phages spanning all four genogroups of the Leviviricetes revealed a highly conserved network of host dependencies, with the notable exception of the F plasmid gene traD. While primary structural receptor components and dsbA mediated disulfide bond formation are universally required across all lineages to ensure F pilus integrity, traD exhibits a strict genogroup-specific requirement during entry, showing variable essentiality across different viral groups despite sharing an identical primary receptor. Our gene dosage screens revealed that an elevated copy number of the hslU protease or the RNA chaperone stpA restricts infection, identifying clear genetic barriers that can perturb the viral life cycle. Parallel assays with filamentous ssDNA phages produced host factor profiles consistent with published literature, while revealing additional variations in host dependency. These screens confirmed that ssDNA phages strictly rely on the host TolQRA complex for entry downstream of pilus engagement. The assays tracked prominent negative fitness signatures across homeostatic clusters, highlighting how the physiological burden of continuous, non-lytic virion extrusion strains the host envelope. Finally, this comparative approach traced the selectivity of our isolation host (E. coli HSF) to a horizontally acquired capsule architecture from Klebsiella. This surface shield excludes a large panel of double stranded DNA phages isolated on diverse E. coli strains, while allowing virions from ssDNA and ssRNA phages to engage the extended F pilus and bypass the barrier via native pilus retraction. Together, this work provides a systematic, class-wide map of single stranded phage-host interactions, bridging classical genetics with modern viral discovery while establishing a robust host platform to access uncultured viral diversity and a functional blueprint to design next generation diagnostics, protein antibiotics, and biocontrol tools to halt horizontal gene transfer.},
}

@article {pmid42780844,
year = {2026},
author = {Zhang, Z and Hou, Z},
title = {Type VI secretion system effectors as modulators of host immunometabolism: organelle stress, nutritional immunity, and therapeutic opportunities.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1951748},
pmid = {42780844},
issn = {1664-302X},
abstract = {Metabolic reprogramming is a central determinant of host defense and pathogen persistence during infection. Although the bacterial type VI secretion system (T6SS) is primarily recognized as a contact-dependent apparatus for interbacterial competition and effector delivery, emerging evidence indicates that T6SS activity can also influence host metabolism at cellular, nutritional, and microbial-community levels. Here, we organize current evidence into three mechanistic tiers: direct biochemical interference with lipids, metabolites, or metal ions; organelle- and signaling-mediated immunometabolic reprogramming; and indirect metabolic effects arising from T6SS-dependent remodeling of microbial communities. T6SS effectors can disrupt endoplasmic-reticulum lipid homeostasis, activate the unfolded protein response and autophagy, alter mitochondrial Ca2+ handling and dynamics, promote redox imbalance, and modulate metabolically sensitive immune pathways including phosphoinositide 3-kinase (PI3K)-Akt, inflammasome, and cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) signaling. T6SS-associated proteins also mediate manganese and zinc acquisition or sequestration, linking microbial nutrient acquisition to host nutritional immunity. At the community level, T6SS-mediated competition may reshape resource allocation, horizontal gene transfer, and microbiome-derived metabolite production. However, while T6SS-induced organelle stress is well established, direct causal links to systemic metabolic diseases, including type 2 diabetes and dyslipidemia, remain unproven. We therefore distinguish direct metabolic measurements from inferences based on organelle damage or signaling changes and discuss strategies to define T6SS-driven metabolic fluxes and evaluate host-directed, anti-virulence, and microbiome-engineering approaches. Viewing the T6SS through an immunometabolic framework may reveal therapeutic vulnerabilities overlooked by conventional models of bacterial toxicity and competition.},
}

@article {pmid42781122,
year = {2026},
author = {López-Carrasco, MA and Purtschert-Montenegro, G and Pinto-Carbo, M and Cárcamo-Oyarce, G and Kalawong, R and Eberl, L},
title = {Lineage-restricted genomic islands drive rhizosphere niche specialization in Pseudomonas capeferrum.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag231},
pmid = {42781122},
issn = {2730-6151},
abstract = {In the rhizosphere, plant growth-promoting rhizobacteria play a pivotal role in plant health by efficiently colonizing roots and enhancing growth through diverse direct and indirect mechanisms. Many of these beneficial traits are associated with genomic islands (GEIs) acquired via horizontal gene transfer, yet their contribution to rhizosphere fitness remains poorly understood. Here, we report the whole-genome sequencing and comprehensive analysis of Pseudomonas putida strain IsoF, a highly efficient root colonizer originally isolated from the tomato rhizosphere that induces systemic resistance in plants. Phylogenomic analysis reclassified IsoF within the P. capeferrum group and revealed an extensive repertoire of GEIs encoding candidate functions to rhizosphere adaptation and plant growth promotion. Notably, IsoF harbours a unique combination of three GEIs absent in closely related strains. Phenotypic characterization and rhizosphere persistence assays using defined deletion mutants demonstrated that these islands significantly contribute to IsoF fitness and competitiveness in the rhizosphere. Together, our findings establish GEIs as key determinants of ecological success in beneficial rhizobacteria and position IsoF as a promising candidate for sustainable biocontrol applications.},
}

@article {pmid42785679,
year = {2026},
author = {Diego, SG and Emmanuelle, J},
title = {Coevolutionary diversification between hosts and their nutritional symbionts in phytophagous hemipterans.},
journal = {Current opinion in insect science},
volume = {},
number = {},
pages = {101623},
doi = {10.1016/j.cois.2026.101623},
pmid = {42785679},
issn = {2214-5753},
abstract = {Hemipteran insects feeding on plant sap rely on obligate microbial symbionts to compensate for the nutritional deficiencies of phloem and xylem sap. Because these bacteria are transmitted maternally over evolutionary timescales, Hemiptera have become a major model system for studying long-term host-microbe codiversification. Recent phylogenomic and comparative genomic studies have greatly expanded taxonomic coverage beyond classical model systems, revealing that ancient codiversification between hosts and nutritional symbionts is widespread across the order, but also that multipartite symbioses, recurrent symbiont acquisition, and symbiont replacement are far more common than previously appreciated. Here, we review current knowledge on the evolutionary dynamics of nutritional symbioses in plant-sucking Hemiptera. We discuss how genome reduction, metabolic complementation, and cellular compartmentalization contribute to the long-term stability of host-symbiont associations, and how horizontal gene transfer and repeated recruitment of novel microbial partners counteract the consequences of genome erosion. We also highlight major gaps in our understanding, including the limited taxonomic sampling across many hemipteran lineages, the ecological and evolutionary consequences of symbiont turnover, and the molecular mechanisms governing bacteriocyte development and symbiont integration. Integrating comparative phylogenomics with functional approaches will be essential for understanding how nutritional symbioses have shaped the diversification and ecological success of Hemiptera.},
}

@article {pmid42787985,
year = {2026},
author = {Ikushima, S and Fukasawa, K and Yoshioka, A and Tochigi, K and Komatsu, H and Kabeya, M and Onuma, M and Tamaoki, M and Hayashi, S},
title = {Human depopulation reshapes antimicrobial resistance dynamics in wildlife through ecological and transmission processes.},
journal = {One health (Amsterdam, Netherlands)},
volume = {23},
number = {},
pages = {101586},
pmid = {42787985},
issn = {2352-7714},
abstract = {Antimicrobial resistance (AMR) in wildlife is often interpreted as a spillover consequence of anthropogenic contamination, but the effects of long-term human depopulation remain poorly understood. We investigated quinolone-resistant Escherichia coli (QRE) and third-generation cephalosporin-resistant E. coli (3CRE) in wildlife and environmental samples from the Difficult-to-Return zones (DRZ), where human activity has been restricted since the 2011 Fukushima Daiichi Nuclear Power Plant accident, and from areas outside the DRZ (OUTSIDE), where human activity is present. Samples were collected from wild boar (n = 326), raccoons (n = 177), masked palm civets (n = 51), other wildlife (n = 39), wallows (n = 5), rivers (n = 9), and ponds (n = 9). Generalized additive models (GAMs) evaluated QRE occurrence using camera-trap-derived wildlife density, land-use variables, and livestock indices; core genome single-nucleotide polymorphism (cgSNP) analysis assessed genomic relatedness and transmission. QRE detection in wild boar was significantly higher in the DRZ, and cgSNP analysis indicated extensive clonal sharing among DRZ wild boar. GAM analysis further showed that QRE carriage increased with local wild boar density, supporting density-associated clonal expansion. In raccoons and masked palm civets, QRE carriage was associated with agricultural land, suggesting an influence of human-modified landscapes. Additionally, bla CTX-M-15 was disseminated across host species via a conserved mobile genetic element, suggesting horizontal gene transfer alongside clonal spread. These findings show that long-term human depopulation can reshape wildlife AMR dynamics and highlight the importance of integrating wildlife population management into One Health-based AMR risk assessments for human reinhabitation.},
}

@article {pmid42788731,
year = {2026},
author = {Rothenburg, S and Megawati, D and Bruneau, R and Tazi, L},
title = {Insights into molecular mechanisms of poxvirus evolution and host range through studies of poxvirus inhibitors of protein kinase R.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0176824},
doi = {10.1128/jvi.01768-24},
pmid = {42788731},
issn = {1098-5514},
abstract = {Protein kinase R (PKR) acts both as a sensor for virus infections, by detecting double-stranded (ds) RNA, and as an antiviral effector by phosphorylating the alpha subunit of eukaryotic translation initiation factor 2 (eIF2). Consequently, viruses have evolved many mechanisms to evade this potent antiviral protein, which in turn led to the fast evolution of PKR. There is an emerging understanding that these molecular arms races have important implications for the virulence and host range of viruses, which was in part propelled by research on PKR and poxvirus PKR inhibitors. At least four direct PKR pathway inhibitors, which either prevent PKR activation, inhibit interaction with eIF2α, or reverse eIF2α phosphorylation, evolved independently in different poxvirus clades, while poxvirus decapping enzymes provide another mechanism to subdue PKR activation via the reduction of dsRNA formation. In addition to discussing the functions and distributions of poxvirus PKR pathway inhibitors, we focus on host species-specific PKR-inhibitor interactions and their consequences for virus host range and virulence, including differential NF-κB pathway activation. We further highlight how research with PKR inhibitor-deficient poxviruses led to seminal discoveries elucidating molecular mechanisms for virus evolution, including gene amplification and horizontal gene transfer.},
}

@article {pmid42791971,
year = {2026},
author = {Wang, H and Zhang, K and Liu, M and Cheng, S and Cordeiro, CM and Sindhøj, E and Liang, J and Zeng, Y and Shen, S and Zhi, S},
title = {Optimized Organic Fertilization Mitigates Antibiotic Resistance Gene Dissemination in Manure-Amended Soils: A Field Study on Nutrient-Microbiome-Antibiotic Resistance Gene Nexus During Cabbage Reproductive Cycle.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antibiotics15090821},
pmid = {42791971},
issn = {2079-6382},
support = {24YFZCSN00270//Tianjin Key Research and Development Program Project/ ; 2023YFD1702000//National Key Research and Development Plan Project/ ; 202402AE090032//Yunnan Science & Technology Planning Project/ ; //the Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences./ ; 202301AT070245//Basic Research Program of Yunnan Province/ ; },
abstract = {Background: Manure-amended agricultural soil is a critical reservoir of antibiotic resistance genes (ARGs), posing escalating threats to environmental health and food safety. However, the temporal trajectories of ARG prevalence throughout the complete reproductive cycle of cash crops, and their mechanistic linkages with fertilization regimes and microbial community succession, remain inadequately understood. Methods: To bridge this knowledge gap, we conducted an in situ field experiment over the entire growth period of Chinese cabbage at a long-term manure-amended farm in Tianjin, China. Six contrasting fertilization strategies were evaluated: unfertilized control (CK1), unfertilized baseline control (CK2), traditional full-rate combined manure-chemical fertilization (TF), traditional half-rate combined manure-chemical fertilization (T1), half-dose sole manure fertilizer (T2), and half-dose sole chemical fertilizer only (T3). Results: Our results demonstrated that ARG abundance and associated mobile genetic elements (MGEs) exhibited a pronounced transient surge immediately post-fertilization, yet reverted to baseline levels by harvest, revealing a tangible resilience of the soil resistome. Notably, the optimized half-organic fertilization (T2) effectively curtailed the proliferation of manure-derived pathogenic taxa while preserving beneficial keystone phyla (e.g., Acidobacteria and Proteobacteria), indicating a trade-off between nutrient provisioning and ecological filtering. Co-occurrence network analysis further identified MB-A2-108, Saccharimonadales, and Rokubacteriales as pivotal hosts for multidrug-resistant ARGs, underscoring that microbial interspecific interactions-rather than taxonomic richness alone-are the primary drivers of resistome succession. Quantitative risk assessment confirmed that the T2 regimen reduced the composite ARG contamination index (CFzone) by 25% relative to conventional full fertilization (TF), while maintaining comparable cabbage yields. Conclusions: Collectively, our findings advocate for precision organic fertilization as a nature-based solution that synchronizes nutrient supply with crop demand, curtails ARG propagation, and mitigates long-term agroecological risks.},
}

@article {pmid42792083,
year = {2026},
author = {Xuan, S and Sheng, J and Chu, Z and Wang, M and Liu, H and Tian, Y and Zhang, H and Guo, X and Liu, J and Wang, G and Liu, Y},
title = {Antimicrobial Resistance and Genomic Characteristics of ESBL-Producing Proteus mirabilis from Farmed Mink in Shandong Province, China.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antibiotics15090933},
pmid = {42792083},
issn = {2079-6382},
abstract = {Background/Objectives: Proteus mirabilis is an opportunistic pathogen and a potential reservoir of clinically important antimicrobial resistance genes in animal production. However, mink-derived P. mirabilis remains poorly characterized. This study investigated multidrug-resistant and extended-spectrum β-lactamase (ESBL)-producing isolates from intensive mink farms, focusing on clinically important β-lactamase genes, their genomic backgrounds, and mobile genetic elements (MGEs). Methods: Among 373 fecal and intestinal-content samples collected from six mink farms in Shandong Province, China, 68 P. mirabilis isolates were recovered. All underwent antimicrobial susceptibility testing, ESBL confirmation, and virulence-associated phenotypic assays. The 39 ESBL-positive isolates underwent whole-genome sequencing, followed by analyses of antimicrobial resistance genes, the pangenome, and MGEs and comparison with 198 publicly available genomes. Results: Of the 373 sampled mink, 68 (18.2%) were P. mirabilis positive, and 39 (10.5%) carried ESBL-producing isolates. Of the 68 isolates, 63 (92.6%) were multidrug resistant, and 39 (57.4%) were ESBL positive. All exhibited strong biofilm formation and urease activity, while 83.8% showed strong swarming motility. Among the sequenced isolates, blaCTX-M genes were identified in 32 isolates and blaNDM-1 in three. Both blaCTX-M-65- and blaNDM-1-positive isolates were distributed across multiple genomic lineages, with blaCTX-M-65 additionally detected in multiple sequence types. This distribution indicates that these genes were not restricted to a single clone but does not demonstrate horizontal gene transfer. MGE-associated features showed same-contig co-occurrence with several resistance genes, notably IS903-blaCTX-M-65 and ISAba125-blaNDM-1. The sequenced isolates also exhibited substantial accessory-genome diversity and widely distributed virulence determinants associated with adhesion, motility, iron acquisition, and toxin-related functions. Conclusions: Mink-derived P. mirabilis exhibited extensive multidrug resistance and carried clinically important β-lactamase genes across diverse genomic backgrounds. These findings support the inclusion of fur-animal production systems in One Health surveillance of antimicrobial-resistant P. mirabilis.},
}

@article {pmid42792794,
year = {2026},
author = {Prakash, S and Saini, S and Bharti, M and Yadav, S and Hivare, P and Rai, NK},
title = {Antibiotic Resistance and the Return to a Pre-Antibiotic Era: A Critical Narrative Review of a Global Catastrophe.},
journal = {Biomedicines},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biomedicines14092053},
pmid = {42792794},
issn = {2227-9059},
abstract = {Antimicrobial resistance is a growing global crisis that threatens to return humanity to a pre-antibiotic era where common infections become deadly. This narrative review synthesizes evidence from 2000 to early 2026, including Global Research on Antimicrobial Resistance data and World Health Organization surveillance, to outline the problem's scale, drivers, and solutions. In 2019, bacterial resistance directly caused 1.27 million deaths and was linked to 4.95 million more. Low- and middle-income countries bear the heaviest burden. ESKAPE pathogens, especially carbapenem-resistant Acinetobacter baumannii and NDM-producing Klebsiella pneumoniae, drive intensive care unit mortality near 50% and cause untreatable neonatal sepsis. One Health drivers include antibiotic overuse in humans, with 30% of prescriptions unnecessary in high-income settings; agriculture, consuming 70% of global antibiotics; and environmental pollution, with resistance genes found in 72% of rivers. Bacteria spread resistance through horizontal gene transfer and mutations such as gyrA S83L, creating pan-drug-resistant strains that make surgeries, transplants, and cancer treatment risky. Economic modeling studies suggest that unchecked antimicrobial resistance could reduce annual global GDP by 1.1-3.8%, with some scenarios projecting losses of up to approximately 5% by 2050, depending on assumptions about healthcare costs, labor productivity, and livestock production. Solutions require subscription-based payment models, enforceable agricultural regulations, integrated genomic surveillance, and equity-focused diagnostics for low- and middle-income countries. Without binding 2030 targets, the post-antibiotic era would become a clinical reality within a decade.},
}

@article {pmid42793212,
year = {2026},
author = {Xiao, Y and Li, X and Qin, H and Li, J and Ma, Z and Su, X and Gao, L and Wang, L},
title = {Mosquito Antimicrobial Peptides: Molecular Diversity, Mechanisms of Action, and Translational Potential.},
journal = {Current issues in molecular biology},
volume = {48},
number = {9},
pages = {},
doi = {10.3390/cimb48090856},
pmid = {42793212},
issn = {1467-3045},
abstract = {Mosquito antimicrobial peptides (AMPs) contribute to innate defense against bacteria, fungi, parasites, and, in some experimental contexts, arboviruses. This narrative review evaluates endogenous mosquito AMP families across Aedes, Anopheles, and Culex species and clearly separates them from heterologous peptides introduced into mosquitoes for transmission-blocking studies. The best-supported endogenous families are cecropins, defensins, gambicin, attacin, and diptericin, although gene repertoires vary among mosquito lineages. Mechanistic evidence is strongest for membrane interaction by individual cecropins and defensins. Evidence for intracellular or redox mechanisms is more limited and peptide- and assay-specific; for example, mitochondrial effects have been demonstrated for Anopheles albimanus cecropin 3 in isolated rat cardiac mitochondria, whereas DNA binding and membrane permeabilization have been shown for an Aedes aegypti cecropin A derivative in Pseudomonas aeruginosa. Scorpine, magainin, and human defensin 5 are not mosquito AMPs and are considered separately as heterologous antiplasmodial effectors. Toll and immune deficiency (IMD) pathways regulate mosquito immune genes through NF-κB-family transcription factors, whereas Janus kinase-signal transducer and activator of transcription (JAK-STAT) is a distinct cytokine-signaling pathway. Translational approaches-including transgenic expression, paratransgenesis, Wolbachia-based control, and peptide engineering-remain promising but require cautious interpretation because efficacy, mechanism, ecological safety, horizontal gene transfer, regulatory oversight, and durability have not been resolved uniformly. By distinguishing direct peptide activity from genetic, expression-only, and inferential evidence, this review provides a more rigorous framework for evaluating mosquito AMPs and their potential use in vector-borne disease control.},
}

@article {pmid42794555,
year = {2026},
author = {Geetha, AA and Soorej, M and Alex, E and Rajesh, D and Babu, NS and Ishani, F and Renjith, S and Sajeev, A and Jacob, JP and Nair, BG and Kumar, G and Madhavan, A and Babu, P},
title = {Aquaculture Pathogens and Antimicrobial Resistance: A One Health Perspective.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188125},
pmid = {42794555},
issn = {1422-0067},
mesh = {*Aquaculture/methods ; Animals ; Humans ; *One Health ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/drug effects/genetics ; },
abstract = {Antimicrobial resistance (AMR) has emerged as a critical global health concern that transcends human, animal, and environmental boundaries. The extensive and often indiscriminate use of antibiotics for disease control and growth promotion has accelerated the evolution and spread of resistant pathogens within the aquaculture sector. This review examines aquaculture-associated AMR through a One Health framework. We explore the molecular mechanisms of resistance such as efflux pumps, enzymatic degradation, mobile genetic elements, and horizontal gene transfer that drive the dissemination of antimicrobial resistance genes among aquatic microorganisms. The review synthesizes evidence linking AMR in aquaculture to public health impacts, including the transmission of resistant bacteria through seafood and environmental exposure. Current regulatory measures and stewardship policies are assessed to identify gaps in implementation, particularly in developing regions where enforcement and public awareness remain limited. Review highlights emerging alternatives such as bacteriophage therapy, engineered probiotics, synthetic microbial communities, and CRISPR-based systems as sustainable approaches to reduce antibiotic dependence. Future research priorities include the integration of genomics, artificial intelligence, and environmental DNA monitoring for precision surveillance. This review emphasis the need for cross-sectoral collaboration, innovation, and global policy coherence to mitigate AMR in aquaculture and safeguard food, environmental, and public health security.},
}

*Aquaculture/methods
Animals
Humans
*One Health
Gene Transfer, Horizontal
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
*Bacteria/drug effects/genetics

@article {pmid42779725,
year = {2026},
author = {Bao, L and Kitten, T and Xu, P},
title = {Specific host translation perturbations promote Tn Smu 1 loss independently of the canonical ImmA regulator.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.15.751695},
pmid = {42779725},
issn = {2692-8205},
abstract = {Integrative and conjugative elements (ICEs) are major drivers of horizontal gene transfer and bacterial genome evolution. Although ICE-encoded regulatory circuits have been extensively characterized, the impact of host physiology on the stability of integrated ICEs remains poorly understood. Here, we identify a host-dependent pathway that links specific host translation perturbations to loss of the ICE Tn Smu1 in Streptococcus mutans . Analysis of host-gene deletion mutants revealed that disruption of fmt , rnjA , or rnjB -three translation-associated host genes-reproducibly promoted Tn Smu1 loss through a mechanism that bypasses the canonical ICE-encoded metalloprotease ImmA but remains dependent on the native attachment site attR . This phenotype was selective, as mutations affecting other essential cellular functions, including protein folding, tRNA modification, cell division, and fatty acid biosynthesis, failed to destabilize Tn Smu1 despite undergoing the same experimental evolution and accumulating adaptive genomic changes. Preventing Tn Smu1 loss in these translation-associated mutants markedly reduced bacterial growth, whereas loss of the element improved fitness, indicating that ICE elimination alleviates the cost associated with Tn Smu1 retention under these conditions. Finally, we show that the relationship between host translation and Tn Smu1 stability extends to a genetically distinct S. mutans clinical isolate, although with strain-dependent penetrance. Together, these findings identify host translational state as an important physiological determinant of Tn Smu1 stability and reveal that bacterial hosts can influence the maintenance of integrated mobile genetic elements through mechanisms that extend beyond element-encoded regulatory circuits.},
}

@article {pmid42779904,
year = {2026},
author = {Tarnopol, RL and Wang, RL and Kim, BY and Whiteman, NK},
title = {Horizontal gene transfer rivals gene duplication as a source of anti-parasitoid immune innovation in the Drosophilidae.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.15.751804},
pmid = {42779904},
issn = {2692-8205},
abstract = {Macroparasites are among the most important agents of natural selection in their host populations, but anti-macroparasite immunity is poorly understood. Vinegar flies (Drosophilidae) and the parasitoid wasps that infect them are emerging models to study how animals defend against macroparasite attack. The canonical anti-parasitoid immune mechanism in insects is melanotic encapsulation, which involves cell-mediated encapsulation coupled with prophenoloxidase (PPO)-mediated melanization of parasitoid embryos. Recently, we discovered the horizontal transfer (HGT) of a bacterially-derived humoral anti-parasitoid effector, Cytolethal distending toxin B (CdtB), across insects, including four drosophilid lineages. Here, we assessed the prevalence of these two anti-parasitoid immune mechanisms in 406 drosophilid and four outgroup species. We found that melanotic encapsulation was relatively uncommon among species with known anti-parasitoid immune responses. While PPO duplications were found in 88 species, the most salient PPO gene underlying melanotic encapsulation, PPO3 , was restricted to Drosophila melanogaster and its close relatives. PPO genes were present in lower copy number per genome in the Drosophilidae than in outgroup lineages and evolved slowly. We found cdtB in the genomes of 93 species and estimated at least 11 independent cdtB gains across the Drosophilidae as early as ~44 mya and as recently as ~6 mya. cdtB acquisition was subsequently associated with higher net diversification rates in some clades. We conclude that humoral immune effectors may play a more important role than previously appreciated in anti-parasitoid immunity in insects and that an immune innovation arising repeatedly from HGT is potentially associated with the evolutionary success of these animals.},
}

@article {pmid42770715,
year = {2026},
author = {Xu, J-W and He, Y-T and Zhou, X and Zhan, X-Y},
title = {Genomic divergence and phenotypic heterogeneity of Legionella longbeachae reveal a putative novel proinflammatory serogroup with genome reduction and mobilome expansion.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0110926},
doi = {10.1128/aem.01109-26},
pmid = {42770715},
issn = {1098-5336},
abstract = {Legionella longbeachae is an emerging respiratory pathogen primarily found in soil environments, yet its genomic architecture and evolutionary strategies remain poorly characterized. Here, through pan-genomic and functional analysis of 242 L. longbeachae isolates, we reveal an open pan-genome driven by extensive horizontal gene transfer and marked functional divergence between core and accessory genomes. We identify a phylogenetically distinct lineage, designated as putative serogroup 3 (sg3), recovered from Chinese environments. This lineage diverges from canonical serogroups 1 and 2 through genome reduction (mean size 4.01 Mb), absence of plasmids, and a truncated O-antigen biosynthesis cluster lacking a key N-acetyltransferase-encoding gene (orf9). In vitro infection models across multiple human cell lines show that sg3 elicits increased host cell death and elevated proinflammatory cytokine transcription in epithelial cells compared to sg1 and sg2. Phylogenetically corrected association analyses revealed no significant link between this phenotype and individual accessory virulence factors. Instead, rank-transformed phylogenetically generalized least squares (PGLS) regression demonstrated a significant positive association with expansion of the mobilome (COG X), while intracellular trafficking (COG U) and defense (COG V) repertoires were contracted. These findings reveal a distinct pathogenic profile in sg3 that differs from the canonical serogroups, characterized by heightened inflammatory activation rather than immune evasion. Our work advances the understanding of L. longbeachae population structure, challenges the reductionist utility of traditional serogrouping, and highlights the potential need for revised diagnostic considerations as well as continued surveillance of lineages displaying enhanced cytotoxicity and proinflammatory responses, which may be associated with mobilome expansion.IMPORTANCELegionella longbeachae is an understudied yet emerging cause of Legionnaires' disease, with a distinct soil-based ecology. Using comparative pan-genomics and functional infection assays across 242 isolates (including 39 newly sequenced from China), we identify a putative novel serogroup (sg3) that has undergone marked genome reduction (4.01 Mb) and completely lost plasmids, contrasting with near-ubiquitous plasmid carriage in sg1/sg2. Despite its streamlined genome, putative sg3 exhibits enhanced cytotoxicity in all tested human cell lines and elevated proinflammatory cytokine expression, particularly in epithelial cells. These phenotypes are not explained by individual virulence genes but are significantly associated with mobilome (COG X) expansion. Our findings question the assumption that genome reduction necessarily diminishes pathogenic potential and suggest that higher-order genomic restructuring, potentially linked to mobilome expansion, may be associated with increased inflammatory responses. Furthermore, they highlight the potential need for continued surveillance and consideration of revised diagnostic approaches to include this rare but possibly underdiagnosed lineage.},
}

@article {pmid42773652,
year = {2026},
author = {Lu, S and Liu, D and Chen, Y and Sun, Q and Chen, L and Sun, T and Zhang, W},
title = {[Recent progress in algal-bacterial symbiotic and mutualistic systems].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {42},
number = {9},
pages = {3884-3904},
doi = {10.13345/j.cjb.260133},
pmid = {42773652},
issn = {1872-2075},
support = {2025YFA0921700//the National Key Research and Development Program of China/ ; 32371486//the National Natural Science Foundation of China/ ; },
mesh = {*Symbiosis/physiology ; *Bacterial Physiological Phenomena ; *Bacteria/metabolism ; Environmental Restoration and Remediation ; },
abstract = {Algal-bacterial symbiotic and mutualistic systems enhance community stability and functional performance through interspecies cooperation and signal exchange, demonstrating considerable potential in environmental remediation and sustainable biomanufacturing. This review systematically summarizes the fundamental interaction types and underlying mechanisms of algal-bacterial symbiosis and mutualism, with a particular focus on enabling technologies for the rational reconstruction of engineered mutualistic consortia and their emerging applications in environmental remediation and biomanufacturing. Different interaction modes, including mutualism, commensalism, parasitism, and endosymbiosis, are comparatively discussed, together with key regulatory mechanisms such as chemical signaling, nutrient exchange, horizontal gene transfer, and homeostasis maintenance under abiotic stress conditions. At the technical level, this paper introduces the recent advances in single-cell dynamic monitoring approaches, artificial intelligence-driven design platforms, and synthetic community engineering strategies integrating both top-down and bottom-up methodologies. Furthermore, this paper discusses the potential applications of algal-bacterial mutualistic systems in wastewater remediation, aquaculture, bioenergy recovery, and sustainable bioproduction and points out the current research challenges related to mechanism understanding, species specificity, long-term system stability, and ecological risk assessment. Finally, this review proposes that interdisciplinary approaches integrating multi-omics analyses, computational modeling, and controllable environmental validation will facilitate the development of efficient, robust, and sustainable algal-bacterial symbiotic systems, thereby providing theoretical guidance and technical support for advancing synthetic biology-driven resource utilization and green biomanufacturing.},
}

*Symbiosis/physiology
*Bacterial Physiological Phenomena
*Bacteria/metabolism
Environmental Restoration and Remediation

@article {pmid42776574,
year = {2026},
author = {Scoglio, GD and Green, DH and Jackson, HO and Purton, S},
title = {Genomic insights into the taxonomy, safety and biotechnological potential of Aphanizomenon flos-aquae and related Nostocales.},
journal = {Microbial genomics},
volume = {12},
number = {9},
pages = {},
pmid = {42776574},
issn = {2057-5858},
mesh = {Multigene Family ; *Aphanizomenon/genetics/classification/metabolism ; Vitamin B 12/metabolism ; *Genome, Bacterial ; Bacterial Toxins/genetics/biosynthesis ; Phylogeny ; Genomics ; Biotechnology ; *Cyanobacteria/genetics/classification/metabolism ; Cyanobacteria Toxins ; },
abstract = {The Nostocales are filamentous cyanobacteria that include bloom-forming, nitrogen-fixing species with major ecological and biotechnological relevance. Owing to their metabolic diversity, nitrogen-fixing capabilities and nutritional profile, they hold potential for various biotechnological applications including the production of nutraceuticals and biofertilizers. However, the capacity of certain Nostocales species to produce cyanotoxins also raises health concerns. This study provides a comparative bioinformatic analysis of 161 Nostocales genomes from the National Center for Biotechnology Information (NCBI) and three newly sequenced Aphanizomenon flos-aquae (AFA) strains, including Klamath AFA, with a focus on taxonomy, cyanotoxin-associated biosynthetic gene clusters (BGCs), natural competence, restriction-modification systems and vitamin B12 metabolism. Our analysis supports reassessment of several AFA-labelled genomes and refines the boundaries of the core AFA cluster. Cyanotoxin-associated BGCs, specifically for anatoxin-a, saxitoxin, cylindrospermopsin and microcystin/nodularin, were detected in only 7.3% of the genomes. Natural competence genes required for horizontal gene transfer were found in 89.6% of the genomes, although the presence of multiple restriction-modification system-associated proteins in Nostocales species, especially Aphanizomenon, Anabaena, Dolichospermum and Nostoc sp. may limit foreign gene acquisition. Additionally, ~30% of the genomes harbour a shared btu operon arrangement associated with B12 import, observed here across multiple Nostocales genera. B12 content in the AFA strains was measured at ~0.4-0.5 µg g[-1] dry biomass and is likely linked to associated B12-producing bacteria. Fluorescent B12 analogue uptake experiments in NIES 4052 and Klamath AFA support a model for the uptake of exogenous B12 in these strains. Together with the detection of cobalamin-producing commensal bacteria, this suggests that B12 in AFA biomass may be linked to cyanobacterium-bacteria interactions. Overall, this study provides a genomic and experimental framework for evaluating the taxonomy, safety, genetic tractability and nutritional potential of AFA and related Nostocales.},
}

Multigene Family
*Aphanizomenon/genetics/classification/metabolism
Vitamin B 12/metabolism
*Genome, Bacterial
Bacterial Toxins/genetics/biosynthesis
Phylogeny
Genomics
Biotechnology
*Cyanobacteria/genetics/classification/metabolism
Cyanobacteria Toxins

@article {pmid42776594,
year = {2026},
author = {Tripathi, M and Kumar, S and Yadav, M and Sehrawat, N and Gangola, S and Sharma, U and Omar, BJ and Prasad, A},
title = {Dissemination of hypervirulent carbapenem-resistant Klebsiella pneumoniae in wastewater.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2026.03100},
pmid = {42776594},
issn = {1588-2640},
abstract = {Klebsiella pneumoniae is a Gram-negative bacterium, which can cause a range of difficult-to-treat infections, like; wound infections, urinary tract infections (UTIs), pneumonia, and other diseases. Recent studies have shown that hypervirulent carbapenem-resistant K. pneumoniae (hv-CRKp) is a single, widespread "super-pathogen" that combines significant clinical complications. This convergence is not exclusive to hospitals, as plasmid-mediated virulence and resistance gene exchange occurs in wastewater and other aquatic habitats. Hospital effluents serve as the main hotspot for CRKp discharge, with substantial clonal spread, according to research from regional wastewater networks. Selective pressures from heavy metals, disinfectants, and antibiotic residues speed up horizontal gene transfer in these intricate microbial communities, encouraging the establishment of hv-CRKp. The molecular mechanisms underlying plasmid fusion and mobility, the role of the wastewater resistome and biofilms as sites of genetic exchange, and the One-Health implications of environmental dissemination are all summarized in this assessment of recent investigations from 2023 to 2025. We show how wastewater-based epidemiology may be utilized as an early warning system to discover novel hv-CRKp lineages by merging data from plasmidomics, metagenomics, and global surveillance. The ecological and molecular continuity that links hospitals, wastewater, and the larger environment must be understood when designing next-generation antimicrobial resistance control initiatives against hv-CRKp. This study concludes by discussing research gaps and intervention ideas to reduce environmental spread.},
}

@article {pmid42777402,
year = {2026},
author = {Altinok, I},
title = {Plastisphere as a global hotspot for antimicrobial resistance: Systematic review and quantitative synthesis.},
journal = {Marine pollution bulletin},
volume = {233},
number = {Pt 3},
pages = {120342},
doi = {10.1016/j.marpolbul.2026.120342},
pmid = {42777402},
issn = {1879-3363},
abstract = {Plastic debris provides colonizable surfaces for microbial biofilms, the plastisphere, which is now recognized as a hotspot for antimicrobial resistance (AMR) amplification and dissemination. This PRISMA 2020-compliant synthesis covers 53 studies. Random-effects meta-analysis of 30 conjugation datasets showed enhanced horizontal gene transfer: pooled log response ratio (lnRR) = 1.93 (95% CI: 1.63-2.23), 6.9-fold (95% CI: 5.1-9.3-fold); heterogeneity was high (I[2] = 85.0%; τ[2] = 0.573; Q = 187.6, df = 29) and the 95% prediction interval spanned 1.5-31.3-fold. Polyvinyl chloride (PVC) biofilms showed the largest sub-group effect (lnRR = 2.72; 95% CI: 1.84-3.60; 15.2-fold), and polymer type was significant as a categorical moderator (QM = 12.3, P = 0.006; R[2] = 29%) but not as a continuous ordinal score (P = 0.15). Antibiotic resistance gene (ARG) concentrations exceeded paired controls by one to three orders of magnitude (median log10 enrichment 1.98; 95-fold). Ampicillin resistance in plastisphere-associated Vibrio spp. reached 68.4% (Wilson 95% CI: 57.3-77.8%), with 32.9% multidrug-resistant. A conceptual five-stage genetic reactor lifecycle model is proposed as a heuristic, not a validated framework, identifying dispersal as the least-evidenced stage. A polymer risk hierarchy (PVC > polyethylene (PE) > polystyrene (PS), with polyethylene terephthalate (PET) lowest for ARG enrichment), an exposure-response framework and four Tier-1 knowledge gaps are established. The evidence base is geographically skewed (38% of studies from Chinese systems), and these estimates describe environmental enrichment, not realized clinical risk. They nonetheless justify incorporating polymer-additive regulation and plastisphere resistome surveillance into One Health strategies and the UN Plastics Treaty.},
}

@article {pmid42778281,
year = {2026},
author = {de Toledo, NA and Van Sluys, MA and Dias, HM},
title = {Evolutionary reconstruction of thiamine biosynthesis pathway: An integrative bioinformatics workflow.},
journal = {Methods in enzymology},
volume = {735},
number = {},
pages = {43-87},
doi = {10.1016/bs.mie.2026.06.014},
pmid = {42778281},
issn = {1557-7988},
mesh = {*Thiamine/biosynthesis/genetics ; *Computational Biology/methods ; Phylogeny ; Workflow ; *Evolution, Molecular ; Bacteria/genetics/metabolism ; Archaea/genetics/metabolism ; *Biosynthetic Pathways/genetics ; Markov Chains ; Eukaryota/genetics/metabolism ; Riboswitch ; },
abstract = {Thiamine (vitamin B1) biosynthesis involves enzymatic activities that exhibit remarkable diversity across the tree of life, including deep sequence divergence, domain rearrangements, lineage-specific duplications and losses, and horizontal gene transfer events. These features complicate computational inference based on single evidence types. This chapter describes a reproducible, modular bioinformatics workflow for pathway-scale comparative analysis of thiamine biosynthesis genes across Bacteria, Archaea, and Eukarya. The workflow integrates four complementary evidence streams: (i) profile-based homolog discovery using Hidden Markov Models (HMMs) with domain architecture validation; (ii) per-family phylogenetic reconstruction to evaluate evolutionary relationships, distinguish orthologs from paralogs, and identify lineage-specific patterns; (iii) detection of TPP riboswitches using covariance models, with an overview of upstream promoter motif discovery as a complementary observational approach; and (iv) transcriptome integration to assess context-dependent gene expression. We further demonstrate how variation in protein domain architecture, particularly single versus multi domain configurations, shape sequence recovery, phylogenetic inference, and evolutionary interpretation. Step-by-step protocols cover computational environment setup, parameter optimization, quality control checkpoints, and interpretation guidelines. The workflow addresses common bioinformatic challenges and annotation inconsistencies across databases. All scripts, HMM profiles, and example datasets are available through GitHub, enabling researchers to apply these methods to thiamine pathway analysis or adapt them for other metabolic pathways with similar evolutionary diversity.},
}

*Thiamine/biosynthesis/genetics
*Computational Biology/methods
Phylogeny
Workflow
*Evolution, Molecular
Bacteria/genetics/metabolism
Archaea/genetics/metabolism
*Biosynthetic Pathways/genetics
Markov Chains
Eukaryota/genetics/metabolism
Riboswitch

@article {pmid42778487,
year = {2026},
author = {Yong, C and Rincón, AFC and Joshi, SH and Memon, R and Gyorgy, A},
title = {Plasmid copy number control offers a versatile tool in synthetic biology applications.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2026.07.005},
pmid = {42778487},
issn = {1879-3096},
abstract = {Plasmids are typically regarded as static delivery vehicles for foreign DNA. Here, we expose the pivotal role that plasmid copy number (PCN) control can play in synthetic biology, not only in Escherichia coli but also in the next-generation bacterial workhorse Vibrio natriegens. We show that the antibiotic selection marker can impact PCN, thus affecting growth and protein production, and that cells can be cotransformed with multiple variants of the same plasmid, with their PCN controlled simultaneously and in unison. We reveal that plasmid loss can be mitigated via the integration of an additional origin of replication (ori) and that PCN control can be leveraged to modulate horizontal gene transfer, which we illustrate within the context of conjugation-based intercellular communication. Finally, we expand the MoClo modular cloning framework with inducible PCN control for rapid prototyping and to enhance the performance of complex biocircuits.},
}

@article {pmid42778666,
year = {2026},
author = {Shin, NR and Kirsch, R and Vogel, H and Riedel, A and Kaltenpoth, M and Pauchet, Y},
title = {Evolutionary dynamics of plant cell wall-degrading enzymes reflects feeding ecology in weevils.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {42778666},
issn = {2399-3642},
support = {PA2808/4-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; *Weevils/genetics/enzymology/physiology/classification ; *Cell Wall/metabolism/enzymology ; Phylogeny ; *Evolution, Molecular ; *Herbivory ; Gene Transfer, Horizontal ; *Biological Evolution ; *Plants/enzymology ; },
abstract = {Many herbivorous beetles depend on plant cell wall-degrading enzymes (PCWDEs) to access the nutritious plant cell content. However, the evolution of PCWDEs in weevils, the most diverse lineage of herbivores, remains poorly understood. Using transcriptomic and genomic analyses of 45 weevil species spanning the majority of existing subfamilies, we identified a total of 13 different PCWDE families, revealing high variability between species. Interestingly, the PCWDE repertoires tracked dietary specialization, with convergent reductions in fungivorous taxa. Furthermore, PCWDE gene family dynamics were driven by both larval and adult specialized herbivory on different plant organs. Despite this complex evolutionary history, phylogenetic analyses place core PCWDE functionalities at the base of the Phytophaga (weevils, leaf beetles, and longhorn beetles) and reveal subsequent horizontal gene transfer (HGT) events from various donors during early Phytophaga diversification. These findings demonstrate that HGTs, gene duplications, and losses shaped PCWDE diversity and facilitated the ecological success of weevils.},
}

Animals
*Weevils/genetics/enzymology/physiology/classification
*Cell Wall/metabolism/enzymology
Phylogeny
*Evolution, Molecular
*Herbivory
Gene Transfer, Horizontal
*Biological Evolution
*Plants/enzymology

@article {pmid42766177,
year = {2026},
author = {Fuad, M and Rabbee, MF and Mahmud, Z and Baek, KH},
title = {Role of extended-spectrum β-lactamase (ESBL) genes in the dissemination of β-lactam resistance within aquatic environments: mechanisms, persistence, and one health implications.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {10},
pages = {},
pmid = {42766177},
issn = {1573-0972},
mesh = {*beta-Lactamases/genetics/metabolism ; *beta-Lactam Resistance/genetics ; *Water Microbiology ; *Enterobacteriaceae/genetics/drug effects/enzymology ; DNA Transposable Elements/genetics ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Humans ; beta-Lactams/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {Antimicrobial resistance of pathogenic bacteria has rapidly increased over the past 20 years, creating a major global health threat. Extended-spectrum β-lactamases (ESBLs) are major drivers of resistance to β-lactam antibiotics, hydrolyzing broad-spectrum cephalosporines and monobactams. ESBL-producing Enterobacteriaceae are widespread across aquatic environments. While previous reviews have broadly described clinical ESBL epidemiology, a comprehensive synthesis explicitly linking aquatic microenvironmental niches, mobile genetic element dynamics, and environmental selection mechanisms remains lacking. This review addresses this gap by critically evaluating how aquatic environments function as active evolutionary reactors rather than mere passive sinks. The dissemination of these ESBL genes depends on conjugative plasmids, insertion sequences, and transposons. Specifically, insertion sequence ISEcp1 mobilizes and enhances the expression of blaCTX-M genes through transposition and strong promoter activity, while IS26 promotes the capture, rearrangement and accumulation of multi-drug resistance determinants within plasmids and transposons. ESBL genes persist in both intracellular and extracellular forms within sediments, biofilms, and microplastic-associated habitats. This review describes the prevalence, mobility, dissemination mechanisms, and environmental-clinical connectivity of ESBL determinants in aquatic systems.},
}

*beta-Lactamases/genetics/metabolism
*beta-Lactam Resistance/genetics
*Water Microbiology
*Enterobacteriaceae/genetics/drug effects/enzymology
DNA Transposable Elements/genetics
Plasmids/genetics
Anti-Bacterial Agents/pharmacology
Humans
beta-Lactams/pharmacology
Gene Transfer, Horizontal

@article {pmid42766741,
year = {2026},
author = {Panossian, B and Kolp, MR and Wu, T and Tallapragada, K and Patel, V and Goldstein, EB and Oliver, KM and Henry, LM and Parker, BJ},
title = {Phenotypic divergence is driven by mobile genetic elements in a heritable insect symbiont.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {39},
pages = {e2607226123},
doi = {10.1073/pnas.2607226123},
pmid = {42766741},
issn = {1091-6490},
support = {IOS2152954//US NSF/ ; R35GM154800//US NIH/ ; BB/W001632/1//UK BBSRC/ ; DBI2109440//US NSF/ ; },
mesh = {Animals ; *Symbiosis/genetics ; *Aphids/microbiology/genetics ; *Interspersed Repetitive Sequences/genetics ; Phenotype ; Plasmids/genetics ; *Enterobacteriaceae/genetics ; Phylogeny ; Gene Transfer, Horizontal ; },
abstract = {Heritable microbes profoundly influence insect biology, yet the traits they confer often evolve rapidly and differ among closely related symbiont strains. Despite their importance, we lack a clear understanding of how novel traits arise in symbionts and how this diversity influences host ecology in nature. The aphid facultative symbiont Regiella insecticola is ideally suited to address this question due to strong lineage-specific variation in host benefits. By generating 20 high-quality genomes, we found that Regiella's evolution is driven largely by gene gains mediated by mobile genetic elements (MGEs). A plasmid (pRILSR1) encoding a type IV secretion system and a highly expressed predicted effector has spread horizontally between distantly related Regiella clades associated with pea aphids. Notably, only pRILSR1-bearing strains confer protection against the fungal pathogen Pandora neoaphidis. Moreover, loss of the plasmid by a protective strain in culture resulted in the loss of protection, indicating that pRILSR1 is required for the defensive phenotype. In a multiyear field study, pRILSR1 frequency varied systematically among host plant-associated pea aphid populations and predicted differences in symbiont-mediated fungal resistance. Together, our results show that gain and loss of a single MGE contributes to divergence in a key adaptive trait, providing a mechanism by which symbiont evolution generates phenotypic differences among host populations.},
}

Animals
*Symbiosis/genetics
*Aphids/microbiology/genetics
*Interspersed Repetitive Sequences/genetics
Phenotype
Plasmids/genetics
*Enterobacteriaceae/genetics
Phylogeny
Gene Transfer, Horizontal

@article {pmid42767306,
year = {2026},
author = {Li, K and Gao, J and Zhang, K and Zhang, J and Zuo, Q and Gao, F and Wang, Y and Guo, Y},
title = {Environmental risks under individual and co-exposure to nisin and cetylpyridinium chloride: From denitrification system disturbance to resistance gene dissemination.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125711},
doi = {10.1016/j.envres.2026.125711},
pmid = {42767306},
issn = {1096-0953},
abstract = {Nisin is a common natural food preservative, and cetylpyridinium chloride (CPC) is a typical quaternary ammonium compounds often applied as a disinfectant to food surfaces. Nisin and CPC frequently coexist in wastewater treatment plants and might pose adverse effects on the microorganisms responsible for nitrogen removal. This short-term batch experiment explored the responses of denitrification systems including nitrogen removal performance, cytotoxicity, resistance genes (RGs), and microbial community under individual and co-exposure to various concentrations of nisin and CPC. 5-80 mg/L nisin had little effect on the denitrification system, whereas 0.5-8 mg/L CPC individually or in combination with 5-80 mg/L nisin caused concentration dependent deterioration of denitrification performance, with total nitrogen removal efficiency even declining to below 5% at the highest tested concentrations. Furthermore, CPC individually or in combination with nisin reduced cell viability, altered microbial community structure, decreased the abundance of the denitrifying functional bacterium Thauera, and enriched Pseudomonas. Nisin and CPC might act synergistically, promoting the proliferation of RGs, with RGs free in water increasing to 9.90 times that of CK under co-exposure to 80 mg/L nisin and 8 mg/L CPC. Nisin and/or CPC might induce co-selection among different RGs, enhancing cross-resistance of bacteria. Positive correlations were observed between mobile genetic elements (intI1, tnpA-04) and multiple RGs, intensifying the potential risk of RGs spreading via horizontal gene transfer. This study revealed the environmental risks of nisin and CPC, providing a reference for assessing their impacts on the biological nitrogen removal process and the potential threat of RGs dissemination.},
}

@article {pmid42767475,
year = {2026},
author = {García-Flórez, A and Leunda-Esnaola, A and Arrufat, P and Kaberdin, VR and Pearman, PB},
title = {Universal single-copy genes and 16S rDNA present incongruent evolutionary histories in vibrio.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108746},
doi = {10.1016/j.ympev.2026.108746},
pmid = {42767475},
issn = {1095-9513},
abstract = {A common technique for the study of the diversity and evolution of microbial communities is 16S rDNA sequencing. However, high sequence identity and variable copy number constrain the application of 16S rDNA in differentiation of closely related taxa and estimation of species relative abundance in environmental samples. A promising alternative is the use of universal single-copy genes as phylogenetic markers. We explore this alternative by analyzing a set of single-copy loci from the genus Vibrio, which comprises more than 100 species of substantial ecological and epidemiological relevance. The phylogenetic histories of these loci, of representative copies of 16S and 23S rDNA genes, and of a collection of partial 16S rDNA sequences were reconstructed using Bayesian inference. Taxon resolution was assessed according to consensus tree topology and clade credibility values. In addition, the congruence among posterior distributions of phylogenetic estimates of the different loci was calculated using Robinson-Foulds distances and visualized with non-metric multidimensional scaling. Phylogenetic analyses reveal that Vibrio single-copy loci produce highly resolved trees in comparison to those of 16S and 23S rDNA sequences. We also observe relatively high congruence among phylogenies of Vibrio single-copy loci while rDNA phylogenies diverge from these. The loci mfd and uvrC are highlighted for further research on Vibrio evolution and analysis of environmental samples. Moreover, possible sources of phylogenetic incongruence between Vibrio single-copy and rDNA loci include differential susceptibility to horizontal gene transfer, as potentially explained by the complexity hypothesis, or lack of phylogenetic information due to limited sequence variability in rDNA sequences.},
}

@article {pmid42768386,
year = {2026},
author = {Pateriya, D and Tanwar, A and Sharma, VK},
title = {Insights into the dynamics of antibiotic resistance genes in the human gut microbiome across populations.},
journal = {Gut pathogens},
volume = {18},
number = {1},
pages = {},
pmid = {42768386},
issn = {1757-4749},
support = {INSACOG//Biotechnology Industry Research Assistance Council/ ; BT/PR50613/MED/32/981/2023//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {The human microbiome serves as a reservoir of antibiotic resistance genes (ARGs), collectively known as the resistome, which has crucial implications for human health. However, the distribution of ARGs across diverse bacterial taxa and their variation across populations, disease states, and body sites remain less well understood. Here, we comprehensively profiled the human resistome using genomic and metagenomic data. Our analysis included 4,744 species-representative gut bacterial genomes and 452 oral bacterial genomes, along with gut metagenomic data from 10,230 individuals across 58 studies encompassing 5,388 healthy and 4,842 disease-associated samples, including underexplored non-Western cohorts. Our analysis revealed variation in the gut resistome across population groups and countries. The oral microbiome exhibited a distinct resistome profile with lower ARG prevalence compared to the gut. Across multiple datasets, ARG abundance was generally higher in inflammatory bowel disease samples compared to healthy samples. Pathogenic taxa such as Enterobacter, Citrobacter, Escherichia, and Klebsiella carried the highest number of ARGs, including clinically relevant ARGs, whereas abundant commensals like Bacteroides and Prevotella contributed to the baseline resistome. Notably, population-level differences in ARG composition appeared to be linked to microbial community structure. Shared ARGs between commensal and pathogenic bacteria provided clues to horizontal gene transfer. These findings provide crucial insights into the ecological and population-level factors shaping the gut resistome, highlighting the roles of both pathogens and commensals in the maintenance and dissemination of antimicrobial resistance.},
}

@article {pmid42768760,
year = {2026},
author = {Sidorov, R and Li, L and Dadvar, A and Ahmad, I and Spring, S and Overmann, J and Römling, U},
title = {Archaeal Genes Code for GGDEF Domain Proteins With Diguanylate Cyclase Activity.},
journal = {Molecular microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mmi.70117},
pmid = {42768760},
issn = {1365-2958},
support = {2022-04865//Swedish Research Council for Natural and Engineering Sciences/ ; //Karolinska Institutet KI Funds 2023/ ; },
abstract = {Cyclic di-GMP is ubiquitous in Bacteria, including members of the deepest branching phyla, but has not yet been detected in Archaea. Thus, whether cyclic di-GMP was present as a signaling nucleotide in the last universal common ancestor (LUCA) of Bacteria and Archaea remains unknown. In this work, bioinformatic analyses and structural modelling identified GGDEF domain proteins in archaeal isolates and encoded by metagenomes of confirmed archaeal origin. In particular, in bacterial model organisms, phenotypic and in vivo assays, in combination with catalytic mutants, suggest that selected archaeal GGDEF domain proteins possess diguanylate cyclase activity. These include the complex RECS-PAS/PAC-PocR-GGDEF-HD-GYP domain protein of Methanocella arvoryzae MRE50, a member of the Stenosarchaea order Methanocellales. While cyclic di-GMP signaling proteins are ubiquitous in Bacteria, their presence seems to be more sporadic in Archaea. It is currently unclear whether cyclic di-GMP signaling proteins have been lost in some lineages, secondarily introduced by horizontal gene transfer into others, or whether both scenarios have occurred.},
}

@article {pmid42764294,
year = {2026},
author = {Liu, H and Qi, Y and Zhang, X and Zhang, T and Zhang, XX and Ma, L},
title = {Systematic citywide analysis reveals ecological connectivity of antimicrobial resistance genes across urban water systems.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42764294},
issn = {2041-1723},
support = {52470217//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Drinking Water/microbiology ; Humans ; Gene Transfer, Horizontal ; *Water Microbiology ; Anti-Bacterial Agents/pharmacology ; Cities ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; Wastewater/microbiology ; Enterobacteriaceae/genetics/drug effects/isolation & purification ; Metagenomics ; *Drug Resistance, Microbial/genetics ; Integrons/genetics ; Bacteria/genetics/drug effects/isolation & purification ; },
abstract = {Antimicrobial resistance (AMR) in drinking water raises public health concerns, while its anthropogenic sources, transmission dynamics, and health risks remain poorly understood, hindering the development of effective strategies to reduce human exposure. Here we conduct a systematic investigation of anthropogenic contributions to AMR across urban water compartments in a megacity, combining metagenomics and culturomics. We identify 1,309 antibiotic resistance genes (ARGs), and tracking their dynamics across microbial communities and fecal Enterobacteriaceae isolates indicates that ecological connectivity establishes a cascading dissemination pathway: wastewater discharge promotes AMR accumulation in natural water bodies, facilitating its persistence in finished drinking water. Critical human-derived ARGs, primarily conferring resistance to beta-lactams and aminoglycosides, are enriched in clinically relevant pathogens. Further analysis reveals synergistic effects of biotic and abiotic drivers, including horizontal gene transfer (HGT), host proliferation, trace metals, disinfectants, and antibiotic residues, acting with connectivity to drive ARG proliferation. Mechanistic insights reveal that integron-mediated HGT captures and rearranges exogenous ARGs, thereby assembling multi-resistant genetic determinants along connected pathways. We establish a risk prioritization framework integrating dynamics, mobility, pathogenicity and clinical relevance to identify high-risk anthropogenic ARGs. These findings elucidate AMR transmission mechanisms via ecological connectivity, informing targeted interventions to disrupt transmission links and mitigate drinking water risks.},
}

*Drinking Water/microbiology
Humans
Gene Transfer, Horizontal
*Water Microbiology
Anti-Bacterial Agents/pharmacology
Cities
*Genes, Bacterial
*Drug Resistance, Bacterial/genetics
Wastewater/microbiology
Enterobacteriaceae/genetics/drug effects/isolation & purification
Metagenomics
*Drug Resistance, Microbial/genetics
Integrons/genetics
Bacteria/genetics/drug effects/isolation & purification

@article {pmid42765727,
year = {2026},
author = {Karačić, J and Singer, L and Bierbaum, G and Parčina, M and Zilles, J and Palmer, B and Karačić, S},
title = {Dental spittoon biofilms as reservoirs of antimicrobial resistance: a longitudinal multi-omics study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0088326},
doi = {10.1128/spectrum.00883-26},
pmid = {42765727},
issn = {2165-0497},
abstract = {Dental chair spittoons are chronically exposed to saliva, aerosols, intermittent water flow, and chemical disinfectants, yet their biofilm ecology and antimicrobial resistance (AMR) dynamics remain poorly defined. We applied longitudinal 16S rRNA gene sequencing, shotgun metagenomics, and culture-based antimicrobial susceptibility testing to biofilms collected across four dental departments at three time points. Community analyses revealed significant temporal succession and department-specific structuring, indicating the establishment of stable, ecologically differentiated biofilm systems. Null-model analysis (Raup-Crick) indicated that community assembly remained predominantly stochastic, although later sampling periods showed modest evidence of increasing ecological filtering. Shotgun metagenomics identified metabolically versatile communities enriched in disinfectant-tolerant environmental taxa, with resistomes dominated by β-lactamases and aminoglycoside-modifying enzymes. Clinically associated plasmid replicons, including IncFII and Col440I, were detected in metagenomically analyzed samples. Culture-based testing of 162 isolates confirmed that 21.7% expressed phenotypic resistance to at least one antimicrobial agent, including multidrug- and carbapenem-resistant representatives of Pseudomonas and Acinetobacter. Together, these findings position dental spittoons as structured aquatic biofilm ecosystems that maintain viable antimicrobial-resistant populations and clinically relevant plasmid replicons under recurrent disturbance, highlighting their ecological role within the broader built-water resistome.IMPORTANCEBiofilms in healthcare environments can act as reservoirs of antimicrobial resistance, yet some potential niches remain poorly studied. Dental chair spittoons are continuously exposed to oral fluids, aerosols, water flow, disinfectants, and residual antimicrobial compounds, creating conditions that may favor biofilm formation and microbial selection. Despite this unique combination of ecological pressures, the microbial communities inhabiting these systems have received little attention. Using a longitudinal multi-omics approach combined with culture-based phenotypic testing, we show that spittoon biofilms harbor diverse microbial communities enriched in antimicrobial resistance determinants, including multidrug-resistant and carbapenem-resistant bacteria. These findings suggest that dental spittoons may represent previously overlooked reservoirs of antimicrobial resistance within clinical environments.},
}

@article {pmid42766112,
year = {2026},
author = {Shang, J and Li, L and Dong, C and Wei, Y},
title = {Bacteriophage-bacteria coevolution: from molecular arms races to ecological and applied perspectives.},
journal = {Archives of microbiology},
volume = {208},
number = {12},
pages = {},
pmid = {42766112},
issn = {1432-072X},
mesh = {*Bacteriophages/genetics/physiology ; *Bacteria/virology/genetics ; *Biological Coevolution ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; CRISPR-Cas Systems ; *Biological Evolution ; Evolution, Molecular ; },
abstract = {Bacteriophages are the most abundant biological entities, driving bacterial evolution through long-term coevolution. Bacteria have evolved diverse defense strategies against phage, including receptor modification, restriction-modification systems, CRISPR-Cas, abortive infection systems, and newly discovered systems such as BREX, DISARM, CBASS, Thoeris, and Zorya. In response, phages deploy countermeasures such as receptor-binding diversification, anti-CRISPR proteins, DNA modification, and inhibitors targeting host immunity. These interactions generate distinct evolutionary dynamics-arms race and fluctuating selection-shaping microbial population structure and ecological stability. Phage-host coevolution promotes microbial diversity, horizontal gene transfer, and regulates community composition across ecosystems. Understanding these processes is critical for applications like phage therapy, microbiome engineering, and biotechnology. This review summarizes molecular mechanisms of bacterial defense and phage counter-defense, discusses coevolutionary models, highlights ecological and applied implications, and outlines future research directions.},
}

*Bacteriophages/genetics/physiology
*Bacteria/virology/genetics
*Biological Coevolution
Gene Transfer, Horizontal
Host-Pathogen Interactions
CRISPR-Cas Systems
*Biological Evolution
Evolution, Molecular

@article {pmid42754197,
year = {2026},
author = {Ye, C and Chen, Y and Yu, X},
title = {Unexpected synergy: Calcium channel blockers and residual chlorine cooperatively accelerate antibiotic resistance dissemination in water systems.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {410},
number = {},
pages = {129168},
doi = {10.1016/j.envpol.2026.129168},
pmid = {42754197},
issn = {1873-6424},
abstract = {The dissemination of antibiotic resistance driven by non-antibiotic pharmaceuticals is an emerging concern warranting further investigation. Calcium channel blockers (CCBs), frequently detected in aquatic environments, have rarely been studied for their role in the spread of antibiotic resistance genes (ARGs). This study examines the impact of two representative CCBs, amlodipine (AML) and verapamil (VER), on conjugative horizontal gene transfer (HGT) under low-level chlorine conditions. A bacterial conjugation system was established using Escherichia coli harboring the conjugative plasmid RP4, under simulated residual chlorine exposure typical of water distribution networks (0.3 mg/L). Conjugation assays revealed that, in the absence of residual chlorine, AML and VER at environmentally relevant concentrations (0.01-100 μg/L) exerted negligible effects on ARG conjugative transfer. Similarly, residual chlorine alone did not significantly enhance HGT. However, the co-occurrence of CCBs and residual chlorine synergistically promoted HGT, yielding a maximal 15.2-fold increase in conjugation frequency. This promotional effect was not mediated by increased cell membrane permeability but was driven by elevated reactive oxygen species production, upregulation of efflux pumps and outer membrane porins, and modulated transcription of conjugation-related genes. Notably, the oxidative stress response gene rpoS was upregulated by over 20-fold, while korA/korB (negative regulators) and kilA/kilB (repressors of vertical transfer) were both downregulated, collectively relieving the repression on conjugative transfer. These findings demonstrate that environmental non-antibiotic pharmaceuticals can synergistically promote ARG dissemination under residual chlorine in water supply systems. This study provides a scientific basis for refining risk assessment frameworks for pharmaceutical contaminants in water.},
}

@article {pmid42757725,
year = {2026},
author = {Liu, S and Xie, S and Song, Y and Li, R and Brenciani, A and Schwarz, S and Zhang, W and Zhu, Y},
title = {Anaerobic bacteria: a neglected reservoir of mobile oxazolidinone resistance genes.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2734670},
doi = {10.1080/19490976.2026.2734670},
pmid = {42757725},
issn = {1949-0984},
mesh = {*Oxazolidinones/pharmacology ; Humans ; *Anti-Bacterial Agents/pharmacology ; Animals ; *Bacteria, Anaerobic/genetics/drug effects/isolation & purification/classification ; *Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences ; Phylogeny ; Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; },
abstract = {Oxazolidinones are critical last-resort antimicrobials against severe infections caused by Gram-positive bacteria, whereas mobile oxazolidinone resistance genes (MORGs, including cfr, optrA, poxtA) severely compromise their clinical efficacy. To date, most surveillance and mechanistic studies focusing on MORGs have focused on aerobic pathogens, while anaerobic commensal and opportunistic bacteria are largely overlooked as hidden resistance reservoirs, leading to critical knowledge gaps under the One Health framework. Here, we identified six MORG-carrying anaerobic gut bacteria belonging to four distinct genera. Notably, this is the first report on the identification of cfr (B) in Gram-negative bacteria and optrA in three previously unreported host species. Genomic dissection further confirmed diverse mobile genetic elements driving horizontal dissemination of MORGs across phylogenetically distant anaerobes. Multiple additional resistance genes coexisted with MORGs in these gut anaerobes. Our findings demonstrate that intestinal anaerobic bacteria constitute a neglected critical reservoir for clinically vital MORGs, highlighting an urgent need for strengthened antimicrobial resistance surveillance of anaerobes across animal and human hosts.},
}

*Oxazolidinones/pharmacology
Humans
*Anti-Bacterial Agents/pharmacology
Animals
*Bacteria, Anaerobic/genetics/drug effects/isolation & purification/classification
*Drug Resistance, Bacterial/genetics
Interspersed Repetitive Sequences
Phylogeny
Gastrointestinal Microbiome
Gene Transfer, Horizontal

@article {pmid42759168,
year = {2026},
author = {Dong, X and Yin, Z and Chen, X and Bai, M and Lei, K and Xu, X and Yan, Z},
title = {Distribution and occurrence characteristics of antibiotic resistance genes in China's nearshore waters: A systematic review (2016-2026).},
journal = {Marine environmental research},
volume = {222},
number = {},
pages = {108416},
doi = {10.1016/j.marenvres.2026.108416},
pmid = {42759168},
issn = {1879-0291},
abstract = {Antibiotic resistance genes (ARGs), as emerging biological pollutants with the capacity for genetic transmission, have been widely detected in China's nearshore aquatic environments and pose potential risks to ecological security and public health. This review systematically synthesizes studies published between 2016 and 2026 on ARGs in China's nearshore waters, with a focus on their occurrence and spatial distribution, source inputs, and mechanisms of transport and dissemination. Overall, ARG abundance generally decreases from estuarine and nearshore waters toward offshore areas, although the specific spatial pattern varies among coastal systems. Estuaries, semi-enclosed bays, and coastal discharge zones are identified as hotspots. Across environmental media, ARGs exhibit multi-interface partitioning among the water column, particles, sediments, biofilms, and biota, with sediments and particle-associated fractions serving as important reservoirs. Urban and industrial wastewater effluents, riverine runoff, agricultural and livestock non-point sources, and nearshore aquaculture together form a complex multi-source input system for ARGs. Physicochemical factors, including salinity, temperature, redox conditions, particle adsorption, and sediment burial, as well as co-selection pressures from antibiotics, heavy metals, and organic pollutants, regulate the persistence and spread of ARGs through mobile genetic elements (MGEs) and horizontal gene transfer. ARGs may alter microbial community structure and biogeochemical cycling, while seafood consumption and coastal exposure represent potential pathways for human exposure to ARGs. This review clarifies the distribution patterns and environmental fate of ARGs in China's nearshore waters and provides a scientific basis for the environmental risk management of emerging pollutants in coastal zones.},
}

@article {pmid42761089,
year = {2026},
author = {Al-Soudy, AS and Rslan, WM and Soulaimani, B and Hajjaji, O and Abd-Elhalim, HM and Drissi, BE and Sobeh, M and Daoud, R and Benhida, R and Mokhtar, MM},
title = {Multi-omics characterization of a rhizosphere-derived Bacillus cereus CBS-B5 strain reveals genomic stability, metabolic versatility, and biosafety-related genomic features for agricultural applications.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1857756},
pmid = {42761089},
issn = {1664-302X},
abstract = {INTRODUCTION: Bacillus cereus strains have potential plant growth-promoting properties but may harbor virulence and antimicrobial resistance (AMR) determinants. This study characterized the rhizosphere-derived B. cereus CBS-B5 strain to assess its functional potential and biosafety-related features.

METHODS: CBS-B5, isolated from sugar beet rhizosphere, was characterized using an integrated multi-omics approach combining phenotypic assays, whole-genome sequencing, phylogenomic and comparative genomic analyses, and metabolomic profiling.

RESULTS: CBS-B5 exhibited visible growth under elevated salinity conditions, demonstrated recovery following heat stress exposure, and strong biofilm formation, but no detectable phosphate solubilization. Whole-genome sequencing revealed a 5.02 Mb genome with 35% GC content, 100% completeness, and 0.03% contamination. Phylogenomic analysis placed CBS-B5 within the B. cereus group. Comparative genomic and functional analyses indicated genomic stability, metabolic versatility, stress-adaptation potential, and diverse biosynthetic gene clusters. Genome plasticity was supported by the presence of mobile genetic elements and horizontal gene transfer events affecting approximately 16% of the proteome. Metabolomic analysis confirmed active metabolic processes, including nitrogen recycling, osmoprotection, and transformation of plant-derived compounds under laboratory conditions. Although virulence-associated genes, including nheABC, cytK, and inhA, and β-hemolytic activity were detected, AMR and virulence determinants showed limited potential for horizontal dissemination. Similarly, AMR genes exhibited low mobility potential and minimal phenotypic resistance beyond intrinsic traits.

DISCUSSION: Overall, CBS-B5 combines genomic stability, metabolic flexibility, and ecological adaptability. From a One Health perspective, the genomic analyses suggest a limited potential for horizontal dissemination of antimicrobial resistance and virulence determinants. However, the presence of chromosomally encoded toxin-associated genes and β-hemolytic activity indicates that additional biosafety evaluation is required before agricultural application.},
}

@article {pmid42762163,
year = {2026},
author = {Silva-Magaña, MA and Mora-Flores, LP and Pita-Galeana, MA and Hernández-Lemus, E and de Anda-Jáuregui, G},
title = {A network dynamical simulation model for the study of antibiotic resistance in microbial communities.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2734703},
doi = {10.1080/19490976.2026.2734703},
pmid = {42762163},
issn = {1949-0984},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; *Bacteria/drug effects/genetics ; Computer Simulation ; Models, Biological ; *Drug Resistance, Bacterial ; *Drug Resistance, Microbial ; },
abstract = {Antibiotic resistance emerges from ecological and evolutionary processes occurring within complex microbial communities. Interactions among microorganisms can shape the pathways through which resistance traits spread and persist, yet many theoretical approaches treat microbial populations as homogeneous compartments. Here we present a simulation-based network dynamical model that represents microbial communities as ecological association networks. In this formulation, nodes correspond to bacterial populations, metapopulations, or taxon-level ecological units, while resistant counterparts represent state-expanded subpopulations associated with the same ecological unit. Edges represent co-occurrence-based ecological proximity rather than direct physical contacts or confirmed horizontal gene transfer events. Using stochastic simulations across multiple network topologies, we explore how structural properties of microbial communities influence the emergence and persistence of resistance. Parameter sweeps across transmission probability, initial resistance fraction, and antibiotic intervention timing allow us to characterize regimes in which resistance either remains localized or spreads through the community. The model produces time series of resistant and susceptible states and snapshots of evolving network configurations, enabling qualitative comparison across simulation scenarios. Our results show that network structure strongly modulates resistance dynamics. Highly clustered networks tend to trap resistance within local neighborhoods, whereas heterogeneous networks with hub nodes facilitate rapid dissemination. Antibiotic perturbations can either suppress resistance or paradoxically accelerate its expansion depending on network topology and intervention timing. These findings should be interpreted as qualitative results from a minimal proof-of-concept model, not as a direct reconstruction of plasmid transfer, species replacement, or patient-specific microbiome responses.},
}

*Anti-Bacterial Agents/pharmacology
*Microbiota/drug effects
*Bacteria/drug effects/genetics
Computer Simulation
Models, Biological
*Drug Resistance, Bacterial
*Drug Resistance, Microbial

@article {pmid42762859,
year = {2026},
author = {Miliotis, G and McDowell, A},
title = {An intact Enterobacteriaceae plasmid sequence in the draft genome assembly of Cutibacterium acnes strain CA17 represents contamination.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {103083},
doi = {10.1016/j.anaerobe.2026.103083},
pmid = {42762859},
issn = {1095-8274},
abstract = {We previously identified an intact Enterobacteriaceae-derived plasmid (pCA17) in the draft genome sequence of C. acnes strain CA17. In the absence of this isolate for laboratory confirmation, we performed in silico analyses, including comparative gene synteny, replicon typing, GC content, and CAI analysis, supporting pCA17 as a likely contaminant.},
}

@article {pmid42763093,
year = {2026},
author = {Vo, T and Hamieh, A and Levy, M and Pontarotti, P and Rolain, JM and Merhej, V},
title = {Characterization of the novel transposon Tn7722 harboring blaNDM-1: Insights into the evolutionary dynamics of resistance in Klebsiella pneumoniae.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2026.09.007},
pmid = {42763093},
issn = {2213-7173},
abstract = {BACKGROUND: Klebsiella pneumoniae is an opportunistic pathogen responsible for invasive infections. The rise of carbapenem-resistant K. pneumoniae, largely driven by acquisition of blaNDM genes, represents a global health threat. In French Polynesia, sporadic cases of NDM-producing Enterobacteriales have been reported. This study characterizes the genomic features of NDM-producing K. pneumoniae isolates from French Polynesia and evaluates the roles of clonal expansion and mobile genetic element (MGE)-mediated horizontal gene transfer in blaNDM dissemination.

MATERIALS AND METHODS: Between July 2006 and September 2021, 17 carbapenemase-producing K. pneumoniae isolates were identified among 715 clinical samples in Tahiti. Whole-genome sequencing using Illumina MiSeq and Oxford Nanopore technologies was performed.

RESULTS: Seven NDM-producing K. pneumoniae strains were identified, five blaNDM-1 and two blaNDM-9 variants. All were resistant to ertapenem (MICs 1 to >32 mg/L), with three resistant to imipenem (MICs 8 to >32 mg/L) and six to meropenem (MICs 2 to >8 mg/L). A novel IS26-mediated composite transposon, Tn7722 (16,246 bp), carrying blaNDM-1, qnrS1 and aph(3')-VI genes, was detected in four isolates on IncF and IncR plasmids. Tn7722-like elements were found in diverse bacterial genomes worldwide, suggesting it facilitates blaNDM transmission across multiple species and regions.

CONCLUSION: NDM-producing K. pneumoniae in French Polynesia remain sporadic but genetically diverse, without evidence of local outbreak. This suggests a contribution of plasmid and Tn7722-associated elements to the diversity and evolution of carbapenem resistance. Ongoing genomic surveillance is vital to track the evolution of high-risk clones and MGEs guiding effective containment.},
}

@article {pmid42750349,
year = {2026},
author = {Liu, M and Wang, Y and Ren, Y and Yang, F and Ren, M and Yu, Q and Zhou, X and Yang, Z and Yang, J},
title = {A horizontally transferred bacterial gene for pantothenic acid biosynthesis regulates diapause and reproduction in the spider mite Amphitetranychus viennensis.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70356},
pmid = {42750349},
issn = {1744-7917},
support = {SJYC2025328//Sanjin Talents Support Program of Shanxi Province/ ; 32572833//National Natural Science Foundation of China/ ; 2026CYJSTX18-15//earmarked fund for Modern Agro-industry Technology Research System/ ; CXGC2023008//Shanxi Agricultural University Scientific and Technological Innovation Capacity Enhancement Program/ ; 2023BQ123//Excellent PhD Scientific Research Startup Project/ ; },
abstract = {Horizontal gene transfer (HGT) has contributed substantially to the evolution of arthropod genomes, yet the functional significance of many horizontally acquired genes remains poorly understood. The hawthorn spider mite, Amphitetranychus viennensis, is a devastating agricultural pest whose high fecundity and overwintering diapause afford its exceptional ecological resilience. Through a genome-wide screen, we identified 37 high-confidence horizontally transferred genes (HTGs) in A. viennensis. Among these candidates, we prioritized AvPBL, a gene encoding pantothenate-β-alanine ligase, for functional characterization because it controls the rate-limiting step of a distinctly non-metazoan pantothenic acid (vitamin B5) biosynthesis pathway. RNAi-mediated suppression of AvPBL significantly reduced transcript abundance and endogenous pantothenic acid levels, triggering a 23.7% reduction in cumulative fecundity and severely compromising the mites' ability to enter winter diapause. Importantly, exogenous pantothenic acid supplementation rescued these reproductive and diapause defects, directly linking the observed phenotypes to the disruption of pantothenic acid biosynthesis. Our results demonstrate that the horizontally transferred bacterial gene AvPBL has been functionally integrated into the endogenous metabolic network of A. viennensis, playing a critical role in vitamin B5 biosynthesis, reproduction, and diapause regulation. These findings provide direct evidence that horizontally acquired metabolic genes can shape key life-history traits and drive adaptive evolution in arthropods.},
}

@article {pmid42752335,
year = {2026},
author = {Khaneshi, M and Faraji Akhijahani, R and Mobayen, G and Shadravan, S and Lahouty, M},
title = {Bacterial Outer Membrane Vesicles in Colorectal Cancer: Interdomain Communication Hubs in Pathogenesis and Immunotherapy.},
journal = {Journal of drug targeting},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/1061186X.2026.2735996},
pmid = {42752335},
issn = {1029-2330},
abstract = {The complex interaction between the intestinal microbiota and host mucosal immunity plays a defining role in colorectal cancer (CRC) development and therapeutic outcomes. Recently, bacterial outer membrane vesicles (OMVs)-nano-sized, lipid-bilayered extracellular particulates released by both commensal and pathogenic microorganisms-have emerged as critical long-range signaling vehicles within the gut. This review provides a comprehensive synthesis of the dual functionalities of OMVs in CRC pathogenesis and oncology. Mechanistically, pathogenic OMVs cross compromised mucosal barriers to drive horizontal gene transfer (HGT) of chimeric episomes, such as SPHINX DNAs and Bovine Meat and Milk Factors (BMMFs), thereby promoting genomic instability and neoplastic transformation. Conversely, there is a paradigm shift toward exploiting next-generation probiotic and engineered OMVs as highly tunable therapeutic platforms. By combining cutting-edge bioengineering strategies-such as biomimetic mineralization to neutralize local tissue acidity and chemotherapeutic packaging-these nanovectors effectively reprogram the immunosuppressive tumor microenvironment (TME). Specifically, optimized OMVs modulate macrophage polarization from an M2 to an M1 phenotype and stimulate CXCL10-mediated CD8+ T-cell infiltration, effectively turning immunologically "cold" tumors "hot." Finally, the great translational challenges regarding systemic endotoxicity, scalability, and target delivery, providing a strategic approach for the integration of OMV-based platforms into synergistic immune checkpoint inhibition regimens.},
}

@article {pmid42754003,
year = {2026},
author = {Chakraborty, T and Chatterjee, M and Das, S and Roy, A and Ramaiah, S and Anbarasu, A},
title = {Biofilm-driven antimicrobial resistance: A review of molecular mechanisms, clinical implications, and therapeutic innovation.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {145},
number = {},
pages = {106028},
doi = {10.1016/j.meegid.2026.106028},
pmid = {42754003},
issn = {1567-7257},
abstract = {Biofilms are structured microbial communities embedded within a self-produced extracellular polymeric substance matrix that promotes persistence under adverse environmental and host-associated conditions. Their clinical importance is primarily associated with increased antimicrobial tolerance, evasion of host immune responses, and persistence in chronic and medical device-associated infections. This review provides an integrated overview of the molecular and genetic determinants governing biofilm development, including surface attachment, matrix biosynthesis, quorum-sensing networks, cyclic-di-GMP signaling, maturation, and dispersal. The contribution of key matrix components, including polysaccharides, extracellular proteins, extracellular DNA, lipids, and water, is considered in relation to biofilm architecture, stability, and cellular adaptation. Clinically relevant biofilm-forming microorganisms, including Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and Candida albicans, are major contributors to chronic infections, healthcare-associated infections, and infections associated with medical devices. The mechanisms contributing to reduced antimicrobial susceptibility in biofilms include restricted drug penetration, metabolic heterogeneity, persister-cell formation, efflux activity, stress-response pathways, and horizontal gene transfer. Conventional in vitro and in vivo biofilm models often fail to fully mimic the complex conditions present within the human host, thereby limiting the clinical translation and therapeutic relevance of experimental findings. In addition, emerging antibiofilm interventions, including quorum-sensing inhibitors, matrix-degrading enzymes, nanoparticle-based delivery systems, antimicrobial peptides, and bacteriophage therapy, are considered alongside the growing application of multi-omics and artificial intelligence for biomarker discovery and therapeutic target identification.},
}

@article {pmid42754122,
year = {2026},
author = {Jia, Y and Luo, S and Wang, X and Li, W and Li, B and Zhang, D},
title = {Novel insight into diversity of active tetracycline-resistant bacteria and genes in sludge by in situ microcapsule-entrapped cultivation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135849},
doi = {10.1016/j.biortech.2026.135849},
pmid = {42754122},
issn = {1873-2976},
abstract = {Antibiotic resistance poses a growing threat to global health and increases healthcare costs. Considering the limitations of traditional methods identifying antibiotic-resistant bacteria and genes, this study established an in situ microcapsule-entrapped cultivation (IMEC) strategy to screen the active tetracycline-resistant bacteria and genes in activated sludge from a wastewater treatment plant. Besides six tetracycline-resistant bacterial genera identified by conventional isolation and direct sequencing, IMEC uncovered extra 20 bacterial genera resistant to tetracycline, and their metabolic activities and tetracycline resistance were confirmed by Raman-Deuterium isotope probing. Among them, Romboutsia, Janthinobacterium, and Hydrogenoanaerobacterium were reported to have tetracycline resistance for the first time. The diversity of active tetracycline-resistant genes identified by IMEC was much lower than that by direct sequencing. In particular, one new tetG-like gene encoding a tetracycline outer periplasmic pump was confirmed by molecular docking. These findings documented the underestimated diversity of tetracycline-resistant bacteria but overestimated diversity of tetracycline-resistant genes in sludge. Overall, IMEC provides an effective tool for resolving active antibiotic-resistant bacteria and genes in activated sludge, offering new insights for water epidemiology.},
}

@article {pmid42747904,
year = {2026},
author = {Danmaigona Godsent-Ogbe, C and No, EG and Zhang, L and Wheeler, T and Dever, JK and He, P and Shan, L},
title = {Whole-genome characterization and phylogenetic placement of Fusarium oxysporum f. sp. vasinfectum isolates.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-11-25-2248-RE},
pmid = {42747904},
issn = {0191-2917},
abstract = {Fusarium wilt of cotton, caused by Fusarium oxysporum f. sp. vasinfectum (Fov), remains a persistent threat to cotton production worldwide. Among the known races, Fov race 4 and its extra-virulent variants cause particularly severe losses in Upland cotton. Although several Fov genome assemblies have been assigned to races, the genomic diversity and evolutionary relationships among pathogenic and non-pathogenic isolates associated with cotton outbreaks remain poorly understood at the whole-genome level. This study addressed these gaps by generating and comparing high-quality genome assemblies of four Fusarium isolates collected from Texas cotton fields: two pathogenic (TX17-24 and TX18-9) and two non-pathogenic (TX17-6 and TX18-6). Draft assemblies were generated using Oxford Nanopore long reads and polished with Illumina reads. Comparative genomic analyses showed that pathogenic isolates possessed larger genomes and more conserved orthologous families, whereas non-pathogenic isolates contained more unique genes. Analyses of predicted secreted effectors, transposable elements, and carbohydrate-active enzymes further distinguished pathogenic and non-pathogenic lineages, suggesting roles in virulence adaptation and genome plasticity. Phylogenomic analyses using k-mer-based, assembly- and alignment-free methods incorporated all available long-read Fov genomes and revealed substantial genetic diversity within races 1 and 4, clustering isolates into multiple sublineages. These findings show that Fov race diversification is underestimated when based on traditional classification schemes and may be shaped by host specialization, geographic separation, or horizontal gene transfer. This work advances our understanding of the genomic diversity and evolutionary dynamics of Fov and establishes a foundation for improved race identification and characterization of Fusarium wilt pathogenesis in cotton.},
}

@article {pmid42748252,
year = {2026},
author = {Segundo-Acosta, PS and Nomura, S and Fernandes-Queiroz, JP and Protasov, E and Kahnt, J and Kaneko, M and Hochberg, G and Shima, S and Murphy, BJ},
title = {Diversity of electron-bifurcating CO2-fixing supercomplexes in methanogens.},
journal = {Science advances},
volume = {12},
number = {38},
pages = {eaed3711},
pmid = {42748252},
issn = {2375-2548},
mesh = {*Carbon Dioxide/metabolism ; Electron Transport ; Electrons ; Oxidation-Reduction ; Aldehyde Oxidoreductases/metabolism/chemistry ; Oxidoreductases/metabolism/chemistry ; *Methanobacteriaceae/metabolism ; Models, Molecular ; Phylogeny ; },
abstract = {In the hydrogenotrophic methanogenic pathway, formylmethanofuran dehydrogenase (Fmd) reduces and fixes CO2, driven by low-potential electrons provided by electron-bifurcating heterodisulfide reductase (Hdr) complexed with electron-donating proteins such as Mvh hydrogenase. Here, we report the structure of a C2-symmetric (Mvh-Hdr)2-Fmd4 supercomplex from a Class I methanogen, Methanothermobacter marburgensis, which is architecturally different from the previously reported ring-shaped D3-symmetric supercomplex of a methanogen belonging to phylogenetically distinct Class II methanogens. In this C2-symmetric form, the redox active sites of Hdr and Fmd are connected by two MvhB polyferredoxins, whose branching electron paths appear to be available for electron transfer to/from other partners. The ancestral form was likely C2 symmetric, whereas D3-symmetric supercomplexes were acquired by horizontal gene transfer, a transition probably helpful for growth in substrate-poor environments.},
}

*Carbon Dioxide/metabolism
Electron Transport
Electrons
Oxidation-Reduction
Aldehyde Oxidoreductases/metabolism/chemistry
Oxidoreductases/metabolism/chemistry
*Methanobacteriaceae/metabolism
Models, Molecular
Phylogeny

@article {pmid42743633,
year = {2026},
author = {He, X and Li, Z and Shen, Z and Feng, C},
title = {Plastisphere as a resistome incubator: Substrate biodegradability escalates compounded genetic risks.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143624},
doi = {10.1016/j.jhazmat.2026.143624},
pmid = {42743633},
issn = {1873-3336},
abstract = {Plastispheres formed on microplastics represent unique hotspots for antibiotic-resistant bacteria, yet how substrate biodegradability shapes resistome profiles remains unclear. To address this gap, this study evaluated the resistome and its associated mobility and pathogenicity risks across nine polymer-specific plastispheres and the surrounding water. Results showed that antibiotic resistance gene (ARG) enrichment was widespread across plastispheres formed on all tested substrates, following a biodegradability-driven gradient that peaked in polyhydroxyalkanoate (PHA). This enrichment was systematically coupled with the co-accumulation of mobile genetic elements (MGEs) and virulence factor genes (VFGs). Host-resolved analysis revealed the selective enrichment of high-risk biomarker taxa in biodegradable plastispheres, particularly Aeromonas and Escherichia, which concurrently harbored antibiotic resistance, genetic mobility, and virulence determinants. Genetic-context analysis revealed contig-level co-localization of these determinants, indicating their potential genetic linkage. Within this structural framework, the co-occurrence of ARGs and MGEs indicated an increased potential for MGE-mediated horizontal gene transfer, whereas the enrichment of VFGs involved in environmental sensing, colonization, and nutrient acquisition suggested potential adaptation to resource competition, thereby potentially contributing to the co-selection of genetically linked ARGs. Substrate biodegradability amplifies both pathways by intensifying these spatial and competitive interactions, rendering plastispheres critical incubators for resistant pathogens in riverine ecosystems. Ultimately, this resistome expansion independent of antibiotic selective pressure reveals the potential ecological hazards of biodegradable plastics, substantiating the need for a systematic reassessment of their widespread use within the "One Health" framework.},
}

@article {pmid42743639,
year = {2026},
author = {Fu, J and Zhao, Y and Lu, J and Dai, Y and Zhang, X and Yang, Y and Ji, B},
title = {Pyrite-mediated antibiotic transformation and antibiotic resistance gene metabolism in recirculation stacking hybrid constructed wetlands.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143616},
doi = {10.1016/j.jhazmat.2026.143616},
pmid = {42743639},
issn = {1873-3336},
abstract = {This study elucidates antibiotic removal mechanisms and antibiotic resistance genes (ARG) attenuation pathways in recirculation stacking hybrid constructed wetlands (RSHCWs) amended with pyrite as a functional substrate. Three pilot-scale RSHCWs with varying pyrite contents were operated to treat sewage spiked with sulfapyridine (SPD), ofloxacin (OFX), and oxytetracycline (OTC). All systems achieved high removal efficiencies for antibiotics (>92% for SPD, >85% for OFX, and >95% for OTC) and ARGs (>90%). Pyrite addition significantly enhanced the adsorption of antibiotic and ARG. Mass balance analysis revealed that degradation/transformation was the key process for antibiotic removal. Pyrite enhanced substrate adsorption, promoted the formation of relatively stable complexes, and facilitated abiotic oxidative transformation and formation of smaller molecular weight transformation products. Major transformation pathways included hydroxylation, bond cleavage, decarboxylation, demethylation, and substitution reactions. Integrated microbial network analyses revealed that ARG attenuation was primarily driven by pyrite mediated adsorption, oxidative damage to antibiotic resistant bacteria, and suppression of resistant bacteria and inhibiting horizontal gene transfer via intensified interspecies microbial competition. Pyrite further altered bacterial diversity, enriching stress-resistant taxa and weakening the association between ARGs and potential host bacteria. Overall, this study underscores the dual function of pyrite in enhancing antibiotic degradation and limiting ARG dissemination.},
}

@article {pmid42744171,
year = {2026},
author = {Xu, X and Yin, J and Peng, D and Li, J and Yang, Z and Qiao, L and Xu, J and Hu, X and Ren, Y and Cheng, B and Mu, Y},
title = {Enrofloxacin metabolism and antibiotic resistance in Monopterus albus differs between pond cage and greenhouse micro-flow aquaculture systems.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125688},
doi = {10.1016/j.envres.2026.125688},
pmid = {42744171},
issn = {1096-0953},
abstract = {Enrofloxacin (ENR) is a fluoroquinolone antibiotic widely used in aquaculture, yet its metabolic fate and resistance selection dynamics remain poorly characterized. Here, we investigated ENR metabolism, tissue distribution, withdrawal periods, gut microbial communities, and antibiotic resistance genes (ARGs) in Monopterus albus reared under pond net cage (PNC) and greenhouse micro-flow (GMF) systems following a 5-day medicated feed treatment (20 mg ENR/kg body weight). Eight ENR metabolites were tentatively identified, with ciprofloxacin (CIP) as the predominant metabolite. The GMF system significantly shortened the estimated withdrawal period to 4050 °C·d compared to 5550 °C·d for PNC (about 30% reduction). Critically, the PNC withdrawal period exceeded the current Chinese regulatory standard of 500 °C·d by more than 10 folds, revealing a substantial gap between existing guidelines and on-farm food safety requirements. Sediment analysis showed that 7.8% of the administered ENR dose persisted as a long term environmental reservoir. Metagenomic sequencing revealed that even a single ENR treatment induced an approximately 10-fold increase in fluoroquinolone resistance genes by day 60 post-treatment, with cross-resistance extending to multiple other antibiotic classes. Aeromonadaceae and Enterobacteriaceae were identified as the primary ARG hosts, and ARG abundance was significantly correlated with mobile genetic element prevalence, suggesting enhanced horizontal gene transfer potential. These findings demonstrate that aquaculture system design profoundly influences antibiotic fate and resistance selection, and that current withdrawal standards are inadequate for scaleless species. System-specific withdrawal guidelines and strengthened antimicrobial stewardship are urgently needed to mitigate environmental and food safety risks from aquaculture antibiotic use.},
}

@article {pmid42746446,
year = {2026},
author = {Zhang, B and Ji, S},
title = {Pangenome of Streptomyces sampsonii and Relatives Highlights Horizontal Gene Transfer and Secondary Metabolism in Environmental Adaptation and Ecological Significance.},
journal = {Ecology and evolution},
volume = {16},
number = {9},
pages = {e74350},
pmid = {42746446},
issn = {2045-7758},
abstract = {Streptomyces sampsonii is a promising biocontrol bacterium, but its genomic basis of adaptation and secondary metabolism remains unclear. Here, we present a chromosome-level genome assembly of S. sampsonii (7.20 Mb, 6015 protein-coding genes) and perform comparative analyses with 95 related Streptomyces species. Phylogenomic and synteny analyses revealed its closest relationship with S. albidoflavus, while extensive structural variations distinguished more distant lineages. Pangenome analysis uncovered 84,178 gene clusters, with pan_shell and pan_cloud genes predominantly enriched in xenobiotic biodegradation, metabolism, and antibiotic biosynthesis, highlighting their roles in ecological adaptation and biocontrol potential. Biosynthetic gene cluster (BGC) analysis identified numerous NRPS, PKS, and terpene pathways, many of which belong to pan_shell and pan_cloud regions, suggesting dynamic evolutionary origins. We further detected 66,260 horizontally transferred (HGT) genes, including 438 in BGCs, underscoring HGT as a major driver of metabolic innovation. Together, these findings provide novel insights into the genomic diversity, adaptive capacity, and secondary metabolic potential of S. sampsonii and its close relatives.},
}

@article {pmid42747194,
year = {2026},
author = {Aguayo, S and Leiva-Sabadini, C and Saavedra, P and Thalhuber, D and Helliwell, E and Merritt, J and Kreth, J},
title = {From Biogenesis to Host Modulation: The Expanding Biology of Oral Streptococcal Membrane Vesicles.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuag049},
pmid = {42747194},
issn = {1574-6976},
abstract = {Bacterial extracellular membrane vesicles (bEVs) provide fundamental biological functions through communication, ecological adaptation, and mediation of host interactions. Gram-positive oral streptococci were long considered to be incapable of bEVs production due to their thick peptidoglycan. In contrast, recent advances in imaging, biochemical isolation, and multi-omics profiling have revealed that bEVs production is common and may represent a general trait of streptococci. This review summarizes current research on the biogenesis, cargo composition, and functional roles of bEVs, with an emphasis on oral streptococcal vesicles and their contributions to oral microbial ecology and host responses. We highlight methodological innovations for isolation and characterization of bEVs that have led to the discovery of species-specific bEVs cargo. Functionally, bEVs participate in diverse biological activities, including horizontal gene transfer, antimicrobial peptide delivery, virulence and redox modulation, and they profoundly influence host immunity by modulating cytokine signaling, epithelial barrier function, and immune pathways. Emerging evidence further suggests active roles in polymicrobial biofilm development and systemic dissemination of microbial signals relevant to health and disease. By integrating biochemical, structural, ecological, and immunological perspectives, this review provides a comprehensive overview of the current state of streptococcal and Gram-positive bEVs research and discusses its translational potential to support oral and general health.},
}

@article {pmid42736213,
year = {2026},
author = {Liu, W and Mei, Q and Tan, M and Zhang, M and Yue, L and Zhang, C and Zhao, F and Zhao, N and Jiang, J and Liu, L and Gao, X and Fang, Y and Liu, D},
title = {Population structure and antibiotic resistance of Salmonella isolates from diseased poultry in Jiangxi Province, China.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107660},
doi = {10.1016/j.psj.2026.107660},
pmid = {42736213},
issn = {1525-3171},
abstract = {Salmonella poses a significant threat to human and animal health. However, the relationship among population diversity, antibiotic resistance, and infection risk remains largely unexplored. In this study, 69 Salmonella strains were isolated from diseased poultry in Jiangxi Province from 2021 to 2024. Using whole-genome sequencing, serotype prediction, MLST, virulence and resistance gene analysis, antibiotic susceptibility testing, and mobile genetic element annotation, we characterized the diversity, resistance profiles, and transmission mechanisms of these strains. The results showed high diversity, with Salmonella enterica subsp. enterica serovar Typhimurium (>60%) and ST19 (62.31%) as the dominant serovar and sequence type, respectively. Several avian isolates were genomically similar to human isolates, indicating potential zoonotic risk. All strains harbored conserved core virulence modules, whereas accessory modules (e.g., cdtB, astA, pefA) varied and may affect pathogenicity. The multidrug resistance rate was 97.1%, with 100% resistance to erythromycin, tilmicosin and tiamulin, and resistance rates of 91.3%, 84.1%, and 71.0% to sulfonamides, enrofloxacin, and ceftiofur, respectively. Sixty-eight resistance genes were identified. Highly conserved antimicrobial resistance gene (ARG) modules (e.g., sul2-aph(3″)-Ib-aph(6')-Id-tet(A)) were shared between chromosomes and plasmids and were flanked by mobile elements such as Tn3 and IS3. Genomic islands (GIs) and plasmids in some strains carried resistance gene clusters highly homologous to those in pathogens from humans, pigs, and chickens, suggesting active horizontal transfer of resistance genes across hosts. This study revealed high diversity, prevalent multidrug resistance, and active horizontal transfer of resistance genes in avian-derived Salmonella from Jiangxi Province, emphasizing the need for cross-host resistance monitoring and antibiotic management within the 'One Health' framework.},
}

@article {pmid42737373,
year = {2026},
author = {Zhan, Z and Zhang, S and Wei, B and Zheng, Y and Li, X and Lin, Q and Chang, J and He, S and Wang, H},
title = {Transferable IncHI2-Associated blaLAP-2 and blaCTX-M-55 Resistance Platforms in Foodborne Salmonella.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
pmid = {42737373},
issn = {2304-8158},
support = {32402222//National Natural Science Foundation of China/ ; },
abstract = {Extended-spectrum β-lactamase genes in foodborne Salmonella enterica can disseminate through mobile multidrug-resistance platforms. IncHI2 plasmids are important resistance vehicles capable of carrying complex resistance regions and facilitating their horizontal transfer across diverse bacterial backgrounds, but the transfer and genomic organization of IncHI2 elements co-carrying blaLAP-2 and blaCTX-M-55 remain insufficiently characterized. This study investigated two multidrug-resistant foodborne isolates recovered in Shanghai in 2022: Salmonella Agona ST13 isolate Sal22C150 and Salmonella Havana ST1527 isolate Sal22P208. Antimicrobial susceptibility testing, whole-genome sequencing, conjugation, plasmid-retention analysis, comparative genomics, as well as strain- and plasmid-level phylogenetic analyses were performed. Both isolates exhibited broad antimicrobial resistance, including resistance to extended-spectrum cephalosporins. In both isolates, blaLAP-2 and blaCTX-M-55 co-transferred with the IncHI2 replicon to Escherichia coli J53 at frequencies of (4.95 ± 0.41) × 10[-5] and (4.46 ± 0.42) × 10[-6] transconjugants per donor cell, respectively. All tested plasmid markers remained detectable through 20 passages without antimicrobial selection. Complete assembly of Sal22P208 confirmed the location of the three β-lactamase genes on the 275,096 bp IncHI2 plasmid pSal22P208. The plasmid contained a conserved conjugative backbone and mosaic accessory regions carrying 15 antimicrobial-resistance determinants together with mercury- and tellurium-resistance loci. SNP-based analysis placed pSal22P208 within a closely related cluster containing six reference IncHI2 plasmids differing by fewer than 30 SNPs and recovered from Salmonella and E. coli of animal, food, and human origin, suggesting a broad distribution of this plasmid lineage across diverse bacterial and ecological backgrounds. Sal22P208 additionally contained a Tn3-associated chromosomal multidrug-resistance region between rpmJ and rpmE that shared extensive structural similarity with a region in Citrobacter braakii LBA3. These findings highlight the role of transferable IncHI2 resistance platforms in the horizontal dissemination and short-term post-transfer maintenance of linked resistance determinants, while chromosomally integrated resistance regions may provide an additional route for the accumulation and inheritance of multidrug resistance in foodborne Salmonella.},
}

@article {pmid42738098,
year = {2026},
author = {Manrique-Sam, C and Rivas-Torres, R and Miranda-Pinto, A and Sanchez Guillen, JC and Apaza-Tosocahua, S and Farfán-Delgado, F},
title = {Molecular and Biosafety Perspectives of Bacterial Self-Healing Concrete: From Sporulation and Biomineralization to Public Health Implications.},
journal = {Materials (Basel, Switzerland)},
volume = {19},
number = {17},
pages = {},
pmid = {42738098},
issn = {1996-1944},
abstract = {Bacterial self-healing concrete has emerged as a bio-based strategy to enhance the durability of cementitious materials and reduce the environmental impact associated with premature infrastructure deterioration. Its functional principle relies on microbially induced calcium carbonate precipitation (MICP), through which bacterial metabolism promotes CaCO3 deposition within cracks. However, self-healing efficiency cannot be explained solely by mineral precipitation capacity. Concrete is a restrictive microbial environment characterized by alkalinity, desiccation, osmotic stress, nutrient limitation and physical confinement. Therefore, effective crack sealing requires a coordinated sequence involving bacterial survival, sporulation, germination, metabolic reactivation, biofilm-associated mineral nucleation and localized biomineralization. This integrative narrative review synthesizes mechanistic, material and biosafety evidence on bacterial self-healing concrete, focusing on spore-forming bacteria such as Bacillus subtilis and related taxa, including Paenibacillus. The evidence indicates that stress tolerance, germination signaling, calcium handling, biofilm establishment and stability, and encapsulation-mediated microenvironmental control are key determinants of performance, but remain insufficiently integrated into materials-oriented studies. Large-scale implementation also requires preventive assessment of strain persistence, genetic stability, horizontal gene transfer, environmental microbiome interactions and life-cycle exposure scenarios. Bacterial self-healing concrete should therefore be understood as a living or bioactive material system whose responsible development depends on the integration of microbiology, molecular biology, materials science, civil engineering, environmental risk assessment, occupational health, and public health.},
}

@article {pmid42742778,
year = {2026},
author = {Elsayed, NS and Abdelsalam, M},
title = {Zoonotic bacterial pathogens in global fish production: transmission, resistance, and one health control strategies.},
journal = {Veterinary research communications},
volume = {50},
number = {6},
pages = {},
pmid = {42742778},
issn = {1573-7446},
mesh = {Animals ; *Fishes/microbiology ; Humans ; One Health ; *Fish Diseases/microbiology/prevention & control/transmission ; Drug Resistance, Bacterial ; *Zoonoses/microbiology/transmission/prevention & control ; Aquaculture ; *Bacterial Zoonoses/transmission/prevention & control/microbiology ; Food Microbiology ; },
abstract = {BACKGROUND: Fish and fishery products are central to global food security, providing high-quality protein and essential micronutrients to populations worldwide. The intensification of aquaculture, expansion of international seafood trade, and growing consumer preference for minimally processed fish products have increased human exposure to bacterial pathogens at multiple points along the production-to-consumption chain.

AIM AND METHODS: This review evaluates bacterial hazards in fish and fish products using recent epidemiological surveillance, field investigations, and systematic reviews. Literature was retrieved from PubMed, Scopus, and Web of Science, and priority was given to peer-reviewed studies and to international food safety agency documentation. Pathogens assessed include Vibrio spp., Aeromonas spp., Listeria monocytogenes, Clostridium perfringens, Salmonella spp., and Escherichia coli, covering transmission dynamics, virulence determinants, antimicrobial resistance (AMR), diagnostic strategies, and evidence-based prevention.

FINDINGS AND CONCLUSIONS: Contamination occurs at distinct stages from aquaculture to consumption, with different risk profiles for each pathogen. Vibrio spp. and Aeromonas spp. are the main ecological hazards in marine and freshwater aquaculture respectively, with confirmed zoonotic potential and climate-sensitive distribution. Salmonella spp. and E. coli reach fish products chiefly through environmental faecal contamination, with multidrug-resistant strains reported across multiple continents. L. monocytogenes poses particular risk in ready-to-eat and cold-smoked products because of its ability to grow at refrigeration temperatures, while C. perfringens remains the least studied hazard in fish matrices. AMR among fish-associated bacteria is an escalating One Health concern, driven by antibiotic overuse in aquaculture and spread through horizontal gene transfer. Effective control requires coordinated One Health action: good aquaculture practices, HACCP-based processing controls, non-thermal preservation technologies, and harmonised AMR surveillance.},
}

Animals
*Fishes/microbiology
Humans
One Health
*Fish Diseases/microbiology/prevention & control/transmission
Drug Resistance, Bacterial
*Zoonoses/microbiology/transmission/prevention & control
Aquaculture
*Bacterial Zoonoses/transmission/prevention & control/microbiology
Food Microbiology

@article {pmid42728443,
year = {2026},
author = {Akinde, SB and Adesoye, AA and Ojo, OO and Oluwajide, OO and Wahab, AA and Olaniyan, OP and Fajoyegbe, ES and Toby-Ogundeji, I and Afolabi-Balogun, NB and Obire, O and Oladipo, EK and Ajadi, FA and Sule, WF and Olasupo, OA and Oyedara, OO and Olaitan, JO},
title = {Genomic Characterisation of Carbapenem-Resistant Klebsiella pneumoniae and Enterobacter hormaechei Clinical Isolates from Nigeria: Evidence of Resistance, Virulence, and Putative Plasmid-Mediated Gene Sharing.},
journal = {Current microbiology},
volume = {83},
number = {11},
pages = {},
pmid = {42728443},
issn = {1432-0991},
mesh = {Nigeria ; *Klebsiella pneumoniae/genetics/drug effects/isolation & purification/pathogenicity/classification ; *Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; *Enterobacter/genetics/drug effects/isolation & purification/pathogenicity/classification ; Humans ; *Carbapenems/pharmacology ; Virulence/genetics ; Microbial Sensitivity Tests ; Whole Genome Sequencing ; Phylogeny ; Genome, Bacterial ; Bacterial Proteins/genetics ; beta-Lactamases/genetics ; *Enterobacteriaceae Infections/microbiology ; },
abstract = {The global proliferation of carbapenem-resistant Enterobacterales (CRE) constitutes one of the most urgent public health threats, yet high-resolution genomic data from sub-Saharan Africa remain critically scarce. We applied whole-genome sequencing (WGS) and comparative phylogenomics to characterise antimicrobial resistance determinants, virulence genes, and mobile genetic elements (MGEs) in three carbapenem-resistant clinical isolates originating from three tertiary hospitals (selected from a broader surveillance collection spanning four facilities) in Osun State, southwestern Nigeria. We purposively selected three isolates, two Klebsiella pneumoniae subsp. pneumoniae (K22, ST411; K31, ST17) and one Enterobacter hormaechei subsp. steigerwaltii (K32, ST45) from a broader surveillance collection of 27 carbapenem-non-susceptible Enterobacterales, to represent phenotypically and genotypically divergent lineages. Resistome analysis revealed extensive plasmid-associated β-lactam and aminoglycoside resistance in K31 (including blaCTX-M-15, blaOXA-1, and blaTEM-1). K32 harboured an intrinsic chromosomal blaACT-17 AmpC gene, while IS26 and ISEcp1 insertion sequences, consistent with transposon-mediated mobilisation, flanked its acquired aminoglycoside and sulfonamide resistance cassettes. K22 lacked detected acquired carbapenemase, ESBL, or plasmid-mediated AmpC genes, indicating that its carbapenem-resistant phenotype may involve non-carbapenemase mechanisms such as porin alteration or efflux-mediated reduced susceptibility; however, this mechanism requires confirmation by direct ompK35/ompK36 sequence analysis and/or phenotypic outer membrane protein profiling. Virulome profiling identified a broader repertoire of siderophore, adhesion, and biofilm genes in both K. pneumoniae isolates than in E. hormaechei. Phylogenomic analysis demonstrated that K22 and K31 cluster within the broader K. pneumoniae population framework but represent distinct high-risk lineages (ST411 and ST17) rather than a single clonal outbreak. Analysis also identified a shared plasmid backbone between K31 and K32, supporting interspecies horizontal gene transfer. These descriptive genomic findings identify clinically relevant resistance and virulence determinants in three purposively selected carbapenem-resistant Enterobacterales from Nigerian tertiary-care hospitals. The detection of shared resistance elements between K. pneumoniae and E. hormaechei suggests possible plasmid-mediated gene sharing. Still, larger WGS studies with long-read sequencing and patient-level epidemiological data are required to define transmission and dissemination patterns.},
}

Nigeria
*Klebsiella pneumoniae/genetics/drug effects/isolation & purification/pathogenicity/classification
*Plasmids/genetics
Anti-Bacterial Agents/pharmacology
*Enterobacter/genetics/drug effects/isolation & purification/pathogenicity/classification
Humans
*Carbapenems/pharmacology
Virulence/genetics
Microbial Sensitivity Tests
Whole Genome Sequencing
Phylogeny
Genome, Bacterial
Bacterial Proteins/genetics
beta-Lactamases/genetics
*Enterobacteriaceae Infections/microbiology

@article {pmid42731179,
year = {2026},
author = {Emetere, ME and Atobatele, BO and Olapade, OT and Popoola, JO and Akinluyi, FO and Owoseni, AA and Irewolede, BA and Aderibigbe, KA},
title = {Indoor Air Quality (IAQ) analysis and 16S rRNA gene sequencing of indoor air pollutants in a 3000-capacity religious auditorium.},
journal = {The Science of the total environment},
volume = {1052},
number = {},
pages = {182237},
doi = {10.1016/j.scitotenv.2026.182237},
pmid = {42731179},
issn = {1879-1026},
abstract = {A thorough molecular and environmental evaluation of microbial isolates and indoor air quality (IAQ) at a place of worship is presented in this work. The study used a dual-methodological approach, including systematic environmental monitoring to assess occupant health concerns and 16S rRNA gene sequencing for taxonomic identification. Four different bacterial isolates were successfully identified by molecular analysis using BLAST and phylogenetic reconstruction: Bacillus tropicus (A11), Leclercia adecarboxylata (A12), Acinetobacter sp. (A13), and Escherichia coli (A14). The evolutionary position of isolate A13 indicated possible horizontal gene transfer, underscoring the existence of flexible, opportunistic pathogens within the indoor environment, whereas isolates A11 and A14 demonstrated significant genetic stability. Concurrently, six sessions of air quality monitoring showed a thermally demanding environment, with humidity (56.00-70.51%) and temperatures (29.21-33.79 °C) continuously surpassing ASHRAE guidelines. The average pollutant concentrations are within WHO and USEPA safety criteria, however, there were outliers that may suggest sporadic pollutant penetration (outdoor) or resuspension of dust. The results demonstrate a clear relationship between increased chemical pollutants (TVOCs) and reduced thermal comfort. To reduce the congregation's acute respiratory and cardiovascular risks, optimal ventilation systems and source-control measures are urgently needed, as evidenced by the presence of clinically relevant microorganisms combined with dangerous pollution levels.},
}

@article {pmid42731589,
year = {2026},
author = {Ma, Z and Zhou, L and Wang, S and Su, Y and Zhu, S and Zhao, Z and Wang, T and Guo, H},
title = {Multidimensional research progress on microbial resistance mechanisms and ecological bioremediation strategies under acid mine drainage stress.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125669},
doi = {10.1016/j.envres.2026.125669},
pmid = {42731589},
issn = {1096-0953},
abstract = {Acid mine drainage (AMD) is a globally pervasive legacy of sulfide ore mining, marked by extreme acidity, high sulfate, and toxic metal loads that destabilize aquatic and terrestrial ecosystems. This review synthesizes how microorganisms function both as sentinels of AMD disturbance and as engines of recovery. Multi-stressor pressures-low-pH, metal toxicity, redox disequilibrium, and nutrient limitation-are resolved at the level of cellular targets, encompassing membrane injury, ROS-driven macromolecule damage, metabolic reprogramming, ion-efflux systems, biomineralization, and horizontal gene transfer. These stresses are then linked to community-level outcomes, documenting niche shifts toward acidophiles, cooperation among sulfur- and iron-cyclers and sulfate-reducing bacteria, and the functional promise of "microbial dark matter." From a gene-to-function perspective, adaptive regulation of proton-handling and metal-homeostasis modules, pathway rewiring, and co-selection of metal and antibiotic resistance are highlighted. On the translational front, sulfate-reducing bioprecipitation, constructed wetlands coupled with microbial fuel cells, and in situ biostimulation/bioaugmentation are evaluated, and their operating windows and failure modes are clarified. Key bottlenecks include low-temperature/low-pH suppression, unresolved microbe-mineral interfacial electron transfer, and incomplete risk governance for resistance genes. An integrative roadmap is outlined: single-cell omics to resolve heterogeneity, synthetic-biology "super-remediators" with programmable control, and Earth Microbiome Project-enabled discovery combined with multi-omics-informed modeling. Overall, a mechanistic, systems-level framework is advanced that couples stress-resilience biology to design rules for scalable, predictable, and sustainable AMD bioremediation.},
}

@article {pmid42733281,
year = {2026},
author = {Shanto, MRH and Ashab Uddin, ASM and Supto, MSM and Mahim, NJ and Howlader, MMR and Ahmed, SSU and Uddin, MB},
title = {Comparative Genomic Analysis of Multidrug-Resistant Escherichia coli Across Poultry-Human-Environmental Interfaces.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70406},
pmid = {42733281},
issn = {2045-8827},
support = {NATP-2/PIU-BARC-44/2017/1663(53)//BARC through the NATP-2 project/ ; },
mesh = {Animals ; *Escherichia coli/genetics/drug effects/isolation & purification/classification ; *Drug Resistance, Multiple, Bacterial/genetics ; Humans ; *Poultry/microbiology ; *Escherichia coli Infections/microbiology/veterinary ; *Genome, Bacterial ; Virulence Factors/genetics ; Whole Genome Sequencing ; Bangladesh ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; *Poultry Diseases/microbiology ; Genomics ; Phylogeny ; *Environmental Microbiology ; },
abstract = {The emergence of multidrug-resistant (MDR) Escherichia coli in poultry represents a critical One Health concern, particularly in developing countries. This study employed a comparative genomic approach to investigate the genomic characteristics, antimicrobial resistance (AMR) profiles, virulence determinants, of poultry-derived MDR E. coli isolates from Bangladesh. Whole-genome sequencing of three representative MDR isolates, identified with 83 globally diverse poultry, human, and environmental E. coli genomes. Pangenome analysis identified the characteristic open pangenome of E. coli, with core genes comprising only 4.6% of the combined dataset. Resistome analysis shown diverse AMR determinants, including blaCTX-M, blaTEM, sul, tet, and qnrS1, associated with antibiotic inactivation and efflux mechanisms. Virulence profiling revealed diverse genes involved in adhesion (fim, csg), iron acquisition (ent, fep, chu), motility, and secretion systems, with core virulence genes exhibiting > 90% sequence identity, whereas accessory virulence genes were more variable. Plasmid analysis demonstrated heterogeneous replicon types, predominantly IncF and Col plasmids, indicating their role in horizontal gene transfer. Jaccard similarity indices revealed moderate to high genetic overlap with global strains (~0.63 for virulence genes and ~0.55 for AMR profiles), suggesting shared evolutionary backgrounds. Phylogenomic and MLST identified all Bangladeshi isolates as ST457, clustering within a globally distributed clonal complex linked to ST10 and ST131 lineages. These findings suggest that the three Bangladeshi poultry-derived E. coli isolates are genetically related to globally circulating strains while harboring extensive resistance and virulence determinants, emphasizing poultry as an important reservoir of MDR pathogens and reinforcing the need for strengthened antimicrobial stewardship and genomic surveillance.},
}

Animals
*Escherichia coli/genetics/drug effects/isolation & purification/classification
*Drug Resistance, Multiple, Bacterial/genetics
Humans
*Poultry/microbiology
*Escherichia coli Infections/microbiology/veterinary
*Genome, Bacterial
Virulence Factors/genetics
Whole Genome Sequencing
Bangladesh
Anti-Bacterial Agents/pharmacology
Plasmids/genetics
*Poultry Diseases/microbiology
Genomics
Phylogeny
*Environmental Microbiology

@article {pmid42733675,
year = {2026},
author = {Chen, T and Yao, Y and Chen, J and Lv, H and Nan, P},
title = {Pathogenesis and Triazole Resistance in Aspergillus fumigatus: A Narrative Review Across the Host Immune Spectrum and One Health Context.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {629247},
pmid = {42733675},
issn = {1178-6973},
abstract = {This narrative review explores triazole resistance and pathogenesis of Aspergillus fumigatus (A. fumigatus) under a unified One Health framework, integrating evidence across host immune spectrums, agricultural environmental selection pressures, veterinary aspergillosis and clinical antifungal management. We illustrate layered host-fungus immune interactions underlying distinct clinical aspergillosis phenotypes, and delineate core resistance mechanisms including cyp51-related target alterations, enhanced efflux pump activity, biofilm-mediated tolerance and adaptive stress response rewiring. Special emphasis is placed on cross-sector transmission pathways of azole-resistant A. fumigatus (ARAF) originating from agricultural ecosystems, as well as surveillance deficits and public health risks linked to animal intermediate hosts. Novel antifungal agents, such as olorofim, fosmanogepix, rezafungin, ibrexafungerp, and T-2307, along with targeted delivery and immunomodulatory adjunct therapies for resistant aspergillosis, are also summarized. Literature published 2020-2026 was retrieved from PubMed via Boolean search strategies, with supplementary manual screening of landmark reference lists to include pivotal earlier studies. Only peer-reviewed original studies, epidemiological surveillance reports, and review articles with complete clinical or experimental datasets were incorporated following rigorous screening. Most studies discuss clinical or agricultural resistance separately, lacking integrated analyses covering human, animal, and environmental dimensions. Major knowledge gaps persist regarding horizontal gene transfer of resistance mutations, cross-species transmission chains, and translational applications of environmental monitoring data. This review summarizes existing research bottlenecks and proposes integrated multi-sector prevention and control strategies from a One Health perspective to curb the growing threat of triazole-resistant aspergillosis.},
}

@article {pmid42734043,
year = {2026},
author = {Alrahimi, J},
title = {Engineered Bacteriophages in Cancer Immunotherapy: Emerging Concepts and Potential Integration with CAR-T Cell Therapy.},
journal = {Folia biologica},
volume = {},
number = {},
pages = {},
doi = {10.14712/fb2026.0018},
pmid = {42734043},
issn = {0015-5500},
abstract = {Due to antigen heterogeneity, restricted immune cell trafficking and an immunosuppressive, nutrient-restricted tumour microenvironment, solid tumours remain resistant to modern immunotherapies. Engineered bacteriophages offer a modular framework to overcome these obstacles: programmable virus-like particles with scalable production. Through genome engineering, capsid decoration with mammalian cell-targeting ligands, or hybrid AAV/phage systems, engineered bacteriophages can display tumour-associated antigens, enhance receptor-mediated uptake and deliver therapeutic payloads such as cytokines, chemokines and suicide genes without naturally infecting mammalian cells. These features support their use as vaccine platforms, immunological adjuvants and targeted gene-delivery vehicles. These may enable more precise, tumour-localized therapeutic intervention. Phages can engage innate immune pathways, including TLR9, TLR3/7/8, cGAS-STING and AIM2, promoting dendritic cell maturation and inflammatory mediators that may convert immunologically "cold" tumours into inflamed microenvironments. Their multivalent antigen display enhances B- and T-cell priming, while cDC1-mediated cross-presentation supports cytotoxic CD8+ T-cell responses and immunological memory. In CAR-T therapy, engineered phages may improve tumour homing through chemokine modulation, support persistence through local cytokine delivery, reduce antigen escape by presenting multiple tumour epitopes, and limit T-cell exhaustion through dominant-negative receptor strategies or local checkpoint blockade. This review summarizes engineering approaches, delivery systems, manufacturing, biodistribution, dosing, and safety issues, including immunogenicity, pre-existing anti-phage antibodies and horizontal gene transfer. It also distinguishes therapeutic engineered phage particles from phage display technologies used for molecular discovery. Despite encouraging results integrating modified bacteriophages with CAR-T cell therapy, the evidence remains mostly preclinical, indicating both substantial translational prospects and crucial obstacles for future clinical development.},
}