@article {pmid42036312,
year = {2026},
author = {Ayukawa, Y and Kaino, M and Yaeno, T},
title = {Horizontal Chromosome Transfer between Pathogenic and Non-pathogenic Fusarium oxysporum Strains Isolated from Cabbage.},
journal = {Microbes and environments},
volume = {41},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME25078},
pmid = {42036312},
issn = {1347-4405},
mesh = {*Fusarium/genetics/pathogenicity/isolation & purification ; *Brassica/microbiology ; *Gene Transfer, Horizontal ; Plant Diseases/microbiology ; *Chromosomes, Fungal/genetics ; Virulence ; },
abstract = {Horizontal chromosome transfer (HCT) has been demonstrated in Fusarium oxysporum. Several pathogenic F. oxysporum strains have been used as donors in HCT experiments, while the non-pathogenic strain Fo47 has mainly been employed as a recipient. It currently remains unknown whether other non-pathogenic F. oxysporum strains are recipients of mobile chromosomes. In the present study, we investigated whether the non-pathogenic strain 08C-3B, obtained from cabbage, acquired the mobile chromosomes of F. oxysporum f. sp. conglutinans strain Cong:1-1, which infects cabbage. We detected HCT between Cong:1-1 and 08C-3B in a conidial anastomosis tube (CAT) fusion-inductive medium, yielding HCT progeny strains that carried scaffolds (SCs) 8 and 9 of Cong:1-1. These progeny strains exhibited reduced colony growth on potato dextrose agar plates and produced no symptoms on cabbage. These results suggest that SC8 and/or SC9 hinder vegetative growth, but do not confer virulence to 08C-3B. We then conducted HCT experiments to assess whether the HCT progeny strain transfers the acquired chromosomes to other strains. However, no progeny strains were obtained, suggesting that 08C-3B does not function as a donor for mobile chromosomes.},
}

*Fusarium/genetics/pathogenicity/isolation & purification
*Brassica/microbiology
*Gene Transfer, Horizontal
Plant Diseases/microbiology
*Chromosomes, Fungal/genetics
Virulence

@article {pmid42037380,
year = {2026},
author = {Koong, J and W Luu, LD and Duggin, IG and Hamidian, M},
title = {Variations in plasmid transfer in Acinetobacter baumannii: insights from epigenetics, strain properties, and experimental conditions.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0348725},
doi = {10.1128/spectrum.03487-25},
pmid = {42037380},
issn = {2165-0497},
abstract = {Plasmid-mediated horizontal gene transfer is a driver of antibiotic resistance dissemination in Acinetobacter baumannii. Here, we investigated the extent to which intrinsic host factors influence plasmid uptake across diverse A. baumannii isolates using electro-transformation and conjugative transfer assays. To enable comparisons, electro-transformation conditions were optimized to minimize technical variability and reveal strain-dependent differences in plasmid uptake. Under the conditions used here, substantial variation in transfer efficiency was observed, including between closely related strains, indicating that plasmid acquisition is strongly influenced by the recipient genetic background. Comparative analyses of electro-transformation and conjugation demonstrated that while experimental parameters such as competent cell density, DNA input, and recipient-to-donor ratios affect transfer efficiency, these factors do not overcome inherent strain-specific barriers. Genome and methylome analyses also revealed extensive diversity in restriction-modification systems and DNA methylation patterns among recipient strains. Moreover, plasmids exhibited altered methylation profiles following transfer into new hosts, consistent with host-driven epigenetic modification. These findings indicate that plasmid transfer efficiency in A. baumannii is determined primarily by strain-specific genetic and epigenetic features rather than transferable experimental conditions. This variability has important implications for interpreting plasmid mobility, host range, and resistance dissemination within this clinically significant species.IMPORTANCEPlasmid-mediated gene transfer is one of the major drivers of antibiotic resistance in Acinetobacter baumannii; however, plasmid transfer protocols remain inconsistent and strain-dependent. By assessing electroporation and conjugation across diverse strains, we identify key experimental and genomic factors, such as test and strain differences, including restriction-modification systems and epigenetic signatures, that influence plasmid uptake. These findings offer practical guidance for optimizing plasmid transfer protocols and highlight strain-level barriers that impact resistance gene dissemination in this critical microorganism.},
}

@article {pmid42038316,
year = {2026},
author = {Abdallah, EM and Alhudhaibi, AM and Dahab, M and Al Noman, A and Sharma, PD and Taha, TH and Nawaz, M},
title = {The WHO priority list of antibiotic-resistant bacteria: challenges and opportunities for next-generation antimicrobial development.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1699987},
pmid = {42038316},
issn = {1663-9812},
abstract = {Antimicrobial resistance (AMR) remains one of the most serious global threats to public health, driven by the rapid emergence and dissemination of multidrug-resistant bacterial pathogens that compromise existing antibiotic therapies. In response, the World Health Organization (WHO) has defined priority lists of antibiotic-resistant bacteria to guide research, innovation, and drug development efforts. This narrative review synthesizes current knowledge on the molecular mechanisms underlying resistance in WHO-priority pathogens, including reduced membrane permeability, efflux pump overexpression, enzymatic drug inactivation, target modification, biofilm formation, and horizontal gene transfer. Beyond mechanistic insights, we critically evaluate the therapeutic limitations of conventional antibiotics, the failure of traditional discovery pipelines, and the growing clinical and economic burden of resistant infections. Emerging strategies, including artificial intelligence-assisted drug discovery, phage therapy, antimicrobial peptides, CRISPR-based systems, resistance-modifying combinations, and natural product-derived compounds and plant compounds, are assessed with emphasis on pharmacological feasibility, translational challenges, and clinical relevance. Particular attention is given to issues of delivery, toxicity, dosing optimization, resistance emergence, regulatory barriers, and real-world implementation. Finally, we highlight the central role of antimicrobial stewardship, surveillance, and a One Health framework integrating human, animal, and environmental sectors in mitigating resistance and sustaining therapeutic effectiveness. Collectively, this review underscores that addressing WHO-priority pathogens will require integrated, multidisciplinary strategies that bridge molecular biology, pharmacology, clinical translation, and public health.},
}

@article {pmid42038416,
year = {2026},
author = {Iranzo, J and Jódar, P and Koonin, EV and Manrubia, S and Cuesta, JA},
title = {A generative model for bipartite gene-sharing networks.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {42038416},
issn = {2331-8422},
abstract = {Gene-sharing networks provide a powerful framework to study the evolution of viruses and mobile genetic elements. These bipartite networks, which link genes to the genomes that contain them, exhibit characteristic degree distributions: a scale-free distribution for genes and an exponential-like decay for genomes. Here, we propose a mechanistic model that explains these patterns through fundamental evolutionary processes including horizontal gene transfer, capture of new genes, emergence of new genomes, and gene loss. Using a mean-field approximation, we derive analytical expressions for the asymptotic gene and genome degree distributions, recapitulating a power-law distribution for genes and an exponential distribution for genomes. Numerical simulations validate these predictions and yield parameter values that closely fit empirical data from dsDNA viruses, RNA viruses, and prokaryotic pangenomes. This simple model with only two parameters provides a generative framework for bipartite gene-sharing networks, offering qualitative and quantitative insights into the main evolutionary forces driving genome plasticity. Setting the gene loss rate to zero, the gene and genome degree distributions of the model closely fit the empirically observed distributions. Thus, evolution of viruses appears to be dominated by gene gain, in agreement with the results of independent reconstructions of viral evolution.},
}

@article {pmid42039843,
year = {2026},
author = {Yao, H and Wang, J and Dong, R and Yi, W and Zhang, M and Zhu, N and Jia, S and Wu, R and Guo, X and Dong, T and Peng, Z and Jiang, L and Li, W and Yang, C and Yuan, M and Guan, Q and Xu, J},
title = {Genomic characterization of vancomycin-resistant Enterococcus faecium and van-carrying mobile genetic elements in a tertiary hospital in northeastern China.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1804495},
pmid = {42039843},
issn = {1664-302X},
abstract = {BACKGROUND: Vancomycin resistant Enterococcus faecium (VREfm) poses a significant healthcare challenge due to its multidrug resistance and genomic plasticity. Vancomycin resistance is commonly mediated by van gene clusters located on transposons, which are often associated with plasmids.

METHODS: 19 VREfm isolates were collected from different departments of the First Hospital of Jilin University between 2019 and 2024. Whole-genome sequencing (WGS) was performed on the strains for comprehensive genomic analysis. Multilocus sequence typing (MLST) was used to determine the sequence types of the strains. Plasmids were grouped based on Mash distance, and plasmid content was analyzed using the MOB-suite tool. Genome-wide comparisons and average nucleotide identity (ANI) analysis were conducted using FastANI. The TnCentral database was used to analyze resistance-associated transposons. The objective was to characterize the genomic diversity of VREfm isolates and the genetic contexts of van-carrying plasmids and transposons.

RESULTS: Among the 19 VREfm isolates, vanA was detected in 16 isolates, while vanM was identified in 3 isolates. MLST analysis revealed five sequence types (ST17, ST68, ST78, ST80, and ST547) with distinct temporal distributions. ST17 and ST68 were more frequently observed among isolates collected between 2019 and 2022, whereas ST78 was more common among isolates collected in 2023-2024 and was associated with multiple plasmid types. These observations suggest differences in lineage composition and plasmid backgrounds across the sampling period. Plasmidome analysis identified 19 plasmid groups, with resistance genes mainly concentrated in four major groups, some of which were shared across different sequence types. Notably, several resistance plasmids lacked functional replicons, suggesting plasmid fragmentation events. Transposon analysis revealed substantial structural diversity among Tn1546 variants, including insertions, deletions, and rearrangements, highlighting the complexity of vanA- and vanM-associated mobile genetic elements across different plasmid and clonal backgrounds.

CONCLUSION: This study provides genomic insights into the diversity and relatedness of VREfm isolates in a tertiary hospital over a 5-year period. The findings describe the diversity of sequence types, plasmid backbones, and van-associated mobile genetic elements within this hospital collection.},
}

@article {pmid42041085,
year = {2026},
author = {Malnak, JC and Montermoso, S and Bushman, FD and Auslander, N},
title = {Uncovering viral protein acquisition events and human-specific folds with pairwise comparisons of predicted protein structures.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msag110},
pmid = {42041085},
issn = {1537-1719},
abstract = {Pairwise sequence comparisons are at the center of molecular evolutionary analyses. However, viral pairwise comparisons are challenging because extreme mutation rates and evolutionary pressure cause genomes to diverge rapidly, limiting detectable sequence similarity to fewer than 3% of virus pairs. To overcome these limitations, we compared viruses based on structural similarity, using predicted protein structures from ColabFold and Foldseek to define protein fold clusters. We represented each virus genome by its protein structural content. Pairwise similarities between viruses were then quantified using the Jaccard index based on the presence or absence of protein fold clusters. Using a recently established viral protein fold database, we compared all pairs of eukaryotic viruses in RefSeq. This approach increased the proportion of comparable viral genome pairs from 2.4% to 16.5%. Using this protein-fold representation of viruses, we were able to accurately predict viral families with an average sensitivity of 85.9%. Investigation of viral families showing limited sensitivity with this approach uncovered a laterally transferred structural cluster (Rep/NS1) broadly shared across diverse viral families and found in the avian lineage of adenoviruses. Sequence homology suggests that this Rep was acquired from Parvoviridae, but the protein is mutant in the ATPase active site, indicating possible exaptation towards a purely DNA binding function. In Gammapapillomaviruses, several E4 clusters were associated with human tropism. In summary, by representing viruses with structural protein clusters, we can classify highly divergent viruses, trace lateral gene transfer, and uncover features associated with viral host range.},
}

@article {pmid42041322,
year = {2026},
author = {Karampatakis, T and Tsergouli, K and Behzadi, P},
title = {Carbapenem-Resistant Serratia marcescens: Genomic Plasticity, Virulence Architecture, and the Expanding Threat of Multidrug Resistance.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/antibiotics15040359},
pmid = {42041322},
issn = {2079-6382},
abstract = {Serratia marcescens is a highly adaptable Gammaproteobacterium with broad ecological distribution and growing clinical importance. Advances in whole-genome sequencing (WGS) and pangenome analysis reveal extensive genomic plasticity, driven by mobile genetic elements (MGEs) such as plasmids, transposons, integrons, prophages, and extracellular vesicles, which collectively accelerate virulence and antimicrobial resistance (AMR) evolution. S. marcescens displays a dynamic accessory genome enriched in resistance and virulence determinants, supporting persistence in diverse environments, including hospital water systems. Clinically, S. marcescens is an emerging opportunistic pathogen associated with severe healthcare-associated infections, ICU outbreaks, and multidrug-resistant "superbug" phenotypes. Its resistome includes intrinsic AmpC β-lactamase, broad efflux systems, and chromosomal determinants conferring resistance to β-lactams, polymyxins, and multiple additional drug classes, while acquired ESBLs and carbapenemases urther limit therapeutic options. Integrating genomic, evolutionary, and clinical insights underscores the urgent need for improved surveillance, mechanistic understanding, and targeted interventions against carbapenem-resistant S. marcescens (CRSM).},
}

@article {pmid42041327,
year = {2026},
author = {Kim, T and Han, Y and Je, S and Kim, M and Song, H},
title = {Genomic Insight into the Mobility of Antibiotic Resistance Genes in Multidrug-Resistant Escherichia coli Isolated from Dewatered Sludge Cakes.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/antibiotics15040364},
pmid = {42041327},
issn = {2079-6382},
support = {K209775002//Chosun University/ ; },
abstract = {Background/Objectives: Municipal wastewater treatment plants (WWTPs) act as reservoirs for antibiotic-resistant bacteria, which pose a threat to global public health. In this study, we used whole-genome sequencing (WGS) to characterize antibiotic resistance genes (ARGs) and their association with mobile genetic elements (MGEs) in five multidrug-resistant (MDR) Escherichia coli isolates from dewatered sludge cake samples collected from a municipal WWTP in Cheongju, Republic of Korea. Methods: Susceptibility to nine antibiotics was evaluated via disk diffusion assay. Among the isolates exhibiting multidrug resistance (MDR) to three or more antibiotic classes, five isolates were randomly selected for whole-genome sequencing using the Illumina NovaSeqX platform. Additionally, we compared the genomic structures of five WWTP isolates with 35 environmental E. coli isolates from South Korea deposited in the NCBI pathogen database. ARGs and MGEs, including plasmids, integrons, and insertion sequences (ISs), were detected in the genome assemblies. Results: ARGs were differentially distributed between chromosomal and plasmid-derived contigs. Efflux pump-related genes were predominantly located on the chromosome across all isolates, whereas several beta-lactamase genes (e.g., blaTEM-30 and blaTEM-33), fluoroquinolone, and tetracycline resistance genes were localized on putative plasmid contigs. Furthermore, we characterized specific MGEs associated with these ARGs, including a class 1 integron gene cassette (dfrA17-aadA5-qacEΔ1-sul1) and an IS-mediated module (mph(A)-mrx-IS6100). Core-genome multilocus sequence typing (cgMLST) revealed that these MDR isolates represented diverse genetic lineages rather than a single clonal cluster. Conclusions: The results from this study highlight the necessity of enhanced post-treatment management of wastewater byproducts and WGS-based surveillance to mitigate the environmental spread of MDR bacteria.},
}

@article {pmid42041359,
year = {2026},
author = {Maroju, PA and Sidhu, AS and Motaganahalli, AR and Minto, RE and Zor, F and Kelley-Patteson, C and Rahimi, R and Hassanein, AH and Sinha, M},
title = {Detection to Disruption: A Comprehensive Review of Bacterial Biofilms and Therapeutic Advances.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/antibiotics15040396},
pmid = {42041359},
issn = {2079-6382},
support = {R01AI165958/NH/NIH HHS/United States ; R21AI171932/NH/NIH HHS/United States ; 831458//Plastic Surgery Foundation/ ; },
abstract = {Bacterial biofilms are structured microbial communities enclosed within a self-produced extracellular polymeric substance matrix composed of polysaccharides, proteins, extracellular DNA, and lipids. This matrix promotes adhesion, structural stability, and the development of heterogeneous microenvironments that restrict antimicrobial penetration and shield bacteria from host immune responses. As a result, biofilms are major contributors to chronic, recurrent, device-related, and difficult-to-treat infections, posing a major challenge for clinical management and antimicrobial stewardship. This review summarizes current understandings of biofilm biology, its clinical relevance, including the stages of biofilm development, the composition and protective roles of the matrix, and the physiological heterogeneity that arises during maturation. It also examines key mechanisms underlying biofilm tolerance and resistance, such as limited antibiotic diffusion, and sequestration, enzymatic inactivation, efflux pump upregulation, persister cell formation, and horizontal gene transfer. In addition, it highlights important clinical settings in which biofilms are implicated, including cystic fibrosis, chronic wounds, osteomyelitis, implant- or device-associated infections, and breast implant illness, in which persistent implant-associated biofilms and the resulting chronic inflammatory milieu have been hypothesized to contribute to local and systemic manifestations in a subset of patients. The review further discusses conventional and emerging approaches for biofilm detection alongwith real-time monitoring. Biofilm-associated infections remain difficult to eradicate because persistence is driven by multiple interconnected protective mechanisms. Effective management therefore requires integrated strategies that combine accurate detection with multifaceted therapies, including antibiotics alongside matrix-disrupting enzymes, quorum-sensing inhibitors, bacteriophages, metabolic reactivators, and nanotechnology-based delivery systems. Advances in multi-omics and system-level modeling will be essential for developing next-generation strategies to prevent, monitor, and treat biofilm-associated disease.},
}

@article {pmid42041381,
year = {2026},
author = {Hossain, H and Ali, MH and Ahmad, T and Sayeed, SSB and Sakib, MAN and Brishty, KA and Saleh, MSJ and Hosen, MM and Ahmed, S and Ahmed, S and Chowdhury, MSR and Rahman, MM},
title = {Mobile Genetic Elements as Central Drivers of Antimicrobial Resistance: Molecular Mechanisms, Evolutionary Ecology, One Health Implications and Control Strategies.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/antibiotics15040418},
pmid = {42041381},
issn = {2079-6382},
support = {SAURES-UGC-2025-26-VABS-117//University Grants Commission of Bangladesh/ ; },
abstract = {Antimicrobial resistance (AMR) represents a global health crisis, driven largely by the mobility of resistance determinants through mobile genetic elements (MGEs). These include plasmids, integrons, insertion sequences, transposons, integrative and conjugative elements (ICEs), and prophages, which together facilitate horizontal gene transfer (HGT) across bacterial species and ecosystems. This review aims to provide a comprehensive synthesis of current knowledge on the types, mechanisms, ecological drivers, and impacts of MGEs in the dissemination of antibiotic resistance genes (ARGs). Methods involved critical evaluation of recent genomic, epidemiological, and ecological studies, alongside case studies of clinically significant resistance outbreaks. Findings highlight how MGEs function as hubs for ARG capture, recombination, and stabilization, enabling the emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) pathogens. We also explored their interactions with ecological pressures such as antibiotics, heavy metals, and biocides, as well as their role in One Health transmission pathways. The significance of this study lies in linking molecular insights with applied strategies, including genomic surveillance, MGE-targeted inhibitors, phage therapy, and CRISPR-based interventions. Understanding MGEs is essential for designing effective interventions to mitigate AMR and protect global health.},
}

@article {pmid42041382,
year = {2026},
author = {Malinoski, L and Silva, GG and Rodrigues, LKI and Carneiro, LF and Gomes, MP},
title = {How Glyphosate and Its Derivatives Influence Antimicrobial Resistance Emergence and Transmission: A One Health Perspective.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/antibiotics15040419},
pmid = {42041382},
issn = {2079-6382},
support = {302226/2022-2//National Council for Scientific and Technological Development/ ; SUS2025831000005//Fundação Araucária/ ; },
abstract = {Background/Objectives: Glyphosate-based formulations are globally pervasive pollutants increasingly recognized as potential contributors to antimicrobial resistance (AMR) in environmental microbiomes. Although glyphosate is designed to inhibit plant 5-enolpyruvylshikimate-3-phosphate synthase, it also affects microbial metabolism, stress response, and genetic exchange. This review synthesizes the pathways through which glyphosate, its metabolite aminomethylphosphonic acid (AMPA), and commercial mixtures influence resistance-associated phenotypes and the dissemination of antibiotic resistance (ABR). Methods: A critical synthesis of the literature was conducted to evaluate the mechanistic and ecological interactions between glyphosate exposure and bacterial resistance in soil, aquatic, and host-associated microbiomes. Results: Experimental evidence showed that sublethal glyphosate exposure induced oxidative stress, altered membrane permeability, activated multidrug efflux pumps, and promoted tolerance phenotypes that could modify antibiotic susceptibility. It also enhances mutation rates and horizontal gene transfer processes associated with the emergence of resistance under controlled conditions. At the community level, glyphosate exposure is associated with microbiome restructuring and enrichment of resistance determinants, often without major shifts in overall diversity of the microbiome. These effects have been reported at environmentally relevant concentrations, although the evidence remains largely derived from laboratory and mesocosm studies. Conclusions: Glyphosate acts as both a biochemical modulator of resistance-related phenotypes and an environmental selective pressure that shapes microbial communities. Its widespread use and environmental persistence position it as a context-dependent contributor to the emergence and dissemination of AMR through interacting mechanistic and ecological pathways. Integrating AMR endpoints into pesticide risk assessments and surveillance frameworks is warranted, in addition to expanded field-based validation.},
}

@article {pmid42042961,
year = {2026},
author = {DeZoysa, AR and Kwan, M and Edison, LK and Barber, R and Glick, L and Denagamage, T and Kariyawasam, S},
title = {Characterization of Antimicrobial Resistance and Potential Zoonotic Risk in Uropathogenic Escherichia coli Isolated from Companion Animals, with Genomic Analysis of Virulence Determinants in a Representative Isolate.},
journal = {Tropical medicine and infectious disease},
volume = {11},
number = {4},
pages = {},
doi = {10.3390/tropicalmed11040101},
pmid = {42042961},
issn = {2414-6366},
support = {16262//American Rescue Plan (ARP) funding for One-Health Research from the Florida Department of Agriculture & Consumer Services (FDACS)/ ; NA//Lisa Conti One Health Initiative from the Department of Comparative, Diagnostic, and Population Medicine at UF-CVM/ ; },
abstract = {Uropathogenic Escherichia coli (UPEC) is a leading cause of urinary tract infections (UTIs) in companion animals. This study characterized 42 UPEC isolates recovered from dogs and cats at the University of Florida, College of Veterinary Medicine Diagnostic Laboratories between 2023 and 2024, focusing on antimicrobial resistance (AMR), virulence gene profiles, biofilm-forming ability, and phylogroup distribution of the isolates. Antimicrobial susceptibility testing (AST) showed that 40.48% of the isolates were resistant to at least one of the tested antibiotics, and 9.52% exhibited multidrug resistance (MDR). Phylogroup B2 was predominant (69.05%), and 61.90% of isolates demonstrated strong biofilm formation in artificial human urine. Virulence gene analysis revealed the presence of genes mediating adhesion (fim, pap, sfa), iron acquisition (fyuA, iro), biofilm formation (csg, bcs, pga, ycg/ymg), motility (fli, mot, flh), and stress response (oxyR, soxR/S, kat). Multiple plasmids carrying AMR and virulence determinants were also identified. The co-occurrence of the traits underscores the potential for persistent and recurrent infections, which can complicate therapeutic outcomes and facilitate horizontal gene transfer (HGT). The detection of antimicrobial-resistant, highly virulent UPEC strains possessing human UPEC traits in companion animals suggests the risk of zoonotic and reverse-zoonotic transmission, particularly in households with close pet-owner interactions. These findings emphasize the importance of judicious antimicrobial use, routine molecular surveillance, and integrated One Health strategies to mitigate the veterinary and public health threats associated with UPEC infections in companion animals.},
}

@article {pmid41845199,
year = {2026},
author = {Zhen, Z and Shuhua, L and Baihe, M and Xin, C and Meiliang, G and Fanxin, L and Lianrui, L},
title = {Genome-wide characteristics, antibiotic resistance, and pathogenicity analysis of Streptococcus parasuis strains isolated from diseased pigs.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41845199},
issn = {1471-2180},
support = {2018CB037//Xinjiang Production and Construction Corps Funding Project/ ; 2022ZD106//Xinjiang Production and Construction Corps Natural Science Technology Development Project/ ; },
abstract = {UNLABELLED: Streptococcus parasuis is currently not only an underestimated zoonotic pathogen but also a bacterial source of infection in food animals, posing a potential threat to global public health. Despite increased reports in recent years, systematic studies in Northwest China remain scarce. However, the lack of complete genomic sequence information has limited in-depth bioinformatics analysis of multidrug-resistant S. parasuis isolated from pigs. This study reports the whole-genome sequencing results of S. parasuis strain A1 isolated from pigs. The A1 genome consists of a single circular chromosome without circular plasmids, establishing it as a potential “blank” vector for constructing standardized gene cloning and expression systems in genetic engineering. Twenty-one antibiotic resistance genes were identified on the bacterial chromosome, conferring resistance to major antibiotics including glycopeptides, macrolides, lincosamides, streptogramins, aminoglycosides, tetracyclines, fluoroquinolones, cephalosporins, polypeptides, and β-lactams. Resistance mechanisms encompass target site modification, target site protection, antibiotic inactivation, and efflux pump-mediated drug efflux, demonstrating potent multidrug resistance potential. Additionally, 113 virulence factors were identified, spanning multiple functional domains including effector protein secretion systems, immune regulation, adhesion, stress survival, and biofilm formation. Among these, six virulence factors relate to nutritional metabolism, primarily involving iron uptake, pyrimidine biosynthesis, purine biosynthesis, and fatty acid metabolism. Antibiotic susceptibility testing confirmed the multidrug-resistant phenotype of this strain. Mouse infection experiments demonstrated that strain A1 exhibits strong pathogenicity, causing lethal infections in mice and significant histopathological damage to organs such as the liver and spleen. Concurrently, levels of pro-inflammatory cytokines (TNF-α, IL-1β, IL-6) were significantly elevated in the serum of infected mice. Whole-genome analysis revealed 24 horizontal gene transfer elements in A1, including 3 genomic islands, 13 transposons, and 8 remnant pre-phage sequences. Furthermore, 196 virulence-attenuating mutations and 10 potential pathogenicity-related deletion sites were identified. Therefore, this study contributes to the development of strategies for preventing and controlling S. parasuis infections and their spread within pig populations. It should be emphasized that this study is based solely on analysis of a single strain, and the generalizability of its conclusions requires validation with additional strains. Furthermore, the correspondence between resistance genes and phenotypes, as well as the specific regulatory and synergistic mechanisms of virulence factors, remain incompletely elucidated and warrant further investigation.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04932-w.},
}

@article {pmid42031315,
year = {2026},
author = {Shan, J and Wang, T and Peng, C and Guo, P and Zhu, H and Luo, D and Wang, Y and Chen, J},
title = {Synchronously enhanced methanogenesis performance and reduced antibiotic resistance genes of cattle manure anaerobic digestion by air nanobubble water.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134704},
doi = {10.1016/j.biortech.2026.134704},
pmid = {42031315},
issn = {1873-2976},
abstract = {The excessive use of antibiotics in livestock farming has made cattle manure (CM) a reservoir for antibiotic resistance genes (ARGs). Anaerobic digestion (AD) can mitigate the risk of spreading ARGs, but its treatment capacity has limitations. This study investigated the effect of air nanobubble water (Air-NBW) on methanogenesis performance and ARGs dynamics during mesophilic and psychrotrophic AD of CM. The results show that Air-NBW enhanced cumulative methane production by 43.4% (mesophilic) and 50.2% (psychrotrophic) by upregulating key functional genes involved in hydrogenotrophic and acetoclastic methanogenesis. Gompertz fitting further showed that the maximum methane yield rate increased by over 62.2% under both temperature conditions. Under mesophilic conditions, Air-NBW had a greater impact on the abundance of mobile genetic elements and the expression of ARG transfer genes than under psychrotrophic conditions. Specifically, Air-NBW led to a 50.7% decrease in mobile genetic elements, a 39.6% downregulation in biofilm-related genes, and a 24.5% upregulation in antioxidant genes, along with a reduction in ARG abundance. This suggests Air-NBW helps lower overall ARG levels. Meanwhile, Air-NBW reduced the abundance of specific ARGs (lnu(D), lsa(B), mph(B), tet(W), tet(T), and tet(Q)) under both temperature conditions. Ultimately, Air-NBW decreased the ecological risk scores by 3.5% (mesophilic) and by 6.8% (psychrotrophic). In summary, Air-NBW can simultaneously boost methane production and mitigate the ecological risks posed by ARGs, with particularly notable performance under psychrotrophic conditions. Therefore, the addition of Air-NBW to the AD of CM shows great application potential in high-latitude cold regions, serving as an efficient and safe treatment approach.},
}

@article {pmid42034426,
year = {2026},
author = {Zhou, N and Wei, R and Yang, S and Hu, F and Feng, Y and Zheng, H},
title = {Antibiotic resistance gene profiles in the gut microbiomes of Apis cerana, Apis mellifera, and Bombus terrestris.},
journal = {Pesticide biochemistry and physiology},
volume = {220},
number = {},
pages = {107059},
doi = {10.1016/j.pestbp.2026.107059},
pmid = {42034426},
issn = {1095-9939},
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Metagenome ; China ; },
abstract = {The gut microbiota of honeybees has been increasingly recognized as a reservoir of antibiotic resistance genes (ARGs). However, comprehensive comparisons of ARG profiles between honeybees and bumblebees inhabiting the same environments are limited. Moreover, the diversity of mobile genetic elements (MGEs) in bee gut microbiomes and their potential role in mediating the horizontal transfer of ARGs have not yet been fully elucidated. In this study, metagenomic sequencing of 48 gut samples from farmed Apis mellifera, Apis cerana, and Bombus terrestris across four regions in China revealed 127 ARG subtypes, which collectively conferred resistance to nine major antibiotic classes. We found that A. mellifera, which carried the highest load of ARGs, concurrently harbored the greatest abundance of MGEs among the three species. Although ARG abundance varied significantly by region, no consistent geographical pattern emerged across the bee species. Importantly, strong positive correlations were detected between the abundances of ARGs and MGEs, particularly between the insertion sequence gene Tn3 and plasmid gene IncQ1. Metagenome-assembled genome analyses further confirmed the co-occurrence of ARGs (sul2, aph(3″)-Ib, and aph(6)-Id) with MGEs (Tn3 and IncQ1) across the three bee species, providing direct evidence that horizontal gene transfer mediated by MGEs contributes to the dissemination of ARGs within bee gut microbiomes. Overall, these findings highlight the critical role of the bee microbiome as a reservoir for ARGs and as a bioindicator for environmental pollutants, providing important insights into the mechanisms of ARG dissemination in ecosystems.},
}

Animals
Bees/microbiology
*Gastrointestinal Microbiome/genetics
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
Metagenome
China

@article {pmid42034610,
year = {2026},
author = {Wang, C and Wang, P and Peng, K and Zhang, H and Zhang, W and Liu, Y and Wang, Z and Li, R},
title = {Cyromazine accelerates the dissemination of antimicrobial resistance genes by promoting the conjugative transfer of the SXT integrative conjugative element.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71554-1},
pmid = {42034610},
issn = {2041-1723},
support = {32473095//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32373061//National Natural Science Foundation of China (National Science Foundation of China)/ ; BK20231524//Outstanding Youth Foundation of Jiangsu Province of China/ ; },
abstract = {Antimicrobial resistance (AMR) is an urgent public health challenge, and the horizontal transfer of antimicrobial resistance genes (ARGs) mediated by mobile genetic elements (MGEs) accelerates its spread worldwide. Despite the recognized role of integrative conjugative elements (ICEs) in conjugative gene transfer, ICE-mediated horizontal gene transfer (HGT) remains underexplored, particularly for SXT ICEs, which are widely disseminated and relevant to animal and human health. Cyromazine, a widely used veterinary drug frequently detected in livestock feces and associated environments, is linked to an increased abundance of ARGs, but the underlying mechanisms remain unclear. Here, we investigate the impact of cyromazine on SXT ICE-mediated ARG transfer and delineate potential mechanisms. We show that cyromazine promotes intra- and inter-species conjugative transfer of SXT ICE and validate this effect in vivo. In environmentally relevant models (feces, soil, and water), cyromazine further enhances SXT ICE transfer and reshapes the community structure of transconjugants. Potential mechanisms include cyromazine-induced ROS accumulation and SOS activation, which may promote SXT ICE excision and induce conjugation-related operons. Enhanced energy production and disrupted membrane homeostasis may further facilitate transfer. Collectively, these findings narrow the gap in ICE-mediated AMR transmission and suggest cyromazine could intensify AMR spread by stimulating SXT ICE conjugative transfer.},
}

@article {pmid42035541,
year = {2026},
author = {Liang, Y and Yang, Z and Zhou, X and Zhao, Q and Wu, Q and Du, J and Wang, H and Guo, WQ},
title = {Why radical oxidation prevails: Dual advantages in sludge valorization and ARG suppression over nonradical pathways.},
journal = {Water research},
volume = {300},
number = {},
pages = {125964},
doi = {10.1016/j.watres.2026.125964},
pmid = {42035541},
issn = {1879-2448},
abstract = {While the efficacy of advanced oxidation processes (AOPs) in sludge valorization is well-established, their associated ecological risks-particularly concerning antibiotic resistance genes (ARGs)-remain a critical blind spot. This knowledge gap is especially significant given the fundamental mechanistic dichotomy between radical and nonradical pathways. Herein, we systematically evaluate two representative systems-sludge-derived biochar-activated peracetic acid (SBC/PAA, nonradical/[1]O2) and nanoscale zero-valent iron-activated peracetic acid (nZVI/PAA, radical/·OH and ·CH3)-focusing on their dual impacts on short-chain fatty acid (SCFA) production and ARG fate. A stark contrast was observed: the mild [1]O2 from SBC/PAA resulted in only a modest increase in SCFA yield but inadvertently increased ARG dissemination potential by enriching mobile genetic elements (MGEs), amplifying host bacteria, and activating stress-induced horizontal gene transfer pathways (oxidative stress, signal transduction and secretory system). In contrast, the highly reactive radicals from nZVI/PAA achieved a dual victory, maximizing SCFA production through efficient cell disruption while concurrently suppressing intracellular and extracellular ARGs via profound genomic damage and functional pathway disruption, with intracellular ARGs (iARGs) and extracellular ARGs (eARGs) further reduced by 46.07% and 45.21% during fermentation. Thus, the distinct chemical effects exerted by the oxidants propagated through the microbial ecosystem, shaping divergent ARG risk trajectories by differentially governing MGEs, hosts, and functional pathways. This insight provides a critical mechanistic foundation for overcoming the trade-off between resource recovery and risk mitigation, shifting the paradigm from the indiscriminate application of AOPs to the strategic selection of oxidation mechanisms for a sustainable and safe sludge treatment future.},
}

@article {pmid42026074,
year = {2026},
author = {Li, L and Wang, H and Chen, X and Kang, J and Xu, Y and Sahu, SK and Lorenz, M and Friedl, T and Campbell, C and Rad-Menéndez, C and Melkonian, B and Wong, GK and Liu, H and Gu, Y and Xu, X and Wei, T and Melkonian, M and Wang, S},
title = {Horizontal gene transfer and diploidy illuminate evolution and stress adaptation in oleaginous Scenedesmaceae (Chlorophyta).},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71696-2},
pmid = {42026074},
issn = {2041-1723},
support = {32300513//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32570763//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Oleaginous microalgae combine high lipid content with the ability to grow under diverse environmental conditions, the oleaginous species of family Scenedesmaceae (Sphaeropleales, Chlorophyta) having emerged as a promising source for biofuels, biostimulants, and bioremediation. This study provides long-read genome sequencing of 38 species/strains of Scenedesmaceae, including 16 chromosome-level genome assemblies, to explore the genomic underpinnings of the exceptional adaptive properties of their vegetative cells. Gene family analysis identifies 'core' and 'dispensible' orthogroups in the Scenedesmaceae and unveils orthogroup expansions and gains in four major metabolic processes that enhance survival of cells under stress: lipid metabolism, sulfur metabolism, resistance to oxidative stress, and heterotrophy. We discover orthogroup gains by horizontal gene transfer (HGT) from non-viridiplant donors in all four processes. Additionally, we identify ten diploid strains, which likely evolved by fusion of gametes and vegetative growth of the diploid cells. We hypothesize that HGT and diploidy fostered adaptive processes in the Scenedesmaceae.},
}

@article {pmid42030144,
year = {2026},
author = {Du, XM and Suo, F and Du, LL},
title = {Gene loss, repression, amplification, and horizontal acquisition shape galactose/melibiose metabolism in fission yeast.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {17},
pages = {e2532532123},
doi = {10.1073/pnas.2532532123},
pmid = {42030144},
issn = {1091-6490},
support = {2024YFA0917400//MOST | National Key Research and Development Program of China (NKPs)/ ; },
mesh = {*Schizosaccharomyces/genetics/metabolism ; *Galactose/metabolism ; *Melibiose/metabolism ; Phylogeny ; Multigene Family ; Gene Transfer, Horizontal ; Gene Deletion ; Gene Amplification ; Gene Expression Regulation, Fungal ; },
abstract = {Natural variation in metabolism is a key driver of microbial adaptation. While galactose utilization is well studied in budding yeasts, it remains poorly understood in the fission yeast Schizosaccharomyces pombe. Here, we reveal extensive natural variation in galactose utilization across S. pombe isolates-from complete deficiency (Gal[-]) to exceptionally fast growth (Gal[F]). Gal[-] strains fall into two classes: one with deletions of the gal gene cluster (via three distinct mechanisms) and another with intact but repressed gal genes. In contrast, Gal[F] is driven by an amplified gene cluster absent from the reference genome-the gal-mel cluster (GMC)-which also confers melibiose utilization (Mel[+]). Mel[+] is exclusively linked to the GMC, except in one strain harboring a standalone melibiase gene. Phylogenetic analyses indicate that horizontal gene transfer may underlie these adaptive traits. Together, our work demonstrates how diverse mechanisms-gene loss, repression, amplification, and horizontal acquisition-shape metabolic diversity and ecological specialization in fission yeast.},
}

*Schizosaccharomyces/genetics/metabolism
*Galactose/metabolism
*Melibiose/metabolism
Phylogeny
Multigene Family
Gene Transfer, Horizontal
Gene Deletion
Gene Amplification
Gene Expression Regulation, Fungal

@article {pmid42031198,
year = {2026},
author = {Su, J and Zhu, R and Fu, D and Zhou, Z and Zheng, N and Cheng, Y and Yao, H},
title = {Surrounding land use patterns drive the distribution characteristics of antibiotic resistance genes in sediments of a typical freshwater lake.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128198},
doi = {10.1016/j.envpol.2026.128198},
pmid = {42031198},
issn = {1873-6424},
abstract = {Antibiotic resistance genes (ARGs) are emerging environmental pollutants, and lake sediments act as their major reservoirs. However, the dynamics of ARG abundance and composition have received little attention in lake sediments under surrounding land use patterns. Here, the sediments of Liangzi Lake areas close to the regions of traditional agriculture (AG), aquaculture (AQ), town construction (TW), and wetland nature reserve (BK, background control) were collected to investigate the abundance and distribution patterns of ARGs. A total of 233 ARGs were detected with the dominant multidrug and β-lactamase resistance classes. PCA and ANOSIM analyses revealed distinct ARG clustering and differences (p = 0.001) among the AG, AQ, TW and BK. AG and AQ exhibited significantly higher ARG diversity, abundance and detection frequency (p < 0.05) compared to BK, indicating the aquaculture and agricultural activity posed the greater risk for ARG dissemination in sediments. Source track analysis showed that aquaculture, human and animal faeces were primary ARG contributors to lake sediments. RDA and Mantel-test analyses demonstrated that the nutrients (OM, TN, C: N), mobile genetic elements (MGEs), and heavy metals significantly influence (p < 0.05) the abundance and composition of ARGs. MGEs played a crucial role in the dissemination of ARGs via horizontal gene transfer (HGT), and potential bacterial hosts showed a strong correlation (p < 0.01) with the abundance of total ARGs. Surrounding land use patterns increased the complexity of co-occurrence patterns among ARGs, MGEs and the hosts in sediments, and potentially stimulated coupling between ARGs and P mineralization genes, thereby further accelerating the ARG transmission. This study provided new insights into how surrounding land use patterns shaped ARG composition and dissemination, and offered a scientific basis for ARG management and prevention in the lake sediments.},
}

@article {pmid42031204,
year = {2026},
author = {Jang, J and Kim, E and Kim, YM and Lee, YM and Yoon, YJ and Park, J},
title = {Spatial distribution of airborne antibiotic resistance genes over the Pacific Ocean: ocean-atmosphere transfer.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128197},
doi = {10.1016/j.envpol.2026.128197},
pmid = {42031204},
issn = {1873-6424},
abstract = {Antibiotic resistance genes (ARGs) are increasingly recognized as global determinants within the 'One Health' framework; however, the diversity of ARGs and their transmission mechanisms across the ocean-atmosphere interface remain poorly understood. In this study, we simultaneously quantified airborne and seawater-derived ARGs along a 3,868 km transect covering Korean coastal waters, the North Pacific Ocean, and the Bering Sea. The normalized relative abundance of ARGs (copies/16S rRNA gene) varied across 10 targeted ARG subtypes, with average values of 1.1×10[-4] ± 5.5×10[-4] copies/16S rRNA gene in aerosol and 1.7×10[-4] ± 1.1×10[-3] copies/16S rRNA gene in seawater. The blaTEM and tetBP genes were dominant subtypes in both matrices, reflecting their roles as core components of the marine resistome. Furthermore, specific genes, including tetA, tetZ, ermB, qnrD, and oqxA, showed proportional enrichment in aerosols, indicating matrix-specific distribution patterns. Exploratory partial canonical correspondence analysis (pCCA) revealed that air mass origin (oceanic vs. terrestrial) and meteorological variables (e.g., air temperature, solar radiation, wind speed, and atmospheric pressure) significantly influence the spatial distribution of airborne ARGs. In addition, Polaribacter sp. and Sediminibacterium sp. were identified as putative microbial hosts potentially facilitating the mobilization of airborne ARGs across the ocean. Strong correlations between intI1 and certain ARGs (e.g., oqxA, ermB, and blaTEM) further suggest the potential role of horizontal gene transfer in resistance dissemination. Our findings provide a critical baseline indicating that airborne ARGs are widely disseminated in remote marine environments, emphasizing the need for global monitoring of the atmospheric resistome.},
}

@article {pmid42021859,
year = {2026},
author = {Hamdi, MF},
title = {Disinfection's impact on the environment, molecular cross-resistance with antibiotics, and modern reduction approaches.},
journal = {Toxicological research},
volume = {42},
number = {3},
pages = {289-306},
pmid = {42021859},
issn = {1976-8257},
abstract = {UNLABELLED: Industrial disinfectant use has become concerning due to its antimicrobial resistance (AMR)- promoting properties, leading to antibiotic and disinfectant co-resistance. This research investigates the genetic processes by which disinfectants enhance bacterial resistance to antibiotics by analyzing multidrug efflux pumps and mobile genetic elements (MGEs). Bacterial cells that encounter disinfectants tend to increase their production of efflux pumps, which simultaneously protect them against disinfectants and various antibiotics. Multidrug resistance in Pseudomonas aeruginosa arises when the bacterium encounters chlorine disinfectants, which activate the MexEF-OprN efflux pump. Horizontal gene transfer (HGT) is an essential factor for the simultaneous selection of both antibiotic- and disinfectant-resistance genes. Scientific evidence demonstrates that chlorination, along with other disinfectants, increases horizontal gene transfer rates, thereby facilitating the exchange of antibiotic resistance genes among bacterial species. The uptake of foreign genetic material occurs through the combined effects of increased membrane permeability and oxidative stress, which promote the process. The development of resistance results from two main mechanisms: horizontal gene transfer and natural genetic adaptations. Bacteria are exposed to disinfectants, which can cause genetic mutations that activate resistance proteins and other defense systems. The resistance of Pseudomonas aeruginosa bacteria to antibiotics increases due to changes in the pmrB gene. Some experimental results indicate that contact with disinfectants may decrease bacterial antibiotic resistance by either slowing bacterial growth or altering the production of virulence factors. This paper highlights the need for stricter regulations on disinfectant use, given their potential to foster the development of multidrug resistance. Further research into the genetic mechanisms underlying disinfectant-induced resistance is essential to understand better and mitigate its impact on public health.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43188-026-00340-4.},
}

@article {pmid42022010,
year = {2026},
author = {Del Mar Quiñonero-Coronel, M and Garcillán-Barcia, MP},
title = {Plasmids serve as vehicles and reservoirs of type VI secretion systems.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag069},
pmid = {42022010},
issn = {2730-6151},
abstract = {The Type VI secretion system (T6SS) is a major determinant of bacterial competition, yet its dissemination across lineages remains unclear. By analyzing 43 213 plasmids and 29 161 chromosomes, we reveal plasmids as an underestimated reservoir and vehicle for T6SS diversification. We identified 405 complete plasmid-encoded T6SSs and 929 orphan islands containing hcp, vgrG, and/or PAAR genes, often independent of full systems. Plasmid-encoded T6SSs are biased toward large replicons, frequently megaplasmids, with distinct stability and mobility traits: orphan island plasmids are enriched in conjugation modules, whereas complete systems are associated with partition and toxin-antitoxin maintenance systems. Phylogenomic analyses show that some plasmid lineages stably integrate T6SSs as core traits, while others undergo recurrent acquisition and diversification. Comparative and ancestral analyses indicate pervasive bidirectional transfers between plasmids and chromosomes, with insertion sequences frequently detected in their vicinity. The presence of near-identical homologs across compartments underscores the capacity of plasmids to transcend phylogenetic barriers and propagate these nanoweapons. Together, our results identify plasmids as dual evolutionary actors in T6SS ecology, functioning as short-term vectors for rapid horizontal spread and as long-term reservoirs that foster stabilization and adaptive diversification.},
}

@article {pmid42022123,
year = {2026},
author = {Yuan, X and Ma, C and Cao, X and Ma, Z and Wu, L and Jiang, P and Yang, Z},
title = {Genomic insights into the global dissemination of linezolid resistance genes in Enterococcus faecium.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1783172},
pmid = {42022123},
issn = {1664-302X},
abstract = {BACKGROUND: Transferable linezolid resistance determinants in Enterococcus faecium, particularly optrA, poxtA, and cfr, have raised increasing global concern due to their potential dissemination across clinical, animal, food, and environmental reservoirs. However, their population distribution, genomic contexts, and associated virulence backgrounds remain incompletely understood.

METHODS: We performed a large-scale genomic analysis of 2,235 publicly available E. faecium genomes to investigate the distribution, sequence types (STs), virulence factors (VFs), and genomic contexts of transferable linezolid resistance genes. Phylogenetic analysis and comparative examination of gene flanking regions were conducted to explore the mechanisms underlying resistance gene dissemination.

RESULTS: A total of 243 genomes (10.9%) carried at least one linezolid resistance gene. poxtA (8.1%) and optrA (6.9%) were more frequently detected than cfr (2.2%). Multiple resistance determinants were simultaneously observed within individual isolates, with optrA + poxtA representing the most frequent gene combination. These resistance genes were distributed across 90 distinct STs, indicating substantial population diversity. Comparative phylogenetic and genomic context analyses revealed significant genetic diversity and a lack of strict phylogenetic clustering, suggesting that horizontal gene transfer mediated by mobile genetic elements plays a major role in the dissemination of these determinants. VF analysis identified 44 virulence genes, with several adherence-associated genes highly conserved across isolates. Notably, certain adherence-related VFs were enriched in isolates harboring multiple resistance genes.

CONCLUSION: Together, these findings highlight the widespread dissemination of optrA-, poxtA-, and cfr-mediated linezolid resistance in diverse E. faecium genomic backgrounds and underscore the important role of horizontal gene transfer in their spread. Continuous genomic surveillance integrating resistance and virulence analyses will be essential for understanding and controlling the global transmission of linezolid-resistant E. faecium.},
}

@article {pmid42022846,
year = {2026},
author = {Singh, I and Kumar, A and Verma, IK and Sharma, D and Singh, AK},
title = {Colistin Resistance in Bacteria: Current Updates on Mechanism of Action and Combating Strategies.},
journal = {The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale},
volume = {2026},
number = {},
pages = {8603173},
pmid = {42022846},
issn = {1712-9532},
abstract = {The rapid development of colistin-resistant bacteria is the biggest global health issue since colistin is referred to as a 'last-hope resource' against life-threatening infections caused by GNB (Gram-negative bacteria). Injudicious and excessive colistin application in clinical, agricultural and veterinary practices, as well as plasmid-mediated horizontal gene transfer and chromosomal mutation, commonly contribute to colistin resistance. The coexistence of the mcr-1 gene with mcr variants, other intrinsic genes and other mechanisms might provide additional resistance strength against colistin. To prevent the emergence of colistin-resistant strains and preserve the therapeutic efficacy of existing antibiotics, we must expand our deep understanding of colistin-resistant strains at the molecular level. This critical review discusses the mechanism of action, various bacterial resistance mechanisms, the presence of mcr genes in bacterial plasmids, hetero-resistance, biofilm formation, the horizontal transfer or dispersion of colistin-resistant genes and combating strategies. Our synthesis underscores the need for strategically aligning mechanistic knowledge with practical therapeutic solutions to combat escalating colistin resistance and inform future medical decision-making and research planning.},
}

@article {pmid42025071,
year = {2026},
author = {Waseem, H and Feng, K and Zhao, B and Yang, X and Liu, M and Wang, J and Li, J and He, Q and Wang, S and Lu, Y and Örmeci, B and Deng, Y},
title = {Diversity and geographic distribution of antibiotic resistance in food waste anaerobic digestion systems.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142168},
doi = {10.1016/j.jhazmat.2026.142168},
pmid = {42025071},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) present in food waste pose a significant environmental and public health challenge, with anaerobic digestion emerging as a promising technology to reduce ARG abundance during waste treatment. In this study, we analyzed the resistomes in 64 anaerobic digestion sludge samples from seven full-scale food waste treatment facilities representing seven Chinese provinces. Across all facilities, a small core set of glycopeptide (van clusters), β-lactamase, aminoglycoside, and macrolide-lincosamide-streptogramin genes accounted for most ARG abundance (70.3%), marking them as critical targets for monitoring and post-treatment at high-risk sites such as Wenzhou. Resistome composition differed significantly among facilities and exhibited moderate correlation with bacterial taxonomic composition, with Firmicutes (Bacillota), Chloroflexota, and Proteobacteria as the major carriers associated with multiple resistance classes. ARG abundance was positively correlated with mobile genetic elements (r = 0.54, p < 0.0001), driven by integrases, transposases, and Tn916. Horizontal gene transfer was largely constrained within phylogenetic boundaries, particularly within Firmicutes (66.67%), limiting cross-phyla ARG dissemination. Resistome variation was driven predominantly by deterministic processes.; these deterministic filters together with regional differences in food-waste composition and MGEs, collectively select for a glycopeptide-dominated, Firmicutes-anchored resistome that is distinct from those in activated sludge and manure digesters.},
}

@article {pmid42025908,
year = {2026},
author = {Leghari, A and Khand, FM and Laghari, S and Lakho, SA},
title = {Climate Change as a Driver of Bovine Mastitis: Impacts on Environmental Pathogen Ecology, Host Susceptibility, and Future Mitigation Strategies.},
journal = {Veterinary journal (London, England : 1997)},
volume = {},
number = {},
pages = {106685},
doi = {10.1016/j.tvjl.2026.106685},
pmid = {42025908},
issn = {1532-2971},
abstract = {Climate change poses an escalating threat to global dairy production by exacerbating the incidence and severity of bovine mastitis, a disease with profound economic and animal welfare implications. This review synthesizes emerging evidence to demonstrate that climate change acts as a multifactorial driver of mastitis risk through interconnected physiological, ecological, and epidemiological pathways. Elevated temperatures and humidity induce host immunosuppression via heat stress, compromising systemic and mammary-specific immune defenses. Concurrently, climatic variables alter the environmental dynamics of key pathogens (e.g., Escherichia coli, Klebsiella spp., Streptococcus uberis), enhancing their survival, proliferation, and biofilm formation. These changes drive extended seasonal risk windows, geographic redistribution of disease pressure, and acute spikes in incidence following extreme weather events. Furthermore, climate change intersects with antimicrobial resistance by increasing disease incidence and antibiotic use, while also promoting environmental persistence and horizontal gene transfer of resistance determinants. To address this compounded challenge, the review outlines a framework for climate-resilient mastitis control, integrating short-term heat abatement and housing adjustments, medium-term nutritional and genetic interventions, and long-term adaptive surveillance within a One Health approach. Proactive, integrated strategies are essential to mitigate the growing threat of climate-amplified mastitis and ensure the sustainability of dairy production systems. Future research must prioritize mechanistic studies, predictive modeling, and economic analyses to translate this knowledge into actionable solutions.},
}

@article {pmid41959466,
year = {2026},
author = {Sapoval, N and Treangen, TJ and Nakhleh, L},
title = {Leveraging spectrum of graph sheaf Laplacian as a genome-architecture-aware measure of microbiome diversity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41959466},
issn = {2692-8205},
abstract = {MOTIVATION: Measures of microbial diversity that can be derived directly from metagenomic sequencing data offer a valuable summary view of the underlying complex systems. Prior work has shown that both taxonomic composition and abundances that are captured by standard diversity measures (e.g., Shannon entropy), and structural variation within the metagenome due to gene duplications, losses and horizontal transfers (HGT), can correlate with the host's health. However, there are no diversity measures available that simultaneously account for the genome architecture and taxonomic composition within the sample. Thus, in this work we propose the spectral energy of a graph sheaf Laplacian as such a measure, and justify its applicability through a simulation study and analysis of biological data.

RESULTS: First, we describe a theoretical framework that allows us to combine the features of genome graphs with the taxonomic data. Then, we explore the sensitivity of the proposed diversity measure to genome rearrangements and HGT events in a simulation study. Finally, we explore applicability of our proposed measure to characterization of diversity of human gut metagenomes. We find our proposed measure to offer better discrimination between healthy controls and inflammatory bowel disease (IBD) patients' samples (n = 403) in the cohorts analyzed.

https://github.com/nsapoval/bd-gsl.},
}

@article {pmid42015495,
year = {2026},
author = {Wang, Z and Feng, Y and You, L and Xu, M and Helwig, K and Li, R and Char, SN and Yang, B and Peters, RJ},
title = {Divergent roles of ent-kaurene oxidase paralogs in rice momilactone biosynthesis.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.70262},
pmid = {42015495},
issn = {1744-7909},
abstract = {Rice (Oryza sativa) is a critically important food crop and a model cereal, with its momilactones among the first discovered phytoalexins. Notably, while momilactone biosynthesis is related to that of the gibberellin (GA) phytohormones, it was acquired via lateral gene transfer of an associated biosynthetic gene cluster (mBGC), but has been suggested to depend on paralog(s) of the ent-kaurene oxidase (KO) required for GA production. Rice contains a five-gene tandem array of the KO family, with three acting in GA biosynthesis (OsKO1-3), while the divergent KO-like OsKOL4 has been shown to catalyze reactions consistent with a role in the production of phytoalexins, such as the phytocassanes and momilactones. Here, building on biochemical characterization of distinct activity for OsKOL5, genetic evidence is provided indicating OsKOL4 is much more important for momilactone biosynthesis, although both play a role in the production of the phytocassanes. Indeed, knock-out lines (kol4, kol5, and kol4/5) are more susceptible, while overexpression increases resistance, to both the fungal blast pathogen Magnaporthe oryzae and bacterial blight pathogen Xanthomonas oryzae. Intriguingly, consistent with previously reported phytotoxicity of momilactone intermediates, a lesion mimic phenotype is observed with kol4 and kol4/5 but not kol5 lines. Concordantly, phylogenomic analysis suggests acquisition of mBGC was preceded by tandem duplication of KO to generate KOL4, with subsequent duplication generating KOL5. Thus, despite the deleterious effects of KOL4 loss, it can be speculated that linkage to the essential KOs may have alleviated such negative selection leading to mBGC recruitment, potentially relevant to plant BGC evolution more generally.},
}

@article {pmid42016008,
year = {2011},
author = {, },
title = {Scientific Opinion on application EFSA-GMO-RX-MON1445 for renewal of the authorisation for continued marketing of cottonseed oil, food additives, feed materials and feed additives produced from cotton MON 1445 that were notified as existing products under Articles 8(1)(a), 8(1)(b) and 20(1)(b) of Regulation (EC) No 1829/2003 from Monsanto.},
journal = {EFSA journal. European Food Safety Authority},
volume = {9},
number = {12},
pages = {2479},
pmid = {42016008},
issn = {1831-4732},
abstract = {This scientific opinion evaluates the risk assessment for the authorisation for continued marketing of genetically modified herbicide tolerant cotton MON 1445 for food and feed produced from it. Cotton MON 1445 contains single copies of functional CP4 epsps and npt II expression cassettes and an aad A gene as non-functional element. Stability of the inserted DNA was confirmed over several generations. Bioinformatic analyses and levels of recombinant proteins did not reveal safety issues. No biologically relevant differences were identified in the compositional, phenotypic and agronomic characteristics of cotton MON 1445 in comparison to its conventional counterpart and its composition fell within the range of non-GM cotton varieties, except for CP4 EPSPS and NPTII proteins. No toxicity and allergenicity issues were identified regarding the newly expressed protens. Products from cotton MON 1445 do not contain viable plant parts. Insert structure in cotton MON 1445 may facilitate the stabilisation of the npt II gene in plasmids of environmental bacteria through double homologous recombination. However, considering the expected low frequency of gene transfer from cotton MON 1445 to bacteria compared to that between bacteria, and the very low exposure to DNA from cotton MON 1445, the EFSA GMO Panel concludes that the contribution of horizontal gene transfer to the environmental prevalence of npt II genes is negligible. Potential interactions of cotton MON 1445 with non-target organisms and the abiotic environment were not considered to be an issue because of low exposure levels. A post-market environmental monitoring plan is not required. The EFSA GMO Panel concludes that the information available for cotton MON 1445 addresses the questions raised by the Member States and that MON 1445-derived products are as safe as products derived from the conventional counterpart in the context of their intended uses.},
}

@article {pmid42017761,
year = {2026},
author = {Moe, R and Piechowiak, KW and Håvarstein, LS and Kjos, M and Straume, D},
title = {LytF contributes to pilus extrusion during natural competence in Streptococcus sanguinis SK36.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0011826},
doi = {10.1128/jb.00118-26},
pmid = {42017761},
issn = {1098-5530},
abstract = {Streptococci may enter a physiological state called competence, during which they express a specific set of genes required for exogenous DNA uptake and its subsequent integration into the genome through homologous recombination. This process, termed natural transformation, facilitates the horizontal acquisition of genetic material, potentially conferring adaptive advantages that enhance bacterial survival under selective pressures. To make homologous DNA available in the surrounding environment, Streptococcus pneumoniae expresses a cell wall hydrolase (CbpD) that lyses and kills closely related species. This process has been coined fratricide, and the acting hydrolase a fratricin. A significant fraction of streptococcal species does not encode a CbpD-like protein, but another competence-induced peptidoglycan hydrolase LytF. It has been speculated that LytF serves the same purpose as CbpD; however, our investigations into the role of LytF in Streptococcus sanguinis revealed no evidence supporting LytF as a fratricin. Instead, we show that LytF is involved in natural transformation by promoting DNA uptake. An essential part of DNA uptake is the competence-induced type IV pilus, which facilitates DNA uptake by pulling nearby DNA toward the cell. By immunoblotting and microscopy imaging, we found that LytF increases extracellular levels of the major pilus component ComGC, suggesting that LytF may modify peptidoglycan to promote pilus extrusion across the cell wall, thereby enhancing the efficiency of DNA uptake.IMPORTANCEStreptococci are a significant cause of severe infections in both humans and animals. They are particularly adept at acquiring new genes through horizontal gene transfer, as they can become competent for natural transformation. This allows them to quickly adapt to selective pressure and spread genes involved in virulence and antibiotic resistance. In Streptococcus sanguinis, the competence-induced peptidoglycan hydrolase LytF has been reported to stimulate natural transformation. Our study contributes to understanding this process by demonstrating that LytF promotes extrusion of the transformation pilus required for DNA uptake.},
}

@article {pmid42019337,
year = {2026},
author = {Yu, B and Jiang, C and Yang, K and Zhang, Y and Gao, Y and Chen, Z and Qian, X and Ouyang, S},
title = {Correlation analysis of heavy metal, antibiotics accumulation, and antibiotic resistance genes induced by long-term biogas slurry application.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129745},
doi = {10.1016/j.jenvman.2026.129745},
pmid = {42019337},
issn = {1095-8630},
abstract = {Biogas slurry (BS), as product of animal manure fermentation, is often used as a fertilizer in farmland. However, the long-term application impact on the soil remains not fully understood. Studies have shown that although long-term application of BS does not lead to excessive antibiotic residues in the soil, it increases the abundance of antibiotic resistance genes (ARGs) and promotes their transfer among potential hosts. The complex co-occurrence of bacteria and ARGs implies enhanced horizontal gene transfer, and the increased abundance of the intl1 gene supports this change. Moreover, the distribution of antibiotic-resistant bacteria and ARGs is closely related to the duration of application. Meanwhile, tetracyclines and fluoroquinolones antibiotics, as well as ARGs, are significantly enriched in soils irrigated with BS, and various potentially pathogenic bacterial genera are present. In addition, the application of BS can increase the soil organic carbon stock and alter the soil bacterial and fungal communities. Long-term application of BS results in the accumulation of tetracyclines and the enrichment of ARGs in the soil. It also has an impact on the diversity of soil microbial functional genes. These findings provide a basis for the formulation of relevant policies and sustainable soil management.},
}

@article {pmid42019627,
year = {2026},
author = {Zhong, X and Bao, H and Zhang, S and Gong, Y and Li, X and Zhang, C and Li, M},
title = {Metabolic module exchange in plant-endophyte coevolution: mechanisms and implications.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.04.054},
pmid = {42019627},
issn = {2090-1224},
abstract = {BACKGROUND: Endophytes establish intimate symbioses with their hosts through long-term coevolution. They are known to promote plant growth, enhance stress resistance, and contribute to the biosynthesis of bioactive compounds. However, despite extensive research on these beneficial roles, a systematic synthesis of their distribution patterns, functional differentiation, and mechanisms of metabolite production remains lacking. This knowledge gap limits our understanding of plant-endophyte coadaptation and hinders its applications in agriculture and medicine.

PURPOSE OF REVIEW: This review critically synthesizes major studies on endophyte diversity, functional specialization, and metabolite biosynthesis. By integrating bibliometric and systematic evidence, we aim to elucidate the essential patterns and possible mechanisms underlying these phenomena-specifically, how endophytes and their host plants achieve functional complementarity and metabolic congruence. We further evaluate the roles of horizontal gene transfer and convergent evolution in enabling both partners to produce identical or structurally similar bioactive metabolites. Significant Scientific Ideas: Endophyte communities are highly structured, forming the basis for their interactions with host plants. Their distribution and functions are host‑ and tissue‑specific: strains from the same tissue of congeneric species show closer phylogenetic relatedness. A clear functional division exists in phytohormone production-bacteria predominantly produce indole-3-acetic acid (IAA), while fungi mainly produce gibberellins (GAs). Roots represent the dominant and most diverse colonization site. Horizontal gene transfer and convergent evolution serve as critical mechanisms enabling metabolic complementation between endophytes and plants. Together, these findings indicate that plant-endophyte coadaptation is underpinned by structured community assembly and functional specialization, rather than by random association.},
}

@article {pmid42020676,
year = {2026},
author = {Purohit, HV and Chakraborty, J and Kothari, RK and Bhatt, AR},
title = {Gene Exchange Mechanisms in Natural and Engineered Probiotics Within the Human Gut Implications for Antibiotic Resistance and Metabolic Modulation.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42020676},
issn = {1867-1314},
}

@article {pmid42020741,
year = {2026},
author = {Wu, L and Mu, DS and An, J and Wang, Y and Fan, X and Lu, DC and Zhang, Y and Xie, Y and Michael, J and Curtis, D and Fan, Y and Wang, Y and Guo, X and Tu, Q and Yan, Q and Gao, Q and He, Z and Deng, Y and Xue, K and Wu, L and Ning, D and Tao, X and Yang, Y and Zhou, J},
title = {Decade-long warming accelerates antibiotic resistance in grassland soils.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42020741},
issn = {1476-4687},
abstract = {Soils are critical reservoirs of antibiotic-resistance genes (ARGs)[1,2], which are strongly shaped by microbial interactions and environmental conditions and are therefore highly sensitive to disturbance[2-6]. Although climate warming is recognized as one of the most significant disturbances to microbial communities and their functions[7-10], its impacts on soil resistomes remain poorly understood. Here we investigated the effects of decade-long experimental warming on ARGs in grassland soils using integrated experimental and computational approaches. Our results revealed that ARG abundance substantially increased (23.9%) under warming-particularly glycopeptide- and rifamycin-resistance genes. Warming specifically enriched Actinomycetota hosts, including various potential plant pathogens, and enhanced ARG mobility. Large-scale unprecedented isolates-based phenotypic analyses also validated that warming increased bacterial resistance to multiple antibiotics. Further mechanistic analyses revealed that warming increased ARG abundance primarily through co-selection of resistance genes physically linked to adaptive traits (for example, thermal tolerance and nitrogen assimilation) and positive selection for thermal tolerance genes, which could be further amplified via horizontal gene transfer. Together, these findings convincingly demonstrate that climate warming substantially accelerates soil antibiotic resistance at genomic, ecological and evolutionary levels, with broad implications for public health and environmental sustainability in a warming world.},
}

@article {pmid42012907,
year = {2026},
author = {Roulet, ME and Garcia, LE and Yu, R and Wang, C and Zhou, R and Sanchez-Puerta, MV},
title = {Circle-mediated HGT shapes the multichromosomal mitochondrial genome of the endoparasitic plant Mitrastemon yamamotoi.},
journal = {The Plant journal : for cell and molecular biology},
volume = {126},
number = {2},
pages = {e70889},
doi = {10.1111/tpj.70889},
pmid = {42012907},
issn = {1365-313X},
support = {PICT2020x2010;01018//Fondo para la Investigación Científica y Tecnológica/ ; 31811530297//National Natural Science Foundation of China/ ; },
mesh = {*Genome, Mitochondrial/genetics ; *Gene Transfer, Horizontal/genetics ; Phylogeny ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genome, Plant/genetics ; DNA, Circular/genetics ; },
abstract = {Horizontal gene transfer (HGT), a well-established driver of genome evolution in prokaryotes, was historically considered rare in plants. However, accumulating genomic evidence supports its occurrence in angiosperms, impacting both nuclear and mitochondrial genomes, particularly in parasitic species that establish vascular connections with their hosts. Despite the increasing recognition of HGT in a few clades of parasitic plants (e.g., Cuscuta, Balanophoraceae, Rafflesiaceae, and Orobanchaceae), the underlying mechanisms and evolutionary consequences of these transfers are still not fully understood, and a few parasitic lineages have not been thoroughly examined yet (i.e., Apodanthaceae, Cytinaceae, Lennoaceae, Mitrastemonaceae). In this study, we assembled the first mtDNA of Mitrastemonaceae. Mitrastemon yamamotoi, a holoparasitic endoparasite in the order Ericales, invades the roots of host trees in the Fagaceae family, creating favorable conditions for HGT. The M. yamamotoi mtDNA exhibits a multipartite structure consisting of 54 circular-mapping chromosomes. Phylogenetic and comparative genomic analyses uncovered extensive HGT from Fagaceae hosts, affecting both coding and non-coding regions. Notably, almost 60% of the M. yamamotoi mtDNA is of foreign origin, and seven chromosomes are entirely foreign, with structural signatures in the donor mtDNA consistent with the recently proposed circle-mediated HGT model. Additionally, we detected six protein-coding genes of foreign origin and one chimeric gene. Remarkably, a foreign atp1 gene has replaced the missing native copy and represents a rare event of functional HGT in plant mitochondria. These results position M. yamamotoi as a valuable model for studying mtDNA evolution and deepening our understanding of the HGT process. Our findings expand the range of lineages in which circle-mediated HGT has been documented, suggesting it is a more widespread and fundamental mode of mitochondrial HGT in plants.},
}

*Genome, Mitochondrial/genetics
*Gene Transfer, Horizontal/genetics
Phylogeny
DNA, Mitochondrial/genetics
Evolution, Molecular
Genome, Plant/genetics
DNA, Circular/genetics

@article {pmid42013709,
year = {2026},
author = {Pelko, T and Jemec Kokalj, A and Regvar, M and Dermastia, M and Vogel-Mikuš, K},
title = {When "biodegradable" is not benign: Microplastic-driven disruption of soil processes and plant-microbe interactions.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142138},
doi = {10.1016/j.jhazmat.2026.142138},
pmid = {42013709},
issn = {1873-3336},
abstract = {The increasing use of biodegradable plastics (BPs) as alternatives to conventional plastics (CPs) is leading to the accumulation of biodegradable microplastics (BMPs) in terrestrial environments. Contrary to assumptions of rapid degradation, BMPs can persist in soil long enough to interact with key biological processes. This review advances the field by proposing a mechanistic framework linking BMP aging and degradation, soil physicochemical transformations, plastisphere assembly, rhizosphere interactions, and plant responses, and by critically evaluating the sources of inconsistency across studies. We show that divergent effects of BMPs can be best explained by four interacting determinants: polymer chemistry and additive composition, aging-driven surface transformations, soil physicochemical properties, and rhizosphere processes including plant-mediated effects. Through these coupled pathways, BMPs can alter aggregation, pore architecture, pH, enzyme activity, and carbon and nutrient cycling, thereby reshaping the soil environment in which microorganisms and roots interact. BMP surfaces can also act as dynamic microbial niches that promote biofilm formation, shift microbial community composition and function, and under certain conditions may facilitate pollutant transport, pathogen persistence, and horizontal gene transfer. Plant responses to BMPs are predominantly indirect and emerge from rhizosphere-mediated processes, which helps explain the wide variability in reported plant responses, ranging from subtle metabolic changes to pronounced growth inhibition. However, current evidence is constrained by short-term studies and insufficient consideration of aged materials. Biodegradability should therefore not be equated with low ecological risk in soils. Progress in this field requires integrative approaches linking BMP properties, plastisphere dynamics, and plant-soil interactions over time.},
}

@article {pmid42002097,
year = {2026},
author = {Ota, Y and Nagahara, Y and Watanabe, R and Isoda, T and Okamoto, K and Saito, R},
title = {Emergence of Klebsiella variicola Harboring blaKPC-2 and blaCTX-M-15 on an IncP-6/IncR Hybrid Plasmid from a Bloodstream Infection Case in Japan.},
journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy},
volume = {},
number = {},
pages = {102970},
doi = {10.1016/j.jiac.2026.102970},
pmid = {42002097},
issn = {1437-7780},
abstract = {OBJECTIVES: Carbapenem-resistant Gram-negative bacteria represent a major global health threat, with Klebsiella pneumoniae carbapenemase (KPC) producers, such as Klebsiella variicola, being particularly concerning due to their association with poor clinical outcomes. Therefore, we aimed to characterize the genome and phenotype of clinical KPC-producing K. variicola isolates in Japan, where such strains are rare.

METHODS: We investigated three K. variicola isolates obtained from blood, urine, and stool samples from a patient with bloodstream infection. The isolates were assessed using antimicrobial susceptibility testing, DNA fingerprinting, whole-genome sequencing analysis, and conjugation assay.

RESULTS: The three K. variicola isolates exhibited resistance or intermediate susceptibility to all β-lactam antibiotics, and DNA fingerprinting revealed identical banding profiles. The isolate from the blood sample harbored blaKPC-2 and blaCTX-M-15 on a hybrid IncP-6/IncR plasmid. Phylogenetic analysis revealed a close relationship between the clinical isolate and a K. variicola strain previously recovered from a sewage tank at the same hospital, despite differences in their antimicrobial resistance gene profiles. The IncP-6/IncR plasmid harbored multiple transposable elements. Additionally, the absence of conjugative transfer suggests that transposon-mediated horizontal gene transfer is the primary mechanism for resistance gene acquisition in the plasmid.

CONCLUSION: This study highlights the emergence of carbapenemase-producing K. variicola in the clinical setting and its potential role as a reservoir for antimicrobial resistance genes. The identification of a novel blaKPC-2/blaCTX-M-15-carrying IncP-6/IncR hybrid plasmid underscores the need for continued surveillance in clinical and environmental contexts to better understand the evolving epidemiology and transmission dynamics of multidrug-resistant bacteria.},
}

@article {pmid42004741,
year = {2026},
author = {Abi, O and Adoud, I and Dihmane, A and Boudarf, H and Lahlou, FA and El Jemli, M and Iskandar, S and Diawara, I and Belrhiti, Z and Balouch, L and Halabi, MK},
title = {A One Health view of antimicrobial resistance in North Africa: Meta-analysis of ESBL-producing Enterobacteriaceae across sectors.},
journal = {One health (Amsterdam, Netherlands)},
volume = {22},
number = {},
pages = {101402},
pmid = {42004741},
issn = {2352-7714},
abstract = {BACKGROUND: Antimicrobial resistance is a growing global health threat, and extended-spectrum β-lactamase-producing Enterobacterales exemplify a critical challenge. Because these organisms circulate across human, animal, food, and environmental reservoirs, a One Health perspective is essential for understanding their epidemiology. However, comprehensive regional syntheses remain limited in North Africa.

METHODS: This systematic review and meta-analysis synthesized evidence from 182 studies published between 2000 and 2024 on ESBL-producing Enterobacterales across North Africa within a One Health framework. We analyzed epidemiological data from human, animal, food, and environmental sources, as well as reported resistance genes, mobile genetic elements, transferability patterns, and clonal diversity associated with ESBL dissemination in the region.

RESULTS: In the human sector, the pooled prevalence estimate (PPE) of ESBL-producing Enterobacterales in clinical infections was 32.9%, with a higher burden in healthcare-acquired infections (37.1%) than in community-acquired infections (20.1%). ESBL carriage was also frequent at admission (34.1%) and increased after hospitalization (51.1%). Among non-human sectors, the PPE was 10.9% in animals, 3.73% in food, and 40.7% in environmental sources. blaCTX-M was the predominant β-lactamase gene family, with blaCTX-M-15 as the leading subtype. Non-β-lactam resistance genes were also frequently reported, indicating broader multidrug resistant backgrounds. Genetic drivers of dissemination included insertion sequences, integrons, and diverse plasmid backgrounds, particularly IncF plasmids. Transferability experiments showed frequent horizontal transfer of ESBL associated resistance, often with co-transfer of non-β-lactam resistance determinants. MLST data identified multiple high-risk clones, including Escherichia coli ST131, ST10, ST405, and ST617, and Klebsiella pneumoniae ST101, ST147, and ST15.

CONCLUSION: ESBL-producing Enterobacterales are widely disseminated across interconnected human, animal, food, and environmental compartments in North Africa. Their regional epidemiology is shaped by a high human burden, substantial environmental reservoirs, frequent multidrug resistant backgrounds, mobile genetic elements, horizontal gene transfer, and the circulation of multiple clonal lineages. These findings highlight the need for strengthened and integrated One Health surveillance in North Africa.},
}

@article {pmid42004950,
year = {2026},
author = {Suarez, LJ and Vargas-Sanchez, PK and Angelov, N and Mylonakis, E and Arce, RM},
title = {Host-pathogen interactions in periodontitis: an integrative interkingdom perspective.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1797726},
pmid = {42004950},
issn = {1664-3224},
abstract = {Periodontitis is an infectious, inflammatory, non-communicable disease characterized by tissue destruction driven by host responses to dysbiotic shifts in oral microbial communities. The subgingival microbiome constitutes a complex ecosystem in which bacteria, fungi, viruses, and archaea interact via interkingdom communication to modulate the inflammatory response through molecular mechanisms that remain largely unknown. This narrative review aims to understand how functional imbalances within the microbiome alter the microenvironment and promote uncontrolled inflammation responsible for periodontal tissue damage, with implications for systemic disease. The search strategy was conducted according to the PRISM-S extension, to include studies evaluating interkingdom host-pathogen interactions at the gingiva interphase leading to microbial and immune dysbiosis. The discovery of fungi acting as opportunistic pathogens highlights their role in enhancing biofilm virulence and exacerbating host responses, contributing to the total inflammatory burden. Similarly, viruses and archaea influence bacterial metabolism through mechanisms including lysis, nutrient recycling, horizontal gene transfer, and interspecies hydrogen transfer. This interkingdom crosstalk disrupts symbiosis, facilitating enhanced biofilm formation, increased production of virulence factors, and antibiotic resistance. A better understanding of the interkingdom perspective necessitates a comprehensive polymicrobial approach to diagnosis and treatment that extends beyond simply controlling bacteria to include the modulation of interkingdom communication systems. Developing new therapeutic alternatives that address these complex interactions is essential for improving outcomes achieved with mechanical therapy and managing the interrelationships between periodontitis and other systemic diseases.},
}

@article {pmid42006025,
year = {2016},
author = {, and Naegeli, H and Birch, AN and Casacuberta, J and De Schrijver, A and Gralak, MA and Guerche, P and Jones, H and Manachini, B and Messéan, A and Nielsen, EE and Nogué, F and Robaglia, C and Rostoks, N and Sweet, J and Tebbe, C and Visioli, F and Wal, JM and Divéki, Z and Fernández-Dumont, A and Gennaro, A and Lanzoni, A and Maria Neri, F and Paraskevopoulos, K},
title = {Scientific Opinion on an application by Dow AgroSciences (EFSA-GMO-NL-2013-116) for placing on the market of genetically modified insect-resistant soybean DAS-81419-2 for food and feed uses, import and processing under Regulation (EC) No 1829/2003.},
journal = {EFSA journal. European Food Safety Authority},
volume = {14},
number = {12},
pages = {e04642},
pmid = {42006025},
issn = {1831-4732},
abstract = {Soybean DAS-81419-2 was developed by Agrobacterium tumefaciens-mediated transformation. It expresses the Cry1F and Cry1Ac proteins to confer resistance to certain lepidopteran species and the PAT protein that confers tolerance to glufosinate ammonium-based herbicides and that was used as a selectable marker gene. The molecular characterisation of soybean DAS-81419-2 did not give rise to safety issues. The agronomic, phenotypic and compositional characteristics of soybean DAS-81419-2 tested under field conditions revealed no relevant differences between soybean DAS-81419-2 and its conventional counterpart that would give rise to any food and feed or environmental safety concerns. There were no concerns regarding the potential toxicity and allergenicity of the newly expressed proteins Cry1F, Cry1Ac and PAT, and no evidence that the genetic modification might significantly change the overall allergenicity of soybean DAS-81419-2. The nutritional value of soybean DAS-81419-2 is not expected to differ from that of non-GM soybean varieties and no post-market monitoring of food/feed is considered necessary. There are no indications of an increased likelihood of establishment and spread of occasional feral soybean DAS-81419-2 plants, unless these plants are exposed to glufosinate ammonium-based herbicides or infested by insect pests that are susceptible to the Cry1F and Cry1Ac proteins. This will not result in different environmental impacts compared to conventional soybean. Considering the scope of this application, interactions with the biotic and abiotic environment were not considered to be an issue. Risks associated with an unlikely but theoretically possible horizontal gene transfer from soybean DAS-81419-2 to bacteria have not been identified. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of soybean DAS-81419-2. The GMO Panel concludes that the soybean DAS-81419-2 is as safe and as nutritious as its conventional counterpart and the tested non-GM reference varieties in the context of its scope.},
}

@article {pmid42006031,
year = {2016},
author = {, and Naegeli, H and Birch, AN and Casacuberta, J and De Schrijver, A and Gralak, MA and Guerche, P and Jones, H and Manachini, B and Messéan, A and Nielsen, EE and Nogué, F and Robaglia, C and Rostoks, N and Sweet, J and Tebbe, C and Visioli, F and Wal, JM and Álvarez, F and Ardizzone, M and Fernández Dumont, A and Liu, Y and Neri, FM and Ramon, M},
title = {Scientific Opinion on an application by DOW AgroSciences LLC (EFSA-GMO-NL-2010-89) for placing on the market the genetically modified herbicide-tolerant maize DAS-40278-9 for food and feed uses, import and processing under Regulation (EC) No 1829/2003.},
journal = {EFSA journal. European Food Safety Authority},
volume = {14},
number = {12},
pages = {e04633},
pmid = {42006031},
issn = {1831-4732},
abstract = {Maize DAS-40278-9 was developed by direct Whiskers-mediated transformation to express the aryloxyalkanoate dioxygenase-1 (AAD-1) protein, conferring tolerance to 2,4-dichlorophenoxyacetic acid (2,4-D) and aryloxyphenoxypropionate (AOPP) herbicides. The molecular characterisation of maize DAS-40278-9 did not raise safety issues. The agronomic, phenotypic and compositional characteristics of maize DAS-40278-9 tested under field conditions revealed no differences between maize DAS-40278-9 and its non-genetically modified (GM) comparator that would give rise to food and feed or environmental safety concerns. There were no concerns regarding the potential toxicity and allergenicity of the newly expressed protein AAD-1, and no evidence that the genetic modification might significantly change the overall allergenicity of maize DAS-40278-9. The nutritional characteristics of maize DAS-40278-9 are not expected to differ from those of non-GM maize varieties and no post-market monitoring of food/feed is considered necessary. Maize DAS-40278-9 is as nutritious as its non-GM comparator and other non-GM commercial varieties. There are no indications of an increased likelihood of establishment and spread of occasional feral maize DAS-40278-9 plants, unless these plants are exposed to the intended herbicides. However, this will not result in different environmental impacts compared to conventional maize. Considering the scope of the application, interactions with the biotic and abiotic environment were not considered an issue. Risks associated with the unlikely but theoretically possible horizontal gene transfer from maize DAS-40278-9 to bacteria were not identified. The post-market environmental monitoring plan and reporting intervals are in line with the scope of the application. In conclusion, the EFSA GMO Panel considers that the information available for maize DAS-40278-9 addresses the scientific comments raised by the Member States and that maize DAS-40278-9, as described in this application, is as safe as the non-GM comparator and non-GM maize reference varieties with respect to potential effects on human and animal health and the environment in the context of the scope of this application.},
}

@article {pmid42007719,
year = {2026},
author = {Porter, NT and Kmezik, C and Lee, Y-H and Siewers, V and Pope, PB and Koropatkin, N and Martens, E and Larsbrink, J},
title = {A system for transferring large genetic loci in Bacteroides enables hemicellulose utilization in Bacteroides thetaiotaomicron and characterization of a locus from an uncultivated strain.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0017626},
doi = {10.1128/aem.00176-26},
pmid = {42007719},
issn = {1098-5336},
abstract = {Bacteria from the Bacteroidota phylum are well-known for their exceptional carbohydrate degradation abilities, which are closely associated with their use of polysaccharide utilization loci (PULs). The native exchange of PULs between different Bacteroidota species via horizontal gene transfer has been confirmed experimentally, and imitating such transfers in vitro can enable detailed studies of PULs from unstudied species in readily tractable hosts and the creation of novel strains. Here, we present a new set of tools and workflow to transfer large genetic loci, such as PULs, into genetically tractable Bacteroides strains. Our method uses a newly designed pICKUP plasmid and derivatives that allow site-specific genome integration and subsequent removal of the plasmid backbone. Thus, an unlimited number of loci may be transferred using the same resistance markers. We validated the pICKUP-based workflow by transfer of a previously characterized mixed-linkage β-glucan utilization locus (MLGUL) into the genome of Bacteroides thetaiotaomicron, which enabled metabolism of mixed-linkage β-glucan by this strain. Subsequent transfer of a PUL from an uncultivated bacterium from the bovine rumen confers the ability to metabolize certain cellooligosaccharides and allows further scrutiny of various genes in the PUL and their involvement in cellooligosaccharide metabolism. The pICKUP-based method presented here expands the toolkit for investigation of PULs and other large loci, including those from intractable or uncharacterized members of the Bacteroidota. A robust method to transfer whole PULs between species also forms the basis for creating custom-tailored PULs and resulting strains, with potential applications in improved gut health and biomass valorization processes.IMPORTANCEThe gut environment is a highly competitive niche, where dietary fiber is a major source of carbon, and polysaccharide utilization loci (PULs) encoded by Bacteroidota species are linked to their dominance in this environment. Our proposed method to study such PULs, especially from non-cultivated or unculturable strains, by transferring them into genetically tractable hosts, represents a valuable alternative to typical studies of isolated PUL-derived proteins. By transferring PULs into culturable hosts, we enable both a better understanding of the PULs' biological roles and modification of the individual encoded genes. Our results show how a single PUL transfer can confer hemicellulose-degrading ability to Bacteroides thetaiotaomicron, which is lacking in the wild-type strain. Transfer of a PUL from a distantly related strain, speculated to confer cellulose-degrading capacity, showcases that this annotation may be incorrect and indicates that the utilization of foreign genetic material depends on species relatedness in the same phylum.},
}

@article {pmid41999584,
year = {2026},
author = {Sheinman, M and Stentella, T and Etheimer, P and Massip, F and Arndt, PF},
title = {Reconstructing the network of horizontal gene exchange in bacteria to differentiate direct and indirect transfers.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evag099},
pmid = {41999584},
issn = {1759-6653},
abstract = {Horizontal gene transfer (HGT) plays a central role in bacterial evolution. Yet, its large-scale dynamics and underlying network structure remain poorly characterized. We present a theoretical framework that models HGT as a continuous stochastic process over a network of bacterial genera and analyze its genomic footprint via the distribution of exact sequence matches shared across taxa-the match length distribution (MLD). We show that different evolutionary regimes imprint distinct statistical signatures on the MLD: single episodic gene transfer events yield exponential distributions, while continuous sustained HGT processes lead to power-law tails. The power-law exponent is analytically linked to the topology of the transfer network, distinguishing between intra-clade transfers and hub-mediated dissemination. Empirical MLDs derived from bacterial genomes recapitulate these predicted patterns. Moreover, we find that defining a genus-specific ``transferability'' parameter that governs pairwise HGT rates, and incorporating a high-transferability hub, accurately reproduces the observed data. Our approach provides a general framework for inferring hidden structure in genomic horizontal transfer processes, enabling quantitative analysis of microbial evolution.},
}

@article {pmid42000334,
year = {2026},
author = {Sarsaiya, S and Jain, A and Chen, J and Gong, Q},
title = {Unlocking non-model organisms with CRISPR-Cas: A roadmap for sustainable biotechnology.},
journal = {Biotechnology advances},
volume = {90},
number = {},
pages = {108890},
doi = {10.1016/j.biotechadv.2026.108890},
pmid = {42000334},
issn = {1873-1899},
abstract = {The reliance on model organisms in biotechnology has advanced our understanding of fundamental biology but has failed to capture the complexity of real-world ecosystems, limiting applications in agriculture, biomanufacturing, and environmental remediation. This review critically evaluates the challenges and opportunities of applying CRISPR-Cas genome editing to non-model organisms, structured around a framework that systematically addresses host-specific barriers, enabling technical solutions, and real-world applications. Key obstacles are first delineated, such as restrictive genetic tools, inefficient DNA repair pathways (including NHEJ-dominance, HDR-deficiency, and polyploidy), and delivery limitations. Subsequently, innovative solutions are explored, including the engineering of Cas variants with expanded PAM flexibility and reduced toxicity, the development of host-adapted delivery systems such as phage-based vectors and conjugative plasmids, and the integration of synthetic biology tools and machine learning for optimization. Alternative, DSB-free modalities-comprising base editing, prime editing, CRISPR-associated transposases (CAST), and recombinase-assisted engineering-are further expanded upon, offering enhanced precision and expanded capabilities for complex genetic modifications. Major findings indicate that these approaches can unlock the potential of non-conventional hosts to address global challenges, such as low-energy biomanufacturing, environmental bioremediation, and carbon capture. It is concluded that bridging the gap between foundational CRISPR research and its real-world applications is imperative. Future efforts should focus on democratizing tools via open-source platforms, advancing delivery systems, establishing ethical governance-with detailed considerations for environmental release, horizontal gene transfer, regional regulatory frameworks, and biosafety in extremophile engineering-and fostering sustainable innovation through synthetic biology integration to fully realize the transformative potential of genome editing in organisms beyond model organisms.},
}

@article {pmid42000515,
year = {2026},
author = {Qiu, Y and Yang, Y and Li, N and Li, X and Lu, Z and Zhou, Z and Feng, S and Liu, Y},
title = {Secondary chlorination enhanced the role of pipe materials in shaping chlorine-resistant microbiome and antibiotic resistome in secondary water supply systems.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142114},
doi = {10.1016/j.jhazmat.2026.142114},
pmid = {42000515},
issn = {1873-3336},
abstract = {Secondary chlorination is often strategically applied in secondary water supply systems (SWSSs) with insufficient disinfectant residuals to suppress microbial regrowth. However, the associated risks posed by chlorine-resistant bacteria (CRB) and antibiotic resistance genes (ARGs) remain unclear. Herein, simulated SWSSs with different pipe materials and chlorine levels were operated for 220 days. Biomass in biofilms and bulk water was markedly reduced following chlorination, and extracellular polymeric substances responded more strongly in stainless steel (SS) pipes, with polysaccharides (70.28%) exhibiting a greater reduction than proteins (37.44%). Meanwhile, chlorination reduced bacterial diversity and reshaped community structure, boosting the contributions of biofilm and particulate phases to waterborne bacteria by 11.47%-15.60% and 17.52%-22.82%, respectively. Chlorination promoted the CRB enrichment (e.g., Nevskia and Sphingomonas), with higher relative abundance in polyvinyl chloride (PVC) pipes and more taxa in SS pipes. The decline in Legionella mitigated potentially pathogenic risks, particularly in chlorinated PVC pipes, despite nine of 13 potential pathogens being chlorine-resistant. Moreover, chlorination generally reduced the ARG absolute abundance but increased their relative abundance, with sulfonamide- and multidrug-ARGs being predominant. Regarding the ARG bacterial hosts, potential pathogens (e.g., Pseudomonas and Enterobacter) posed the highest risk, followed by non-pathogenic CRB (e.g., Herbaspirillum and Sediminibacterium) and chlorine-sensitive bacteria (e.g., Runella and Isosphaera). Vertical gene transfer dominated ARG transmission, while horizontal gene transfer occurred more readily in the water phase and was promoted in chlorinated PVC pipes. These findings provide novel insights into the microbial risk and antibiotic resistome, and may guide pipe material selection and disinfection optimization within SWSSs.},
}

@article {pmid42000565,
year = {2026},
author = {Wan, X and Zhan, J and Chen, Z and Wu, B},
title = {Ventilation-driven microbial and antimicrobial resistance divergence in intensive poultry houses and the associated public health risks.},
journal = {Research in veterinary science},
volume = {206},
number = {},
pages = {106196},
doi = {10.1016/j.rvsc.2026.106196},
pmid = {42000565},
issn = {1532-2661},
abstract = {Ventilation strategies in intensive poultry production systems play a critical role in shaping airborne microbial communities and the dissemination of antibiotic resistance, with potential implications for environmental and public health. In this study, bioaerosols from closed (mechanically ventilated) and open (naturally ventilated) chicken houses were systematically characterized using high-throughput metagenomic sequencing to compare microbial community composition and antibiotic resistance gene (ARG) profiles under contrasting ventilation regimes. Open chicken houses exhibited significantly higher microbial diversity (P < 0.05), reflecting increased environmental microbial inputs, while the relative abundance of the potentially antibiotic-resistant pathogen Staphylococcus aureus was also elevated. In contrast, closed chicken houses facilitated the accumulation of a core microbial community, including potential pathogens such as Helicobacter pullorum and Clostridium perfringens. Closed chicken houses showed a greater enrichment of macrolide resistance genes. In addition, the overall abundance of ARGs, expressed as ARG copies per 16S rRNA gene, was significantly higher in closed houses than in open houses (P < 0.05). Although total ARG abundance was lower in open chicken houses, the proportion of contigs harboring both ARGs and mobile genetic elements (MGEs) was significantly higher (P < 0.05), indicating increased potential for horizontal gene transfer. These findings reveal differences in microbial diversity and associated health risks between different poultry production systems and underscore the importance of optimizing ventilation strategies to control pathogen transmission and the spread of antibiotic resistance.},
}

@article {pmid42001010,
year = {2026},
author = {Monecke, S and Braun, SD and Diezel, C and Müller, E and Reinicke, M and Coleman, DC and El-Adawy, H and Keane, OM and Moawad, AA and Piccinini, R and Ehricht, R},
title = {Staphylococcus aureus sequence type 71 is a chimera that emerged twice.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12777-w},
pmid = {42001010},
issn = {1471-2164},
}

@article {pmid41993328,
year = {2026},
author = {Villa, JF and Kondekar, S and Fauconnet, Y and Machouri, M and Lacrouts, C and Veaute, X and Guérois, R and Rocha, EPC and Andreani, J and Radicella, JP},
title = {Unveiling a missing component of the atypical type IV secretion system required for natural transformation of Helicobacter pylori.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.01.715814},
pmid = {41993328},
issn = {2692-8205},
abstract = {UNLABELLED: Exchange of genetic information by natural transformation shapes bacterial evolution. In Helicobacter pylori it is thought to drive its unusually high recombination rate, which has a crucial role in the evolution of virulence and the propagation of antibiotics resistance genes. While in most cases uptake of the incoming DNA into the periplasm is mediated by type IV pili, in H. pylori this initial step of natural transformation requires ComB, a unique competence-specific type IV secretion system (T4SS). The mechanisms by which ComB mediates DNA uptake are still poorly understood, since T4SS are usually involved in an opposite process of DNA export. Here, we identify a gene (hp1421) that is absolutely required for uptake of the transforming DNA into the periplasm, although distant from the comB operons. We show that hp1421 codes for a hexameric ATPase from the VirB11 family. HP1421 is present in the cytoplasm and interacts with ComB4, another ATPase of the T4SS inner membrane subcomplex. The structural modelling and functional analysis of HP1421 and its interaction with ComB4 indicate that HP1421 is a missing component of the ComB inner-membrane subcomplex that we propose to name ComB11. Phylogenetic analyses show that comB11 is a H. pylori core gene and suggest that the competence-dedicated ComB T4SS was a recent acquisition within Helicobacteraceae. Hence, co-option of the T4SS for DNA transformation requires nearly all the proteins that were previously essential for DNA conjugation.

AUTHOR SUMMARY: The capacity of bacteria to exchange genetic information contributes in the case of pathogens to the spreading of antibiotic resistance and virulence factors. For Helicobacter pylori, a Gram-negative pathogen that colonises about half of the world population and is at the origin of diseases such as ulcers and gastric cancers, natural transformation is the major mechanism of horizontal gene transfer. However, H. pylori uses a very unusual system to capture and internalise the foreign DNA. Indeed, a Type 4 secretion system mediates this process. Here, we identify a so far missing and essential component of the T4SS, coded by a gene distant from the operon coding the other subunits. Through a combination of structural modelling, biochemical and microscopy approaches we show that this ATPase is an indispensable part of the ComB T4SS. Our study provides new insights into the mechanism by which the peculiar ComB T4SS works backwards to allow the passage of the tDNA from the bacterial environment into the periplasm.},
}

@article {pmid41993802,
year = {2026},
author = {Baker, BA and Leroy, RB and López-García, P and Eme, L and Moreira, D},
title = {Methanonatronarchaeia are deep-branching ancestrally methanogenic archaea distant from Halobacteria.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag071},
pmid = {41993802},
issn = {2730-6151},
abstract = {Since their discovery, the phylogenetic placement of the extremely halophilic, methanogenic Methanonatronarchaeia has remained controversial. Different studies have variably placed this lineage as sister to the archaeal class Halobacteria (haloarchaea) or as a deep-branching euryarchaeal group. These conflicting results may reflect methodological artefacts linked to the strong amino acid compositional bias characteristic of halophilic archaea and evolutionary model misspecification. Here, we reanalyse published phylogenomic datasets using site-heterogeneous mixture models that mitigate such biases. Our analyses consistently recover Methanonatronarchaeia as a deep-branching lineage basal to the Methanotecta, independent of the inclusion of the recently described Ordosarchaeia. We further show that Ordosarchaeia do not constitute a distinct lineage but fall within the previously described Halorutilales and Afararchaeaceae. Re-examination of the methyl-coenzyme M reductase phylogeny indicates that the placement of Methanonatronarchaeia mcr genes is best explained by vertical inheritance, without invoking horizontal gene transfer from unknown donors. Together, our results support ancestral methanogenesis within this lineage and its independent adaptation to extreme halophily.},
}

@article {pmid41995266,
year = {2026},
author = {Patel, V and Kucuk, RA and Haines-Eitzen, BR and Russell, JA and Oliver, KM},
title = {Emergent symbiont strains provide thermally robust protection against co-evolved and novel parasitoids of introduced pea aphids.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag098},
pmid = {41995266},
issn = {1751-7370},
abstract = {Climate change and biological invasions pose synergistic threats; however, organisms may rapidly adapt through microbial symbiosis. We investigated how defensive symbionts in invasive pea aphids, Acyrthosiphon pisum, respond to emerging threats. Previously rare strains of the protective symbiont Hamiltonella defensa increased from <0.5% to 58% in aphid populations over just a few years. Bioassays revealed that these strains confer reciprocal, enemy-specific defences. One strain (C11) protected against Praon pequodorum, a native parasitoid that only began attacking pea aphids post-introduction, but provided no defence against the co-evolved parasitoid Aphidius ervi. Conversely, a closely related strain (C9) protected strongly against A. ervi but not P. pequodorum. When the APSE bacteriophage was spontaneously lost from H. defensa C11 during cultivation, protection against P. pequodorum was completely eliminated, experimentally confirming the essential role of phage-encoded defences. Cultivation-assisted genomic analyses implicate divergent phage virulence cassettes in enemy-targeted defence, creating complementary protection portfolios within populations. The modular architecture of APSE phages enables rapid acquisition of novel capabilities through horizontal gene transfer. Critically, both strains maintained robust anti-parasitoid defence under simulated heatwave conditions, in contrast to previous findings in which modest temperature increases disabled protection in other H. defensa strains. Our findings demonstrate the potential for heritable symbionts to provide rapid adaptive responses to anthropogenic stressors within ecological timescales, representing a widespread mechanism for host persistence under accelerating global change and having important implications for biological control and ecosystem management.},
}

@article {pmid41995362,
year = {2026},
author = {Han, Y and Zhou, X-Q and Tang, X-X and Teng, M-J and Xiang, P and Nie, R-T and Pei, Y-F and Zhang, K and Zheng, D-Q and Yang, F},
title = {Comparative functional genomics of Saccharomyces cerevisiae reveals genetic determinants of stress tolerance and ethanol fermentation.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0363225},
doi = {10.1128/spectrum.03632-25},
pmid = {41995362},
issn = {2165-0497},
abstract = {Saccharomyces cerevisiae strains from diverse origins exhibit distinct phenotypic traits, providing valuable diversity and adaptability for industrial applications. Here, we conducted a comparative analysis of phenotypic and genomic features across 41 S. cerevisiae strains with clear industrial niche associations, aiming to identify genetic determinants underlying stress resistance and ethanol fermentation efficiency. These strains displayed niche-specific growth advantages under fermentation-related stress conditions, yet none showed broad tolerance. During ethanol fermentation using wheat and sorghum substrates, ethanol yields varied from 0.42 to 0.48 g ethanol/g glucose, with strains exhibiting superior maltose utilization achieving higher ethanol titers. Substantial variation was also observed in glycerol and acetic acid production, and a strong negative correlation was detected between their yields. Whole-genome sequencing revealed that chromosomal aberrations, DNA recombination-mediated chromosomal rearrangements, loss of heterozygosity, and gene gain or loss were major genetic factors contributing to phenotypic diversity. Furthermore, identification of novel genes acquired through horizontal gene transfer expanded the genetic repertoire of Saccharomyces strains. An additional SOD2 gene obtained from Torulaspora microellipsoides contributed to oxidative stress tolerance. Furthermore, our results demonstrate that whole-genome duplication in S. cerevisiae enhances maltose utilization and ethanol production in starchy substrate fermentation. Together, these findings offer novel mechanistic insights into the genomic evolution of yeast in industrial/ecological niches.IMPORTANCEThis study systematically analyzed phenotypic diversity and genomic variations across 41 diverse Saccharomyces cerevisiae strains. Key findings include strain-specific stress resistance linked to ecological niches, a strong glycerol-acetic acid negative correlation in starchy substrate fermentation, horizontal transfer-acquired SOD2 enhancing oxidative tolerance, and genome duplication boosting maltose utilization and ethanol yield. These results uncover niche-specific genetic mechanisms driving S. cerevisiae adaptive evolution and provide references for screening of strains with improved industrial traits.},
}

@article {pmid41997245,
year = {2026},
author = {Wang, X and Wang, X and Ai, S and Wu, F and Xi, J and Li, J and Liu, Z},
title = {Harnessing native microbes: Intermittent aeration for bioremediation of phenolic compounds contaminated freshwater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134641},
doi = {10.1016/j.biortech.2026.134641},
pmid = {41997245},
issn = {1873-2976},
abstract = {Phenolic pollutants pose persistent risks to freshwater ecosystems due to their toxicity, structural diversity, and resistance to biodegradation. This study investigated microbial community dynamics, gene-level adaptation, and biostimulation strategies for phenolic removal using native microbial community. Metagenome analyses revealed marked taxonomic shifts under phenolic stress, with engineered systems favoring modular cooperative degradation, whereas the natural community relied on dominance of stress-resistant taxa and inter-phylum horizontal gene transfer (HGT). Functional profiling identified 28 candidate KEGG Orthologs (KOs), including oxidative, ring-cleaving, and energy-support genes, enriched across core degraders such as Pseudomonas, Sphingobium, and Bordetella. Biostimulation assays demonstrated oxygen availability as the primary limiting factor: intermittent aeration (IA) enhanced phenolic degradation by 29%, while IA combined with activated carbon (IA + AC) achieved up to 75% improvement, especially for complex compounds like bisphenol A (BPA) and nitrophenol. Predictive modeling based on KO abundance and stimulation methods (R[2] = 0.75-0.88) successfully predicted degradation performance across 50 natural samples. While IA + AC provided the most consistent improvement, 15 communities achieved comparable efficiencies under IA alone, highlighting context-dependent biodegradation capacities linked to HGT and metabolic pathway diversity. These findings establish a scalable predictive framework and emphasize the importance of tailoring biostimulation strategies to native microbial capacities, offering a practical route for in situ bioremediation of phenol-contaminated freshwater systems.},
}

@article {pmid41794678,
year = {2026},
author = {Li, D and Fan, Z and Wang, S and Su, Y and Yuan, M and Fang, H and Wang, R and Gao, H and Bai, H and Mao, D and Luo, Y},
title = {Plasmid-mediated convergence of multidrug resistance and hypervirulence in community-acquired Klebsiella pneumoniae in Tianjin, China.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41794678},
issn = {1471-2180},
support = {42377426//National Natural Science Foundation of China/ ; 2020YFC1806904//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Klebsiella pneumoniae is a major bacterial pathogen responsible for community- and hospital-acquired infections. Although strains associated with hospital-acquired disease have been well described, the genomic and phenotypic characteristics of community-acquired K. pneumoniae among community-acquired isolates from this setting remain insufficiently understood. This study aimed to characterize the molecular features, antimicrobial resistance patterns, and virulence-associated traits of community-acquired strains isolated from a tertiary hospital in Tianjin.

RESULTS: A total of 27 community-acquired K. pneumoniae underwent whole-genome sequencing and comprehensive phenotypic assessment. Molecular typing revealed that the dominant lineages included ST11-KL64-O1/O2v1, ST268-KL20-O1/O2v1, and ST15-KL102-O1/O2v2. All isolates carried at least one virulence-associated gene as defined by established hvKp markers and produced high levels of siderophores (> 30 µg/mL). Most strains displayed multidrug-resistant phenotypes and simultaneously possessed virulence determinants, indicating the frequent detection of multidrug-resistant hypervirulent K. pneumoniae among the studied community-acquired isolates. Genomic analysis showed that the coexistence of resistance and virulence traits was largely associated with horizontal gene transfer mediated by mobile genetic elements such as plasmids, insertion sequences, and transposons. Replicons of the IncHI1B and IncFIB plasmid families were frequently linked to virulence-associated genes. Functional assays, including Galleria mellonella infection, biofilm formation, macrophage infection, and serum resistance testing, confirmed the pathogenic potential of these strains. Integrated genomic and phenotypic findings suggested that multiple virulence factors collectively enhance pathogenicity through immune evasion, increased biofilm production, and modulation of host responses.

CONCLUSIONS: Community-acquired K. pneumoniae strains analyzed in this study exhibit a concerning combination of multidrug resistance and enhanced virulence. The convergence of these traits, largely associated with mobile genetic elements, represents an emerging public health concern and underscores the need for strengthened surveillance and targeted control measures.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04867-2.},
}

@article {pmid41987615,
year = {2026},
author = {Eliwa, AI and Eldahshan, MM},
title = {CRISPR-Cas at a crossroads: from microbial immunity to precision biotechnology.},
journal = {Journal of immunoassay & immunochemistry},
volume = {},
number = {},
pages = {1-24},
doi = {10.1080/15321819.2026.2658465},
pmid = {41987615},
issn = {1532-4230},
abstract = {Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) form RNA-guided adaptive immune systems in bacteria and archaea that mediate sequence-specific defense against invading genetic elements. Beyond their ecological role in restricting bacteriophage infection and horizontal gene transfer (HGT), CRISPR-Cas systems have been repurposed as programmable nucleases, enabling rapid, scalable, and precise genome engineering. Over the past decade, CRISPR platforms, most prominently Cas9, have transformed functional genomics, accelerated target discovery and drug development, and progressed from experimental tools to clinically evaluated gene and cell therapies. In parallel, growing attention has focused on both native and engineered roles of CRISPR-Cas in shaping HGT, plasmid ecology, and antimicrobial resistance (AMR), as AMR continues to expand globally. In this Review, we integrate advances spanning eukaryotic genome editing and prokaryotic antimicrobial applications. We summarize CRISPR-Cas classification and molecular mechanisms, highlighting spacer acquisition, guide RNA biogenesis, target recognition, and nucleic acid cleavage. We then examine how cellular DNA repair pathways influence editing outcomes and discuss strategies to enhance precision. We further review delivery strategies, such as conjugative plasmids, bacteriophages and phagemids, extracellular vesicles, and nanoparticles, together with evolutionary countermeasures encoded by mobile genetic elements, including anti-CRISPR proteins. Finally, we outline current limitations.},
}

@article {pmid41988040,
year = {2026},
author = {Seguí, G and Piñeiro-Iglesias, B and Salvà-Serra, F and Karlsson, R and Moore, ERB},
title = {Resolving taxonomic uncertainties in the genus Haemophilus: a genomics-based approach for the reclassification of species within genera of the family Pasteurellaceae and proposal of four novel genera and one novel species.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1798515},
pmid = {41988040},
issn = {1664-302X},
abstract = {INTRODUCTION: The taxonomy of species within the genus Haemophilus, within the family Pasteurellaceae, shows extensive polyphyly, causing long-standing taxonomic ambiguities that complicate clinical, epidemiological and evolutionary research. Traditional classifications based on phenotypes and comparative 16S rRNA gene sequence analyses have resulted in discrepancies in defining genera and species, necessitating a thorough genome-based reevaluation. In this study, we have conducted an integrated phylogenomic analysis of the type strains of 90 species, covering all genera with validly published names within the family Pasteurellaceae, focusing on the historically-problematic Haemophilus genus.

METHODS: We used whole-genome sequencing, core proteome phylogeny and genome-wide similarity analyses to assess and define genus and species boundaries.

RESULTS: Results from phylogenomic analyses identified four well-supported species-clades within Haemophilus, revealing several misclassified species. Comparative POCP and AAI analyses, using genomic sequence data, showed that traditional genus-level thresholds (≥50% for POCP and 60-80% for AAI) of calculated protein content are insufficient to resolve species of genera with extensive horizontal gene transfer, whereas more stringent cutoffs aligned better with phylogenomic groupings. ANI and dDDH analyses effectively delineated species-level boundaries but offered limited detail for higher taxonomic ranks. Analyses of virulence factors found conserved sets of core genes known to be crucial for colonization, immune evasion and iron uptake, along with genus- and species-specific factors, indicating ecological adaptations. Functional annotation and metabolic pathway analysis highlighted universal processes and phylogenetic lineage-specific features.

DISCUSSION: Overall, our comprehensive genomic approach has elucidated a reliable phylogenetic-based taxonomy of Haemophilus, detected misclassified species, recognized new genera and supports a biologically meaningful taxonomy for Pasteurellaceae. These results establish the basis for accurate species identification, clinical diagnostics, evolutionary research and functional studies within this medically and veterinarily important family.},
}

@article {pmid41989184,
year = {2026},
author = {Peng, Z and Zhu, N and Yi, W and Jiang, L and Dong, T and Wu, R and Jia, S and Guo, X and Luo, Z and Guan, Q},
title = {Pan-genome insights into type VI secretion systems and their functional repertoires in Enterobacter.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0178125},
doi = {10.1128/msystems.01781-25},
pmid = {41989184},
issn = {2379-5077},
abstract = {The Enterobacter genus contains 23 species that include common nosocomial pathogens capable of causing a wide variety of infections. We obtained all available Enterobacter genomes and retained 4,805 high-quality genomes after quality control. Genome sequencing analysis of Enterobacter species revealed the presence of type VI secretion systems (T6SS) in these bacteria, but systematic analysis and comparison of these systems among different species are limited. We found that these bacteria code for three distinct types of T6SS, each with a unique set of diverse predicted effectors. Whereas at least 14 effectors are found in each strain, the number of immunity proteins is considerably fewer. By demonstrating a correlation between the abundance of known T6SS-associated proteins and the presence of T6SS, we proposed a comparative genomics model to evaluate the correlation between unknown T6SS-associated ortholog proteins and T6SSs. Among the homologous groups most strongly associated with T6SS, we potentially identified several effectors. It is conceivable that our methodology could be scaled to survey additional bacterial genera for novel T6SS effectors, thereby providing fresh perspectives and directions for subsequent biological experiments.IMPORTANCEEnterobacter species are important human pathogens that can cause severe conditions like pneumonia, urinary tract infections, and bacteremia. As Gram-negative bacteria, they frequently carry diverse T6SS loci, which are often associated with bacterial virulence and are also one of the important causes of bacterial infection. T6SS effectors play a critical role in interbacterial competition and virulence during infection. VgrG proteins are essential T6SS components that form the spike structure and mediate effector delivery, making them critical for bacterial competition and virulence. However, systematic studies on their distribution and function remain limited. Here, we analyzed all available high-quality Enterobacter genomes and revealed that T6SS diversity is shaped by both species' evolution and horizontal gene transfer (HGT). We proved that it is feasible to measure the biological relevance of unknown functional proteins to the T6SS through statistical analyses. This high-throughput approach provides a new perspective for future research on T6SS functionality, especially in Enterobacter.},
}

@article {pmid41990170,
year = {2026},
author = {Hirano, H and Tsuji, N and Chiba, S and Nureki, O},
title = {Structural basis for DNA processing and membrane translocation by ComEC in natural transformation.},
journal = {Science (New York, N.Y.)},
volume = {392},
number = {6795},
pages = {311-316},
doi = {10.1126/science.aea3485},
pmid = {41990170},
issn = {1095-9203},
mesh = {Cryoelectron Microscopy ; *DNA, Single-Stranded/metabolism/chemistry ; *Bacterial Proteins/chemistry/metabolism/ultrastructure ; *DNA, Bacterial/metabolism/chemistry ; *Transformation, Bacterial ; *Membrane Proteins/chemistry/metabolism/ultrastructure ; Cell Membrane/metabolism ; Protein Domains ; *Gene Transfer, Horizontal ; Escherichia coli/genetics ; },
abstract = {Natural transformation is one of the major pathways of horizontal gene transfer in bacteria, enabling the acquisition of extracellular DNA and its integration into the host genome. ComEC is a membrane protein responsible for DNA translocation in this process, yet its precise function and structure have remained elusive. Here, we report cryo-electron microscopy structures of ComEC in DNA-free, single-stranded DNA (ssDNA)-bound, and double-stranded DNA (dsDNA)-bound forms, together with biochemical analyses. These structures reveal that ComEC cleaves one strand of dsDNA at its extracellular domain and guides the remaining strand into a positively charged pore formed within the membrane domain. These findings provide a structural basis for the long-hypothesized roles of ComEC in both DNA processing and translocation across the inner membrane during natural transformation.},
}

Cryoelectron Microscopy
*DNA, Single-Stranded/metabolism/chemistry
*Bacterial Proteins/chemistry/metabolism/ultrastructure
*DNA, Bacterial/metabolism/chemistry
*Transformation, Bacterial
*Membrane Proteins/chemistry/metabolism/ultrastructure
Cell Membrane/metabolism
Protein Domains
*Gene Transfer, Horizontal
Escherichia coli/genetics

@article {pmid41990660,
year = {2026},
author = {Hassan, S and Yaseen, A and Wani, HK and Sabreena, and Zaman, M and Bali, BS and Ganai, BA and Ganiee, SA and Shah, AJ},
title = {Microplastics as genetic vectors for environmental DNA: A review on adsorption mechanisms, plastisphere genetics, and ecotoxicological implications.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {142078},
doi = {10.1016/j.jhazmat.2026.142078},
pmid = {41990660},
issn = {1873-3336},
abstract = {Environmental DNA (eDNA) has emerged as a highly sensitive, non-invasive biomonitoring tool for biological community profiling and ecotoxicological assessment in aquatic systems affected by microplastics. In natural environments, it predominantly exists as extracellular DNA (free or particle-associated genetic fragments), and its physicochemical behavior governs its fate. Despite rapid advances in both eDNA-based monitoring and microplastic research, the combined influence of these factors on the environmental fate, transport, and interpretation of molecular signals remains poorly understood. Failure to account for these interactions risks systematic bias in exposure assessment and community composition inference. Here, we critically review and analyze existing evidence on eDNA-microplastic interactions and highlight their implications for spatial and temporal bias in molecular ecological analysis. The physicochemical and biological mechanisms governing DNA adsorption and environmental fate are evaluated, demonstrating that eDNA-microplastic interactions are modulated by polymer chemistry, surface aging, ionic strength, microbial colonization, and hydrodynamic transport. Plastisphere biofilms further act as genetic hotspots that concentrate and redistribute extracellular DNA, antibiotic resistance genes, and mobile genetic elements under co-contaminant exposure. This review applies structured genetic-information scoring and hierarchical synthesis to link microplastic traits with molecular-level risk. The synthesis indicates that small (<200 μm) aromatic, hydrophobic microplastic fragments, films and fibers exhibit the highest genetic risk scores, accompanied by a shift from descriptive 16S profiling toward functional antibiotic resistance genes and eDNA-mediated horizontal gene transfer signals. Based on the synthesized evidence, we identify environmental variability, ambiguity in origin and persistence of eDNA on the microplastic surfaces, limited quantitative resolution, and insufficient standardization as key methodological constraints. Accordingly, targeted solutions are proposed to close technical gaps and outline priority directions for future research.},
}

@article {pmid41990750,
year = {2026},
author = {Gonzalez Pastor, B and Shkoporov, AN and Hill, C},
title = {Not just passengers: Phages as agents of genetic exchange in fecal microbiota transplantation.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.03.017},
pmid = {41990750},
issn = {1934-6069},
abstract = {Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridioides difficile infection and is increasingly being explored for other microbiota-associated diseases. However, general research has largely focused on bacterial engraftment, overlooking the contribution of the gut virome. In this perspective, we highlight phage-mediated horizontal gene transfer (HGT) as a potentially influential process occurring following FMT. Donor-derived phages may potentially influence community structure, engraft in resident bacteria, and modulate microbial functions or host physiology. In addition, temperate phages are well-equipped to mobilize bacterial genes, such as metabolic functions, stress-response traits, and antibiotic resistance determinants, raising the possibility that gene flow could well contribute to FMT outcomes. We propose a conceptual model in which phages act as bidirectional mediators of adaptation, not only accompanying bacterial communities but also influencing gut ecosystems in subtle, yet potentially consequential, ways.},
}

@article {pmid41991299,
year = {2026},
author = {Li, Y and Ye, ZH and Wang, JL and Peng, ZX and Wu, YN},
title = {[Cross-host transmission of bacterial antibiotic resistance: research progress on ecological pattern and mechanism].},
journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]},
volume = {60},
number = {4},
pages = {612-621},
doi = {10.3760/cma.j.cn112150-20250423-00347},
pmid = {41991299},
issn = {0253-9624},
support = {2024YFE0106300//National Key Research and Development Program of China/ ; 32172314//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Animals ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; *Drug Resistance, Microbial ; Livestock ; Bacteria/drug effects ; },
abstract = {Antimicrobial resistance (AMR) constitutes a global public health crisis, its transmission networks deeply entrenched at the animal-environment-human health interface. This review systematically elucidates the mechanisms underlying the emergence and characteristics of dissemination of AMR within China's livestock and poultry farming sector. It reveals the core pathways by which structural contradictions between antibiotic use and regulation drive the cross-boundary migration of resistance genes via manure, soil, water bodies, and the food chain. Molecular mechanism studies demonstrate that the synergistic interplay between the evolution of resistance phenotypes and horizontal gene transfer accelerates the formation of multi-drug resistance phenotypes under the co-selective pressure exerted by antibiotic residues and environmental stressors. This review pioneers the integration of a collaborative application framework for multi-dimensional genomic technologies in AMR research, elucidating how this framework provides technical support for resistance source-tracing and risk assessment by deciphering the transmission trajectories of antibiotic resistance genes (ARGs), the evolution of resistance lineages, and host adaptation. Concurrently, it identifies barriers to cross-system data integration as a critical bottleneck for precise prevention and control. Grounded in the "One Health" concept, this review advocates for the construction of a comprehensive "animal-environment-human" analytical framework to uncover key nodes in cross-boundary transmission. It further proposes coupling multi-omics, artificial intelligence, and big data technologies to establish a novel, integrated "monitoring-prediction-intervention" prevention paradigm. Through the deep integration of science and technology with governance strategies, this approach aims to optimize interventions across the entire chain from farm to fork, thereby providing a scientific decision-making basis for curbing the global spread of AMR.},
}

Humans
Animals
*Drug Resistance, Bacterial
Anti-Bacterial Agents/pharmacology
Gene Transfer, Horizontal
*Drug Resistance, Microbial
Livestock
Bacteria/drug effects

@article {pmid41991609,
year = {2026},
author = {Banks, EJ and Bárdy, P and Tran, NT and Nguyen, PM and Stojilković, B and Gozzi, K and Maqbool, A and Le, TBK},
title = {A bacterial CARD-NLR-like immune system controls the release of gene transfer agents.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41991609},
issn = {2058-5276},
support = {221776/Z/2/Z//Wellcome Trust (Wellcome)/ ; 224067/Z/21/Z//Wellcome Trust (Wellcome)/ ; NA//Lister Institute of Preventive Medicine/ ; BB/X01097X/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/X01097X/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/X01097X/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; NA//Royal Commission for the Exhibition of 1851/ ; },
abstract = {Bacteria use immune systems to detect and defend against mobile genetic elements including phages. Gene transfer agents (GTAs) are domesticated prophages with phage-like characteristics including the ability to induce host cell lysis for gene transfer. Whether GTAs elicit or avoid bacterial immune systems is poorly understood. Here, a transposon mutagenesis with deep sequencing screen in Caulobacter crescentus identified a tripartite system, LypABC, essential for GTA-mediated cell lysis and gene transfer. LypABC resembles a caspase recruitment domain-nucleotide-binding leucine-rich repeat (CARD-NLR) anti-phage defence system. LypABC is dispensable for DNA packaging into GTA particles but required for host cell lysis, involving the peptidase domains of LypA and LypC, and the ATPase domain of LypB. As LypABC overproduction is toxic, strict regulation through the transcriptional repressor CdxB is required. CdxB binds the promoters of lypABC and of essential GTA activator genes, coupling GTA activation to host cell lysis. Our findings suggest that bacterial immune systems can be co-opted to support horizontal gene transfer by GTAs.},
}

@article {pmid41792596,
year = {2026},
author = {Jafari, E and Pourakbari, B and Asadi Karam, MR and Azizian, R and Sotoudeh Anvari, M and Mamishi, S},
title = {Antimicrobial resistance patterns and carbapenemase gene distribution in pediatric Pseudomonas aeruginosa isolates: molecular and epidemiological insights from an Iranian referral center.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41792596},
issn = {1471-2180},
abstract = {BACKGROUND: Antimicrobial resistance in Pseudomonas aeruginosa represents a major challenge in pediatric healthcare, yet molecular epidemiological data from children in the Middle East are limited. This study aimed to characterize antimicrobial resistance patterns, carbapenemase gene profiles, and transmission dynamics in a tertiary pediatric hospital in Iran.

METHODS: We analyzed 110 P. aeruginosa isolates from pediatric patients (December 2023-August 2024) using disk diffusion susceptibility testing, PCR detection of carbapenemase genes (blaIMP, blaKPC, blaNDM, blaOXA, blaSIM, blaSPM, and blaVIM), and RAPD-PCR genotyping. Multivariate logistic regression analysis was used to identify predictors of resistance.

RESULTS: Carbapenem resistance (CR) affected 40.9% of isolates, with 37.3% multidrug-resistant (MDR) and 10.0% extensively drug-resistant. Among CR isolates, blaVIM (68.9%) and blaNDM (55.6%) predominated, with 49.1% harboring multiple carbapenemase genes. Age was a significant predictor of antimicrobial resistance (p < 0.05 for most antibiotics). Children < 5 years demonstrated significantly lower resistance compared to those > 10 years, with the strongest associations observed for fluoroquinolones (ciprofloxacin: AOR = 0.046 (CI: 0.010–0.212), p < 0.001; norfloxacin: AOR = 0.061 (CI: 0.013–0.283), p = 0.002) and some β-lactams (meropenem: AOR = 0.196 (CI: 0.062–0.623), p = 0.021). Gender showed no significant association with resistance across all antibiotics tested (p > 0.05). Gene coexistence was a significant predictor for β-lactams (imipenem: AOR = 1.968 (CI: 1.314–2.946), p = 0.001). RAPD-PCR revealed 23 genetic clusters, with ward-specific clustering patterns suggesting nosocomial transmission, particularly in intensive care units (ICUs).

CONCLUSION: This study demonstrates an alarming burden of carbapenemase-producing P. aeruginosa among Iranian pediatric patients, with age-dependent antibiotic resistance, frequent co-existence of carbapenemase genes suggesting horizontal gene transfer, and ward-specific genetic clustering consistent with nosocomial transmission. These observations underscore the necessity for age-focused therapeutic strategies, intensified ICU surveillance, and targeted antimicrobial stewardship.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04833-y.},
}

@article {pmid41982285,
year = {2026},
author = {Fu, Z and Yang, P and Wu, J and Zhang, G and Feng, Y},
title = {Exploring the evolutionary landscape of mitochondrial genomes in the sunflower family (Asteraceae).},
journal = {Plant diversity},
volume = {48},
number = {2},
pages = {278-288},
pmid = {41982285},
issn = {2468-2659},
abstract = {Asteraceae, the largest family of flowering plants, comprises more than 26,000 species worldwide, many of which serve as crops, medicinal herbs, and ornamentals. While substantial genomic resources are available for nuclear and chloroplast genomes, mitochondrial genomes (mitogenomes) in this family remain poorly explored, limiting an integrated understanding of its genomic evolution. Here, we assembled 38 complete mitogenomes representing 12 subfamilies and 22 tribes. Our analyses revealed substantial size variation, with notably larger mitogenomes in early-diverging lineages. We also observed extensive structural rearrangements across subfamilies and tribes. Although the gene content is largely conserved, we identified notable mutations, horizontal gene transfer events, and losses of RNA editing sites. We reconstructed a comprehensive mitochondrial phylogeny of Asteraceae, which revealed both congruent and conflicting relationships with phylogenies based on plastid and nuclear markers. Furthermore, our fragment analysis of total mitochondrial DNA demonstrated that the differential retention of ancestral sequences significantly influences mitogenome size variation in Asteraceae. This study provides a systematic mitogenomic resource, offering novel insights into the evolutionary dynamics of this major plant family.},
}

@article {pmid41982879,
year = {2026},
author = {Wang, R and Wang, X and Meng, Q and Liu, X and Yan, H and Zhang, Z and Fu, Y and Liang, A},
title = {Detection and functional analysis of horizontal gene transfer events in the ciliate Euplotes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1782463},
pmid = {41982879},
issn = {1664-302X},
abstract = {BACKGROUND: Horizontal gene transfer (HGT), the movement of heritable materials between distantly related organisms, is a key evolutionary force shaping eukaryotic genomes. Euplotes are free-living unicellular eukaryotes belonging to the phylum Ciliophora, and are tended to establish endosymbiotic relationships with different bacteria. However, the scale of HGT in Euplotes, and its possible roles in driving their diversification and adaptation remains unexplored.

METHODS: A large-scale phylogeny-based bacterial HGT detection was performed across five genome sequenced Euplotes. Gene structure and expression of the HGT-acquired genes were analyzed based on the transcriptome data. Putative functions of these genes were annotated based on BLAST search in the protein family (Pfam), the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Quantitative polymerase chain reaction (qPCR) and RNA interference (RNAi) were performed to validate the function of the prevalent HGT-acquired genes encoding mannan endo-1,4-β-mannosidase (Man) from E. amieti.

RESULTS: We systematically examined HGT in five Euplotes genomes and found that they acquired a total of 342 genes exhibiting diverse functions, including enzymes involved in carbohydrate metabolism, sulfur metabolism, and the cell signaling. HGT-acquired genes displayed similar genomic features with the native genes, including GC content, the proportion of intron-contained gene, and coding sequences (CDS) length, implying ancient acquisition events. Five putative endosymbiont-derived genes encoding glycoside hydrolases from E. vannus were identified. Furthermore, among the 342 HGT candidates, only seven HGT families were putatively transferred into the last common ancestor of all five Euplotes. Further qPCR analysis showed that the mRNA levels of mannan endo-1,4-β-mannosidase A (Ea-ManA) and mannan endo-1,4-β-mannosidase B (Ea-ManB) increased after feeding with Chlorogonium elongatum in E. amieti. Knockdown of Ea-Man genes by RNAi increased mortality which suggested that Ea-Man genes are essential for E. amieti.

CONCLUSION: Based on these findings, we suggest that the endosymbionts of Euplotes are potential donor organisms for HGT-acquired genes, and HGT is a prevalent mechanism that is actively used in Euplotes to expand their adaptive capabilities.},
}

@article {pmid41985106,
year = {2026},
author = {Sun, Q and Lin, Y and Ping, Q and Zhao, Y and Wang, X and Wang, L and Li, Y},
title = {Breaking the Pharmaceutical-ARG Nexus in Wastewater: Mechanistic Insights into Risk Mitigation by a Novel Riboflavin/Ultraviolet/Peracetic Acid Disinfection Process Unveiled by Multiomics.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c16102},
pmid = {41985106},
issn = {1520-5851},
abstract = {Wastewater treatment plants (WWTPs) serve as critical reservoirs and dissemination hotspots for pharmaceuticals and antibiotic resistance genes (ARGs), posing significant threats to environmental and public health. In this study, a novel riboflavin/ultraviolet/peracetic acid (RF/UV/PAA) disinfection process was developed to enhance the removal of these emerging contaminants. The process achieved superior performance in degrading 29 pharmaceuticals and eliminating 106 ARGs and 13 mobile genetic elements (MGEs), attributed to the action of both radical and non-radical species. The underlying risk mitigation potential was further elucidated through multiomics analyses. The results revealed that the RF/UV/PAA process suppresses ARG dissemination through a triple-mechanism pathway, directly inactivating host bacteria; blocking vertical gene transfer; enhancing pharmaceutical removal, which alleviates the selection pressure for resistance; and disrupting horizontal gene transfer (HGT) through MGE destruction and alterations in membrane permeability, extracellular polymeric substance secretion, adenosine triphosphate synthesis, and cellular motility. Notably, our results also suggest that non-antibiotic pharmaceuticals promote the MGE-mediated HGT of ARGs, challenging the conventional antibiotic-centric paradigm. This study not only establishes RF/UV/PAA disinfection as an effective technology for the synergistic removal of pharmaceuticals and ARGs in wastewater but also provides critical mechanistic insights to mitigate ARG dissemination via WWTP effluents.},
}

@article {pmid41985881,
year = {2026},
author = {Kansal, S and Kundu, J and Sharma, V and Mamik, SK and Soni, S and Angrup, A and Biswal, M and Walia, K and Ray, P and Taneja, N},
title = {Genomic insights into carbapenem- and colistin-resistant Klebsiella pneumoniae reveal co-occurrence of resistance and virulence determinants in India.},
journal = {Indian journal of medical microbiology},
volume = {},
number = {},
pages = {101114},
doi = {10.1016/j.ijmmb.2026.101114},
pmid = {41985881},
issn = {1998-3646},
abstract = {BACKGROUND: Carbapenem- and colistin-resistant Klebsiella pneumoniae poses a major challenge to critical care due to limited therapeutic options. Combined with hypervirulence, the infections caused by multi-drug-resistant isolates become exceptionally difficult to treat, often resulting in prolonged illness and higher mortality.

METHODS: We analysed 65 clinical isolates of carbapenem and colistin resistant K. pneumoniae using whole genome sequencing to characterize resistance, virulence, and associated mobile genetic elements that may facilitate horizontal gene transfer.

RESULTS: The isolates represented 17 sequence types, with ST147, ST231 and capsular loci KL64 and KL51 being the most prevalent. Pan-genome analysis revealed high genetic diversity with an open genome structure. Resistance genes were widely distributed where carbapenem resistance was primarily mediated by NDM-1 or OXA-232 in combination with mutations in OmpK35/36 porin. Colistin resistance was mostly associated with mutations in mgrB, pmrB, or crrB genes though 30% of phenotypically resistant isolates lacked known determinants, suggesting the presence of additional unknown mechanisms. Virulence factors included frequent detection of yersiniabactin with aerobactin (iucA) and hypermucoidy loci (rmpA) in subset of isolates.

CONCLUSION: The co-occurrence of resistance and virulence determinants in multiple genomes suggests that highly pathogenic and multidrug resistant K. pneumoniae strains are already circulating in India. The detection of multiple IncF and Col-type plasmids, known to facilitate the mobilization of antimicrobial and virulence genes, further highlights the potential for future convergence events. Collectively, this study provides a genomic snapshot and valuable baseline for India, emphasising the importance of continued surveillance to monitor and contain the emergence of high-risk convergent lineages.},
}

@article {pmid41977780,
year = {2026},
author = {Garcia, LE and Roulet, ME and Garay, LA and Sanchez-Puerta, MV},
title = {Genomic Footprints of Multiple Host Lineages in the Mitochondrial and Nuclear Genomes of the Holoparasite Prosopanche americana.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
pmid = {41977780},
issn = {2223-7747},
support = {PICT2019-03067//Fondo para la Investigación Científica y Tecnológica/ ; M048-T1//Universidad Nacional de Cuyo/ ; },
abstract = {Horizontal Gene Transfer (HGT) is a hallmark of the evolution of parasitic plants, facilitated by the haustorial connection. While mitochondrial HGT is widespread, the extent of nuclear HGT and the long-term retention of foreign genetic material in holoparasitic lineages remain poorly understood. This study explores the genomic architecture of Prosopanche americana (Hydnoraceae), a non-photosynthetic holoparasite currently specialized on Fabaceae. Through a comparative phylogenomic approach integrating draft mitochondrial genomes (mtDNA) and nuclear transcriptomes of P. americana, we identified a multi-layered landscape of foreign DNA. The mtDNA of P. americana contains 18 foreign regions (>500 bp) primarily derived from Solanales, Malvales, and Fabales. Notably, 13 of these regions are shared with P. panguanensis, indicating they were acquired in their common ancestor before speciation and ecological shift. In the nuclear genome, we identified 303 horizontally acquired transcripts (99 orthogroups) with high confidence. Functional analysis revealed an enrichment of foreign genes involved in metabolic pathways and plastid functions (e.g., photosystems and thylakoids) exclusively derived from the ancestral host order Solanales. Our results demonstrate that the genome of P. americana acts as a "molecular fossil," preserving evidence of past ecological interactions with diverse host lineages. The disparity in HGT footprints between the current host (Fabaceae) and ancestral hosts suggests a period of high genomic plasticity followed by host specialization, providing new insights into the timing and dynamics of horizontal gene flow in holoparasitic Piperales.},
}

@article {pmid41980940,
year = {2026},
author = {Lu, Z and Li, R and Zhou, K and Li, S and Sun, S and Liu, J and Zhao, L and Chen, S and Liu, K and Yuan, X and Shao, Z},
title = {Tick-vectored mobilization of antibiotic resistance genes: transboundary dissemination across wildlife-livestock-vector-environment interfaces.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00986-w},
pmid = {41980940},
issn = {2055-5008},
support = {2024SF-YBXM-289//Key Research and Development Projects of Shaanxi Province/ ; 82473689//National Natural Science Foundation of China/ ; 82273689//National Natural Science Foundation of China/ ; WW25Z01SF027//Wuwei City Science and Technology Plan Project/ ; },
abstract = {Antibiotic resistance genes (ARGs) are emerging as critical environmental contaminants across diverse ecological interfaces. To dissect evidence of microbiome and resistome in the different interconnected interfaces of ecotone, we conducted a field investigation of the microbiome and resistome of marmots, along with coexisting domestic sheep, ticks and their cave soils within the same ecological habitat. We used shotgun metagenomics with metagenome-assembled genomes (MAGs), species-resolved binning, ARG identification, source-tracker analyses, and horizontal gene transfer (HGT) network analysis to examine potential cross-interface dissemination. The composition of the mammalian gut microbiome was primarily comprised of Firmicutes, while ticks and soils exhibited distinct clusters that were predominantly dominated by Proteobacteria. The observed resistance mechanisms manifested niche-specific patterns, with target alteration predominating in mammals, whereas ticks exhibited elevated antibiotic inactivation/efflux strategies, and soils prioritized efflux mechanisms. Metagenomic assembly from these four groups yielded 5339 metagenome-assembled genomes (MAGs), of which 1481 met medium- or high-quality standards. Ticks exhibited 72% species similarity and 52% ARG concordance with marmots, while soils conserved 32% ARGs and >86% toxin genes with mammals. Our findings demonstrate that the transboundary dissemination of ARGs across different ecological interfaces, necessitates integrated surveillance of antimicrobial resistance at ecological boundaries to mitigate public health risks.},
}

@article {pmid41968559,
year = {2026},
author = {Patel, AK and Singh, N and Bala, VC and Dash, PP and Goswami, PK and Chatterjee, S},
title = {Antimicrobial Resistance: Global Challenges, Resistance Mechanisms and Mitigation Strategies.},
journal = {Recent advances in anti-infective drug discovery},
volume = {},
number = {},
pages = {},
doi = {10.2174/0127724344421494251207174255},
pmid = {41968559},
issn = {2772-4352},
abstract = {Antimicrobial resistance (AMR) poses a significant threat to global public health and economic stability, driven by the overuse and misuse of antibiotics in human medicine, veterinary practice, and agriculture. The spread of resistance mechanisms, such as enzymatic degradation, efflux pumps, and horizontal gene transfer, further exacerbates this issue, particularly in low-resource settings. This review aims to summarize the current understanding of antimicrobial resistance, including its molecular mechanisms, global challenges, economic burden, and innovative mitigation strategies such as antimicrobial stewardship, phage therapy, antimicrobial peptides, and CRISPR-based approaches. A comprehensive literature review was conducted using scientific databases such as PubMed, Scopus, and Web of Science to gather recent studies, reviews, and guidelines related to AMR. Relevant data on resistance mechanisms, global trends, clinical implications, and mitigation strategies were synthesized to provide an integrated overview of current challenges and solutions. The review highlights how AMR contributes to increased mortality, prolonged illness, and healthcare costs, while barriers such as limited antibiotic research and diagnostic capacity hinder progress. Integrated approaches, including antimicrobial stewardship, vaccination, phage therapy, and CRISPR-based therapies, are essential to reduce resistance. Additionally, global initiatives like surveillance systems and public awareness campaigns play a vital role in controlling the spread of resistant infections. Addressing AMR requires coordinated global efforts involving stewardship programs, novel therapeutics, education, and surveillance systems. Sustainable action can reduce antibiotic misuse and delay resistance development, securing effective treatments for future generations.},
}

@article {pmid41969565,
year = {2026},
author = {Kavagutti, VS and Beavogui, A and Wiart, N and Wincker, P and Oliveira, PH},
title = {Defensomes, counter-defensomes, and the remodeling of microbial communities.},
journal = {PNAS nexus},
volume = {5},
number = {4},
pages = {pgag073},
pmid = {41969565},
issn = {2752-6542},
abstract = {Bacteria and mobile genetic elements (MGEs) have coevolved for billions of years in an enduring evolutionary arms race, leading to the emergence and diversification of a vast arsenal of defense and counter-defense systems. In the last recent years, high-throughput screening methods and genome-resolved metagenomics have markedly enhanced our understanding of the diversity and abundance of immune systems across cultured and uncultured microorganisms. This fueled subsequent interest in better understanding the dynamic tri-kingdom interplay between bacteria, bacteriophages, and eukaryotic cells, and led to renewed efforts to improve alternative antibacterial phage-based therapies. Here, we discuss the evolutionary and ecological dynamics underlying the bacteria-MGE arms race, recent findings on bacterial defensomes, MGE counter-defensomes, holodefensomes, and their key role in the development of microbiome-targeted therapies. To this end, we argue why and how highly conserved anti-MGE defense systems should be prioritized as promising targets for the development of next-generation bacterial inhibitors with broad biomedical relevance, supported by a comprehensive analysis of their distribution and diversity across bacteria.},
}

@article {pmid41969793,
year = {2026},
author = {Lellouche, J and Di Castro, H and Maschiah, N and Paikin, S and Zvereva, M and Tchernov, D and Scheinin, A and Cohen, E and Meron, D},
title = {One Health Surveillance of Antimicrobial Resistance in the Eastern Mediterranean: The Blackchin Guitarfish as a Case Study.},
journal = {GeoHealth},
volume = {10},
number = {4},
pages = {e2025GH001680},
pmid = {41969793},
issn = {2471-1403},
abstract = {Antimicrobial resistance (AMR) poses a global One Health challenge, linking human, animal, and environmental health. Marine environments and organisms are increasingly recognized as reservoirs of antimicrobial-resistant bacteria and mobile genetic elements. This study investigates the prevalence of antibiotic non-susceptible bacteria and resistance genes in juvenile Glaucostegus cemiculus blackchin guitarfish along the Israeli Mediterranean coast. Between 2023 and 2024, 19 specimens were sampled from Ma'agan Michael, Acer, and Evtach. Swabs from skin, gills, and mouth were cultured on selective and chromogenic media, followed by identification using matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF MS) and antimicrobial susceptibility testing. Resistance genes were screened by quantitative PCR (qPCR), with CTX-M beta-lactamases (bla CTX-M) variants sequenced and phylogenetically analyzed. A total of 162 bacterial isolates were obtained, of which 54% were identified to 26 species across eight families, primarily Staphylococcaceae (39%) and Bacillaceae (36%). Several clinically relevant pathogens were detected, including Staphylococcus aureus, Pseudomonas spp., and Escherichia coli. Reduced susceptibilities were observed in 31 isolates from 10 specimens, with multidrug resistance identified in P. mendocina, P. stutzeri, and E. coli. Skin samples yielded the highest proportion of resistant isolates. Importantly, the bla CTX-M-185 extended-spectrum β-lactamase gene was detected in six individuals, with sequences closely related to those of human-associated strains, suggesting anthropogenic origins. These findings demonstrate that juvenile guitarfish harbor clinically significant resistant bacteria and genes, highlighting the marine environment as a potential reservoir of AMR. Integrating endangered species into AMR surveillance highlights the importance of for environmental monitoring and conservation strategies within a One Health framework.},
}

@article {pmid41971533,
year = {2026},
author = {Huang, H and Ghosh, D and Worrich, A},
title = {A One Health perspective on bacterial extracellular vesicles as mediators of antimicrobial resistance spread.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag052},
pmid = {41971533},
issn = {2730-6151},
abstract = {Antimicrobial resistance (AMR) is a global health threat requiring a One Health approach across human, animal, and environmental sectors. Bacterial extracellular vesicles (BEVs), membrane-bound particles secreted by bacteria, have emerged as potential vectors of antibiotic resistance and mediators of horizontal gene transfer. Found across clinical, agricultural, and natural environments, BEVs carry resistance genes, mobile genetic elements, and virulence factors. They protect genetic cargo, function without direct cell contact, and can cross ecological boundaries more easily than whole bacteria. This review synthesises current knowledge on BEVs in AMR transmission, highlights their cross-sector potential, and identifies key research gaps. Recognising their role is essential for improving AMR surveillance and informing future mitigation strategies.},
}

@article {pmid41972339,
year = {2026},
author = {Panda, A and Sarkar, S and Gupta, A and Tiwari, V},
title = {Computational and experimental targeting of TraH-TraU interaction in Acinetobacter baumannii inhibits type IV secretion system (T4SS) mediated transfer of the tetracycline resistance gene.},
journal = {Journal of biomolecular structure & dynamics},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/07391102.2026.2642908},
pmid = {41972339},
issn = {1538-0254},
abstract = {Antimicrobial resistance genes are transferred through conjugation-based horizontal gene transfer, which relies on the type IV secretion system (T4SS) for DNA transfer. Thus, conjugation inhibitors hold promise for controlling the spread of resistance genes among Gram-negative bacteria. Conjugation involves more than twenty proteins encoded by the tra operon. This study focuses on identifying inhibitors that can target critical protein-protein interactions within the conjugative machinery of A. baumannii. Protein-protein interaction analysis, binding energy calculations and dissociation constant (Kd) estimations suggest that the TraH-TraU interaction is stronger than other interactions among the selected Tra proteins. TraH-TraU plays a vital role in DNA transfer and mating pair stabilisation during conjugation and was therefore selected for further investigation. Fifty-eight potential inhibitors were shortlisted based on literature, and their interactions with the TraH-TraU complex were evaluated through molecular docking, Gibbs free energy and Kd calculations, and L42, L50, L53, L55, L56, L57 and L58 were selected. Molecular dynamics simulations further confirmed the stable binding of these compounds with the TraH-TraU complex, which was followed by ADMET analysis and cytotoxicity prediction. Based on that, myristic acid and picolinic acid were selected for further studies, including longer MD simulations. Principal component analysis revealed that myristic acid induces stronger restriction of the essential dynamics of the TraH-TraU complex than picolinic acid, suggesting better inhibition of the conformational flexibility required for conjugative function. Subsequent conjugation assays demonstrated that myristic acid effectively inhibited conjugation at lower concentrations compared to picolinic acid. Scanning electron microscopy (SEM) analysis confirmed that both compounds disrupted the conjugation pilus. Hence, these findings suggest that myristic acid inhibits conjugation-based transfer of resistance genes by targeting the TraH-TraU interaction in Gram-negative bacteria and can be used further to inhibit horizontal gene transfer among bacteria.},
}

@article {pmid41972581,
year = {2026},
author = {Qabel, RA and Xu, M and Li, C and Zhang, C and Zhang, C and Huang, Y and Xiong, G and Maser, E and Guo, L},
title = {Phage Frontiers: Genomic and Functional Profiling of Novel Virulent Agents Targeting Foodborne Enterobacteriaceae.},
journal = {Biology},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/biology15070578},
pmid = {41972581},
issn = {2079-7737},
support = {20230203162SF//Department of Jilin Province Science & Technology/ ; },
abstract = {Foodborne pathogens of Enterobacteriaceae are becoming an increasing global concern, with multidrug-resistant strains posing significant risks to food safety and public health, especially in high-risk products like dairy. This research focused on isolating, biologically characterizing, and genomically profiling new bacteriophages that target key Enterobacteriaceae members as potential biocontrol agents. Eight phages were isolated from wastewater using four bacterial hosts and analyzed through transmission electron microscopy, one-step growth analysis, adsorption kinetics, host range evaluation, whole-genome sequencing, comparative genomics, phylogenetic analysis, proteomic profiling, and virion assembly pathway characterization. All eight isolates exhibited icosahedral heads with contractile tails typical of Myoviridae morphology, demonstrated broad-spectrum lytic activity against 21 bacterial strains (infectivity: 47.6-95.2%), showed high adsorption efficiencies (84.75-99.98%), and had burst sizes ranging from 11 to 166 particles per cell. Genome sizes varied from 103 to 170 kb with coding densities between 92-96%. Importantly, none contained antimicrobial resistance genes, virulence factors, or lysogeny-associated elements, confirming their strictly lytic lifestyles and favorable biosafety profiles. Phylogenetic and comparative analyses indicated mosaic genomic structures influenced by horizontal gene transfer rather than host phylogeny. These findings provide a robust biological and genomic basis for evaluating these phages as potentially safe and effective alternatives to antibiotics in controlling foodborne Enterobacteriaceae, pending further in situ validation.},
}

@article {pmid41972769,
year = {2026},
author = {Mukhopadhyay, S and Debnath, F and Chakraborty, D},
title = {The missing thread of One Health efforts: improper drug disposal as an overlooked driver of antimicrobial resistance.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0058625},
doi = {10.1128/msphere.00586-25},
pmid = {41972769},
issn = {2379-5042},
abstract = {With gradual recognition of the components and the stakeholders, "One Health approach" became a global strategy for mitigating antimicrobial resistance (AMR). However, the role of improper pharmaceutical disposal, particularly antimicrobials at the household level, remains largely overlooked within One Health strategies. Expired and unused medicines are frequently discarded into household waste, drains, or open environments. The bioactive pharmaceutical residues enter soil, surface water, groundwater, and sediments. Conventional waste management and wastewater treatment systems are not designed to remove these compounds, resulting in chronic, low-level environmental exposure. Such sub-inhibitory concentrations of antimicrobials exert sustained selective pressure on environmental microbial communities, which promotes the emergence, persistence, and dissemination of resistant bacteria. Discarded antimicrobials persist in aquatic and terrestrial ecosystems, reshape microbial communities, disrupt nutrient cycling, and accelerate horizontal gene transfer. The environmental resistome, a vast genetic reservoir connecting environmental microbes with human and animal pathogens, plays a key role in resistance amplification. Evidence from India and other low and middle-income countries reveals the widespread presence of "clinically important resistance genes," including extended-spectrum β-lactamases and carbapenemases, in non-clinical environments. Residues and resistant bacteria can bioaccumulate in aquatic organisms and livestock, facilitating transmission through food chains and communities and often beyond routine surveillance. Despite its significance, household pharmaceutical waste management is largely absent from national and global AMR action plans. Incorporating safe drug disposal may serve as the missing thread in the One Health, apart from environmental monitoring and ecopharmacovigilance, which are critical to reduce environmental selection pressure and resistance propagation.},
}

@article {pmid41974411,
year = {2026},
author = {Ahmad, F and Sun, C and Muhammad, A and Shao, Y},
title = {Microplastics and pathogen risk across ecosystems: From biofilm to antimicrobial resistance and host susceptibility.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128128},
doi = {10.1016/j.envpol.2026.128128},
pmid = {41974411},
issn = {1873-6424},
abstract = {Microplastics (MPs) are ubiquitous in terrestrial and aquatic ecosystems, where they rapidly acquire organic coatings and biofilms (the plastisphere) and interact with co-occurring chemical pollutants. However, the conditions under which MPs become ecologically relevant in increasing disease risk remain underexplored. A key controversy is that microbial detection or enrichment on MPs is often treated as evidence of pathogen "vectoring," yet most studies do not quantify viability/infectivity, detachment, or delivered dose to hosts under environmentally realistic conditions. This review synthesizes evidence on MP-pathogen interactions and dispersal across ecosystems and reframes "MPs as vectors" through a vectorial-capacity lens that distinguishes association from transmission relevance and links MP-mediated risk to measurable dose delivery at host-relevant interfaces. Across ecosystems, evidence supports biofilm-driven persistence and enrichment of opportunistic taxa, but direct demonstrations of MP-mediated infection remain limited. We further highlight an unresolved issue, whether MPs confer unique transmission advantages compared with size-matched natural particulates that also sorb microbes and contaminants but are rarely used as comparators. We examine host susceptibility as a risk multiplier: MP exposure can compromise epithelial barriers via oxidative stress, modulate innate immunity, and disrupt microbiome-mediated colonization resistance. Plastisphere biofilms may also function as eco-evolutionary microhabitats that enrich antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs), with plausible enhancement of horizontal gene transfer, although field-scale attribution is still scarce. Finally, we outline priorities for standardized evidence grading, comparator-based study designs, and quantitative metrics (loading, viability decay, detachment kinetics) to enable risk attribution and guide monitoring and mitigation.},
}

@article {pmid41966564,
year = {2026},
author = {Liu, J and Yan, C and Zhang, S and Zeng, G and Ma, S and Dai, J and Huang, H and Li, Y and Yu, F and Shangguan, YX and Xu, H and Liu, H},
title = {Effects of pig bone‑derived hydroxyapatite on contaminated manure composting: Humification, copper/zinc immobilization, and high‑risk antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {141984},
doi = {10.1016/j.jhazmat.2026.141984},
pmid = {41966564},
issn = {1873-3336},
abstract = {The high-value utilization of livestock manure remains a critical challenge due to co-contamination with heavy metals (Cu/Zn) and antibiotic resistance genes (ARGs), particularly high-risk ARGs that threaten public health. Here, pig bone-derived bio-based hydroxyapatite was incorporated into aerobic composting to comprehensively explore its effects on humification, heavy metals (Cu/Zn) passivation, and ARGs dissemination, as well as the underlying microbial mechanisms. Results demonstrated that bio-based hydroxyapatite prolonged the thermophilic phase, increased humus and humic acid contents by 27.9% and 31.4% respectively, and significantly up-regulated functional genes involved in carbon degradation (e.g., pox for lignin, amyA for starch, xylA for hemicellulose) and carbon fixation (e.g., accA in HP/HB cycle, acsA in WL pathway). The bioavailable fractions of Cu and Zn were reduced by 38.56% and 13.78% via complexation with humic substances and bio-based hydroxyapatite's surface functional groups. Notably, total ARGs abundance decreased by 26.1%, with Rank I and II high-risk ARGs reduced by 58.74% and 81.82% relative to the control. Bio-based hydroxyapatite also reduced the abundance of mobile genetic elements by 29.73% and inhibited the proliferation of Salmonella, a key ARGs host genus. Mechanistically, bio-based hydroxyapatite promoted stochastic microbial community assembly, enhanced cooperative interspecies interactions, and constrained horizontal gene transfer by alleviating oxidative stress (ROS/SOS pathway) and reducing bacterial motility (chemotaxis and flagellar assembly). These findings elucidated the multi-dimensional regulatory role of bio-based hydroxyapatite in synergistically improving compost quality and mitigating co-occurring ecological risks, providing valuable insights for the safe resource utilization of contaminated livestock manure.},
}

@article {pmid41967706,
year = {2026},
author = {Yang, B and Zhang, M and Zhu, S and Wang, Z and Liu, Y},
title = {Natural flavonoids inhibit plasmid conjugation via iron chelation and zinc-responsive envelope stress.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.04.011},
pmid = {41967706},
issn = {2090-1224},
abstract = {INTRODUCTION: Plasmid-mediated bacterial conjugation is a major driver of horizontal gene transfer (HGT) via direct cell-to-cell contact, significantly accelerating the dissemination of antimicrobial resistance (AMR). Given the limited pipeline of new antibacterial agents, conjugation inhibitors represent a promising alternative strategy to curtail resistance spread.

OBJECTIVES: This study aims to identify potent natural compounds that block resistance transmission and elucidate their underlying molecular mechanisms.

METHODS: We conducted conjugation assays to screen plant-derived flavonoids for inhibitory activity against resistant plasmid transfer. Structure-activity relationship (SAR) analysis was employed to delineate the impact of specific substituent groups. Transcriptomic profiling and gene knockout experiments identified and validated critical functional genes. Cell surface hydrophobicity, adhesion and aggregation assays provided mechanistic evidence of gene function in the conjugation process.

RESULTS: Herein, we demonstrate that the majority of plant-derived flavonoids potently inhibit the conjugative transfer of two distinct plasmids both in vitro and in vivo. SAR analysis reveals that flavonoids with lower lipophilicity (log P), particularly those bearing hydroxyl groups, exhibit superior inhibitory efficacy. Conversely, isopentenyl-substituted flavonoids display attenuated activity. Mechanistically, scutellarein, a representative hydroxylated flavonoid, disrupts bacterial iron homeostasis, triggering zinc-responsive envelope stress response (ESR) activation. Zinc influx induces intracellular protective responses mediated by ZraP and glutathione (GSH), whose depletion reduces membrane permeability, reactive oxygen species (ROS) levels and electron transport chain (ETC) activity. Concurrently, GSH oxidation to glutathione disulfide (GSSG) upregulates bhsA expression, altering surface hydrophobicity and flagellar motility, thereby diminishing intercellular adhesion, aggregation and physical encounter frequency.

CONCLUSION: Collectively, our findings uncover the critical roles of iron homeostasis perturbation and ESR activation in controlling plasmid conjugation, underscoring the therapeutic potential of natural flavonoids in mitigating the AMR crisis.},
}

@article {pmid41968065,
year = {2026},
author = {Benzerara, K and Millet, M and Skouri-Panet, F and Gaschignard, G and Mehta, N and Bezard, M and Caumes, G and Chevrier, DM and Dezi, M and Duverger, A and Guigner, JM and Gutiérrez-Preciado, A and Lefevre, CT and López-García, P and Menguy, N and Monteil, CL and Pehau-Arnaudet, G and Penard, E and Pereiro, E and Scandola, C and Travert, C and Vantelon, D and Duprat, E and Callebaut, I and Moreira, D},
title = {Intracellular Amorphous Calcium Carbonate Biomineralization in Methanotrophic Gammaproteobacteria Was Acquired by Horizontal Gene Transfer From Cyanobacteria.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70270},
doi = {10.1111/1462-2920.70270},
pmid = {41968065},
issn = {1462-2920},
support = {ANR-24-CE44-5543//Agence Nationale de la Recherche/ ; ANR-21-CE01-0010//Agence Nationale de la Recherche/ ; 307110/ERC_/European Research Council/International ; 787904/ERC_/European Research Council/International ; },
mesh = {*Gene Transfer, Horizontal ; *Biomineralization ; *Calcium Carbonate/metabolism ; *Cyanobacteria/genetics/metabolism ; Phylogeny ; *Methylococcaceae/genetics/metabolism ; *Gammaproteobacteria/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Some bacteria genetically control the biomineralisation of intracellular amorphous calcium carbonates (iACC) with potential implications for microbial physiology, evolution, bioremediation and biogeochemical cycling. Until now, this capacity has been documented in Cyanobacteria, the giant gammaproteobacterium Achromatium and a few magnetotactic Pseudomonadota and Nitrospirota. Here, we report the discovery of iACC biomineralisation in members of the Methylococcaceae, a family of aerobic methanotrophic Gammaproteobacteria. A homologue of the ccyA gene, a diagnostic marker for iACC formation in Cyanobacteria, was identified in several Methylococcaceae genomes, based on the conserved C-terminal (GlyZip)3 domain of the encoded calcyanin protein. Moreover, two cultivated strains, Methylococcus geothermalis and Methylococcus mesophilus, whose genomes contained the ccyA gene, were consistently shown to form iACC. The ccyA genes of Methylococcaceae and Microcystis share higher sequence similarity than with other Cyanobacteria, suggesting horizontal gene transfer (HGT) from an ancestral Microcystis-like cyanobacterium to Methylococcaceae. This finding extends the known taxonomic distribution of ccyA and suggests that the capability to biomineralize iACC was acquired by HGT. The discovery of iACC in methane-oxidising Methylococcaceae highlights a previously unrecognised coupling between calcium carbonate biomineralisation and methane cycling in aquatic environments, suggesting an overlooked role of iACC formation in microbial carbon storage and local geochemical regulation.},
}

*Gene Transfer, Horizontal
*Biomineralization
*Calcium Carbonate/metabolism
*Cyanobacteria/genetics/metabolism
Phylogeny
*Methylococcaceae/genetics/metabolism
*Gammaproteobacteria/genetics/metabolism
Bacterial Proteins/genetics/metabolism

@article {pmid41958893,
year = {2026},
author = {Zhan, Y and Ma, X and Guo, X and Zhang, M and Cui, C and Li, W and Yan, S and Cui, S and Yang, X and Guo, Y},
title = {Genomic Characterization of Clostridium botulinum Isolates from Soil and Soybean Samples in High-Incidence Regions - Xinjiang, Inner Mongolia, and Qinghai PLADs, China, 2024.},
journal = {China CDC weekly},
volume = {8},
number = {9},
pages = {238-245},
pmid = {41958893},
issn = {2096-7071},
abstract = {Foodborne botulism is prevalent in northwestern China, linked to traditional homemade foods. Recently, some cases have been linked to commercial vacuum-packaged ready-to-eat meat products. Soil is a potential contamination source, yet genomic information on environmental isolates from high-incidence regions remains scarce.

WHAT IS ADDED BY THIS REPORT?: This study presents the first genomic characterization of 23 C. botulinum isolates obtained from soil and soybean samples in Northwest China. Four botulinum neurotoxin subtypes, A5(B3), B2, B3, and B4, were identified, each demonstrating notable geographic and metabolic diversity. Subtype-specific genomic adaptations, transposase insertions, and an incomplete prophage carrying bont in one isolate were observed, suggesting historical horizontal gene transfer.

Soils in high-incidence regions may act as persistent reservoirs of C. botulinum, emphasizing the need for targeted evidence-based public health interventions. Strengthening hygiene and sanitation practices during food processing, along with enhanced surveillance of both traditional and commercial food products, are essential to prevent future foodborne botulism outbreaks in endemic regions.},
}

@article {pmid41959308,
year = {2026},
author = {Sakdinan, B and Sinha, A and Qadri, F and Khan, AI and Nelson, EJ and Shapiro, BJ},
title = {Species-specific prophage induction by ciprofloxacin in human gut metagenomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.11.711154},
pmid = {41959308},
issn = {2692-8205},
abstract = {UNLABELLED: Antibiotics are known to trigger prophage induction in controlled laboratory settings, but it remains unclear whether this also occurs within microbiomes in nature. Current methods investigating the link between antibiotics and prophage induction within the human gut rely on in vitro culturing of human gut bacterial isolates. Using a metagenomic approach, we aimed to measure prophage induction and whether it is associated with antibiotic exposure. Across two independent human cohorts, we compared prophage to bacterial host read depth ratios (P:H) across known or measured antibiotic exposures. We found that induction is not broadly associated with antibiotic exposures at the level of the overall microbiome, but that ciprofloxacin increases P:H ratios in specific bacterial species. We documented heterogeneous trajectories of P:H ratios over the course of antibiotic exposure, sometimes increasing and remaining high, or returning to baseline. This study complements experimental models by providing in vivo evidence of induction in the human gut.

IMPORTANCE: Bacteriophages are viruses that infect a bacterial host. The lytic and lysogenic cycles are the two classic outcomes of phage infection. In the lytic cycle, the phage immediately replicates and lyses its host to release new viral particles. In the lysogenic cycle, the phage, now called a prophage, integrates its genome into that of its host without killing it. Prophages can switch to the lytic cycle in a process called induction, in which the viral genome is replicated, the host cell is lysed, and viral particles are released. The most immediate consequence of induction is host cell death which can impact bacterial populations and communities. Since prophages are mobile genetic elements that can move between bacteria, they are also an important vehicle for horizontal gene transfer. While induction has been well studied in vitro , whether and how induction occurs within the complex microbial ecosystem in humans is less well characterized. Understanding prophage induction in vivo is therefore critical in corroborating in vitro observations.},
}

@article {pmid41959403,
year = {2026},
author = {Maier, J and Gin, C and Rabasco, J and Spencer, W and Bass, A and Duerkop, BA and Callahan, B and Kleiner, M},
title = {TrIdent - An R package to automate transductomics analysis of virus-like particle mediated DNA mobilization.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.31.715651},
pmid = {41959403},
issn = {2692-8205},
abstract = {BACKGROUND: Transduction is a form of horizontal gene transfer in which bacterial DNA is packaged and transferred by virus-like particles (VLPs). Transductomics is a sequencing-based method used to detect DNA carried by VLPs. During transductomics analysis, reads from a sample's ultra-purified VLPs are mapped to metagenomic contigs assembled from the same sample's whole-community. The read mapping produces coverage patterns that require a time-consuming manual inspection and classification process which makes the method's use unfeasible for datasets with many samples.

RESULTS: We developed a novel algorithm, TrIdent (Transduction Identification), that uses pattern-matching to automate the transductomics data analysis and that is available as an R package (https://jlmaier12.github.io/TrIdent/). There is no software equivalent to TrIdent so we compared TrIdent's classifications of transductomics datasets to classifications made by human classifiers. TrIdent's classifications were generally comparable to the manual classifications on a previously generated, manually classified transductomics dataset. When applied to newly generated transductomics data from the murine microbiota, TrIdent agreed with two independent human classifiers as much as the two independent human classifications agreed with each other. TrIdent classified transductomics datasets in a fraction of the time needed by human classifiers, and the classifications produced by TrIdent are fully reproducible. We used TrIdent to explore three murine gut transductomes and found that bacterial DNA associated with the Oscillospiraceae and Turicibacteraceae families was highly enriched in the DNA packaged by VLPs as compared to the whole community metagenomes.

CONCLUSIONS: The TrIdent software is a more accessible, more efficient, and more reproducible alternative to the manual inspection of read coverage patterns previously required for transductomics data analysis. To demonstrate the application of TrIdent, we analyzed transductomics datasets from murine fecal pellets and showed that specific low abundance bacterial families appear to be heavily involved in transduction.},
}

@article {pmid41961820,
year = {2026},
author = {Ojaswini, and Pal, S and Dhibar, A and Chandra, K and Rangarajan, A and Shukla, SP},
title = {Cellular remodeling of ovarian follicular epithelial cells transmits an obligate nutritional endosymbiont in a scale insect.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {16},
pages = {e2532091123},
doi = {10.1073/pnas.2532091123},
pmid = {41961820},
issn = {1091-6490},
support = {Ramalingaswami Fellowship//Department of Biotechnology, Ministry of Science and Technology, India (DBT)/ ; SRG/2021/000600//Department of Science and Technology, Ministry of Science and Technology, India (DST)/ ; },
mesh = {Animals ; *Symbiosis/physiology ; Female ; *Hemiptera/microbiology/genetics ; *Epithelial Cells/microbiology/metabolism ; Oocytes/microbiology/metabolism ; *Ovarian Follicle/cytology/microbiology ; },
abstract = {Many insects show complex associations with vertically transmitted endosymbionts. Here, we describe unique cellular remodeling of the oocyte's follicular epithelial cells into endosymbiont-bearing tubular structures in the ensign scale insect Insignorthezia insignis (Hemiptera: Ortheziidae). Vitellogenic oocytes develop a bulge-like distension at the posterior pole. Here, follicular epithelial cells undergo extensive cellular reorganization, remodeling their actin cytoskeleton and plasma membrane to produce cellular protrusions. These tubular protrusions, which are densely packed with the endosymbiont, subsequently detach from the epithelial layer and migrate along the developing embryonic germ band, thus facilitating the endosymbiont's transovarial transmission. We further report a flavobacterial endosymbiont with an eroded genome of 0.86 Mb that encodes genes for amino acids, vitamins, and fatty acid biosynthesis. Genes for pantothenate and biotin biosynthesis, which were absent from the endosymbiont genome, were found to be horizontally acquired by the host genome from bacteria other than the symbiont, demonstrating host-symbiont metabolic complementarity and genome coevolution. The symbiont's nutrient-provisioning genes were expressed both in the host's adult stage, which feeds exclusively on nutrient-deficient plant phloem, as well as in the embryonic stages. Notably, experimental depletion of the endosymbiont from the embryonic stage caused high mortality, while the surviving nymphs exhibited severe phenotypic abnormalities, including the absence of body wax. Our results highlight the intricate and synergetic coordination between endosymbionts and the developing embryo, indicating broader phenotypic consequences in scale insects via symbiont-mediated nutritional supplementation.},
}

Animals
*Symbiosis/physiology
Female
*Hemiptera/microbiology/genetics
*Epithelial Cells/microbiology/metabolism
Oocytes/microbiology/metabolism
*Ovarian Follicle/cytology/microbiology

@article {pmid41962241,
year = {2026},
author = {Lin, Z and Pang, S and Xu, T and Zhou, YL and Zhang, C and Qian, PY and Zhang, S},
title = {Marine plastisphere expands the ecological niche and evolutionary dynamics of nrfA-dependent nitrite ammonifying bacteria.},
journal = {Water research},
volume = {299},
number = {},
pages = {125879},
doi = {10.1016/j.watres.2026.125879},
pmid = {41962241},
issn = {1879-2448},
abstract = {The marine plastisphere affects nitrogen cycling processes, but its role in nrfA-dependent nitrite ammonification, a critical phase of dissimilatory nitrate reduction to ammonium (DNRA) with important implications for nitrogen retention and greenhouse gas dynamics, remains unexplored. In this study, we analyzed 269 plastisphere metagenomes and eight metatranscriptomes from global public datasets. The plastisphere contained elevated nrfA levels compared to seawater, and nrfA transcripts were consistently detected. A total of 285 putative nrfA-dependent nitrite ammonifying bacteria were identified, including 156 novel genera. Most plastisphere MAGs overlapped with other examined marine biofilms, whereas 109 MAGs were uniquely detected in plastisphere samples within the analyzed comparative datasets. Functional studies revealed diverse electron-donor utilization strategies supporting DNRA in plastisphere microorganisms. Evolutionary analyses showed that nrfA genes were distributed across different phyla through horizontal gene transfer, whereas purifying selection limited sequence divergence. These findings highlight a previously underappreciated genetic and transcriptional potential for DNRA in plastic-associated biofilms at the particle scale, with implications for nitrogen retention within plastisphere microhabitats.},
}

@article {pmid41962374,
year = {2026},
author = {Zhou, LT and He, DH and Li, J and He, RX and Ma, SJ and Gong, GY and Zou, XS and Li, S and Zhou, YF and Hu, WJ},
title = {Dynamics and drivers of last-resort antibiotic resistance genes during pilot-scale aerobic fermentation of municipal sludge and subsequent bok choy pot trials.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {141891},
doi = {10.1016/j.jhazmat.2026.141891},
pmid = {41962374},
issn = {1873-3336},
abstract = {Sludge from wastewater treatment plants may exacerbate environmental dissemination of last-resort antibiotic resistance genes (LARGs) when applied to land. However, LARG behavior during aerobic sludge fermentation and subsequent soil-plant transfer remains poorly understood. This study specifically targeted LARGs beyond common ARGs and coupled pilot-scale fermentation with bok choy cultivation to resolve their dynamics and compartmentalization. Using metagenomic sequencing with correlation and network analyses, we identified environmental drivers and inferred potential hosts. Optimized fermentation conditions (maintaining >50 °C for 10 days) reduced moisture to 30%, lowered the C/N ratio to 24.7, and achieved germination indices of 85%-90%. Fermentation promoted microbial succession, enhanced metal passivation and organic matter humification, and reduced antibiotic and ARG abundance, with total antibiotic degradation reaching 49.19% in the thermophilic phase. LARG abundance increased by 47.6% in the mesophilic phase due to cell lysis and MGE release, then declined by 9.7% in the thermophilic phase and 47.8% during maturation. Although fermentation stabilized sludge, specific genes (e.g., KPC-22 and poxtA) rebounded, driven by horizontal gene transfer and physicochemical changes. Subsequent planting demonstrated that a 10%-15% sludge application rate optimized bok choy agronomic performance and improved soil antibiotic degradation. Across soil, rhizosphere, and phyllosphere, LARGs exhibited distinct compartmentalization patterns. Network analysis further indicated that LARGs were primarily associated with indigenous soil taxa (e.g., Streptomyces) rather than potential pathogens (e.g., Klebsiella). Consequently, the impact on the core transmission network was minor, suggesting that appropriately fermented sludge application presents a controllable ecological risk and supports its safe utilization under the studied conditions.},
}

@article {pmid41963319,
year = {2026},
author = {Manzano-Morales, S and Gabaldón, T},
title = {Phylogenomics of Asgard archaea reveals a unique blend of prokaryotic-like horizontal transfer and eukaryotic-like gene duplication.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71534-5},
pmid = {41963319},
issn = {2041-1723},
abstract = {Asgard archaea hold a pivotal position in the tree of life as the closest known relatives to eukaryotes and are therefore crucial for understanding eukaryogenesis. Earlier genomic analyses revealed that Asgard genomes are remarkably larger than those of other archaea and contain a significant number of genes seemingly acquired from bacteria. However, the precise contributions of horizontal gene transfer and gene duplication in shaping Asgard genomes remain largely unknown. Here, we present a comprehensive phylogenomic analysis to dissect the evolutionary dynamics of Asgard genomes, quantifying gene duplication, loss, and both inter- and intra-domain gene transfer events. Our findings reveal that gene transfer is widespread throughout Asgard evolution, predominantly affecting metabolic genes at the periphery of interaction networks. However, our analyses demonstrate that gene duplications, rather than horizontal gene transfers, are the primary drivers behind the increased genome sizes observed in Asgard archaea. This unique evolutionary signature in Asgard archaea-a blend of pervasive prokaryotic-like gene transfer alongside significant eukaryotic-like gene duplication-is consistent with their phylogenetic placement and offers novel insights into the genomic transitions that likely underpinned eukaryogenesis.},
}

@article {pmid41748559,
year = {2026},
author = {He, W and Xiong, R and Zheng, M and Zhang, T and Zhang, Y and Wang, Q and Zhao, C and Huang, T and Liu, Y and Tian, Y and Tabl, KM and Mao, X and Li, P and Feng, G and Bai, X and Liu, Q and Yan, W and Liao, Y and Zhang, J and Yin, P and Wu, A},
title = {Specialized aldo-keto reductases trigger complete degradation of mycotoxin deoxynivalenol.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41748559},
issn = {2041-1723},
mesh = {*Trichothecenes/chemistry/metabolism ; *Aldo-Keto Reductases/metabolism ; *Nocardioides/enzymology/genetics ; *Bacterial Proteins/genetics/metabolism ; Plants, Genetically Modified/enzymology ; Cryoelectron Microscopy ; Gene Transfer, Horizontal ; *Mycotoxins/chemistry/metabolism ; Arabidopsis ; },
abstract = {The mycotoxin deoxynivalenol (DON) poses severe threats to human and animal well-being globally. Enzymatic degradation is the most effective way to eliminate DON toxicity, yet no catalytic process for complete degradation of DON has been uncovered. Here, we show that a metabolic pathway initiated by C3-epimerization and C8-reduction is responsible for complete degradation of DON in the DON-metabolizing bacterium Nocardioides sp. S5-5. Two horizontally transferred aldo-keto reductase genes, DONepi and DONrd, have evolved to orchestrate C3-epimerization and C8-reduction respectively. Notably, the octameric-structured DONepi alone catalyzes C3-epimerization of DON by steering the rigid-body rotation of the transient 3-keto intermediate for stereoinverting reduction. Moreover, DONrd can catalyze the C8-reduction of DON and its C3-epimerized product 3-epi-DON simultaneously to form C8-hydroxyl products, which facilitates the further degradation by a potential oxidase and other putative enzymes. DONepi expression in transgenic plants confers resistance to DON, representing potential for controlling mycotoxin contamination pre- and postharvest.},
}

*Trichothecenes/chemistry/metabolism
*Aldo-Keto Reductases/metabolism
*Nocardioides/enzymology/genetics
*Bacterial Proteins/genetics/metabolism
Plants, Genetically Modified/enzymology
Cryoelectron Microscopy
Gene Transfer, Horizontal
*Mycotoxins/chemistry/metabolism
Arabidopsis

@article {pmid41928146,
year = {2026},
author = {Saif, NA and Elghaish, RA and Badr, E and Mouftah, SF and Shawky, SM and Pascoe, B and Sheppard, SK and Elhadidy, M},
title = {Pathoadaptive evolution and clonal dissemination of community- associated methicillin-resistant Staphylococcus aureus in Egypt.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {},
pmid = {41928146},
issn = {1471-2334},
abstract = {BACKGROUND: Staphylococcus aureus is a major public health concern and is classified as a priority pathogen by the World Health Organization (WHO) with the global rise of methicillin-resistant S. aureus (MRSA) infections. Community-associated MRSA (CA-MRSA) strains have become increasingly important in both community and healthcare settings. This study aimed to investigate the genomic diversity, evolution, resistome, and virulome of CA-MRSA isolates circulating in Egypt to better understand their persistence, adaptation, and public health implications.

METHODS: A total of 123 CA-MRSA isolates were collected from clinical settings in Alexandria, Egypt. Methicillin resistance was first determined phenotypically using cefoxitin resistance, followed by genotypic confirmation through detection of the mecA gene.Whole-genome sequencing and comparative genomic analyses were performed to characterize sequence types, clonal complexes, SCCmec elements, resistance determinants, and virulence factors. Phylogenetic relationships were reconstructed to assess evolutionary divergence, and network analysis was used to explore associations between resistance and virulence gene profiles.

RESULTS: Eight distinct clonal complexes (CCs) were identified, dominated by CC121-SCCmecV (15%), CC1-SCCmecV (14%), CC15-SCCmecV (9%), CC1-SCCmecVI (7%), and CC8-SCCmecV (6%). Five novel sequence types (ST8157–ST8161) were discovered and deposited in pubMLST, indicating ongoing local evolution. Within CC8, two divergent lineages (ST239 and ST8) harbored unique SCCmec elements, reflecting significant phylogenetic differentiation. Globally important epidemic clones such as ST239-III-MRSA and ST22-IV-MRSA (EMRSA-15) were also detected. Network analysis revealed broad ecological adaptability, with livestock-associated CC97 and healthcare-associated CC5 harboring genes for immune evasion and biofilm formation. The detection of yopB in CC97 and yscT in CC5, genes typically found in Yersinia species, suggests horizontal gene transfer as a mechanism of adaptation. The high prevalence of fosB (fosfomycin resistance) and elevated fusidic acid resistance (39%) further underscores the emergence of multidrug resistance.

CONCLUSIONS: This large-scale genomic analysis reveals the coexistence of globally disseminated and locally evolved CA-MRSA lineages in Egypt. The findings underscore the adaptive potential of Egyptian MRSA populations and their contribution to regional AMR dynamics. Continued genomic surveillance within a One Health framework is essential for monitoring MRSA evolution, informing control measures, and mitigating the spread of resistance in both community and clinical settings.

CLINICAL TRIAL: Not applicable.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-026-13097-w.},
}

@article {pmid41953073,
year = {2026},
author = {Tang, L and Yang, W and Yang, L and Lv, Y and Zhang, J},
title = {Targeting Horizontal Gene Transfer to Combat Antimicrobial Resistance: A Review of Mechanisms, Drivers, and Multi-Omics Strategies.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {589962},
pmid = {41953073},
issn = {1178-6973},
abstract = {The widespread dissemination of antibiotic resistance genes in bacteria primarily relies on horizontal gene transfer (HGT), a phenomenon that has profound implications for global healthcare and animal husbandry. Therefore, elucidating the key mechanisms of HGT is crucial for controlling the global spread of resistance genes. Horizontal gene transfer can occur not only through classical pathways such as conjugation, transformation, and transduction but also involves non-classical mechanisms including gene transfer agents, outer membrane vesicles, and nanotubes. This process is mediated by various mobile genetic elements, such as plasmids, bacteriophages, transposons, integrons, integrative and conjugative elements (ICEs), and integrative and mobilizable elements (IMEs). HGT is typically regulated by a combination of host-specific intrinsic factors and external environmental conditions. To address the spread of resistance, numerous detection and prevention tools targeting this mechanism have been developed. This article focuses on the process of HGT and its associated mobile genetic elements, systematically analyzes key factors influencing this process, summarizes sequencing and bioinformatic technologies used for monitoring HGT, and explores prevention strategies informed by genomic, proteomic, and metabolomic approaches. The aim is to provide a theoretical foundation and practical guidance for the control of drug-resistant bacteria.},
}

@article {pmid41953456,
year = {2026},
author = {Ivanova, M and Mourão, J and Szarvas, J and Tosun, ES and Lacy-Roberts, N and Thornval, NR and Záborcki, Z and Jánosi, S and Garcia-Fierro, R and Beloeil, PA and Liebana, E and Guerra, B and Hendriksen, RS and Kjeldgaard, JS},
title = {Human-associated NDM-5-producing multidrug-resistant Escherichia coli detected in retail beef and pork in Hungary, 2021.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1793862},
pmid = {41953456},
issn = {2673-7647},
abstract = {BACKGROUND: Carbapenem-resistant Enterobacterales pose a significant public health threat, particularly when detected in food-producing animals and retail meat. Although carbapenems are not used in European Union animal production, sporadic cases of carbapenemase-producing Escherichia coli have emerged across multiple European countries since 2019. The detection of human-associated carbapenemase genes in meat raises concerns about potential transmission to humans through the food chain.

METHODS: In this study, we characterize three multidrug-resistant (MDR) E. coli isolates harboring bla NDM-5 recovered from retail beef and pork in Hungary in 2021. E. coli isolates were subjected to phenotypic antimicrobial susceptibility testing using broth microdilution, conjugation experiments, and genotypic characterization through whole-genome sequencing using Illumina and Oxford Nanopore platforms. Hybrid assemblies enabled comprehensive comparative genomic and plasmid analyses.

RESULTS: All three isolates belonged to the human-associated uropathogenic clone ST405 (O102:H6) and were clonally related with a maximum of two single nucleotide polymorphisms. They exhibited identical genomic profiles conferring resistance to carbapenems, cephalosporins, fluoroquinolones, tetracycline, and azithromycin. Comparative genomic analysis revealed close genetic relationships with human clinical isolates from Australia and the United Kingdom, suggesting international dissemination. The bla NDM-5 gene was located on conjugative IncFII-IncFIB hybrid plasmids (approximately 132 kb) closely related to clinical plasmids from human isolates in the United States, differing only by the absence of a bla CTX-M-15-ISEcp1 transposition unit.

CONCLUSION: The detection of human-associated bla NDM-5-carrying E. coli ST405 in retail meat represents a serious food safety concern, highlighting potential transmission routes to humans and emphasizing the need for enhanced surveillance and epidemiological investigations.},
}

@article {pmid41955011,
year = {2026},
author = {López Sánchez, A and Scholz, GE and Stadler, PF and Lafond, M},
title = {From Small Parsimony to Horizontal Gene Transfer: Inferring Horizontal Transfer and Gene Loss for Single-Origin Characters.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {15578666261426009},
doi = {10.1177/15578666261426009},
pmid = {41955011},
issn = {1557-8666},
abstract = {The simple underlying pattern of presence-absence of a character within a species tree provides useful steps to trace complex evolutionary histories. Character-based models such as perfect transfer networks and its galled variant aim to leverage this information to predict horizontal gene transfers. Under the assumption that characters have a single origin, are rarely lost, and can be transferred horizontally, they remain an efficient inference method for almost tree-like scenarios. Nevertheless, they can sometimes predict overly complicated scenarios, and its simplest structural variants are too restrictive for practical uses. With the goal of extending this model to include loss events, we present a Sankoff-Rousseau-like algorithm that aims to recover the simplest possible scenarios that combine gene transfers and losses using solely the single character information already contained in a given species tree. We establish a link between the small parsimony problem and the inference of scenarios with a minimum number of losses and transfers, allowing losses and transfers to have a user-defined penalization for this end. We also explore the utility of our model for tracing possible highways of gene transfers by presenting a real case study on a dataset of bacterial species and Kyoto Encyclopedia of Genes and Genome functions as characters.},
}

@article {pmid41955379,
year = {2026},
author = {Righi, L and Stutzmann, S and Bader, L and Lemopoulos, A and Blokesch, M},
title = {Competence-mediated DNA uptake diversifies Vibrio cholerae sedentary chromosomal integrons.},
journal = {Science (New York, N.Y.)},
volume = {392},
number = {6794},
pages = {194-201},
doi = {10.1126/science.aed0645},
pmid = {41955379},
issn = {1095-9203},
mesh = {*Vibrio cholerae/genetics/virology/metabolism ; *Integrons/genetics ; *Gene Transfer, Horizontal ; *DNA, Bacterial/genetics/metabolism ; *Chromosomes, Bacterial/genetics ; Bacteriophages ; },
abstract = {Bacteria often survive viral attack and environmental stress by sharing genes that enhance their defenses. The cholera pathogen Vibrio cholerae carries a sedentary chromosomal integron (SCI), a genetic element containing hundreds of mostly promoterless gene cassettes, about 10% of which encode antiviral systems. Cassettes are thought to reshuffle under stress to the favorable first array position, yet the SCI in pandemic V. cholerae has remained static for more than 60 years. In this study, we show that SCI diversification efficiently occurs by horizontal transfer linked to the genus's aquatic lifestyle: DNA released from lysed cells is taken up by naturally competent vibrios and integrated into the first position of the SCI array, the primary site of strong expression, where it confers resistance to phage and potentially other threats.},
}

*Vibrio cholerae/genetics/virology/metabolism
*Integrons/genetics
*Gene Transfer, Horizontal
*DNA, Bacterial/genetics/metabolism
*Chromosomes, Bacterial/genetics
Bacteriophages

@article {pmid41956298,
year = {2026},
author = {Zuo, Q and Gao, J and Zhang, J and Lu, T and Zhang, K and Li, K and Gao, F and Wang, Y and Guo, Y},
title = {Masked ecological risk: Stable anammox performance conceals resistance genes propagation under short-term non-antibiotic antimicrobials stress.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134574},
doi = {10.1016/j.biortech.2026.134574},
pmid = {41956298},
issn = {1873-2976},
abstract = {Dioctadecyldimethylammonium chloride (DODMAC) and potassium sorbate (PS) are two prevalent non-antibiotic antimicrobials that frequently co-exist in sewage. However, their impacts on anaerobic ammonium oxidation (anammox) systems remains unclear. This study investigated the short-term effects of single and combined DODMAC (0.5 and 8 mg/L) and PS (5 and 20 mg/L) stress over 40 operational cycles. Remarkably, anammox activity was not inhibited, and a metabolic shift led to pronounced NO3[-]-N accumulation under 8 mg/L DODMAC stress. Total nitrogen removal efficiency was maintained or slightly enhanced under PS stress due to stimulated denitrification. However, this seemingly stable performance under short-term stress masked a critical ecological threat: significant enrichment of resistance genes (RGs). The abundance of intracellular RGs increased substantially, with intI1 (an integron gene) reaching up to 8.5 times that of CK under the stress of DODMAC and/or PS. Network analysis identified Bdellovibrio, Dokdonella and Acinetobacter as key potential RGs hosts enriched (p < 0.05). Horizontal gene transfer mediated by mobile genetic elements (especially intI1) was the primary driver of RGs dissemination. These findings demonstrated that functional stability did not equate to ecological safety. This highlighted the urgent need to look beyond conventional performance metrics when assessing the environmental impacts of emerging contaminants.},
}

@article {pmid41947428,
year = {2026},
author = {Rinke, JL and Franke, L and He, D and Fischer, ML and Vizueta, J and Eicholt, LA and Larsen, RS and Xiong, Z and Cunningham, P and Henry, LM and Kaltenpoth, M and Gadau, J and Zhang, G and Boomsma, JJ and Schrader, L},
title = {Comparative analysis of 163 ant genomes reveals recurrent horizontal gene transfer from bacteria to ants.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giag043},
pmid = {41947428},
issn = {2047-217X},
abstract = {BACKGROUND: Horizontal gene transfer (HGT) from bacteria can drive phenotypic innovation and adaptation in eukaryotes. Ants are likely carriers of HGT-derived genes, as they have repeatedly established mutualistic associations with vertically transmitted bacterial symbionts with direct access to the germline. However, the prevalence of HGT across ants and most other insects remains virtually unexplored.

RESULTS: Here, we systematically investigated the genomes of over 160 species of ants and uncovered 497 protein-coding HGT events in 85 species, predominantly derived from intracellular symbionts. Among these, we identified several HGTs likely underpinning functional innovations, primarily by mediating immune-system adaptations or facilitating nutritional niche expansions. Several of these HGTs were conserved in sequence and synteny across multiple species, consistent with strong signatures of purifying selection over up to 40 million years. Functional and structural analysis of a horizontally acquired Xanthine-guanine phosphoribosyltransferase gene of Cardiocondyla ants reveals deep entrenchment of this protein in basic energy metabolism of the host, facilitated by the enzyme's substrate promiscuity.

CONCLUSIONS: This study provides insights into the abundance and diversity of HGT from bacteria in the evolutionary history of ants. Furthermore, our comparative and functional analyses suggest that many of the horizontally acquired genes serve adaptive functions in ants, most prominently by expanding metabolic pathways or modulating immune responses.},
}

@article {pmid41949588,
year = {2026},
author = {Sunmonu, GT and Coldbeck-Shackley, RC and Graham, RMA and Leong, LE and Ogunniyi, AD and Sheppard, AE},
title = {Genomic characterization of mobile genetic elements associated with antimicrobial resistance in Streptococcus pneumoniae from Australia.},
journal = {Microbial genomics},
volume = {12},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001662},
pmid = {41949588},
issn = {2057-5858},
mesh = {*Streptococcus pneumoniae/genetics/drug effects/classification/isolation & purification ; *Interspersed Repetitive Sequences/genetics ; Australia ; Anti-Bacterial Agents/pharmacology ; Humans ; Pneumococcal Infections/microbiology ; Genome, Bacterial ; Drug Resistance, Multiple, Bacterial/genetics ; Macrolides/pharmacology ; *Drug Resistance, Bacterial/genetics ; Genomics ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; },
abstract = {The emergence and spread of antimicrobial resistance (AMR) in Streptococcus pneumoniae threatens current antibiotic treatment strategies. While β-lactams remain the first-line therapy for pneumococcal infections in Australia, resistance to macrolides, tetracyclines and other antibiotics, driven by resistance genes carried on mobile genetic elements (MGEs), is increasingly reported. In this study, we conducted a comprehensive analysis of 573 S. pneumoniae genomes from South Australia, Queensland and Victoria to investigate the distribution of MGEs and their association with acquired AMR genes. Resistance genes and MGEs were identified using AMRFinderPlus and MobileElementFinder. Serotypes, sequence types and global pneumococcal sequence clusters (GPSCs) were assigned using SeroBA, MLST and the GPS pipeline. Out of the 573 genomes, 547 passed quality checks. Tn916-like (Tn916, Tn6002, Tn2010, Tn6003 and ICESpnTw19F14) and Tn5253-like (Tn5253, ICESpn529IQ) integrative conjugative elements carried various combinations of ermB, mefA, msrD, tetM, catA and catA16 genes, supporting horizontal gene transfer as a key mechanism of resistance spread. Macrolide and tetracycline resistance genes co-occurred in 192/239 (80.7%) MGE-positive genomes. The most common MGE-positive serotypes were 33F/ST717/GPSC3 (15.6%, n=30), serotype 4/ST2759/GPSC162 (15.1%, n=29), serotype 15A/ST63/GPSC9 (7.3%, n=14), serotype 23A/ST338/GPSC5 (5.7%, n=11), serotype 15A/ST8625/GPSC9 (3.6%, n=7) and serotype 19A/ST3111/GPSC932 (3.6%, n=7). Our results reflect global trends of MGE-associated resistance in expanding non-vaccine serotypes (such as 15A and 23A) and multidrug-resistant clones. These findings underscore the evolutionary role of MGEs associated with AMR in shaping the pneumococcal resistome and highlight the continuous need for genomic surveillance to inform antibiotic stewardship and vaccine strategies in Australia.},
}

*Streptococcus pneumoniae/genetics/drug effects/classification/isolation & purification
*Interspersed Repetitive Sequences/genetics
Australia
Anti-Bacterial Agents/pharmacology
Humans
Pneumococcal Infections/microbiology
Genome, Bacterial
Drug Resistance, Multiple, Bacterial/genetics
Macrolides/pharmacology
*Drug Resistance, Bacterial/genetics
Genomics
Gene Transfer, Horizontal
Microbial Sensitivity Tests
Multilocus Sequence Typing

@article {pmid41933200,
year = {2026},
author = {Gopu, V and Bhattacharya, S and Bejerano-Sagie, M and Zhuang, M and Nevo, Y and Yakovian, O and Shraiteh, B and Ravins, M and Guria, MK and Kahan, T and Maček, B and Rosenshine, I and Ben-Yehuda, S},
title = {A family of endonucleases blocks nanotube-mediated plasmid exchange.},
journal = {Nature microbiology},
volume = {11},
number = {4},
pages = {960-975},
pmid = {41933200},
issn = {2058-5276},
support = {810186//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; SPP2389//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Plasmids/genetics/metabolism ; *Bacillus subtilis/genetics/enzymology ; *Gene Transfer, Horizontal ; *Nanotubes/chemistry ; *Endonucleases/metabolism/genetics ; Conjugation, Genetic ; Bacterial Proteins/metabolism/genetics ; },
abstract = {Horizontal transfer of small non-conjugative plasmids is primarily attributed to transformation, transduction or comobilization with conjugative elements; however, transfer through intercellular membranous nanotube conduits can also occur. Here we show that nanotube-dependent plasmid exchange (NPex) operates bidirectionally between bacteria, enabling plasmid donation and, to a lesser extent, plasmid acquisition. We identified a Bacillus subtilis isolate, BSB1, deficient in NPex and show that a prophage-encoded factor, YokF, blocks plasmid transmission. YokF is an endonuclease that localizes to the membrane of donor bacteria, where it interacts with the nanotube component, FlhA, to impede plasmid transfer through DNA degradation. We further show that YokF provides an advantage to donor bacteria by restricting the sharing of beneficial plasmids with competing neighbouring cells. Bioinformatics and functional analyses revealed that YokF homologues are widespread across Gram-positive bacteria, representing a conserved family of gatekeepers that restrict plasmid flow via NPex.},
}

*Plasmids/genetics/metabolism
*Bacillus subtilis/genetics/enzymology
*Gene Transfer, Horizontal
*Nanotubes/chemistry
*Endonucleases/metabolism/genetics
Conjugation, Genetic
Bacterial Proteins/metabolism/genetics

@article {pmid41944871,
year = {2026},
author = {Tereshonok, D and Evsyukov, S and Stepanova, A},
title = {Specific features of rol-gene polymorphism of Rhizobium rhizogenes.},
journal = {Archives of microbiology},
volume = {208},
number = {6},
pages = {},
pmid = {41944871},
issn = {1432-072X},
support = {126012015839-6//Ministry of Science and Higher Education of the Russian Federation/ ; 126012015839-6//Ministry of Science and Higher Education of the Russian Federation/ ; 126012015839-6//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Polymorphism, Genetic ; Plant Roots/microbiology ; *Bacterial Proteins/genetics ; Plant Diseases/microbiology ; *Rhizobium/genetics ; *Genes, Bacterial ; Agrobacterium ; },
abstract = {Bacterium Rhizobium rhizogenes has the unique ability to cause hairy root disease. Symptoms of this disease occur when the bacterial genes rolA, rolB, rolC, and rolD, contained in plasmid T-DNA, are expressed after integration into the plant genome. A biotechnological method for obtaining fast-growing in vitro cultures of hairy roots capable of synthesizing secondary metabolites is based on this feature. Also, the ability of the bacterium to mediate horizontal gene transfer may have led to the appearance of rol-gene homologs in plant genomes, which by now have been found in a wide range of species. The variability of rol-genes may play an important role in the evolution of the whole mechanism of natural transformation, as it can potentially affect the physiological properties of transformed plants. The sequence analysis revealed a significant overall degree of variability in rol-genes between bacterial strains. But at the same time, a part of rol-gene sequences remained conserved in both bacterial and plant genomes. A detailed study demonstrated that in all of the considered bacterial rol-genes, as well as in plant genes potentially capable of expression in full-length form, the variability was represented by either nucleotide substitutions or insertions and deletions of multiples of three, which did not permit reading frame displacement.},
}

*Polymorphism, Genetic
Plant Roots/microbiology
*Bacterial Proteins/genetics
Plant Diseases/microbiology
*Rhizobium/genetics
*Genes, Bacterial
Agrobacterium

@article {pmid41946252,
year = {2026},
author = {Deng, B and Ren, ZH and Ren, CY and Zhao, HP},
title = {Inhibiting Cr(VI)-mediated ARG dissemination in wastewater: Synthetic antioxidant-, extracellular polymeric substance-, and nuclease-producing microbiome targeting ROS, MGEs, and ARG-MRG co-occurrence.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {141985},
doi = {10.1016/j.jhazmat.2026.141985},
pmid = {41946252},
issn = {1873-3336},
abstract = {Heavy metals (HMs) trigger the sustained enrichment and dissemination of antibiotic resistance genes (ARGs) by exerting selective pressure, and there is an urgent need for effective and environmentally friendly control strategies. Herein, we found that long-term (180 d) hexavalent chromium [Cr(VI)] stress (10 mg/L) could facilitate the enrichment of multidrug-resistant plasmids (e.g., blaTEM and sul1) and significantly increase (p < 0.05) the conjugative transfer frequency. Subsequently, we constructed a synthetic carotenoid- and extracellular nuclease gene exeM-producing microbiome centered on Deinococcus radiodurans R1, which synthesizes and secretes extracellular polymeric substances (EPS) via the Wzx/Wzy-dependent pathway, thereby alleviating environmental oxidative stress by adsorbing Cr(VI) (over 85%) and scavenging ROS (approximately 18-26-fold). qPCR results demonstrated that the synthetic microbiome effectively reduced ARG abundances, along with the mobile genetic elements traG and intI1 (by more than one order of magnitude, MGEs) and the metal resistance gene chrA (by more than two orders of magnitude, MRG). Electron microscopy and metagenomic analysis demonstrated that the synthetic microbiome could further reduce the co-occurrence of ARGs and MRGs (e.g., tetA, chrA, and chrB) by impairing plasmid integrity and preserving cell membrane integrity (ompC, oprC, plsB, and fabR), thus inhibiting horizontal gene transfer. In addition, it reduced the abundance of Pseudomonadota (the host harboring ARGs and MGEs, p < 0.05) by 33-48%. This study provides a sustainable bioremediation strategy for controlling the dissemination of ARGs in heavy metal-polluted wastewater.},
}

@article {pmid41937731,
year = {2026},
author = {Kong, JF and Phang, HC and Wan Kamal, WHB and Ng, Y and Mohamad, S and Kee, PE and Liew, KB},
title = {Role of Probiotics in Oral Health: A Review From Microbial Balance to Clinical Applications.},
journal = {Current pharmaceutical biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113892010421039251206192855},
pmid = {41937731},
issn = {1873-4316},
abstract = {A diverse microbial community exists within the human oral cavity that plays an essential role in maintaining health or inducing diseases such as dental caries, periodontal disease, and halitosis. Probiotics, live microorganisms that provide health benefits when consumed in adequate amounts, have been found to be promising as a means of modulating the oral microbiome and combating these diseases. This review incorporates present knowledge about the mechanism of probiotic action, including competitive exclusion of pathogens, antimicrobial metabolite production, biofilm disruption, and immune modulation. Efficacy against pathogenic bacteria like Streptococcus mutans and Porphyromonas gingivalis has been proven by prominent probiotic groups Lactobacillus, Bifidobacterium, and Streptococcus, resulting in oral microbial homeostasis. Clinical applications of probiotics include prevention of caries, plaque reduction, and management of gingivitis and periodontitis, with research focusing on strain-specific effects. Emerging trends include precision probiotics tailored to each oral condition, postbiotics as strong alternatives (formerly "strong contenders"), and innovative delivery systems to enhance viability and colonization. The hurdles of strain specificity, regulatory gaps, and inconsistencies of clinical outcome continue. Safety concerns, while rare, represent possible risks of horizontal gene transfer and opportunistic infections in immunocompromised hosts. Future directions lie in genetic modification, new delivery methods, and standard clinical protocols to enhance probiotic function. This review emphasizes the clinical potential of probiotics as adjunctive treatments in oral medicine, with the caveat that further work is needed to overcome current challenges and enhance their therapeutic efficacy.},
}