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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid42734856,
year = {2026},
author = {Lavanya, E and Iruthayasamy, J and Soodamani, A and Petchimuthu, M and Angappan, S and Murugavel, K and Muthusamy, K},
title = {Microbial consortia for pesticide biodegradation: mechanisms, cross-class pathways, and translational challenges.},
journal = {Biodegradation},
volume = {37},
number = {5},
pages = {},
pmid = {42734856},
issn = {1572-9729},
mesh = {Biodegradation, Environmental ; *Microbial Consortia ; *Pesticides/metabolism ; *Bacteria/metabolism/genetics ; },
abstract = {The use of synthetic pesticides estimated at 4.1 million metric tons annually worldwide, has led to widespread contamination of soils and aquatic environments, with documented risks to ecosystem integrity and human health. Physicochemical remediation methods are costly and often generate secondary pollutants and toxic intermediates, making microbial bioremediation a lower-residue alternative to physicochemical treatment. Because pesticide degradation in natural environments is rarely achieved by single microbial species, this review critically synthesizes evidence on multi-species microbial consortia-natural, synthetic, and genetically engineered for the biodegradation of six major pesticide classes: organophosphates, carbamates, pyrethroids, neonicotinoids, organochlorines, and triazines. Integration of the ecological mechanisms underlying consortium synergism (sequential metabolic cooperation, metabolic division of labour, biosurfactant-mediated bioavailability enhancement, horizontal gene transfer, and extracellular enzyme cooperation) with the enzymatic and genetic basis of degradation for each pesticide class, and evaluate how emerging tools like multi-omics profiling, CRISPR-based strain engineering, immobilisation technologies, synthetic consortium design, and AI-assisted optimisation are reshaping consortium design. Reported removal efficiencies are consistently higher for consortia than for monocultures across the studies reviewed here, though direct comparisons vary by pesticide class and experimental design. The review closes by evaluating the principal barriers to field-scale translation, strain persistence, ecological risk and regulatory approval, and monitoring of introduced strains and proposes a tiered framework for matching consortium design to contamination scenario. To date, this is the review to integrate ecological interaction mechanisms, class-specific enzymatic pathways, and translational technologies for pesticide-degrading consortia within a single framework.},
}

Biodegradation, Environmental
*Microbial Consortia
*Pesticides/metabolism
*Bacteria/metabolism/genetics

@article {pmid42735657,
year = {2026},
author = {Wu, C and Shang, X and Cui, Z and Li, Q and Shan, X and Bai, Y and Hu, Q and Jin, H and Sun, Y and Xu, D},
title = {Marine particulate matter serves as a hotspot for enriching pathogenic bacteria and disseminating antibiotic resistance genes.},
journal = {Marine pollution bulletin},
volume = {233},
number = {Pt 3},
pages = {120360},
doi = {10.1016/j.marpolbul.2026.120360},
pmid = {42735657},
issn = {1879-3363},
abstract = {In coastal ecosystems, free-living (FLB) and particle-attached bacteria (PAB) occupy distinct niches, but their pathogenic and antibiotic resistance gene (ARG) reservoirs are lacking. Using molecular approaches, we compared the composition, pathogenic diversity, ARGs abundance, and microbial interactions of FLB and PAB communities from the Bohai Sea. We found PAB had higher diversity, heterogeneity, and network complexity than FLB. PAB hosted 233 potential pathogenic taxa (vs. 169 in FLB), with Escherichia spp., Staphylococcus spp., and Vibrio spp. dominant. Parallel qPCR analysis confirmed that the abundance of Escherichia coli, Vibrio spp., and Pseudomonas aeruginosa were significantly higher in PAB communities, whereas Staphylococcus aureus was more abundant in FLB communities. Among the ten targeted ARGs, eight were significantly more abundant in PAB communities, with sul1, NDM-1, and qacEΔ1-01 being the most dominant subtypes in the study region. Importantly, a significant positive correlation between the total abundances of ARGs and mobile genetic elements was observed exclusively in PAB communities, suggesting that particle surfaces serve as hotspots for horizontal gene transfer (HGT). Our results not only reinforce the role of HGT as a key mechanism for ARG dissemination in marine bacteria, but also highlights that such transfer likely occurred across the interface between FLB and PAB communities, forming a dynamic, interconnected network for ARG exchange. Collectively, this study highlights the critical role of marine particles in structuring microbial communities, enriching pathogens, and facilitating antibiotic resistance propagation, offering important insights for assessing ecological and public health risks in coastal waters.},
}

@article {pmid42735830,
year = {2026},
author = {Ma, Y and Ge, Y and Liu, C and Wang, M and Xiao, Z and Liu, X and Song, T and Zhou, Q and Xiao, L},
title = {Pathogenic microbiomes on jellyfish reveal health risks beyond envenomation.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {},
number = {},
pages = {109307},
doi = {10.1016/j.toxicon.2026.109307},
pmid = {42735830},
issn = {1879-3150},
abstract = {Jellyfish stings pose a growing public health concern in coastal regions, yet secondary bacterial infections arising from venom-induced tissue damage remain largely unexplored. Here we used shotgun metagenomics to characterize the surface microbiomes of Rhopilema esculentum, Chrysaora quinquecirrha and Stomolophus meleagris, profiling bacterial composition, virulence factors, antibiotic resistance genes and mobile genetic elements. We observed distinct host-specific microbiome signatures, with R. esculentum harboring the highest abundance of virulence-associated genes and notable enrichment of WHO priority pathogens including Staphylococcus aureus and Acinetobacter baumannii. Resistance genes conferring tetracycline, glycopeptide and fluoroquinolone resistance were prevalent across all species. Transposases comprised over 45% of mobile genetic elements, indicating substantial horizontal gene transfer potential. Validation using newly developed TaqMan qPCR assays across eight jellyfish species including the three aforementioned and five additional species, confirming that all harbored at least one opportunistic pathogen. These findings establish jellyfish surfaces as underappreciated reservoirs of antibiotic-resistant pathogens and highlight a potential, but as yet unproven, route of pathogen exposure following envenomation.},
}

@article {pmid42721553,
year = {2026},
author = {Yang, Z and Yuan, J and Liu, X and Huang, T and Wang, C and Wang, Y and Chen, Y and Li, X and Tang, L},
title = {Spatiotemporal dynamics and dual-transfer mechanisms of the riverine resistome under antibiotic and metal co-pollution in the Xiangjiang River Basin.},
journal = {Water research},
volume = {308},
number = {Pt A},
pages = {126847},
doi = {10.1016/j.watres.2026.126847},
pmid = {42721553},
issn = {1879-2448},
abstract = {The co-pollution of antibiotics and heavy metals severely exacerbates the dissemination of antimicrobial resistance, yet the distinct mechanisms driving resistome assembly across complex environmental matrices remain poorly understood. This study characterizes the spatiotemporal dynamics of the resistome under multi-pollutant stress within the water-sediment system of the Xiangjiang River, a basin historically impacted by intensive heavy metal smelting and contemporary antibiotic discharges. We elucidate a phase-dependent "dual-track" mechanism governing resistance evolution. In the flowing aqueous phase, particularly during wet-season runoff events, sub-inhibitory antibiotics serve as a primary stimulant that promotes a high potential for rapid horizontal gene transfer, facilitating the structural consolidation of multidrug resistance genes with highly mobile genetic elements. Conversely, in benthic sediments, persistent heavy metal legacies exert deterministic selective pressure that restructures the microbial host community, strongly implicating host-dependent vertical gene transfer as the dominant pathway for resistome enrichment. Crucially, our in vitro transformation models demonstrate that antibiotics and heavy metals exert a potent combined promotion effect on genetic exchange during co-exposure, with both contaminants concurrently driving the significant elevation of horizontal mobility. This potent co-selection transforms the riverine ecosystem into a dynamic "genetic reactor", enabling environmental microbiomes to acquire broad-spectrum resistance traits through singular transfer events. Ultimately, our findings highlight the urgent need for integrated water-sediment management and the synchronized co-regulation of mixed contaminants to mitigate escalating ecological and public health risks.},
}

@article {pmid42723086,
year = {2026},
author = {Afkhamian, A and Saffari Natanzi, A and Jafaridarabjerdi, M and Aghaei, S and Haghjou, A and Shafiei, M and Bashkandi, AH and Shahraki, S and Reiter, RJ and Haddad Kashani, H and Yang, Y},
title = {Virobiome-mediated regulation of microbiota-gut-brain axis signaling and neuroimmune homeostasis.},
journal = {Cell communication and signaling : CCS},
volume = {24},
number = {1},
pages = {},
pmid = {42723086},
issn = {1478-811X},
mesh = {Humans ; *Homeostasis ; Animals ; *Signal Transduction ; *Brain/immunology/metabolism ; *Gastrointestinal Microbiome ; *Virome ; },
abstract = {The human gut-brain axis (GBA) is increasingly recognized as a complex bidirectional communication system integrating microbial, neural, endocrine, and immune networks that shape neurological health. While bacterial contributions to this dialogue have been extensively characterized, the viral component of the gut ecosystem, the virome, has emerged as an important component associated with host physiological regulation. This review synthesizes evidence suggesting that bacteriophages and eukaryotic viruses may contribute to microbial and immune homeostasis and may influence signaling along the microbiota-gut-brain axis. In experimental studies, Bacteriophages have been shown to influence microbial community structure through lytic and lysogenic cycles, horizontal gene transfer, and metabolic modulation, indirectly regulating production of neuroactive metabolites such as short-chain fatty acids and tryptophan derivatives which in turn have been linked to blood brain barrier integrity and modulate microglial activation. In observational human studies and experimental models, eukaryotic viruses including Epstein Barr virus and cytomegalovirus have been associated with systemic inflammation, molecular mimicry, and cytokine dysregulation, amplifying neuroimmune cascades implicated in Alzheimer's disease (AD), multiple sclerosis (MS), autism spectrum disorder (ASD), and major depressive disorder (MDD). The convergence of viral-bacterial interactions highlights a transkingdom signaling network shaping neuroinflammatory tone and influencing disease susceptibility. Emerging experimental strategies, including precision phage therapy, engineered probiotics incorporating CRISPR-based antiviral systems, and fecal virome transplantation (FVT), are being explored as potential approaches to modulate virome-microbiome interactions. Integration of multiomics platforms with artificial intelligence-driven modeling will be critical for clarifying the temporal and mechanistic relationships between virome dynamics and neurological function. Collectively, these insights highlight the gut virobiome as a potentially important contributor to neuroimmune equilibrium and illuminate avenues for microbiome-informed diagnostics and interventions in neurodegenerative and neuropsychiatric disorders. This review therefore highlights the often underappreciated role of the gut virobiome and proposes an integrative conceptual model linking virome dynamics with microbiota-gut-brain axis signaling.},
}

Humans
*Homeostasis
Animals
*Signal Transduction
*Brain/immunology/metabolism
*Gastrointestinal Microbiome
*Virome

@article {pmid42725757,
year = {2026},
author = {Dörr, L and Ghosh, R and Schweikert, M},
title = {Bacterial R-bodies with common morphologies and unrolling dynamics are phylogenetically scattered, indicating extensive lateral gene transfer and wide application potential.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0086426},
doi = {10.1128/aem.00864-26},
pmid = {42725757},
issn = {1098-5336},
abstract = {Refractile bodies (R-bodies) of gram-negative bacteria are large proteinaceous assemblies, rolled up in the form of an Archimedean spiral. They exhibit rapid rod-like reversible extension in the micrometer range when cued by chemical environmental triggers and have potential for synthetic biology and biochip applications. Initially described for the Paramecium endosymbionts Caedibacter taeniospiralis and Caedimonas varicaedens, R-bodies have since been discovered in many classes of Pseudomonadota, both in endosymbionts and in non-endosymbionts. However, despite the fact that the genetics and morphologies, as well as the unrolling kinetics of R-bodies from different species, show considerable diversity, no recent study has integrated these aspects into a single framework. The latter would be advantageous for the creation of an R-body biotechnology toolbox, where different properties determine the application area. Here, we have examined the R-bodies from six different Pseudomonadota, comprising both phylogenetically diverse endosymbionts and non-endosymbionts. Comparison of the morphologies of the rolled-up and unrolled forms, obtained using electron microscopy and high-quality images, to their corresponding genetic data indicates that extensive lateral gene transfer has occurred, which confounds a common framework based on these data. However, we have also studied the R-body extension and retraction kinetics using high frame-rate light microscopic video recordings, where we show for the first time that R-bodies can be classified into two classes, showing "fast burst" or "slow" acid-induced extension kinetics, respectively. We propose that this criterion may, in fact, be the most useful for the choice of an R-body tool for biotechnological purposes.IMPORTANCER-bodies are unique proteinaceous macromolecular structures capable of massive reversible extension in response to external environmental triggers without the input of chemical energy. They comprise only a few small polypeptides, which makes them potentially highly amenable to tuning via genetic engineering, as well as being exceptionally stable. These properties would be highly desirable in biotechnology and synthetic biology, as well as in biochip applications, where a controlled mechanical extensor might play an integral part in a nanoscale molecular machine. So far, only R-bodies from a single species, Caedibacter taeniospiralis, have been characterized extensively. However, in recent years, genomic information has revealed that a panoply of R-bodies are widely distributed among gram-negative phyla, although studies have generally not included morphological data. This study brings these two areas together to provide a holistic overview of the field and also reveals new insights into key dynamic aspects of R-body extension.},
}

@article {pmid42727463,
year = {2026},
author = {Fan, Y and Guo, X and Lyu, J and Wang, X and He, Y},
title = {Planetary health and pharmacology: Addressing the ecological impact and circular threat of pharmaceuticals.},
journal = {Ecotoxicology and environmental safety},
volume = {323},
number = {},
pages = {120787},
doi = {10.1016/j.ecoenv.2026.120787},
pmid = {42727463},
issn = {1090-2414},
abstract = {Drug safety science has expanded beyond patient-level pharmacovigilance to address the environmental consequences of pharmaceutical use. Pharmaceuticals are now detected across diverse ecosystems, but traditional single-compound, high-dose toxicological frameworks remain inadequate for evaluating chronic, low-dose, multi-compound environmental exposures. This review provides a mechanistic analysis of pharmaceutical ecotoxicity, tracing how molecular interactions with conserved biological targets in non-target organisms translate into population-level ecological effects. Synthetic estrogens activate nuclear hormone receptors at nanogram-per-liter concentrations, driving reproductive failure through receptor-mediated transcriptional reprogramming. Psychoactive drugs disrupt neurotransmitter systems conserved across vertebrates, altering predator avoidance and reproductive behavior at sub-microgram-per-liter levels. Anti-inflammatory drugs cause species-specific toxicity through differential phase II metabolism, as the diclofenac-vulture crisis demonstrates. Anticancer agents produce genotoxic effects in aquatic organisms through the same DNA-damaging mechanisms underlying their therapeutic activity. A unifying theme emerges when these endpoints are considered alongside antimicrobial resistance: sub-inhibitory antibiotic concentrations in environmental hotspots select for resistant bacteria and accelerate horizontal gene transfer, with resistance genes returning to human pathogens through water, food, and occupational exposure, completing a circular threat linking environmental contamination to clinical treatment failure. Mitigation strategies are evaluated across the pharmaceutical lifecycle, including biodegradable molecular design, manufacturing discharge controls, antimicrobial stewardship, and advanced wastewater treatment. The analysis demonstrates that effective intervention requires targeting root causes across the pharmaceutical lifecycle rather than relying on end-of-pipe remediation, and that integrating environmental sustainability into pharmaceutical safety assessment is essential for protecting both ecological and human health.},
}

@article {pmid42713726,
year = {2026},
author = {Cao, Y and Zhu, LJ and Wang, T and Yu, W},
title = {The Conjugative Megaplasmid pMD9A Mediates Transferring Antibiotic Resistance Genes.},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {10766294261484663},
doi = {10.1177/10766294261484663},
pmid = {42713726},
issn = {1931-8448},
abstract = {Pseudomonas asiaticais an emerging opportunistic pathogen with a broad host range. Current evidence suggests that some isolates exhibit multidrug resistance, which may complicate treatment. In this study, a multidrug-resistant P. asiatica strain MD9 was isolated from aquaculture water. We aimed to characterize its complete genome sequence and investigate the role of its conjugative megaplasmid pMD9A in the horizontal transfer of antibiotic resistance genes. The genome of MD9 consists of one circular chromosome (5,956,782 bp, with a G + C content of 62.5%) and one circular megaplasmid, pMD9A (455,169 bp, with a G + C content of 56.5%). Genome annotation identified 65 antibiotic resistance genes and 148 putative virulence factor-encoding genes in the MD9 genome. The megaplasmid pMD9A carries 29 antibiotic resistance genes conferring resistance to β-lactams, chloramphenicol/florfenicol, aminoglycosides, and macrolides. A class 1 integron (intI1) and multiple autonomous conjugative transfer elements were identified in pMD9A. Conjugation experiments demonstrated that the β-lactam resistance gene blaOXA-246 could be horizontally transferred from the donor MD9 strain to the recipient Escherichia coli 25DN strain. The megaplasmid pMD9A not only carries a broad array of antibiotic resistance genes, but also facilitates their horizontal spread among environmental bacteria, thereby potentially contributing to the dissemination of multidrug-resistant bacteria.},
}

@article {pmid42714165,
year = {2026},
author = {Xia, Y and Cai, L and Ding, B and Su, B and Zhang, R},
title = {Megamimivirus double-stranded DNA linear genomes flanked by highly diverse terminal inverted repeats.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0082526},
doi = {10.1128/jvi.00825-26},
pmid = {42714165},
issn = {1098-5514},
abstract = {UNLABELLED: Giant viruses have fundamentally expanded our understanding of virology by challenging the conventional boundaries of both virion size and genome complexity. However, the scarcity of isolates has left many of their unique biological features unexplored. Here, we report the isolation and characterization of four new giant virus species belonging to the subfamily Megamimivirinae, sampled from distinct environments across China. Among these, Megavirus daqingense is the first giant virus isolated from an oil reservoir; it exhibits virion stability under high salinity, chloroform exposure, and elevated temperatures, suggesting fitness adaptations to subsurface conditions. Using a hybrid sequencing approach that integrates short- and long-read technologies, we assembled complete linear genomes for all four isolates, each flanked by long terminal inverted repeats (TIRs). Comparative genomic and synteny analyses identified 29 distinct TIRs from 46 megamimivirus genomes. Gene content within these TIRs was highly diverse, with no orthologous proteins conserved across all repeats. Furthermore, TIR genes experienced weaker purifying selection than those in non-TIR regions (i.e., the genomic regions excluding the TIRs), consistent with their role as drivers of genome plasticity. Notably, we discovered for the first time that identical tRNA genes are shared between TIRs and non-TIR regions of eukaryotic viruses. Collectively, our work provides insights into the structural and evolutionary complexity of megamimiviruses, revealing TIRs as reservoirs of genetic diversity and hotspots for gene transfer, thereby playing a pivotal role in shaping the dynamic architecture of giant virus genomes.

IMPORTANCE: Terminal inverted repeats (TIRs) are critical structural elements at the termini of linear genomes essential for fundamental processes such as recombination, replication, and integration across diverse organisms. However, the inherent limitations of short-read sequencing technologies have left the complete structure, diversity, and evolutionary significance of long TIRs in giant viruses unexplored. In this study, we leverage hybrid sequencing and comparative genomic analyses to unveil the complexity of TIRs across the subfamily Megamimivirinae. We demonstrate that TIRs are dynamic genomic hotspots characterized by remarkable gene diversity and unexpected conservation of specific tRNA genes. These findings establish TIRs as key drivers of genome plasticity, serving as hotspots for horizontal gene transfer and genetic innovation. By resolving the long-hidden terminal structures of megamimivirus genomes, this work provides a foundational framework for understanding how TIRs shape the evolution of giant viruses and, more broadly, advances our understanding of genome architecture in large DNA viruses.},
}

@article {pmid42715613,
year = {2026},
author = {Christensen, JM and Neilson, EHJ},
title = {A plant-centric view of class B flavin-dependent monooxygenase evolution and diversity.},
journal = {The Plant journal : for cell and molecular biology},
volume = {127},
number = {5},
pages = {e71106},
doi = {10.1111/tpj.71106},
pmid = {42715613},
issn = {1365-313X},
support = {0054890//Novo Nordisk Fonden/ ; 1051-00083B//Danmarks Frie Forskningsfond/ ; 1131-0002B//Danmarks Frie Forskningsfond/ ; },
mesh = {Phylogeny ; *Evolution, Molecular ; *Mixed Function Oxygenases/genetics/metabolism ; *Oxygenases/genetics/metabolism ; *Flavins/metabolism ; *Plant Proteins/genetics/metabolism ; *Viridiplantae/genetics/enzymology ; *Plants/genetics/enzymology ; },
abstract = {Flavin-dependent monooxygenases (FMOs) are ancient enzymes present throughout all kingdoms of life. FMOs utilize flavin-based cofactors to incorporate an oxygen atom into their substrate, altering its chemical properties. Class B FMOs are enriched throughout the plant kingdom, catalyzing essential reactions for plant development and defense, including auxin biosynthesis and systemic acquired resistance. Despite these essential metabolic roles, class B FMO functional characterization remains relatively limited, with no common evolutionary framework for FMO diversity across the plant kingdom currently available. By mining genomes representing 78 major Viridiplantae lineages, we present a curated dataset and comprehensive plant-centric phylogenetic analysis of class B FMOs, classifying eight distinct families: BVMO, N-Ox, N-Ox like 1, SeedlessFMO, S-Ox, S-Ox like 1, S-Ox like 2, and YUCCA. Most families evidently originate from an algal progenitor, although disparate degrees of FMO prevalence within and across families suggest multiple acquisition events in plants via horizontal gene transfer. Structural modeling and domain architecture analysis provide a refined framework for class B FMO diversity in plants delivering new insights into protein diversity and evolution. This plant-centric focus on class B FMOs provides an important resource that will facilitate further biochemical and functional characterization within plant development and response to environmental change.},
}

Phylogeny
*Evolution, Molecular
*Mixed Function Oxygenases/genetics/metabolism
*Oxygenases/genetics/metabolism
*Flavins/metabolism
*Plant Proteins/genetics/metabolism
*Viridiplantae/genetics/enzymology
*Plants/genetics/enzymology

@article {pmid42709849,
year = {2026},
author = {Holtgrefe, N and van Iersel, L and Meuwese, R and Murakami, Y and Schestag, J},
title = {PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {15578666261481955},
doi = {10.1177/15578666261481955},
pmid = {42709849},
issn = {1557-8666},
abstract = {Phylogenetic diversity (PD) plays an important role in biodiversity, conservation, and evolutionary studies by measuring the diversity of a set of taxa based on their phylogenetic relationships. In phylogenetic trees, a subset of k taxa with maximum PD can be found by a simple and efficient greedy algorithm. However, this algorithmic tractability is lost when considering phylogenetic networks, which incorporate reticulate evolutionary events such as hybridization and horizontal gene transfer. To address this challenge, we introduce PaNDA (Phylogenetic Network Diversity Algorithms), the first software package and interactive graphical user-interface for exploring, visualizing, and maximizing diversity in phylogenetic networks. PaNDA includes a novel algorithm to find a subset of k taxa with maximum diversity, running in polynomial time for networks of bounded scanwidth, a measure of tree-likeness of a network that grows slower than the well-known level measure. This algorithm considers the variant of PD on networks in which the branch lengths of all paths from the root to the selected taxa contribute towards their diversity. We demonstrate the scalability of this algorithm on simulated networks, successfully analyzing level-15 networks with up to 200 taxa in seconds. We also provide a proof-of-concept analysis using a phylogenetic network on Xiphophorus species, illustrating how the tool can support diversity studies based on real genomic data. The software is easily installable and freely available at https://github.com/nholtgrefe/panda. Additionally, we extend the definition of PD to semi-directed phylogenetic networks, which are mixed graphs increasingly used in phylogenetic analysis to model uncertainty of the root location. We prove that finding a subset of k taxa with maximum diversity remains NP-hard on semi-directed networks, but do present a polynomial-time algorithm for networks with bounded level.},
}

@article {pmid42711294,
year = {2026},
author = {Peng, Y and Woods, LC and Perlaza-Jimenez, L and Lappan, R and Jespersen, M and Dong, X and Holland, SR and Chown, SL and Leung, PM and Greening, C},
title = {Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42711294},
issn = {2041-1723},
support = {FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; MGS and MITS//Monash University (MU)/ ; },
mesh = {Antarctic Regions ; *Gene Transfer, Horizontal ; *Soil Microbiology ; Phylogeny ; *Selection, Genetic ; Hydrogenase/genetics ; *Adaptation, Physiological/genetics ; Metagenome ; Aldehyde Oxidoreductases/genetics ; Bacteria/genetics/classification ; Multienzyme Complexes ; },
abstract = {Terrestrial Antarctica harbors compositionally diverse and functionally distinct microbial life. Yet the eco-evolutionary processes underlying adaptation to Antarctica's polyextreme conditions remain largely unknown. Here, we address how horizontal gene transfer (HGT) and de novo mutations influence microbial adaptation in 16 Antarctic soils using combined short- and long-read datasets. Phylogenetic reconciliation and mobile genetic element analysis of 676 metagenome-assembled genomes show frequent HGT across communities. While transferred genes span diverse functional categories, those involved in energy metabolism are exchanged at higher frequency. Genes for aerotrophy, i.e. the consumption of atmospheric trace gases to provide energy, carbon, and hydration, are among the most frequently disseminated. Approximately a quarter of carbon monoxide dehydrogenases and [NiFe]-hydrogenases are predicted to be horizontally acquired and are often associated with mobile genetic elements. Analysis of polymorphisms suggests widespread purifying selection, particularly for aerotrophy genes, providing further evidence that aerotrophy is critical for microbial survival in Antarctica. Genetic variation in hydrogenases is tightly associated with predicted protein structures, with intense selection acting on critical sites preserving stability and function. Together, these findings show that previously unrecognized eco-evolutionary dynamics shape the composition and function of Antarctic microbial communities, and confirm aerotrophy is a strongly selected and horizontally disseminated trait.},
}

Antarctic Regions
*Gene Transfer, Horizontal
*Soil Microbiology
Phylogeny
*Selection, Genetic
Hydrogenase/genetics
*Adaptation, Physiological/genetics
Metagenome
Aldehyde Oxidoreductases/genetics
Bacteria/genetics/classification
Multienzyme Complexes

@article {pmid42713434,
year = {2026},
author = {LeCuyer, TE and Monahan, J and Farrell, K and Adams, K and Walters, A and McClendon, D and Fox, A and Bianchi, JR},
title = {Antimicrobial susceptibility patterns of commensal fecal bacteria isolated from pigs with an intentional genomic alteration that included the selectable marker gene nptII.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1885937},
pmid = {42713434},
issn = {1664-302X},
abstract = {INTRODUCTION: Animals with intentional genomic alterations (IGAs) hold promise for meeting increasing worldwide demand for animal-source proteins. As part of regulatory risk assessment for introducing animals with IGAs into the food chain, monitoring commensal bacterial microbiota is recommended due to concern that antimicrobial resistance genes used during IGA selection could be transferred, via horizontal gene transfer, to gastrointestinal or environmental bacterial populations, potentially contributing to antimicrobial resistance. The objective of this study was to assess the antimicrobial susceptibility patterns in commensal bacteria isolated from fecal samples of GalSafe™ pigs that have an IGA that includes the aminoglycoside resistance gene nptII.

METHODS: Antimicrobial resistance rates observed in Escherichia coli, Salmonella, Campylobacter and Enterococcus isolated from GalSafe™ pigs were compared to resistance rates observed in conventional pigs at slaughter. Bacterial isolates were tested for antimicrobial resistance genes by PCR and one isolate underwent whole genome sequencing.

RESULTS: In total, 137 bacterial isolates recovered from 55 fecal samples collected from 47 individual adult GalSafe™ pigs were evaluated. Prevalence of antimicrobial resistance in GalSafe™ pigs was generally similar to, or lower than, resistance prevalence reported from conventional pigs at slaughter, based on National Antimicrobial Resistance Monitoring System (NARMS) data. Higher resistance rates in GalSafe™ pigs were observed only for quinolones in Campylobacter coli (ciprofloxacin and nalidixic acid) and nitrofurantoin in Enterococcus spp. One isolate (E. coli) was positive for nptII neomycin resistance gene, the same gene used for IGA selection in GalSafe™ pigs, and the remaining 136 isolates were negative for nptII. However, the positive isolate did not appear to contain nptII derived from the GalSafe™ pig genome as the sequences flanking the gene did not match the IGA.

DISCUSSION: We did not detect evidence of nptII gene transformation into bacterial species of potential human health importance in this population of GalSafe™ pigs.},
}

@article {pmid42709738,
year = {2026},
author = {Le, YH and Azumah, JD and Khong, DT and Nguyen, TN and Appiah-Kwarteng, C and Matsui, K and Yamamoto, M and Tanaka, K and Yamamoto, Y},
title = {Comparative prevalence of the mercury resistance gene merA in human feces, food, and environmental water from Japan, Vietnam, and Ghana.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0357976},
pmid = {42709738},
issn = {1932-6203},
mesh = {Humans ; Ghana ; Vietnam ; Animals ; *Feces/microbiology ; Japan ; *Mercury/toxicity ; Water Microbiology ; Meat/microbiology ; *Drug Resistance, Bacterial/genetics ; Chickens ; },
abstract = {In this study, we investigated the prevalence and abundance of the mercury resistance gene merA in human feces, retail chicken meat, and environmental water samples collected from Japan, Vietnam, and Ghana. A real-time PCR assay developed in this study demonstrated high specificity toward merA sequences from more than 12 bacterial species. Using this assay, merA was detected in 6.8% of human fecal samples in Japan (n = 29), in contrast to significantly higher rates observed in Vietnam (70.2%, n = 47) and Ghana (97.4%, n = 39). Similar geographic trends were evident in the chicken meat samples: 18.5% in Japan (n = 27), 66% in Vietnam (n = 91), and 90% in Ghana (n = 10). Environmental water samples showed a consistently high merA detection rate across all countries (75-100%, n = 21), with substantially higher gene copy numbers in Vietnam and Ghana than in Japan. merA was detected in some water samples, even when total mercury concentrations were below the detection limit, indicating that molecular detection may offer greater sensitivity than traditional physicochemical methods. Mercury-resistant bacteria were successfully isolated and cultured, and Citrobacter freundii was identified as the representative strain. Genomic analysis revealed that merA was located on an IncFIB plasmid, flanked by insertion sequences, suggesting its potential for horizontal gene transfer. These findings highlight merA as a promising biomarker for environmental mercury exposure and support the utility of fecal merA analysis as a proxy for assessing mercury-related public health risks.},
}

Humans
Ghana
Vietnam
Animals
*Feces/microbiology
Japan
*Mercury/toxicity
Water Microbiology
Meat/microbiology
*Drug Resistance, Bacterial/genetics
Chickens

@article {pmid42641524,
year = {2026},
author = {Meng, Y and Gao, P and Liang, H and Wei, Z and Ren, X and Pan, H and Feng, H and Hu, S},
title = {Transmission dynamics and driving mechanisms of antibiotic resistance genes through a chronosequence of saline-sodic rice cultivation.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143380},
doi = {10.1016/j.jhazmat.2026.143380},
pmid = {42641524},
issn = {1873-3336},
mesh = {*Oryza/growth & development ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Soil/chemistry ; *Genes, Bacterial ; Gene Transfer, Horizontal ; Salinity ; Agriculture ; },
abstract = {Rice cultivation reclaims saline-sodic soils and improves fertility, but may also promote antibiotic resistance genes (ARGs) accumulation and horizontal transfer, posing ecological risks. This study investigated long-term co-evolution of soil properties, microbial communities, ARGs, and mobile genetic elements (MGEs) across a 1-78 year cultivation chronosequence in saline-sodic fields. Results indicated that prolonged cultivation effectively alleviated soil salinization and increased fertility. Microbial communities shifted directionally, with functional taxa enriched, while opportunistic pathogen-containing genera peaked during 5-20 years. ARGs abundance and diversity increased markedly after five years and peaked at 10-20 years. Multidrug efflux pump genes persisted throughout the chronosequence, whereas aminoglycoside resistance genes declined after 30 years. MGEs activity increased over time and was significantly correlated with key ARGs. Path analysis identified improved soil properties as the primary direct driver of ARGs accumulation, while cultivation-induced declines in microbial diversity indirectly promoted ARGs dissemination by weakening the community's suppression of MGEs-mediated horizontal transfer. Collectively, long-term rice cultivation not only ameliorated saline-sodic soils but also created a dynamic, stage-specific resistome, with the 5-20 year period representing a critical risk window for ARGs propagation. These findings highlight the need to integrate ARGs monitoring into soil health assessments for sustainable management of reclaimed saline-sodic lands.},
}

*Oryza/growth & development
*Soil Microbiology
*Drug Resistance, Microbial/genetics
Soil/chemistry
*Genes, Bacterial
Gene Transfer, Horizontal
Salinity
Agriculture

@article {pmid42705771,
year = {2026},
author = {Shah, N and Munir, A and Shafiq, M and Shoaib, M},
title = {From commensal to pathobiont: The emergence of virulence-enhanced Escherichia coli in China's food-animal systems - insights with future implications.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120414},
doi = {10.1016/j.foodres.2026.120414},
pmid = {42705771},
issn = {1873-7145},
mesh = {Animals ; China/epidemiology ; *Escherichia coli/pathogenicity/genetics/drug effects ; *Food Microbiology ; Virulence/genetics ; *Escherichia coli Infections/epidemiology/microbiology/veterinary ; Humans ; Virulence Factors/genetics ; Drug Resistance, Bacterial/genetics ; *Foodborne Diseases/microbiology/epidemiology ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {A fundamental shift in Escherichia coli epidemiology is being driven by convergence of virulence determinants and antimicrobial resistance within linked human-animal-environment systems. In China, the rapid growth of food-animal production, extensive antimicrobial use, and complex food networks are accelerating the emergence and dissemination of virulence-enhanced E. coli pathobionts. This review synthesizes recent epidemiological, genomics, and outbreak data to characterize China's evolving landscape of food-animal-associated E. coli. We highlight a significant shift from classical pathotypes to hybrid lineages that simultaneously carry virulence factors and last-resort antibiotic resistance determinants, including mcr-1, tet(X4), and blaNDM. These traits disseminate rapidly via plasmid-mediated horizontal gene transfer, facilitating rapid adaptation and enabling cross-sectoral One Health transmission. National surveillance, foodborne outbreak investigations, and whole-genome sequencing data show that food-animal reservoirs are active evolutionary niches that drive pathogen diversity and fitness, rather than serving merely as contamination sources. Whole-genome sequencing also pinpoints high-risk clones (e.g., ST394) and plasmid-mediated co-selection of virulence and AMR. The emergence of hybrid pathotypes (e.g., STEC/ETEC) and AMR-virulence co-selection challenges traditional classification and limits the effectiveness of conventional surveillance approaches. The 2017 colistin ban reduced mcr-1, yet ongoing resistance and emerging tet(X4) demand integrated surveillance. Collectively, these findings call for reconceptualizing E. coli as a dynamic genomic entity embedded within a unified ecological network. Addressing this threat requires an integrated One Health strategy including genomic surveillance, agricultural antimicrobial stewardship, and coordinated food-environment-clinical monitoring to prevent high-risk clone emergence and global spread.},
}

Animals
China/epidemiology
*Escherichia coli/pathogenicity/genetics/drug effects
*Food Microbiology
Virulence/genetics
*Escherichia coli Infections/epidemiology/microbiology/veterinary
Humans
Virulence Factors/genetics
Drug Resistance, Bacterial/genetics
*Foodborne Diseases/microbiology/epidemiology
Anti-Bacterial Agents/pharmacology
Gene Transfer, Horizontal

@article {pmid42706609,
year = {2026},
author = {Sun, YZ and Su, JW and Elsheikha, HM and Lou, WB and Song, YH and Li, JM and Liu, F and Cai, R and Leng, X and Gong, QL and Zhang, XX},
title = {Farming reshapes the gut resistome, virulome, and mobilome of Cervidae.},
journal = {Virulence},
volume = {17},
number = {1},
pages = {2728506},
doi = {10.1080/21505594.2026.2728506},
pmid = {42706609},
issn = {2150-5608},
mesh = {Animals ; Gene Transfer, Horizontal ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Deer/microbiology/virology ; Metagenome ; Interspersed Repetitive Sequences ; Virulence Factors/genetics ; Plasmids/genetics ; Bacteriophages/genetics ; Virome ; Bacteria/genetics/drug effects/classification ; Agriculture ; },
abstract = {The rapid expansion of cervid farming raises concerns about antimicrobial resistance (AMR) dissemination, yet its impact on the Cervidae gut microbiome remains poorly characterized. We integrated 89 newly sequenced fecal metagenomes with 599 publicly available datasets, comprising 285 metagenomes from farmed cervids and 370 from wild cervids, to construct a catalog of 15,494 non-redundant metagenome-assembled genomes (MAGs) representing 2,401 species. Our analysis demonstrates that farming profoundly reshapes the gut microbiome's functional composition. Specifically, farmed cervids exhibited significantly higher relative abundance, diversity, and heterogeneity of antimicrobial resistance genes (ARGs) compared to wild counterparts. We observed a robust synergistic relationship between ARGs, virulence factor genes, and mobile genetic element (MGE)-associated genes, identifying 70 ARG-MGE combinations as evidence of potential horizontal gene transfer. Plasmid profiling further suggested that a subset of ARGs may be associated with conjugative plasmids, with plasmid-associated ARGs being significantly more abundant in farmed than in wild cervids. Virome analyses indicated that bacteriophages, particularly Siphoviridae, may serve as mobile reservoirs for ARGs. Notably, Cervidae shared 268 ARG types with humans, including 23 high-risk genes associated with resistance to clinically important antibiotics (e.g. tetX1, vanRD, and bla-CTX-M-178), with Escherichia coli as a key cross-host carrier. These findings highlight that human-impacted cervid gut microbiomes are significant environmental reservoirs of clinically relevant AMR, underscoring the necessity for enhanced antibiotic stewardship and resistance surveillance in managed wildlife within a One Health framework.},
}

Animals
Gene Transfer, Horizontal
*Gastrointestinal Microbiome/genetics
Feces/microbiology
*Deer/microbiology/virology
Metagenome
Interspersed Repetitive Sequences
Virulence Factors/genetics
Plasmids/genetics
Bacteriophages/genetics
Virome
Bacteria/genetics/drug effects/classification
Agriculture

@article {pmid42706795,
year = {2026},
author = {Guo, HD and Zhang, ZJ and Ling, MF and Sun, CX and Guo, Y and Liu, XB and Zhu, KS and Xiang, H and Qian, HY and Tan, AJ},
title = {A horizontally acquired gene mediates insect cocoon pigmentation in the eri silkmoth, Samia ricini.},
journal = {Zoological research},
volume = {47},
number = {5},
pages = {1691-1702},
doi = {10.24272/j.issn.2095-8137.2025.447},
pmid = {42706795},
issn = {2095-8137},
mesh = {Animals ; *Gene Transfer, Horizontal ; *Bombyx/genetics/physiology ; *Pigmentation/genetics/physiology ; },
abstract = {Holometabolous insects make cocoons during larval-pupal metamorphosis to protect the pupal phase. The materials used for cocoon construction vary widely. Lepidopteran insects typically secrete silk to form cocoons, which display diverse colors. The eri silkworm, Samia cynthia ricini, is an economically important domesticated species that mostly produces white cocoons, with some varieties producing red cocoons. The enzyme kynureninase (KYNU), acquired from bacteria by horizontal gene transfer, has previously been implicated in insect coloration, while the tryptophan metabolite 3-hydroxyanthranilic acid (3-HAA) has been identified as a red pigment. However, exactly how KYNU is involved in cocoon pigmentation remains unclear. Here, we report that a horizontally transferred bacterial gene encoding KYNU regulates red cocoon formation. Metabolomic analysis revealed a high accumulation of 3-HAA in red cocoons, confirming its role as the primary pigment and associating the coloration with tryptophan metabolism. Quantitative real-time polymerase chain reaction (qPCR) analysis indicated that SrKYNU is highly expressed in the silk glands and significantly downregulated in the red cocoon strain compared to the white cocoon strain. Genomic sequencing identified a 141 bp deletion in the upstream regulatory region of KYNU in the red cocoon strain compared to the white cocoon strain. Dual-luciferase assays confirmed that this deletion significantly reduced promoter activity. CRISPR/Cas9 knockout of SrKYNU in the white-cocoon strain resulted in mutants producing red cocoons with elevated 3-HAA content. These findings reveal that the horizontally transferred gene SrKYNU exhibits tissue-specific expression and regulates cocoon coloration in S. ricini, illustrating that horizontal gene transfer can play an important role in regulating an insect physiological process.},
}

Animals
*Gene Transfer, Horizontal
*Bombyx/genetics/physiology
*Pigmentation/genetics/physiology

@article {pmid42708308,
year = {2026},
author = {Miron, RJ and Ahmad, P and Sculean, A},
title = {Understanding exosomes: A history of EV-erything.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.70092},
pmid = {42708308},
issn = {1600-0757},
abstract = {BACKGROUND: Extracellular vesicles (EVs), including exosomes, have emerged as fundamental regulators of cell-to-cell communication and are increasingly recognized for their therapeutic and diagnostic promise. While EV research has expanded remarkably over the past two decades, the discipline is rooted in a much longer history of observations, conceptual progress, and technological innovations that gradually transformed the comprehension of these nanosized particles. This review offers a historical perspective on the evolution of EV biology, underscoring the pivotal discoveries, researchers, and community-mediated initiatives that have shaped the contemporary domain.

METHODS: A narrative review of the literature was conducted to assess major milestones in EV research, from the earlier descriptions of cell-free particulate material to modern progress in EV biology, standardization, and translational medicine. Particular emphasis was placed on landmark investigations that redefined the biological importance of EVs and on the development of international frameworks that enhanced reproducibility and methodological rigor.

RESULTS: Early studies characterized EV-like particles as sedimentable plasma components or cellular waste, culminating in Peter Wolf's description of "platelet dust" in 1967. Subsequent research by Crawford, Johnstone, Stahl, Raposo, Ratajczak, and others established EVs as bioactive structures contributing to vesicle biogenesis, antigen presentation, and horizontal gene transfer of genetic information. Progress in particle characterization, molecular profiling, and imaging approaches further demonstrated EVs as intricate carriers of proteins, lipids, metabolites, and nucleic acids capable of mediating diverse physiological and pathological mechanisms. In parallel, the establishment of the International Society for Extracellular Vesicles (ISEV) and the successive MISEV guidelines offered a pivotal foundation for standardization, transparency, and reproducibility across the discipline.

CONCLUSION: The history of EV research reflects a remarkable transition from observations of poorly understood extracellular particles to the recognition of EVs as key modulators of biological communication and potential therapeutic systems. As technological capabilities, standardization efforts, and translational applications continue to advance, EVs are poised to play an increasingly important role in the future of precision medicine.},
}

@article {pmid42708931,
year = {2026},
author = {Li, Q and Shi, K and Cui, HL and Zhang, YQ and Li, BZ and Gao, BY and Liang, B},
title = {Divergent Evolutionary Trajectories of Pseudomonas aeruginosa PAO1 under Trace versus Preservative-Level Antimicrobial Methylisothiazolinone Exposure.},
journal = {Environmental science & technology},
volume = {60},
number = {35},
pages = {24851-24862},
doi = {10.1021/acs.est.6c05943},
pmid = {42708931},
issn = {1520-5851},
support = {JCYJ20240813105125034//Shenzhen Science and Technology Innovation Program/ ; SYSPG20241211173609007//Shenzhen Science and Technology Innovation Program/ ; 2023B1515020077//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 52322007//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Pseudomonas aeruginosa/drug effects/genetics ; *Thiazoles/pharmacology ; Animals ; Anti-Infective Agents/pharmacology ; },
abstract = {Isothiazolinones are widely used nonantibiotic antimicrobials with high electrophilic reactivity toward bacterial protein thiols. Although this reactivity leads to rapid degradation and low environmental persistence, their potential to drive cryptic microbial evolution remains poorly understood. Here, we focused on methylisothiazolinone (MIT), a widely used isothiazolinone, and conducted a 60-cycle experimental evolution of Pseudomonas aeruginosa PAO1 across a concentration gradient spanning environmentally relevant (10 μg/L) to preservative-use (8-16 mg/L) levels. We demonstrate an exposure-level-dependent bifurcation in evolutionary strategies. Trace-level MIT exposure enhanced horizontal gene transfer capacity (from 0.0520 ± 0.0006 to 0.0764 ± 0.0008) through membrane remodeling, including elevated membrane potential, reduced extracellular polymeric substances, and 2.79-fold induction of indole signaling. In contrast, preservative-level MIT exposure drove key mutations (e.g., mexR deletion) and metabolic-transcriptional rewiring, increasing minimal inhibitory concentrations of Meropenem by 8- to 16-fold with minimal fitness costs. Furthermore, the 16 mg/L-evolved lineages exhibited hypervirulence, causing 100% mortality within 24 h in a Galleria mellonella model compared to 90% ancestral survival. These findings demonstrate that even trace exposure to highly bioactive antimicrobials can reshape microbial evolution and accelerate resistance emergence, highlighting unrecognized evolutionary risks and providing a critical scientific basis for refining their risk assessment and management frameworks.},
}

*Pseudomonas aeruginosa/drug effects/genetics
*Thiazoles/pharmacology
Animals
Anti-Infective Agents/pharmacology

@article {pmid42694502,
year = {2026},
author = {Hu, X and Yuan, Y and Yang, Z and Chu, Y and Huang, T and Zhao, K},
title = {Next-generation anti-infective drugs in the post-antibiotic era: focusing on anti-virulence agents targeting the bacterial quorum sensing system.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1935576},
pmid = {42694502},
issn = {2235-2988},
mesh = {*Quorum Sensing/drug effects ; Humans ; *Bacteria/drug effects/pathogenicity ; *Bacterial Infections/drug therapy/microbiology ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Virulence/drug effects ; Drug Resistance, Multiple, Bacterial ; *Anti-Infective Agents/pharmacology/therapeutic use ; Virulence Factors/antagonists & inhibitors ; Animals ; },
abstract = {Antimicrobial resistance is a critical global public health challenge, with drug-resistant infections contributing to more than one million deaths annually. The widespread dissemination of multidrug-resistant bacteria poses a severe threat to the management of infectious diseases. Bacterial evolution via genetic mutation and horizontal gene transfer diminishes antimicrobial efficacy, often leading to therapeutic failure, increased morbidity and mortality. However, the development of novel antibiotics lags far behind the rapid evolution of drug-resistant bacteria. Therefore, scientists worldwide have committed to exploring alternative therapeutic strategies for bacterial infections. The key question is which strategy holds the greatest promise of addressing the predicament of traditional antibiotics and being recognized as "next-generation anti-infective drugs". This narrative review summarizes several of the most promising alternative treatment strategies against bacterial infections, emphasizing the core strengths and limitations of each strategy. A critical comparative analysis reveals that no single strategy can simultaneously satisfy the demands of acute therapy, broad patient coverage, and resistance evasion, underscoring the need for context-dependent and sequential deployment. Moreover, among these alternatives, anti-virulence therapeutic strategies, particularly those targeting the bacterial quorum sensing (QS) system, represent a major and extensively studied approach, although their clinical translation remains nascent. This review delineates the molecular mechanisms and therapeutic potential of QS-targeting anti-virulence agents. Furthermore, we candidly assess the extant biological, pharmacological, and clinical barriers impeding their clinical translation, providing perspectives on future research directions to harness these next-generation anti-infective paradigms effectively.},
}

*Quorum Sensing/drug effects
Humans
*Bacteria/drug effects/pathogenicity
*Bacterial Infections/drug therapy/microbiology
*Anti-Bacterial Agents/pharmacology/therapeutic use
Virulence/drug effects
Drug Resistance, Multiple, Bacterial
*Anti-Infective Agents/pharmacology/therapeutic use
Virulence Factors/antagonists & inhibitors
Animals

@article {pmid42696881,
year = {2026},
author = {Xia, R and Shi, T and Zhao, J and Li, G and Luo, W and Xu, Z},
title = {Signal competition versus metabolic inhibition: Divergent fates of antibiotic resistance genes under N-acyl-L-homoserine lactone-targeted quorum quenching in composting.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143482},
doi = {10.1016/j.jhazmat.2026.143482},
pmid = {42696881},
issn = {1873-3336},
abstract = {Quorum sensing (QS) mediates biofilm formation and antibiotic resistance gene (ARG) transfer via signaling molecules, yet whether disrupting QS via quorum quenching restrains ARG dissemination during composting remains unclear. Here, vanillin and eugenol were supplemented at the beginning and mature stages to regulate ARG dynamics. Initial vanillin application effectively disrupted QS pathways and enhanced the removal of ARGs and MGEs by over 20% and 40%, respectively. Mechanistically, vanillin and eugenol competitively bound to acyl-homoserine lactone (AHL) receptors, triggering transient AHL accumulation and enhancing the functional potential for extracellular polymeric substance (EPS) production and type IV secretion system. Vanillin subsequently suppressed bacterial adhesion and conjugation by reducing genes related to EPS secretion (e.g. wacL), conjugation pilus assembly (e.g. trbC), and flagellar motility (e.g. fliE). This suppression reduced the number of mobile high-risk ARGs and attenuated horizontal gene transfer dominated by Pseudomonadota and Bacillota. Additionally, vanillin suppressed vertical gene transfer at the mature stage via inhibiting the growth of Gram-negative ARG hosts. Conversely, eugenol inhibited respiratory complexes IV/V, blocked ATP synthesis and temperature elevation, weakening thermal inactivation of ARG hosts (e.g. Pseudomonadota) and elevating ARG abundance. These findings provide a targeted approach for source control of ARGs in organic waste valorization.},
}

@article {pmid42697647,
year = {2026},
author = {Huang, C and Dai, X and Chen, Y and Ge, H and Zhang, L and Yu, Y and Fang, H},
title = {Chitosan mitigates the dissemination of antibiotic resistance genes caused by metalaxyl in the soil-earthworm system.},
journal = {Pesticide biochemistry and physiology},
volume = {223},
number = {},
pages = {107278},
doi = {10.1016/j.pestbp.2026.107278},
pmid = {42697647},
issn = {1095-9939},
mesh = {Animals ; *Chitosan/pharmacology ; *Oligochaeta/drug effects ; Soil Microbiology ; *Alanine/analogs & derivatives/toxicity/pharmacology ; *Fungicides, Industrial/toxicity/pharmacology ; *Drug Resistance, Microbial/genetics ; *Soil Pollutants/toxicity ; Soil/chemistry ; Bacteria/genetics/drug effects ; Gene Transfer, Horizontal/drug effects ; },
abstract = {The widespread use of agricultural fungicides can lead to residual contamination and accelerate the emergence and spread of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) in soil ecosystems. Developing green remediation strategies that simultaneously reduce fungicide residues and mitigate antibiotic resistance risks is therefore beneficial for soil pollutant control. Here, we investigated the effects of chitosan (CHI) on the dissipation of metalaxyl (MET) enantiomers and their influence on the soil-earthworm resistome and microbiome through pot experiments and metagenomics analysis. The results showed that CHI significantly accelerated MET dissipation in soil and reduced its bioaccumulation in earthworms. MET enantiomers, particularly S-MET, promoted the dissemination of ARGs, including high-risk ARGs, in the soil-earthworm system, whereas CHI suppressed these effects, likely by limiting the potential for mobile genetic element (MGE)-mediated horizontal gene transfer (HGT). Compared with the corresponding treatments without CHI amendment, CHI amendment reduced the total relative abundance of ARGs by 16.8%-24.7% in soil and by 34.1%-58.3% in earthworm guts. Furthermore, CHI reshaped microbial community structure in both soil and earthworm gut samples by driving ecological niche differentiation of Actinomycetota and Pseudomonadota and reduced ARG host abundance. These findings offer practical insights for controlling contamination by fungicides and ARGs in agricultural soils.},
}

Animals
*Chitosan/pharmacology
*Oligochaeta/drug effects
Soil Microbiology
*Alanine/analogs & derivatives/toxicity/pharmacology
*Fungicides, Industrial/toxicity/pharmacology
*Drug Resistance, Microbial/genetics
*Soil Pollutants/toxicity
Soil/chemistry
Bacteria/genetics/drug effects
Gene Transfer, Horizontal/drug effects

@article {pmid42697668,
year = {2026},
author = {Zhu, S and Liu, X and Yang, X and Wu, W and Ahmed, T and Jiang, H and Ding, T},
title = {Amplicon and metagenomic sequencing reveal thifluzamide drive rhizosphere microbial structural shifts and functional adaption.},
journal = {Pesticide biochemistry and physiology},
volume = {223},
number = {},
pages = {107299},
doi = {10.1016/j.pestbp.2026.107299},
pmid = {42697668},
issn = {1095-9939},
mesh = {*Rhizosphere ; Fungi/drug effects/genetics ; Oryza/microbiology ; Bacteria/drug effects/genetics ; Metagenomics ; *Fungicides, Industrial/pharmacology ; Soil Microbiology ; *Microbiota/drug effects ; Metagenome ; },
abstract = {Thifluzamide (TF) is a widely used phenyl urea fungicide in rice production; however, its impacts on the structural composition and functional dynamics of the rhizosphere microbiome remain poorly understood. Here, we systematically investigated the effects of TF on the structure, interactions, and functional potential of the rice (Oryza sativa L.) rhizosphere microbiome using integrated amplicon sequencing and metagenomic approaches. TF application significantly altered both bacterial and fungal community composition, bacterial diversity was markedly reduced, whereas fungal diversity increased. With bacterial diversity markedly reduced while fungal diversity increased. Beta-diversity analyses revealed strong treatment-driven community separation, indicating pronounced TF-induced microbial restructuring. Co-occurrence network analysis demonstrated reduced complexity and connectivity in bacterial networks but increased negative co-occurrence patterns within fungal communities, suggesting contrasting stability responses between microbial kingdoms. Metagenomic profiling further revealed substantial functional shifts, including the differential enrichment of KEGG and COG pathways associated with xenobiotic metabolism. Notably, while total ARG abundance remained stable, TF exposure altered the resistome profile by selectively enriching specific classes of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and mobile genetic elements (MGEs). Strong positive correlations between MGEs and ARGs highlighted an elevated potential for horizontal gene transfer. Metagenome-assembled genome (MAG) analysis identified specific TF-enriched bacterial taxa, including Methylophilus, Sulfurospirillum, and Azospirillum, which harbored genes involved in pesticide degradation and xenobiotic transformation. Collectively, these findings demonstrate that TF profoundly reshapes the rice rhizosphere microbiome by altering microbial diversity, interaction networks, resistance gene profiles, and functional capacities. This study provides genomic insights into fungicide-microbiome interactions, underscoring the potential ecological implications associated with TF application, while identifying candidate microbial taxa that may contribute to pesticide degradation and rhizosphere microecology resilience.},
}

*Rhizosphere
Fungi/drug effects/genetics
Oryza/microbiology
Bacteria/drug effects/genetics
Metagenomics
*Fungicides, Industrial/pharmacology
Soil Microbiology
*Microbiota/drug effects
Metagenome

@article {pmid42700597,
year = {2026},
author = {Pan, M and Shen, L and Feng, J and Li, Z and Wu, L and Wu, R and Du, S and Liu, H},
title = {Metagenomic analysis of florfenicol and microplastics effects on microbial function and antibiotic resistome in rice seedling rhizosphere soil.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143454},
doi = {10.1016/j.jhazmat.2026.143454},
pmid = {42700597},
issn = {1873-3336},
abstract = {Antibiotics enrich antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in farmland, but the contribution of microplastics (MPs) to this process remains unclear. Here, through metagenome analysis, we revealed the add-on effects of PE and PLA on ARGs and VFGs enrichment in rice seedling rhizosphere soil under florfenicol (FF) stress. Compared with controls, root iron plaque content decreased by 35%, 66% and 69% under FF, FF + PE and FF + PLA treatments, disrupting microbial iron balance and activating ABC transporter pathways. Loss of beneficial/core microbes weakened community resistance; bacteria were more sensitive to stress than fungi. Among 945 ARGs and 391 VFs detected, antibiotic efflux abundance rose by 184% under FF, while mobile genetic elements (MGEs) increased from 0.5% to 38.1%, facilitating horizontal ARG transfer. In addition to horizontal gene transfer (HGT) mediated by mobile genetic elements (MGEs), our finding suggests a potential mechanism by which virulence factors (VFs) may promote ARG enrichment through the accumulation of tissue-damaging free radicals. Only one ARG-carrying human pathogen existed in controls, whereas six multi-drug-resistant pathogens emerged under combined pollution. This study provides new insights into the environmental risks of the add-on effects of MPs under antibiotics stress and contributing to the "One Health" goal.},
}

@article {pmid42705770,
year = {2026},
author = {Li, X and Guan, Z and Zhang, J and Wang, Y and Guo, T and Fan, R and Jiang, H and Han, R and Yang, Y},
title = {From farm to gut: ecological filtering and risk interpretation of antimicrobial resistance in dairy products.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120415},
doi = {10.1016/j.foodres.2026.120415},
pmid = {42705770},
issn = {1873-7145},
mesh = {*Dairy Products/microbiology ; Animals ; Humans ; *Drug Resistance, Bacterial/genetics ; *Food Microbiology ; Anti-Bacterial Agents/pharmacology ; Risk Assessment ; *Gastrointestinal Microbiome ; Bacteria/drug effects/genetics ; Milk/microbiology ; Food Handling ; },
abstract = {Antimicrobial resistance (AMR) is increasingly recognized as a food safety and public health challenge that extends beyond clinical settings to animal production, food processing, and host-associated microbial ecosystems. Dairy products represent an important interface linking farm environments, processing systems, and the human gastrointestinal tract. However, current evidence on AMR in dairy products remains fragmented. Most studies have focused on detecting antibiotic-resistant bacteria, antimicrobial resistance genes, and mobile genetic elements, whereas less attention has been given to whether these determinants remain viable or functionally relevant after processing and gastrointestinal exposure. This review examines AMR determinants in dairy products from a farm-to-gut perspective. We summarize major upstream reservoirs and entry routes of resistance determinants along the dairy chain and evaluate their distribution across raw milk and processed dairy products. A central argument of this review is that dairy processing should be interpreted as an ecological filter rather than a simple decontamination step, because it can reduce viable microorganisms while reshaping the persistence, localization, and transfer potential of resistance-related signals. We further discuss the ecological barriers that dairy-associated AMR determinants must overcome before becoming biologically meaningful host risks, including gastrointestinal survival, microbial competition, horizontal gene transfer, colonization, persistence, and functional expression. Detection alone should not be equated with public health risk. Instead, AMR assessment in dairy systems should move beyond descriptive surveillance toward multilayered interpretation of viability, mobility, persistence, functional activity, and host relevance. This risk-oriented framework provides a basis for distinguishing molecular presence from functional transmission relevance, identifying critical control points across the dairy chain, supporting AMR management in dairy products.},
}

*Dairy Products/microbiology
Animals
Humans
*Drug Resistance, Bacterial/genetics
*Food Microbiology
Anti-Bacterial Agents/pharmacology
Risk Assessment
*Gastrointestinal Microbiome
Bacteria/drug effects/genetics
Milk/microbiology
Food Handling

@article {pmid42692727,
year = {2026},
author = {Javaid, A and Tabassum, N and Karthikeyan, A and Kim, YM and Khan, F},
title = {Genomic determinants underlying biogenic amine detoxification phenotypes in food-associated lactic acid bacteria: Mechanism, evolutionary origin, and relevance to fermented food safety.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 1},
pages = {120335},
doi = {10.1016/j.foodres.2026.120335},
pmid = {42692727},
issn = {1873-7145},
mesh = {*Biogenic Amines/metabolism ; *Lactobacillales/genetics/metabolism ; Phenotype ; Phylogeny ; *Food Safety ; *Fermented Foods/microbiology ; *Genome, Bacterial ; *Food Microbiology ; Gene Transfer, Horizontal ; Fermentation ; Genomics ; Inactivation, Metabolic/genetics ; },
abstract = {Biogenic amines (BAs) are toxic metabolites that accumulate in fermented foods and pose significant food safety concerns. Although several lactic acid bacteria (LAB) have previously been reported to exhibit strain-specific BA-degrading phenotypes, the genetic determinants underlying these activities have remained largely uncharacterized. Here, we analyzed 8251 LAB genomes to validate BA-degrading phenotypes. We predicted five BA-associated genes, including two direct biogenic amine-degrading genes (BADGs), mco and patA, and three polyamine-modifying genes (PMGs), speG, paiA, and bltD. Among BADGs, mco was broadly distributed across LAB and strongly enriched across food-associated niches. patA, organized within a conserved potD-glnB-potABC-patA cassette, is a putative, functionally distinct BADG in LAB, revealing a nitrogen-responsive polyamine uptake-catabolism module. Phylogenomics, phylogenetic reconciliation, and synteny analysis established that all five genes entered the LAB through episodic horizontal gene transfer followed by lineage-specific fixation. GC compositional bias and mobile genetic element association further corroborated the horizontal origin of the two BADGs. Structural analysis confirmed the conservation of catalytic core residues of BADGs across LAB, indicating strong purifying selection. Phenotype-to-genotype correlation with experimentally reported LAB suggested mco as a reliable genomic predictor of degrading phenotype. Integration of degradation and biosynthetic profiles predicted multiple LAB species capable of both synthesizing and degrading BA, along with 1823 genomes with degradation potential but lacking detectable BA biosynthesis genes. This study provides the first large-scale genome framework linking BA-degrading phenotypes with their genetic determinants in LAB and offers a rational basis for selecting BA-detoxifying strains for fermented food applications.},
}

*Biogenic Amines/metabolism
*Lactobacillales/genetics/metabolism
Phenotype
Phylogeny
*Food Safety
*Fermented Foods/microbiology
*Genome, Bacterial
*Food Microbiology
Gene Transfer, Horizontal
Fermentation
Genomics
Inactivation, Metabolic/genetics

@article {pmid42693304,
year = {2026},
author = {Izuazu, C and Browne, C},
title = {Probability of Antibiotic Resistance During Treatment in Stochastic PK/PD-Based Bacterial Model with Distinct Drug and Mutation Modes.},
journal = {Bulletin of mathematical biology},
volume = {88},
number = {10},
pages = {},
pmid = {42693304},
issn = {1522-9602},
support = {DMS 2413769//National Science Foundation/ ; },
mesh = {Stochastic Processes ; *Anti-Bacterial Agents/pharmacokinetics/pharmacology/administration & dosage ; Mutation ; *Drug Resistance, Bacterial/genetics ; *Models, Biological ; Markov Chains ; Bacteria/drug effects/genetics ; Mathematical Concepts ; Humans ; *Bacterial Infections/drug therapy/microbiology ; Computer Simulation ; Gene Transfer, Horizontal ; },
abstract = {Mathematical models, e.g., differential equations and stochastic processes, have gained considerable attention for understanding evolution of antibiotic resistance. However, most existing models assume standing genetic variation and do not consider the possibility of random or drug-induced mutation of reference bacterial strains. Therefore, we propose a pharmacokinetics/pharmacodynamics (PK/PD)-based continuous-time Markov chain considering the competition and mutation between sensitive and resistant bacterial within an infected host during treatment. The proposed model is approximated as a generalized birth-death process with immigration, allowing for explicit derivation of the probability resistant population establishes during treatment. Besides capturing the stochasticity of de novo emergence of a resistant bacterial strain, we explore the effects of different antibiotic modes of action, horizontal gene transfer, nutrient availability and drug pharmacokinetics on antibiotic resistance. We find that replication-targeting (biostatic) drugs suppress resistance more than death-targeting (biocidal) drugs. Like prior works, we obtain maximized resistance at intermediate drug concentrations, however the consideration of de novo mutation magnifies the superiority of higher doses in preventing resistance emergence.},
}

Stochastic Processes
*Anti-Bacterial Agents/pharmacokinetics/pharmacology/administration & dosage
Mutation
*Drug Resistance, Bacterial/genetics
*Models, Biological
Markov Chains
Bacteria/drug effects/genetics
Mathematical Concepts
Humans
*Bacterial Infections/drug therapy/microbiology
Computer Simulation
Gene Transfer, Horizontal

@article {pmid39929992,
year = {2026},
author = {Habig, M and Patneedi, SK and Stam, R and De Fine Licht, HH},
title = {Horizontal transfer of accessory chromosomes in fungi - a regulated process for exchange of genetic material?.},
journal = {Heredity},
volume = {135},
number = {8},
pages = {590-596},
pmid = {39929992},
issn = {1365-2540},
support = {NNF23OC0086230//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Chromosomes, Fungal/genetics ; *Fungi/genetics ; Genome, Fungal ; Metarhizium/genetics ; Codon ; },
abstract = {Horizontal transfer of entire chromosomes has been reported in several fungal pathogens, often significantly impacting the fitness of the recipient fungus. All documented instances of horizontal chromosome transfers (HCTs) showed a marked propensity for accessory chromosomes, consistently involving the transfer of an accessory chromosome while other chromosomes were seldom, if ever, co-transferred. The mechanisms underlying HCTs, as well as the factors regulating the specificity of HCTs for accessory chromosomes, remain unclear. In this perspective, we provide an overview of the observed propensity in reported cases of horizontal chromosome transfers. We hypothesize the existence of a signal that distinguishes mobile, i.e., horizontally transferred, accessory chromosomes from the rest of the donor genome. Recent findings in Metarhizium robertsii and Magnaporthe oryzae, suggest that a mobile accessory chromosome may contain putative histones and/or histone modifiers, which could generate such a signal. Based on this, we propose that mobile accessory chromosomes may encode the machinery required for their own horizontal transmission, implying that HCT could be a regulated process. Finally, we present evidence of substantial differences in codon usage bias between core and accessory chromosomes in 14 out of 19 analysed fungal species and strains. Such differences in codon usage bias could indicate past horizontal transfers of these accessory chromosomes. Interestingly, HCT was previously unknown for many of these species, suggesting that the horizontal transfer of accessory chromosomes may be more widespread than previously thought, and therefore an important factor in fungal genome evolution.},
}

*Gene Transfer, Horizontal
*Chromosomes, Fungal/genetics
*Fungi/genetics
Genome, Fungal
Metarhizium/genetics
Codon

@article {pmid42535547,
year = {2026},
author = {Evseeva, D and Pecrix, Y and Kucka, M and Weiler, C and Franzl, C and Vlková-Žlebková, M and Colombi, E and Chan, YF and Poussier, S and Wicker, E and McCann, HC},
title = {Interspecies Exchange of Mobile Genetic Elements During a Plant Disease Outbreak.},
journal = {Genome biology and evolution},
volume = {18},
number = {9},
pages = {},
pmid = {42535547},
issn = {1759-6653},
mesh = {*Plant Diseases/microbiology ; Phylogeny ; *Interspersed Repetitive Sequences ; *Ralstonia/genetics/pathogenicity/classification ; Disease Outbreaks ; Gene Transfer, Horizontal ; Evolution, Molecular ; Ralstonia solanacearum/genetics ; },
abstract = {Outbreak sequencing provides insight into the origin and evolutionary processes acting on emerging pathogens. Sequencing a historic multihost outbreak of Ralstonia spp. in Martinique shows the outbreak was caused by two lineages that diverged at separate times from mainland populations. One lineage (Ralstonia pseudosolanacearum I-18) was originally introduced from Asia to South America, where it became well established prior to its dissemination to Martinique, where it retains a signature of specialization on solanaceous hosts. The novel lineage first identified during the outbreak (Ralstonia solanacearum IIB-4NPB) arose from a mainland population endemic to the Americas prior to its arrival in Martinique, where host-range expansion was observed. In contrast to minor changes in secreted effector protein repertoires, the emergent R. solanacearum IIB-4NPB acquired a novel integrative and conjugative element (ICERsoRUN1145). After identifying all Ralstonia spp. ICEs and mapping their spatial and phylogenetic distribution among Ralstonia spp. sampled during the outbreak, we found closely related ICEs circulating in mainland populations of R. pseudosolanacearum, indicating likely exchange between introduced and endemic Ralstonia spp. The family of ICEs in Ralstonia (ICERs) has a conserved bipartite structure and display a striking pattern of functional specialization in each cargo gene insertion hotspot: the first hotspot is a target for metabolic gene acquisition, and the second is a target for defense element acquisition. This work provides unparalleled phylogenetic and spatial resolution of an unusual outbreak and highlights the role of horizontal transfer in shaping the ecological success of an emerging pathogen.},
}

*Plant Diseases/microbiology
Phylogeny
*Interspersed Repetitive Sequences
*Ralstonia/genetics/pathogenicity/classification
Disease Outbreaks
Gene Transfer, Horizontal
Evolution, Molecular
Ralstonia solanacearum/genetics

@article {pmid42690738,
year = {2026},
author = {Qi, F and Qiu, S and Sang, Z and Han, H and Zhang, G and Wei, Y and Pan, G and Zhang, Z and Zhang, H and Zhen, C and Xia, J},
title = {Plant-Derived BtHCYP Promotes Phloem Feeding and Fecundity in Bemisia tabaci.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c05658},
pmid = {42690738},
issn = {1520-5118},
support = {PC2024B01010//China Agricultural University/ ; 2022RC015//Chinese Universities Scientific Fund/ ; 2022YFD1401201//National Key Research and Development Program of China/ ; NA//National Top Young Talents Program of China/ ; SKLJRP2505//State Key Laboratory of Agricultural and Forestry Biosecurity/ ; },
abstract = {Bemisia tabaci is a destructive agricultural pest with a remarkable capacity to exploit diverse host plants. Horizontally transferred genes (HTGs) have recently been implicated in this adaptive success, yet the functions of most HTGs in the whitefly remain unclear. Feeding behavior is crucial for nutrient acquisition and reproduction in piercing-sucking insects, but whether HTGs contribute to host adaptation by regulating feeding remains largely unknown. Here, we identified BtHCYP, a plant-derived HGT gene in B. tabaci encoding a cysteine protease. Biochemical and in vivo assays confirmed that BtHCYP retained cysteine protease activity. RNA interference-mediated silencing of BtHCYP significantly reduced whitefly fecundity. Electrical penetration graph on cotton plants analyses further revealed that BtHCYP knockdown impaired phloem feeding. Collectively, these findings demonstrate that a plant-derived HTG can enhance whitefly fecundity and efficient phloem feeding, as BtHCYP silencing reduced oviposition by 27.6%, highlighting a potential molecular target for whitefly management.},
}

@article {pmid42678601,
year = {2026},
author = {Schell, CM and Magi, G and Simoni, S and Massacci, FR and Albini, E and D'Achille, G and Paoletti, C and Carriera, F and Morroni, G and Mingoia, M and Zhu, Y and Zhang, W and Du, XD and Krüger-Haker, H and Schwarz, S and Bernstein, JC and Giovanetti, E and Brenciani, A},
title = {Genomic insights into an optrA-carrying plasmid associated with linezolid resistance in clinical Enterococcus faecalis isolates, Argentina.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42678601},
issn = {1435-4373},
support = {U23A20241//National Natural Science Foundation of China/ ; },
abstract = {The spread of the transferable optrA gene poses an increasing threat to the clinical efficacy of oxazolidinones. Here, we characterized a novel optrA-carrying plasmid, pEfa-optrA-Arg, from a linezolid-resistant Enterococcus faecalis clinical isolate from Argentina. The 68,653-bp conjugative plasmid harbored optrA together with multiple antimicrobial resistance genes and showed high similarity to a plasmid previously identified in a bovine isolate from Switzerland. pEfa-optrA-Arg, or a closely related variant, was also detected in E. faecalis isolates from several Argentinian hospitals, highlighting the role of horizontal gene transfer in the spread of antimicrobial resistance across human and animal reservoirs within the One Health continuum.},
}

@article {pmid42679012,
year = {2026},
author = {Fan, S and Wang, L and Liu, C and Li, H and Qi, H and Du, P and Guo, J},
title = {Hypervirulence-associated pseudo-compound transposons as fundamental mobile units driving cross-species virulence dissemination in Enterobacteriaceae.},
journal = {PLoS pathogens},
volume = {22},
number = {9},
pages = {e1014513},
pmid = {42679012},
issn = {1553-7374},
mesh = {Virulence/genetics ; *DNA Transposable Elements/genetics ; Plasmids/genetics ; *Enterobacteriaceae/genetics/pathogenicity ; Gene Transfer, Horizontal ; *Enterobacteriaceae Infections/microbiology/genetics ; Humans ; Klebsiella pneumoniae/genetics/pathogenicity ; },
abstract = {BACKGROUND: The rapid global spread of hypervirulence in Enterobacteriaceae, particularly in carbapenem-resistant Klebsiella pneumoniae, poses a significant public health threat. However, the key genetic vehicles and mechanisms driving horizontal transfer of hypervirulence-associated genes (iucA, iroB, rmpA, rmpA2, and peg-344) remain poorly defined, limiting effective surveillance.

METHODS: We performed a large-scale genomic survey of 2,869 virulence-associated plasmid sequences and 2,337 complete Enterobacteriaceae chromosomes. Using comparative genomics and evolutionary analyses, we systematically identified and characterized Hypervirulence-associated Pseudo-Compound Transposons (Hva-PCTs), defined as structured mobile elements in which hypervirulence-associated genes are flanked by insertion sequences.

RESULTS: Our results demonstrate that hypervirulence-associated genes are transmitted primarily as discrete IS-bounded units, which we term Hva-PCTs. We identified 29 distinct plasmid-borne Hva-PCTs (pHva-PCTs) and 30 chromosomal Hva-PCTs (cHva-PCTs). These modules show clear species-specific patterns: iucA/iroB-associated Hva-PCTs mainly originate in Escherichia coli and spread through IncFIB-containing multi-replicon plasmids (commonly combined with IncFIC(FII) and/or IncFII, while rmpA/rmpA2/peg-344-containing modules originate in K. pneumoniae and are disseminated via IncHI1B/repB plasmids. Three Hva-PCTs were detected on both plasmids and chromosomes (xHva-PCTs). In one clinical K. pneumoniae isolate (LS356), the identical composite module was present on both replicons. Simpler sub-modules, such as ISKqu3-rmpA2-iucA_1-IS102 and IS102-rmpA-peg-344-iroB_1-IS1A, frequently co-occur on the same plasmid; when positioned in tandem, they reconstitute the full composite structure. This assembly pattern is further supported by a partial duplication event in plasmid pP901. CD-HIT clustering (80% nucleotide identity and 90% coverage) showed that 13 of 22 major clusters contained both plasmid and chromosomal copies, with intra-cluster identities >80% across multiple sequence types and host species.

CONCLUSION: Hypervirulence-associated genes in Enterobacteriaceae are disseminated mainly as IS-flanked Hva-PCTs rather than solely through intact virulence plasmids. These modules exhibit strong but not absolute host specificity. The presence of identical Hva-PCTs on plasmids and chromosomes suggests inter-replicon mobility, while their stepwise assembly from simpler sub-modules highlights modular accretion as a key evolutionary process. Tracking Hva-PCTs as distinct mobile units may complement existing plasmid- and gene-centric surveillance approaches for hypervirulent and convergent strains. Experimental validation of their transposition activity and phenotypic effects is still required.},
}

Virulence/genetics
*DNA Transposable Elements/genetics
Plasmids/genetics
*Enterobacteriaceae/genetics/pathogenicity
Gene Transfer, Horizontal
*Enterobacteriaceae Infections/microbiology/genetics
Humans
Klebsiella pneumoniae/genetics/pathogenicity

@article {pmid42680011,
year = {2026},
author = {Vo, T and Merhej, V and Isber, C and Pontarotti, P and Bittar, F and Rolain, JM},
title = {Global lessons from antibiotic resistance: metformin-hydrolyzing genes in transposable elements, a new threat for type II diabetic patients?.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2026.08.026},
pmid = {42680011},
issn = {2213-7173},
abstract = {OBJECTIVES: To investigate the evolutionary origin, genomic mobility, and potential dissemination of metformin-hydrolyzing genes (mfmAB), and to assess whether environmental selection by metformin pollution may drive the emergence of transferable pharmaceutical-degrading traits analogous to antibiotic resistance.

METHODS: Large-scale comparative genomics was performed using publicly available bacterial genomes carrying mfmAB homologs. Phylogenomic reconstruction, average nucleotide identity analysis, genomic context comparison, plasmid characterization, and insertion sequence mapping were used to infer evolutionary history and identify mechanisms of horizontal gene transfer.

RESULTS: mfmAB homologs were identified in twelve Aminobacter and three Pseudomonas genomes within a conserved ∼8.2 kb gene cluster. Phylogenomic analyses showed that metformin-degrading capacity emerged independently in multiple Aminobacter lineages across distinct continents, consistent with convergent evolution under anthropogenic selective pressure. Genomic comparisons indicated a chromosomal origin of mfmAB, followed by mobilization onto conjugative plasmids through IS1182-mediated transposition. In Pseudomonas, additional IS3/IS6-mediated transposition events integrated mfmAB into diverse plasmid backbones, frequently within composite transposons also encoding guanylurea and biguanide degradation pathways (guuH, bguH). These findings reveal a dynamic modular assembly of metabolic functions facilitating adaptation to pharmaceutical pollutants.

CONCLUSIONS: Metformin pollution appears to promote the emergence and mobilization of pharmaceutical-degrading genes through mechanisms paralleling antibiotic resistance evolution. Although no clinical impact has yet been demonstrated, the potential spread of such genes into human-associated microbiomes and their possible co-selection with antibiotic resistance determinants represent an emerging One Health concern. Environmental surveillance of pharmaceutical-degrading genes is warranted to anticipate future threats to drug efficacy.},
}

@article {pmid42684534,
year = {2026},
author = {Chavan, M and Bramhe, C and Sangani, K and Patel, N and Chavda, P and Satyavolu, V and Patidar, V and Baghatharia, S and Shekh, S and Joshi, M and Sabara, P and Chatterjee, S and Joshi, C and Patel, A},
title = {Assessment and tracking of antimicrobial resistance in Escherichia coli as a one health perspective.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {9},
pages = {},
pmid = {42684534},
issn = {1573-0972},
support = {GSBTM/RSS/e-file/30/2024/0021/05258544//Network Program on Antimicrobial Resistance, Superbugs and One Health/ ; },
mesh = {*Escherichia coli/genetics/drug effects/classification/isolation & purification ; Gene Transfer, Horizontal ; Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *One Health ; Genome, Bacterial ; India ; Polymorphism, Single Nucleotide ; Humans ; Animals ; *Escherichia coli Infections/microbiology/veterinary ; Phylogeny ; },
abstract = {Genomics has emerged as a powerful tool for addressing the global scenario of antimicrobial resistance (AMR) in the world. The chances of strain circulation across diverse ecosystems has led us to understand the situation from one health point of view. The study examined 897 Escherichia coli genomes across healthcare (n = 615), veterinary and fisheries (n = 219), and environment (n = 63) from Gujarat, India, from 2022 to 2025. The genomes were characterized by sequence type (ST), serotype, and phylogroup analysis to identify the dominant clonal lineages. Furthermore, antibiotic resistance genes (ARGs) and plasmids were analyzed to understand the movement of horizontal gene transfer (HGT). The putative transmission events across sectors were identified using single-nucleotide polymorphisms (SNPs) with distance thresholds of 0, 1, 2, 5, 10, 20, and 50. We reported the presence of internationally reported dominant clonal lineage ST131-B2-O25:H4 across all settings. The healthcare isolates carried a heavy burden of ARGs than the environment and veterinary and fisheries sectors (median 9 vs. 5 vs. 1 gene per isolate), which is consistent with the use of clinical antimicrobial use exerting the dominant selective pressure in this dataset. Plasmid clustering identified 505 distinct clusters, of which 64 were detected across all three sectors, carrying acquired resistance genes namely mphA, sul1, blaCMY-59, qnrS1, and tetA on predominantly IncF (IA, IB, IC, II) replicons. Resistance genes and mobile genetic elements (IS3, IS5, and IS66) were classified by co-location confidence. Potential transmission events and co-circulation both within and across niches were indicated by overlapping clusters. Genomic clustering and mobility patterns of plasmids identified in the E. coli strains are consistent with the possible clonal and plasmid-mediated spread from healthcare to the veterinary and fisheries and the environment sectors. This study's convenience-based sampling and cross-sectoral design do not establish confirmed or directional transmission. These findings support a One Health framework for AMR surveillance, prioritizing biosecurity, antimicrobial stewardship, and infection prevention and control across sectors.},
}

*Escherichia coli/genetics/drug effects/classification/isolation & purification
Gene Transfer, Horizontal
Plasmids/genetics
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
*One Health
Genome, Bacterial
India
Polymorphism, Single Nucleotide
Humans
Animals
*Escherichia coli Infections/microbiology/veterinary
Phylogeny

@article {pmid42687087,
year = {2026},
author = {Ren, Y and Li, X and Ju, L and Yao, Y and Chen, X and Wang, X},
title = {A fitness advantage from the pLVPK plasmid fuels the global spread of a carbapenem-resistant hypervirulent Klebsiella pneumoniae high-risk clone: ST11-KL64.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42687087},
issn = {1618-1905},
abstract = {BACKGROUND: The global emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP), particularly the ST11-KL64 subclone acquiring pLVPK-like virulence plasmids, represents a critical public health threat. This study investigates the epidemiological dominance and molecular mechanisms underlying ST11-KL64's fitness advantage over KL47 variants.

METHODS: We performed comparative genomic analysis on 43,722 K. pneumoniae genomes (2011-2022) from 112 countries, focusing on ST11-CRKP strains. Capsular typing (KL64 vs. KL47), virulence gene profiling (aerobactin, RmpADC), and plasmid stability analysis were conducted using Kleborate, RAST, and PlasmidFinder. Plasmid-chromosome interactions were characterized through hybrid assembly approaches.

RESULTS: ST11-KL64 demonstrated rapid expansion post-2016, surpassing KL47 as China's dominant CRKP subtype (40.5% vs. 28.9%), with regional predominance in Zhejiang (62.3%) and Sichuan (58.7%) provinces. Notably, 94.8% of KL64 strains maintained intact pLVPK plasmids with high aerobactin carriage (60.5%), while KL47 exhibited frequent plasmid fusion (58.8% with IncFIB[pNDM-Mar]) or chromosomal integration (41.4%), resulting in lower virulence potential (27.3% aerobactin+). Genomic analysis revealed KL64's superior plasmid stability (71.2% gene retention vs. KL47's 43.6%) and clinical correlation with severe outcomes (OR = 2.34, 95%CI 1.67-3.28).

CONCLUSION: The ST11-KL64 subclone's epidemiological success stems from stable pLVPK plasmid maintenance, enabling simultaneous carbapenem resistance and hypervirulence. These findings highlight the urgent need for genomic surveillance targeting plasmid-mediated virulence in CRKP outbreaks, particularly in critical care settings where horizontal gene transfer may accelerate strain evolution.},
}

@article {pmid42674632,
year = {2026},
author = {Li, Y and Yu, Z and Kang, Y and Wu, S and Engelstädter, J and Carvalho, G and Batstone, D and Guo, J},
title = {Chlorination Enhances Bacterial Invasion and Conjugative Transfer of Antibiotic Resistance Genes in Biofilms.},
journal = {Environmental science & technology},
volume = {60},
number = {33},
pages = {23148-23161},
doi = {10.1021/acs.est.6c04433},
pmid = {42674632},
issn = {1520-5851},
support = {DE250100902//Australian Research Council/ ; DP220101526//Australian Research Council/ ; },
mesh = {*Biofilms/drug effects ; Halogenation ; Chlorine ; Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Pseudomonas putida ; Conjugation, Genetic ; Escherichia coli ; Gene Transfer, Horizontal ; Pseudomonas aeruginosa ; },
abstract = {Biofilms are widespread in water distribution systems and consist of bacterial cells with extensive cell-to-cell contact, a prerequisite for plasmid-mediated conjugative transfer of antibiotic resistance genes (ARGs). Although plasmid-mediated conjugative ARG transfer has been extensively studied, our understanding of how conjugation occurs within spatially structured bacterial biofilms and how chlorine disinfection influences the conjugation process remains limited. This study systematically investigated the effects of chlorine exposure on biofilm disruption, resistant bacteria invasion, and the conjugative transfer of ARGs in both monoculture and multispecies biofilms composed of Escherichia coli, Pseudomonas putida, and Pseudomonas aeruginosa. Results showed that free chlorine significantly enhanced plasmid-mediated ARG transfer in biofilms at an initial dose of 5 mgCl/L. This could be due to the disruption of recipient biofilm structure, which facilitated donor colonization of the biofilms and close contact with the recipient bacteria. The hotspots for ARG conjugative transfer in the biofilms shifted from the surface (18 ± 2 μm) to the inner layer (27 ± 3 μm) under free chlorine exposure in the multispecies biofilm model. Moreover, a mathematical model was developed to simulate the long-term dynamics of gene transfer within biofilms under free chlorine exposure. The simulation results indicated that exposure to 5 mgCl/L promoted deeper colonization of donor cells and enhanced the dissemination of ARGs throughout the biofilm. Collectively, our findings provide a mechanistic link between biofilm structural disruption, bacterial invasion, and accelerated ARG horizontal transfer in biofilms under free chlorine exposure.},
}

*Biofilms/drug effects
Halogenation
Chlorine
Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
Pseudomonas putida
Conjugation, Genetic
Escherichia coli
Gene Transfer, Horizontal
Pseudomonas aeruginosa

@article {pmid42675331,
year = {2026},
author = {Sun, P and Wang, X and Qiu, Y and Liu, H and Long, Y and Fang, C},
title = {Microplastics and antibiotic resistance genes in landfills: interaction mechanisms, environmental risks, and composite pollution implications.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {9},
pages = {},
pmid = {42675331},
issn = {1573-2959},
mesh = {*Microplastics/analysis ; *Drug Resistance, Microbial/genetics ; *Waste Disposal Facilities ; *Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; },
abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) widely coexist and interact in landfills, forming novel composite pollution. This review reveals their occurrence characteristics, migration mechanisms, interaction risks, and ecological threats in landfills. Landfills accumulate MPs, primarily composed of polyethylene, polypropylene, and polystyrene, with abundance and fragmentation increasing with depth. They migrate via leachate while undergoing continuous aging, and their dispersion is further exacerbated by reduced particle size and enhanced surface hydrophilicity. Meanwhile, aged MPs can provide attachment surfaces for plastisphere-like biofilms and may serve as carriers for pathogens and bacteria because of their large specific surface area and oxygen-containing functional groups. MP-associated biofilms may facilitate horizontal gene transfer (HGT) by increasing microbial contact opportunities and, under some experimental conditions, by promoting oxidative stress responses and membrane permeability changes. ARGs spread across species via HGT and show a significant association with heavy metals. Concomitantly, heavy metal resistance genes may modulate ARG expression, while ARG abundance is also influenced by landfill age, seasonal variations, and pH. Coexistence of MPs, ARGs, and heavy metals triggers co-selection pressure, amplifying composite pollution. Composite pollutants may migrate through soil-water systems and potentially enter food webs, with possible accumulation in organisms; however, evidence directly linking landfill-derived pollutants to human tissue exposure remains limited. The concealed and complex pollution hinders remediation, necessitating coordinated solutions. The lack of detailed policies, standardized methodologies, and inconsistent research strategies hinder cross-study comparisons. This article is aimed at summarizing the occurrence, migration, and interaction patterns of emerging pollutants in landfills and at providing a basis for systematic management and future risk warning.},
}

*Microplastics/analysis
*Drug Resistance, Microbial/genetics
*Waste Disposal Facilities
*Environmental Monitoring
*Water Pollutants, Chemical/analysis

@article {pmid42675958,
year = {2026},
author = {Abdulhassan, AA and Hamid, HH and Al-Lami, SM and Saber, ZM},
title = {Molecular Characterization of OXA Carbapenemase Genes in Acinetobacter Baumannii Isolated from Different Clinical Samples.},
journal = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology},
volume = {60},
number = {4},
pages = {445-457},
doi = {10.33594/000000882},
pmid = {42675958},
issn = {1421-9778},
mesh = {*Acinetobacter baumannii/genetics/isolation & purification/drug effects/enzymology ; *beta-Lactamases/genetics/metabolism ; Humans ; *Bacterial Proteins/genetics/metabolism ; Microbial Sensitivity Tests ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Acinetobacter Infections/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Polymerase Chain Reaction ; },
abstract = {BACKGROUND/AIMS: Acinetobacter baumannii is an opportunistic gram-negative pathogen and an increasingly important cause of hospital-acquired infections, particularly in intensive care units. Its remarkable ability to rapidly acquire resistance mechanisms, especially against carbapenems, represents a major public health concern. This study aimed to investigate the molecular detection and characterization of OXA-type carbapenemase genes in A. baumannii isolates collected from various clinical sources in Baghdad, Iraq.

METHODS: Between March and July 2025, 36 non-repetitive A. baumannii isolates were obtained from patients with different infections. Identification was performed using standard biochemical tests, CHROMagar Acinetobacter, and the VITEK 2 system and was confirmed by PCR amplification of the intrinsic blaOXA-51 gene. Antimicrobial susceptibility testing was conducted according to CLSI guidelines. The prevalence of blaOXA-23, blaOXA-24, blaOXA-51, and blaOXA-58 genes was determined by PCR. Selected PCR products were sequenced and subjected to phylogenetic analysis.

RESULTS: Extensive antimicrobial resistance was observed among the isolates, particularly to carbapenems, with resistance rates of 83.3% for imipenem and 72.2% for meropenem. High resistance rates were also detected for fluoroquinolones and aminoglycosides, whereas colistin and tigecycline retained comparatively greater activity. PCR screening revealed prevalence rates of 100% for blaOXA-51, 86.1% for blaOXA-23, 69.4% for blaOXA-24, and 47.2% for blaOXA-58. Multiple blaOXA genes were detected in more than half of the isolates, suggesting horizontal gene transfer and local clonal expansion. Phylogenetic analysis demonstrated high similarity between local isolates and international reference strains, supporting the widespread dissemination of resistance determinants. Several nucleotide substitutions were identified within the blaOXA-23 and blaOXA-24 genes.

CONCLUSION: The findings indicate that blaOXA-23 is the predominant contributor to carbapenem resistance among A. baumannii isolates in Baghdad, while blaOXA-24 and blaOXA-58 are also increasingly prevalent. The observed resistance patterns and phylogenetic relationships underscore the importance of continuous molecular surveillance, antimicrobial stewardship, and effective infection control measures to limit the spread of multidrug-resistant A. baumannii. These data contribute valuable regional information to the global understanding of antimicrobial resistance epidemiology.},
}

*Acinetobacter baumannii/genetics/isolation & purification/drug effects/enzymology
*beta-Lactamases/genetics/metabolism
Humans
*Bacterial Proteins/genetics/metabolism
Microbial Sensitivity Tests
Phylogeny
Anti-Bacterial Agents/pharmacology
Carbapenems/pharmacology
Acinetobacter Infections/microbiology
Drug Resistance, Multiple, Bacterial/genetics
Polymerase Chain Reaction

@article {pmid42593117,
year = {2026},
author = {Choi, H and Hwang, M and Navarathna, DH and Jinadatha, C},
title = {Plasmid-mediated dissemination of blaKPC-3 and multidrug resistance genes among different species of Klebsiella.},
journal = {Microbiology spectrum},
volume = {14},
number = {9},
pages = {e0125426},
pmid = {42593117},
issn = {2165-0497},
support = {VASEQCURE//US Department of Veterans Affairs/ ; },
mesh = {*Plasmids/genetics/metabolism ; *Drug Resistance, Multiple, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *beta-Lactamases/genetics/metabolism ; Humans ; *Klebsiella/genetics/drug effects/classification/isolation & purification/enzymology ; Carbapenems/pharmacology ; Klebsiella Infections/microbiology ; *Bacterial Proteins/genetics/metabolism ; Klebsiella pneumoniae/genetics/drug effects ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; Whole Genome Sequencing ; Genome, Bacterial ; Multigene Family ; },
abstract = {Carbapenem resistance is a serious threat to public health because carbapenems are used as last-resort antibiotics. Carbapenem resistance gene KPC (Klebsiella pneumoniae carbapenemase) inactivates a broad range of β-lactam substrates. In this manuscript, we examined intra-host transmission of blaKPC-3 via interspecies gene transfer. Two carbapenem-resistant Klebsiella pneumoniae isolates and one Klebsiella michiganensis isolate were identified from two patients. Genetic relations of these isolates were investigated with whole-genome sequencing (WGS). Hybrid assembly of bacterial genomes showed the three isolates carried plasmids that harbor common antimicrobial resistance (AMR) gene clusters that confer multidrug-class resistance, including carbapenems. Our results suggest that AMR gene clusters are disseminated across the species as fragments rather than as complete, intact plasmids.IMPORTANCEAn antimicrobial resistance gene cluster encompassing multiple drug classes on plasmids could lead a drug-susceptible pathogen to gain multidrug resistance. Interspecies gene transfer enables K. michiganensis to become multidrug-resistant through the acquisition of clustered, plasmid-encoded resistance genes spanning multiple antibiotic classes.},
}

*Plasmids/genetics/metabolism
*Drug Resistance, Multiple, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
*beta-Lactamases/genetics/metabolism
Humans
*Klebsiella/genetics/drug effects/classification/isolation & purification/enzymology
Carbapenems/pharmacology
Klebsiella Infections/microbiology
*Bacterial Proteins/genetics/metabolism
Klebsiella pneumoniae/genetics/drug effects
Microbial Sensitivity Tests
Gene Transfer, Horizontal
Whole Genome Sequencing
Genome, Bacterial
Multigene Family

@article {pmid42674242,
year = {2026},
author = {Liu, F and Zhang, L and Zhao, Q and Cheng, M and Xu, Z and Li, T and Xu, S and Shen, Q and Wang, H and Zhang, C},
title = {Prevalence of Third-Generation Cephalosporin-Resistant Salmonella in Animals in China: The Key Role of ESBL, AmpC, and Other β-Lactamase Strains in the Genome.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107992},
doi = {10.1016/j.ijantimicag.2026.107992},
pmid = {42674242},
issn = {1872-7913},
abstract = {OBJECTIVE: To elucidate the drug resistance characteristics, epidemiological distribution, and molecular mechanisms of third-generation cephalosporin-resistant Salmonella from animal sources in China during 2016-2024.

METHODS: Antimicrobial susceptibility testing, serotyping, and whole-genome sequencing (WGS) were employed.

RESULTS: Salmonella exhibited the highest resistance rate to ampicillin (91.9%), followed by sulfisoxazole (87.4%) and tetracycline (83.1%). Among these, strains producing extended-spectrum β-lactamases (ESBLs) accounted for 67.1% and were widely prevalent in chickens and ducks; their dominant resistance gene, blaCTX-M-55, is closely associated with IncI2 and is co-driven by ISEcp1, ISKpn26, IS150, and IS103. 6.2% of the strains carried cephalosporinases (AmpC), primarily from chickens, with blaCMY-59 associated with ISEcp1 as the predominant genotype. An additional 27.1% carried other β-lactamases, mostly from pigs, with the predominant genotype being blaTEM-1 associated with IS406. Notably, the carbapenemase gene blaNDM-1/5 was detected only in strains producing other β-lactamases and was associated with ISSbol and ISRor2. Serotype distribution showed that S. Kentucky predominantly carried ESBLs and AmpC, while S. Enteritidis was dominated by other β-lactamases. Phylogenetic analysis revealed that serotype is the primary factor determining the structure of Salmonella clonal groups, and the acquisition of resistance to third-generation cephalosporins in Salmonella may depend on both clonal transmission and horizontal gene transfer.

CONCLUSION: This study is the first to untangle the differences in animal distribution and serotype associations of third-generation cephalosporin-resistant Salmonella over the past decade and to elucidate, at the genomic level, the formation mechanisms and transmission pathways underlying different resistance phenotypes.},
}