@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.},
}

@article {pmid41877513,
year = {2026},
author = {Hassen, B and Abbassi, MS},
title = {Occurrence of integrons and their gene cassette arrays in Aeromonas species in aquatic environments: a narrative review.},
journal = {International journal of environmental health research},
volume = {36},
number = {9},
pages = {2612-2629},
doi = {10.1080/09603123.2026.2647896},
pmid = {41877513},
issn = {1369-1619},
mesh = {*Aeromonas/genetics ; *Integrons/genetics ; *Water Microbiology ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Gene Transfer, Horizontal ; },
abstract = {Antibiotic-resistant bacteria (ARB) and their associated antibiotic resistance genes (ARGs) represent a growing threat in clinical settings. ARB and ARGs from environmental ecosystems can persist in their native habitats and potentially transfer to human and animal pathogens. Aeromonas spp. has emerged as a notable nosocomial pathogen and is increasingly recognized as a bioindicator of antibiotic resistance in aquatic environments. Thus, Aeromonas spp. may play a pivotal role in the mobilization and dissemination of ARGs. This review synthesizes current literature on the presence and diversity of integrons, genetic elements that facilitate the horizontal transfer of resistance genes, within Aeromonas spp. isolated from aquatic ecosystems. Class 1 integrons are the most frequently reported in Aeromonas, although class 2 integrons have also been detected across various species and geographic regions. A substantial proportion of integron-positive Aeromonas isolates exhibit multidrug resistance (MDR). Moreover, diverse gene cassettes arrays have been identified in different Aeromonas strains, reflecting a high level of genetic variability. In conclusion, Aeromonas spp. represent a significant reservoir and vector for ARGs in aquatic systems, with the potential to transfer these resistance determinants to other pathogenic bacteria through drinking water and the food chain, thereby posing a public health risk.},
}

*Aeromonas/genetics
*Integrons/genetics
*Water Microbiology
*Drug Resistance, Bacterial/genetics
Genes, Bacterial
Gene Transfer, Horizontal

@article {pmid42386527,
year = {2026},
author = {Son, JH and Lawlor, MA and Virani, M and Cao, W and Levine, MT and Ellison, CE},
title = {Convergence and conflict among telomere-specialized transposons across 60 million years of Drosophilid evolution.},
journal = {Genome research},
volume = {36},
number = {9},
pages = {1800-1817},
doi = {10.1101/gr.281112.125},
pmid = {42386527},
issn = {1549-5469},
mesh = {Animals ; *Telomere/genetics ; *DNA Transposable Elements/genetics ; *Evolution, Molecular ; Phylogeny ; Retroelements ; *Drosophilidae/genetics ; *Drosophila/genetics ; Gene Transfer, Horizontal ; Genome, Insect ; },
abstract = {The Drosophila telomere is one of the best-studied examples of active transposable elements (TEs) benefiting, rather than harming, the host genome. All Drosophila species lack telomerase, and most species instead have telomeres composed of head-to-tail arrays of specialized retrotransposons. These TEs ostensibly act as mutualists by elongating chromosome ends, but evidence from species closely related to Drosophila melanogaster suggests that telomeric transposons may also antagonize their host genome. Importantly, the limited number of Drosophila species characterized thus far has precluded our ability to delineate idiosyncrasies from universal evolutionary forces and genetic mechanisms that shape the history of these TEs. Here, we have surveyed long-read genome assemblies of more than 100 species of Drosophila, identifying a total of 396 telomeric TE families. Our findings show that these telomere-specialized elements evolve dynamically and also undergo striking convergent evolution: The complete loss of telomeric TEs has occurred repeatedly across the genus, whereas individual telomeric TE lineages have repeatedly lost one of their two protein-coding genes. These elements have also repeatedly undergone horizontal transfer between distantly related Drosophila lineages and have repeatedly captured host gene fragments that promote their selfish suppression of host TE-silencing systems. Furthermore, telomere specialization itself appears to have evolved convergently, as some nontelomeric families have gained the ability to target their insertions to telomeres. These results provide unprecedented resolution into the evolution of these unusual TEs and highlight several novel mechanisms by which they evolve in conflict both with each other and their host genome despite the essential telomere function they provide.},
}

Animals
*Telomere/genetics
*DNA Transposable Elements/genetics
*Evolution, Molecular
Phylogeny
Retroelements
*Drosophilidae/genetics
*Drosophila/genetics
Gene Transfer, Horizontal
Genome, Insect

@article {pmid42668177,
year = {2027},
author = {Yan, S and Wu, K and Zhang, M and Tan, D and Zhan, L and Li, B and Yang, X and Yang, Z and Li, W and Guo, Y and Lei, C},
title = {Genomic insights into Salmonella enterica serovar Corvallis from China 2014-2023: A foodborne bacterial pathogen for antimicrobial resistance carriage and potential global transmission.},
journal = {Food microbiology},
volume = {141},
number = {},
pages = {105236},
doi = {10.1016/j.fm.2026.105236},
pmid = {42668177},
issn = {1095-9998},
mesh = {*Salmonella enterica/genetics/drug effects/isolation & purification/classification ; China/epidemiology ; Animals ; Chickens/microbiology ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Drug Resistance, Bacterial ; *Genome, Bacterial ; Phylogeny ; Serogroup ; *Foodborne Diseases/microbiology/epidemiology ; *Salmonella Infections/microbiology/transmission ; Plasmids/genetics ; Meat/microbiology ; Genomics ; Drug Resistance, Multiple, Bacterial/genetics ; Polymorphism, Single Nucleotide ; },
abstract = {Nontyphoidal Salmonella (NTS) is a leading zoonotic bacterial pathogen and a major cause of foodborne illness worldwide. Salmonella enterica subsp. enterica serovar Corvallis (S. Corvallis) has recently emerged in China as a serotype of concern, showing an elevated antimicrobial resistance (AMR) profile. We analyzed 260 S. Corvallis isolates collected through the China National Foodborne Disease Surveillance Program between 2014 and 2023, together with 598 publicly available genomes from global sources. Antimicrobial resistance determinants, pan-genome dynamics, phylogenetic structure, and patterns of global dissemination were characterized in an integrated framework. Isolates from the chicken production chain (chicken meat and slaughter-environment samples) harbored significantly more AMR genes (ARGs) than those of human origin. Correlation network analysis revealed consistent associations between specific plasmid replicons and ARGs: IncHI2 co-occurred with aadA16, dfrA27, and sul1; IncQ1 with floR; and IncA/C2 with dfrA12 and aadA2, with IS26 likely mediating their co-mobilization. SNP analysis demonstrated genetic distances ranging from 0 to 350 SNPs between isolates, with a substantial proportion showing ≤10 SNP differences, suggesting potential transmission events. Geographically, strains clustered predominantly around China, the United Kingdom, and countries in the Americas, with ST1541 as the dominant sequence type. Transmission inference further highlighted strong cross-regional links between UK and Chinese isolates. The co-occurrence of China-enriched ARGs with specific mobile genetic elements (MGEs) supports an evolutionary scenario in which a highly virulent, multidrug-resistant S. Corvallis clade has emerged through the combined effects of cross-regional dissemination and MGE-driven horizontal gene transfer, plausibly shaped by localized antimicrobial selection pressure. These findings underscore how regional antimicrobial use practices, particularly within the poultry production chain, can shape the evolution of resistant zoonotic pathogens with global transmission potential, and argue for coordinated One Health surveillance of emerging NTS serotypes.},
}

*Salmonella enterica/genetics/drug effects/isolation & purification/classification
China/epidemiology
Animals
Chickens/microbiology
*Anti-Bacterial Agents/pharmacology
Humans
*Drug Resistance, Bacterial
*Genome, Bacterial
Phylogeny
Serogroup
*Foodborne Diseases/microbiology/epidemiology
*Salmonella Infections/microbiology/transmission
Plasmids/genetics
Meat/microbiology
Genomics
Drug Resistance, Multiple, Bacterial/genetics
Polymorphism, Single Nucleotide

@article {pmid42668373,
year = {2026},
author = {Peng, Z and Zhuang, H and Liu, R and Li, F and Zhang, S and Du, P and Zheng, H and Sun, J and Quereda, JJ and Wu, Z},
title = {Multidrug-resistant and virulent Streptococcus suis strains detected in clinically healthy pigs in Guangdong and Guangxi, China.},
journal = {Veterinary research},
volume = {57},
number = {1},
pages = {},
pmid = {42668373},
issn = {1297-9716},
support = {No.2023YFD1800503//National Key Research and Development Program of China/ ; No.KCXFZ20230731094003006//Shenzhen Science and Technology Program/ ; No. ZDCYKCX20250901093300001//Shenzhen Key Industry Research and Development Program/ ; },
mesh = {Animals ; *Streptococcus suis/pathogenicity/drug effects/genetics ; *Streptococcal Infections/veterinary/microbiology/epidemiology ; China/epidemiology ; *Swine Diseases/microbiology/epidemiology ; Swine ; Virulence ; *Drug Resistance, Multiple, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Sus scrofa ; Mice ; Genetic Variation ; Zebrafish ; Humans ; },
abstract = {Streptococcus suis is a major zoonotic pathogen, and strains originating from clinically healthy pigs pose an increasingly serious threat to human health. This study investigated 315 S. suis isolates collected from clinically healthy pigs in Guangdong and Guangxi provinces between 2024 and 2025. Among these isolates, 34 capsular polysaccharide (cps) types were identified, with 40.63% belonging to cps types associated with human infections. The isolates exhibited high genetic diversity, distributed across 80 sequence types (STs), 13 clonal complexes (CCs), and five minimum core genomes (MCGs). Animal infection models demonstrated that a considerable proportion of healthy-pig-derived strains displayed high virulence in zebrafish and mouse models. Cytotoxicity assays confirmed that isolates belonging to CC1, CC7, CC17, CC94, and CC108 caused significant cytotoxicity toward A549 and hBMEC cells. Alarmingly, 96.82% of the isolates were multidrug-resistant, and notably, 29.84% showed resistance to penicillin. Furthermore, various integrative and conjugative elements (ICEs) and prophages were identified in these strains. Homology analysis revealed that ICEs carried by highly virulent healthy-pig-derived strains shared high similarity with those from highly virulent human-derived strains and even human-derived Streptococcus agalactiae, raising concerns about the possible dissemination of virulence-associated determinants via ICEs. This study highlights the emergence of multidrug-resistant and highly virulent S. suis strains in healthy pig populations. The dual threat of pathogenicity and antimicrobial resistance, coupled with the horizontal gene transfer capacity of ICEs and prophages, constitutes a serious public health risk, underscoring the urgent need for enhanced surveillance.},
}

Animals
*Streptococcus suis/pathogenicity/drug effects/genetics
*Streptococcal Infections/veterinary/microbiology/epidemiology
China/epidemiology
*Swine Diseases/microbiology/epidemiology
Swine
Virulence
*Drug Resistance, Multiple, Bacterial
*Anti-Bacterial Agents/pharmacology
Sus scrofa
Mice
Genetic Variation
Zebrafish
Humans

@article {pmid42668380,
year = {2026},
author = {Feurstein, C and Bachmann, L and Heber, L and Dobbert, B and Jung, S},
title = {A superfamily of bioactive proteins from fungi - are these secondary metabolites?.},
journal = {Fungal biology and biotechnology},
volume = {13},
number = {1},
pages = {},
pmid = {42668380},
issn = {2054-3085},
support = {DFG, GRK2473 "Bioactive Peptides" - project number 392923329//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Since decades, fungi are leveraged in biotechnology to produce high-value compounds used in multiple economic sectors. Strain and process optimisation is based on a comprehensive understanding of the production organism on the cellular and molecular level. Among three antifungal protein families in fungi, consisting of small cysteine-stabilised proteins, it has been shown that, for some family members, bioactivities are also associated with additional functions in their hosts, e.g., carbon metabolism, autophagy, or asexual development. These proteins are interesting as alternative source of novel antifungal drugs. However, their potential impact on biotechnological production is not yet elucidated.

RESULTS: In this study, we introduce the antifungal bubble protein "AgBP", from Aspergillus giganteus and further elucidate the reservoir of bioactive proteins in fungi. We used NCBI PSI-BLAST and subsequent phylogenetic and structural analyses of the Antifungal Protein (AFP), Bubble Protein (BP), and Neosartorya fischeri antifungal protein 2 (NFAP2) family members. We could identify further putative members: 165 AFP-, 102 BP-, and 219 NFAP2-like proteins. Six of the AFP and all 219 NFAP2 family members are not yet assigned on InterPro. All proteins were exclusively identified in fungi. To our best knowledge, this is the first study to report this group of bioactive proteins is shared among the two divisions of Ascomycetes and Basidiomycetes. Phylogenetic tree analyses demonstrate restricted taxonomic distribution within single genera. Furthermore, the comparison of the tertiary structures of all members of the three AFP families clearly separates them from each other and from non-fungal small cysteine-stabilised antifungal proteins.

CONCLUSION: We hypothesise that the three protein families represent a distinct superfamily of evolutionary related proteins. We further hypothesise that these proteins could be categorised as secondary metabolite like molecules of ribosomal origin. For brevity, we named this superfamily BPF (bioactive proteins from fungi). The distribution of BPF members is presumably driven by horizontal gene transfer. Furthermore, we hypothesise that BPF members likely serve rather different biological roles than merely acting as antimicrobials. Their hypothetical classification as potential secondary metabolite like proteins in combination with their occurrence among several biotechnologically relevant fungal genera, e.g., Aspergillus, Penicillium, Trichoderma, Schizophyllum, etc., emphasises their potential relevance for genetic and metabolic engineering.},
}

@article {pmid42669367,
year = {2026},
author = {Li, J and Liu, Y and Zhang, J and Zhang, Y and Wang, X and Han, X and Zhang, S and Zhao, Z and Dong, S},
title = {Pilot-scale simultaneous coupling ozonation and biodegradation for enhancing pollutant removal and mitigating antibiotic resistance genes in penicillin intermediate wastewater.},
journal = {Bioresource technology},
volume = {463},
number = {},
pages = {135749},
doi = {10.1016/j.biortech.2026.135749},
pmid = {42669367},
issn = {1873-2976},
abstract = {Penicillin intermediate wastewater contains recalcitrant organics and residual antibiotics that favor the enrichment of antibiotic-resistant bacteria and the dissemination of antibiotic resistance genes (ARGs). In this study, a pilot-scale simultaneous coupling ozonation and biodegradation (SCOB) system was applied to treat the secondary biochemical effluent of penicillin intermediate wastewater. The reactor achieved stable operation under selected conditions of a 6 h hydraulic retention time, a 2 h ozone supply period, and an ozone dosage of 5 mg/(L·h). Compared with the standalone biodegradation system, the SCOB system enhanced chemical oxygen demand removal by 25.90%, UV254 removal by 31.34%, and a 34.93-fold increase in chroma removal. The SCOB system attenuated both chronic and acute toxicity in the effluent. Microbial analyses revealed that, despite lower biomass, microbial activity increased by 21.04% in the SCOB system, accompanied by distinct community succession, with Proteobacteria, Actinobacteria, and Chloroflexi as the dominant phyla and Hyphomicrobium as the dominant genus. The SCOB system also reduced intracellular reactive oxygen species levels and suppressed ARGs abundance and dissemination. The total abundance of ARGs decreased by 10.34%, while multidrug resistance plasmids were reduced by 25.40%. This study provides engineering guidance for developing pilot-scale SCOB as an advanced treatment strategy for simultaneously achieving pollutant removal and ARGs risk mitigation in antibiotic-containing wastewater.},
}

@article {pmid42674139,
year = {2026},
author = {Jiang, K and Pan, X and Zhu, S and Dang, Z and Yang, Z and Huang, L and Pan, X and Zou, X and Zhang, J and Guo, Y and Zhang, W and Li, Z and Cong, X and Wang, Z},
title = {Cellulose/polyester-blended microplastics amplify plastisphere pathogen and antibiotic resistome risks.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135752},
doi = {10.1016/j.biortech.2026.135752},
pmid = {42674139},
issn = {1873-2976},
abstract = {Microplastics (MPs) are important vectors for antibiotic resistance genes (ARGs) in anaerobic digestion systems, yet the risks posed by cellulose/polyester-blended materials remain poorly understood. In this study, commercial airlaid paper (AP; 45 % cellulose and 55 % polyester), polyethylene (PE), polypropylene (PP), and polystyrene (PS) were incubated in anaerobic reactors for 60 days. Biofilm characterization, extracellular polymeric substances (EPS) analysis, 16 S rRNA sequencing, and metagenomics were used to compare plastisphere formation, microbial assembly, ARG/mobile genetic element (MGE) profiles, and potential pathogen composition. Owing to its fibrous structure and bioavailable cellulose fraction, AP exhibited the highest biofilm biomass and EPS content. In contrast, PE, PP, and PS induced stronger interfacial stress, especially PS, as indicated by increased reactive oxygen species, lactate dehydrogenase release, and enrichment of oxidative stress, SOS response, and multidrug efflux pump related genes. Metagenomic analysis showed that fully synthetic MPs mainly enriched multidrug resistance genes, whereas AP selectively enriched polymyxin resistance genes, particularly Mcr-5.1 and Mcr-5.2. AP also exhibited the highest ARG-MGE co-localization rate (12.7 %) and antibiotic resistance risk. Overall, these findings identify polymer composition as a key factor shaping plastisphere resistome assembly and indicate that cellulose/polyester-blended materials require specific consideration in sludge-associated antimicrobial resistance risk assessments.},
}

@article {pmid42665237,
year = {2026},
author = {Yang, L and Wei, D and Li, Y and Chen, X},
title = {Algae-to-host horizontal gene transfer in Paramecium bursaria is associated with host adaptation during endosymbiosis.},
journal = {Molecular phylogenetics and evolution},
volume = {225},
number = {},
pages = {108726},
doi = {10.1016/j.ympev.2026.108726},
pmid = {42665237},
issn = {1095-9513},
abstract = {Paramecium bursaria maintains a stable endosymbiosis with green algae, yet the evolutionary consequences of this association remain unclear. Here, we screened the host genome for algal-derived horizontally transferred genes (HTGs) using a lineage-aware workflow designed to detect horizontal gene transfer (HGT) between two defined lineages. We identified 16 candidate HTGs, including four putative newly transferred genes and 12 homologous transferred genes, most of which were functionally associated with redox homeostasis and metabolism. Five HTGs showed symbiosis-dependent expression. RNAi knockdown of GH32s and SATs reduced host proliferation, total cell area, and motility, while GH32s knockdown also reduced endosymbiont load. Duplication patterns suggest that most transfers may have occurred after the P. bursaria lineage diverged from the sampled Paramecium species but before its lineage-specific whole-genome duplication (WGD). The HTGs also showed host-associated shifts in GC content and gene length, while representative HTGs retained conserved domains and functional motifs. Together, our results support algae-to-host HGT in P. bursaria and suggest that some transferred genes may contribute to metabolic integration during endosymbiosis.},
}

@article {pmid42667423,
year = {2026},
author = {Sarkar, MP and Pal, A},
title = {Comparative phylogenomics of bacterial urease systems reveals architectural conservation, lineage-specific specialization, and candidate horizontal transfer.},
journal = {Molecular genetics and genomics : MGG},
volume = {301},
number = {1},
pages = {},
pmid = {42667423},
issn = {1617-4623},
mesh = {*Urease/genetics ; Phylogeny ; *Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Evolution, Molecular ; Genomics/methods ; *Bacteria/genetics/enzymology/classification ; Bacterial Proteins/genetics ; Helicobacter/genetics/enzymology ; },
abstract = {Urease is a nickel-dependent, multi-gene bacterial system that contributes to nitrogen acquisition, pH homeostasis, and ecological adaptation, yet most comparative studies rely on single-gene markers such as ureC. Here, we analyzed 237 complete genomes from a stratified bacterial panel integrating ecological and genome-level metadata, annotation-guided screening, profile-HMM detection, locus reconstruction, and species-tree comparison. Within this panel, 149 genomes encoded at least one complete urease locus, 11 contained candidate but incomplete neighborhoods, and 77 lacked any supported urease locus. At the locus level, we recovered 173 urease-associated neighborhoods, including 150 canonical ureABC loci, 7 Helicobacter AB fusion loci, and 16 partial or split loci. The canonical three-subunit architecture therefore dominated the dataset, whereas the Helicobacter-type configuration persisted as a small but stable lineage-restricted alternative. Eight genomes encoded duplicated complete canonical systems, and in each case, both loci mapped to the same top-level assembly sequence record. Their paired loci differed in gene order and typically shared only about 62-63% concatenated ureABC identity, consistent with older divergence or secondary acquisition rather than recent exact duplication. Comparison of the concatenated ureABC gene tree with the species tree identified 12 candidate incongruent loci, all involving complete canonical systems. A manual review of the strongest examples highlighted ecologically coherent modules in nitrifiers and marine cyanobacteria, as well as nickel- and hydrogenase-associated urease neighborhoods in enteric bacteria. Together, these results establish bacterial urease as a broadly conserved but evolutionarily flexible genomic component shaped by architectural conservation, lineage-specific specialization, duplication, and occasional intergeneric transfer.},
}

*Urease/genetics
Phylogeny
*Gene Transfer, Horizontal
Genome, Bacterial/genetics
Evolution, Molecular
Genomics/methods
*Bacteria/genetics/enzymology/classification
Bacterial Proteins/genetics
Helicobacter/genetics/enzymology

@article {pmid42667975,
year = {2026},
author = {Li, J and Zhu, C and Chai, G and He, F and Song, Z and Chen, Z and Chen, M and Yi, Z},
title = {Progressive evolutionary trajectories of mitochondrion-related organelles in anaerobic ciliates (Eukaryota, Alveolata) revealed by APM ciliates and a facultatively anaerobic spirotrichean species.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108721},
doi = {10.1016/j.ympev.2026.108721},
pmid = {42667975},
issn = {1095-9513},
abstract = {Ciliates are an excellent model for studying convergent transitions from mitochondria to mitochondrion-related organelles (MROs) in protists. Despite our growing knowledge of adaptive evolution in ciliate MROs, the progressive evolutionary trajectories within anaerobic ciliate lineages and the MRO metabolisms of facultatively anaerobic ciliates remain unexplored. In this study, we predicted MRO metabolisms of eight species within the anaerobic monophyletic APM (Armophorea-Muranotrichea-Parablepharismea) clade and a facultative anaerobe from its sister class Spirotrichea. Our main results are as follows: (1) During their adaptation to anaerobic environments, the MRO electron transfer chain (ETC) components and their associated functions have been progressively lost in the APM clade. (2) The MRO of the last common ancestor of Armophorea likely possesses complexes Ⅰ, Ⅱ, and Ⅴ, but lacks functional complexes Ⅲ and Ⅳ. Subsequently, during their adaptation to anaerobic environments, the armophorean lineage has further lost complex Ⅴ in the order Clevelandellida and Metopida. (3) In the MRO of the facultatively anaerobic ciliate Heterodeviata sinica, complexes Ⅲ and Ⅳ are absent, and alternative oxidases (AOX) play a key role in adaptation to fluctuating dissolved oxygen levels. (4) The fused [FeFe]-hydrogenase appears to have been acquired by the last common ancestor of ciliates through horizontal gene transfer (HGT), followed by multiple independent losses. Our results provide insights into the progressive adaptations of anaerobic ciliates to the low-oxygen environments.},
}

@article {pmid42663479,
year = {2026},
author = {Liu, M and Su, X and Huang, X and Yang, X and Chen, Y and Xu, J and He, Y},
title = {Top-down/bottom-up consortia achieve robust γ-HCH degradation and reduced methanogenic contribution in wetlands.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0113326},
doi = {10.1128/aem.01133-26},
pmid = {42663479},
issn = {1098-5336},
abstract = {UNLABELLED: Generalist non-obligate organochlorine-degrading bacteria (ODB) play an important role in the bioremediation of γ-hexachlorocyclohexane (γ-HCH), yet their ecological roles and functional mechanisms remain underexplored. In this study, we used both "top-down" and "bottom-up" strategies to construct two functional consortia (M and Y13) based on non-obligate ODB. Both consortia demonstrated efficient degradation in sediment microcosms, reducing γ-HCH (C/C0) to 63.0% (M) and 56.1% (Y13). Simultaneously, functional microbial consortia inoculation significantly suppressed the CO2 reduction methanogenesis pathway compared with the non-inoculated group (P < 0.05), as evidenced by a marked decline in the CH4/CO2 ratio in inoculated groups. The well-known degradation gene pceA was enriched in the Y13 group, and the co-localization of pceA-encoding contigs with mobile genetic elements was identified. Notably, Enterococcus was found to have successfully colonized inoculated groups. It has strong environmental evolutionary adaptability and might acquire organochlorine-degrading genes through horizontal gene transfer under pollution stress. The broad applicability of non-obligate ODB (e.g., Enterococcus) makes them a promising candidate for future environmental remediation efforts, breeding new avenues of "One Health" win-win solutions in carbon reduction during pollution remediation for wetlands.

IMPORTANCE: γ‑Hexachlorocyclohexane (γ‑HCH) is a representative organochlorine pesticide and a well‑known persistent organic pollutant that poses significant risks to ecosystems and human health. Microbial anaerobic degradation is a key process in the natural attenuation and engineered cleanup of γ‑HCH contamination. The effective application of obligate organohalide-respiring bacteria often requires precise management. In parallel, newly discovered non‑obligate organohalide-respiring bacteria capable of degrading γ‑HCH have emerged as promising alternatives, yet their performance and ecological interactions in realistic sediment systems remain poorly understood. This study examines the degradation mechanisms and microbial ecology of non-obligate organohalide-respiring bacterial functional consortia in complex media. The findings provide critical insights for developing effective bioaugmentation strategies for lindane‑contaminated coastal wetlands and may offer a useful framework for managing other recalcitrant halogenated pollutants in similar environments.},
}

@article {pmid42663501,
year = {2026},
author = {Du, J and Du, J and Qiu, L and Zhou, Q and Jin, M and Chen, J and Wu, W},
title = {The vector effect of microplastics and nanoplastics: co-transport and ecological risks of chemical pollutants and antibiotic resistance genes in the soil-water continuum.},
journal = {Drug and chemical toxicology},
volume = {},
number = {},
pages = {1-26},
doi = {10.1080/01480545.2026.2717208},
pmid = {42663501},
issn = {1525-6014},
abstract = {Microplastics (MPs) and nanoplastics (NPs) act as dynamic environmental vectors across the soil-water continuum, allowing them to enter organisms through direct ingestion, leading to potential tissue accumulation. Under specific exposure conditions, these vectors can undergo trophic transfer through food chains, contributing to combined toxicological risks. This paper reviews how the adsorption and co-transport behaviors of chemical pollutants by MPs and NPs are collectively regulated by the intrinsic physicochemical properties of the material and environmental weathering processes. The formation of the "plastisphere" on the surface of these particles provides a physical substrate that selectively enriches microbial communities and mobile genetic elements (MGEs). Under specific combined chemical stresses, this localized enrichment can act as a precursor to facilitate the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs), although the actual occurrence of HGT remains highly context-dependent. Additionally, MPs and NPs exacerbate their ecotoxicological impacts by operating via an "adsorption-ingestion-release" pathway within host gastrointestinal tracts, significantly influencing the dynamic bioavailability and combined toxicity (e.g., synergistic, antagonistic, or additive) of co-existing pollutants across multiple trophic levels. Given the numerous unresolved scientific challenges-such as the lack of standardized quantification methodologies for complex soil matrices and the poorly understood biomagnification of composite pollutant mixtures-there is a pressing need to promote further research through AI-driven coupled kinetic models and a comprehensive "One Health" risk assessment paradigm.},
}

@article {pmid42664264,
year = {2026},
author = {Tuffet, R and Acacia, E and Coluzzi, C and Charpentier, X and Koffel, T and Venner, S},
title = {Ecological theory sheds light on plasmid diversity and dynamics.},
journal = {PLoS biology},
volume = {24},
number = {8},
pages = {e3003918},
pmid = {42664264},
issn = {1545-7885},
mesh = {*Plasmids/genetics ; Genome, Bacterial/genetics ; Gene Transfer, Horizontal ; Bacteria/genetics ; Evolution, Molecular ; *Genetic Variation ; Ecology ; Models, Genetic ; },
abstract = {Bacterial genomes are remarkably dynamic, shaped by horizontal gene transfer. Plasmids are key actors in this process, fueling rapid bacterial adaptation to stresses such as antibiotics. Yet, plasmids follow evolutionary trajectories of their own, defying traditional genetic frameworks. Beyond the co-evolution of traits directly involved in plasmid-host relationships, it is now essential to draw from ecological theory to understand plasmid assemblages. By viewing plasmids as ecological entities competing for a shared resource, the bacterial host, we show that their distribution within bacterial genomes mirrors the structure of ecological communities. Our minimal stochastic model, inspired by community ecology, reveals that plasmid diversity arises from the combined action of niche differentiation and neutral processes. These results challenge deterministic views of genome organization, highlighting the central role of stochasticity and drift. This work establishes a theoretical bridge between microbial genomics and ecology, offering a new framework to understand-and potentially control-the evolution of bacterial genomes.},
}

*Plasmids/genetics
Genome, Bacterial/genetics
Gene Transfer, Horizontal
Bacteria/genetics
Evolution, Molecular
*Genetic Variation
Ecology
Models, Genetic

@article {pmid42661048,
year = {2026},
author = {Abdella, B and Shokrak, NM and Mohamed, RA and El-Helow, ER},
title = {The prc gene as a high-resolution proxy for Aeromonas genus-wide clonal genealogy, phylogenomic validation and superiority over traditional MLST.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42661048},
issn = {2045-2322},
mesh = {*Aeromonas/genetics/classification ; Phylogeny ; *Multilocus Sequence Typing/methods ; Genome, Bacterial ; Recombination, Genetic ; *Bacterial Proteins/genetics ; Evolution, Molecular ; Genetic Markers ; },
abstract = {Aeromonas spp. are critical aquatic pathogens affecting global aquaculture and human health, yet their taxonomy is frequently confounded by persistent horizontal gene transfer and high recombination rates. While whole-genome sequencing offers definitive resolution, many laboratories remain dependent on biochemical profiling or multi-locus sequence typing (MLST) due to cost and infrastructure constraints. To address this diagnostic gap, a two-phase phylogenomic study to identify a robust single locus genetic marker was conducted. In the discovery phase, we analyzed 22 high-quality complete Aeromonas type strain genomes to quantify the evolutionary impact of recombination and selection of new marker candidate, followed by a validation phase involving high-quality 374 genus-wide assemblies. Our results indicate that an elevated recombination-to-mutation ratio (r/m ≈ 1.70) is associated with reduced phylogenetic congruence of standard MLST loci, including gyrB, groL, and recA. In contrast, the prc gene exhibited the highest congruence with the recombination-filtered clonal genealogy (score = 0.94). Within the 95-96% ANI species boundary, the prc gene identity consistently remained more than 97%. This observed prc stability may be associated with functional constraints related to its predicted role in the periplasm. We therefore propose that a prc gene phylogeny and sequence identity threshold of > 97% could serve as a rapid and cost-effective marker for preliminary species-level assignment and epidemiological surveillance of Aeromonas spp., particularly in settings where a whole-genome sequencing is not readily available.},
}

*Aeromonas/genetics/classification
Phylogeny
*Multilocus Sequence Typing/methods
Genome, Bacterial
Recombination, Genetic
*Bacterial Proteins/genetics
Evolution, Molecular
Genetic Markers

@article {pmid42663137,
year = {2026},
author = {Zeng, K and Shen, W and Cai, J},
title = {Clonal spread of linezolid-, tigecycline-, and vancomycin-resistant Enterococcus faecium isolates co-harbouring transferable optrA, vanA and tet(M) variant.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {81},
number = {9},
pages = {},
doi = {10.1093/jac/dkag292},
pmid = {42663137},
issn = {1460-2091},
support = {81971988//National Natural Science Foundation of China/ ; },
mesh = {*Enterococcus faecium/genetics/drug effects/isolation & purification/classification ; Humans ; *Tigecycline/pharmacology ; *Linezolid/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Plasmids/genetics ; *Bacterial Proteins/genetics ; Electrophoresis, Gel, Pulsed-Field ; China/epidemiology ; Whole Genome Sequencing ; *Gram-Positive Bacterial Infections/microbiology/epidemiology ; Carbon-Oxygen Ligases/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Conjugation, Genetic ; Vancomycin Resistance/genetics ; DNA Transposable Elements ; Intensive Care Units ; },
abstract = {OBJECTIVES: This study investigated the clonal dissemination and molecular basis of linezolid-, tigecycline- and vancomycin-resistant E. faecium (LTVRE) isolates in a surgical intensive care unit (SICU) of a Chinese hospital.

METHODS: Three LTVRE isolates collected from patients in the SICU were subjected to antimicrobial susceptibility testing and whole-genome sequencing analysis. S1 nuclease pulsed-field gel electrophoresis was performed to verify the topology of plasmids. Conjugation experiments were conducted to evaluate the transferability of resistance determinants.

RESULTS: WGS analysis demonstrated that the three LTVRE belonged to the same clone (Sequence Type 78). The optrA and vanA genes were co-located on a transferable large linear plasmid (327.5 kb in size) and contributed resistance to linezolid and vancomycin. A tet(M) variant carrying a phenylalanine-to-isoleucine substitution at Position 473 (F473I) was identified within a Tn916-like transposon. Although chromosomally encoded, this element retains the capacity for horizontal transfer to E. faecium BM4105RF and conferred tigecycline resistance.

CONCLUSIONS: Our findings reveal a resistance dissemination strategy in which plasmid-borne and chromosomal mobile genetic elements independently or cooperatively drive the spread of resistance to last-line antibiotics and highlight the urgent need for enhanced surveillance of multidrug-resistant E. faecium, such as LTVRE.},
}

*Enterococcus faecium/genetics/drug effects/isolation & purification/classification
Humans
*Tigecycline/pharmacology
*Linezolid/pharmacology
*Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
Plasmids/genetics
*Bacterial Proteins/genetics
Electrophoresis, Gel, Pulsed-Field
China/epidemiology
Whole Genome Sequencing
*Gram-Positive Bacterial Infections/microbiology/epidemiology
Carbon-Oxygen Ligases/genetics
*Drug Resistance, Multiple, Bacterial/genetics
Gene Transfer, Horizontal
Conjugation, Genetic
Vancomycin Resistance/genetics
DNA Transposable Elements
Intensive Care Units

@article {pmid42663464,
year = {2026},
author = {Ramoneda, J and Vinod, DP and Ma, Y and Ruan, C and Schmidt, J and Manhart, M and Angst, DC and Johnson, DR},
title = {Spatial constraints determine the spread of plasmid-encoded antibiotic resistance between bacterial colonies.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0053126},
doi = {10.1128/msystems.00531-26},
pmid = {42663464},
issn = {2379-5077},
abstract = {Plasmid transfer among bacteria is an important driver of the spread of antibiotic resistance. Surface-associated bacterial biomass is a hotspot for plasmid transfer due to the dense spatial packing of cells, but this biomass is often sparse (composed of discrete bacterial colonies). Compared to plasmid dynamics within a single colony, the determinants of plasmid transfer between discrete colonies are less understood. Yet, colonies routinely physically collide with each other as they grow and expand across surfaces. Here, we experimentally demonstrate that collisions between colonies of Stutzerimonas stutzeri and Escherichia coli enable the spread of an antibiotic resistance-encoding plasmid, with the extent of transfer determined by the spatial distance between bacterial inocula. To better understand how spatial constraints influence the mechanisms underlying inter-colony plasmid spread, we applied an individual-based model simulating plasmid dynamics between colliding colonies. Our simulations quantitatively predict how the probabilities of plasmid transfer and loss affect plasmid spread as colonies grow and collide. These effects are modulated by the distances between colonies and the spatial positioning of plasmid-carrying cells along the collision boundary. Our study reveals that inter-colony plasmid transfer is determined by the interplay between plasmid transfer, plasmid loss, and spatial constraints, expanding our understanding of plasmid dynamics in the spread of antibiotic resistance genes.IMPORTANCEThe spread of antibiotic resistance between spatially discrete microbial colonies is poorly understood, despite its relevance to persistent colonization on a variety of surfaces (e.g., medical devices, dental plaque, wound infections, indoor plumbing, etc.). Here, we combined experiments and individual-based modeling to show that physical collisions between growing colonies enable the spread of plasmids carrying antibiotic resistance genes. The extent of transfer depends on the initial spatial distance between colonies, the probabilities of plasmid transfer and loss, and the local spatial intermixing of plasmid-carrying and -free cells along the collision boundary. These findings reveal how the interplay between plasmid biology and microbial spatial organization governs the spread of antibiotic resistance and provide a quantitative framework for predicting plasmid dynamics in spatially structured environments.},
}

@article {pmid42654995,
year = {2026},
author = {Wang, E and Zhang, Y and Yue, R and Wang, Y and Ma, X and Zhang, G and Jin, L},
title = {Plant-Microbiome Interactions in Medicinal Plants: A Synergistic Partnership for Biomass Production and Secondary Metabolite Accumulation.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
pmid = {42654995},
issn = {2076-2607},
support = {GSRAS-06//Gansu University Of Chinese Medicine/ ; CARS-21//Gansu University Of Chinese Medicine/ ; 2025A-116//Gansu University of Traditional Chinese Medicine/ ; 25JRRA1171//Gansu University of Traditional Chinese Medicine/ ; Northwest China-Tibet Medicine Collaborative Innovation Center (2026)//Gansu University of Traditional Chinese Medicine/ ; 2025KJZC00005//Northwest Institute of Eco-Environment and Resources/ ; },
abstract = {Medicinal plants are important sources of secondary metabolites (SMs), but their production is constrained by resource shortages, low cultivation efficiency, and continuous cropping obstacles. As the "second genome" of host plants, the plant microbiome is deeply involved in plant growth and development, stress adaptation, and the accumulation of bioactive compounds, providing new pathways for the sustainable utilization of traditional Chinese medicine resources. This review summarizes the mechanisms by which the plant microbiome regulates biomass formation and SM accumulation in medicinal plants. Microorganisms can promote plant nutrient acquisition, enhance resistance to biotic and abiotic stresses, and regulate root architecture and hormonal signaling. Meanwhile, microorganisms can also participate in the remodeling of secondary metabolic networks in medicinal plants through elicitor- and effector protein-mediated signal transduction, regulation of metabolic gene expression, redistribution of photosynthetic carbon sources and metabolic precursors, and their own biosynthetic capacities. From the perspective of co-evolution, plants and their microbiomes constitute symbiotic systems formed through long-term interactions. Plants can selectively recruit specific microbial taxa through root exudates, SMs, and signaling molecules, whereas microorganisms influence plant adaptability and medicinal material quality through colonization, metabolic feedback, and horizontal gene transfer. This review proposes that a synergistic regulatory pattern of "close phylogenetic relatedness-similar secretions-similar microbial communities" may exist between medicinal plants and microorganisms. This pattern suggests that closely related medicinal plants may share similar core microbial taxa, which may help reveal the intrinsic mechanisms underlying specific microbial recruitment and the quality formation of geo-authentic medicinal materials. Furthermore, the design of synthetic microbial communities (SynComs) can be achieved based on the identification of shared functional genes and the screening of indigenous core functional strains.},
}

@article {pmid42655709,
year = {2026},
author = {Corrêa, BA and Medinilha Pancher, T and Calandriello Calio, D and Tassi, AD and Pereira, LR and Carrillo, D and Harakava, R and Novelli, VM and Kitajima, EW and Ramos-González, PL and Freitas-Astúa, J and Gonzalez-Ibeas, D},
title = {Identification of Partitivirus-like RdRPs in the Brevipalpus yothersi Genome Supports Viral-to-Arthropod Horizontal Gene Transfer.},
journal = {Viruses},
volume = {18},
number = {8},
pages = {},
pmid = {42655709},
issn = {1999-4915},
support = {2023/08989-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
mesh = {Animals ; *Gene Transfer, Horizontal ; *RNA-Dependent RNA Polymerase/genetics/chemistry ; Phylogeny ; *Mites/genetics/virology ; Viral Proteins/genetics ; *RNA Viruses/genetics/enzymology ; Genome ; *Arthropods/genetics/virology ; },
abstract = {RNA-dependent RNA polymerases (RdRPs) are essential enzymes involved in RNA virus replication and eukaryotic RNA silencing. They are generally absent in vertebrates but present in some invertebrate lineages, such as nematodes and certain arthropods. Brevipalpus yothersi is a phytophagous mite of agricultural relevance due to its role as a vector of plant-infecting viruses. We have identified two RdRPs on the genome of this mite species that, unexpectedly, are not of eukaryotic origin. Phylogenetic reconstruction and comparisons of 3D protein structures revealed similarity with viral RdRPs of the Partitiviridae family. Both RdRPs retain conserved catalytic motifs at the protein sequence level, and expression was confirmed by RNAseq and qPCR across mite developmental stages, with a peak during the nymphal stage. K-mer profiles showed similarity with mite endogenous genes, suggesting gene amelioration after the integration, or being derived from a viral donor already adapted to the mite. Our study also identified orthologs in other Brevipalpus species, but not in other Acari relatives, supporting that the horizontal gene transfer event is circumscribed to the Brevipalpus genus. These findings highlight an intriguing case of viral gene domestication in arthropods that might influence their developmental biology and the host-virus interaction.},
}

Animals
*Gene Transfer, Horizontal
*RNA-Dependent RNA Polymerase/genetics/chemistry
Phylogeny
*Mites/genetics/virology
Viral Proteins/genetics
*RNA Viruses/genetics/enzymology
Genome
*Arthropods/genetics/virology

@article {pmid42656412,
year = {2026},
author = {Pearl, S and Anbarasu, A},
title = {Comparative genomics of carbapenem resistant and susceptible clinical Acinetobacter baumannii reveals lineage-associated mobilization of acquired carbapenemase determinants: an integrative in silico genomics approach.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1886564},
pmid = {42656412},
issn = {2235-2988},
mesh = {*Acinetobacter baumannii/genetics/drug effects/classification/enzymology/isolation & purification ; *Carbapenems/pharmacology ; *beta-Lactamases/genetics ; *Genomics/methods ; *Bacterial Proteins/genetics ; Humans ; *Anti-Bacterial Agents/pharmacology ; Genome, Bacterial ; Acinetobacter Infections/microbiology ; Interspersed Repetitive Sequences ; Genotype ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; Virulence Factors/genetics ; Computer Simulation ; Plasmids/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Carbapenem resistant Acinetobacter baumannii (CRAB) is recognized as one of the most critical priority pathogens by the World Health Organization due to its persistence in nosocomial settings, extensive antimicrobial resistance, and increasing dissemination at the global level. Despite the escalating availability of genomic data, genotype-phenotype integrated studies exploring the genetic determinants associated with carbapenem resistance remain limited.

METHODS: In this study, a comprehensive comparative genomics was performed using publicly available 395 clinical A. baumannii genomes, comprising of 267 CRAB and 128 carbapenem susceptible A. baumannii (CSAB). Comparative genomic analyses included sequence types (STs), virulence factors (VFs), antimicrobial resistance genes (ARGs), and mobile genetic elements (MGEs) characterization. Pangenome-wide association study (PanGWAS) was performed to test the associations between genotypes and carbapenem resistance phenotype.

RESULTS: CRAB genome subset demonstrated higher abundance of ARGs (acquired carbapenemases in particular), plasmids, carbapenem resistance-associated insertion sequences, and integrons than CSAB genomes. PanGWAS identified six positively associated genes (relE, umuC, hphA, hsmA, hphR, and fecI) significantly enriched in CRAB population. Core SNP phylogeny integrated with STs and acquired carbapenemase genes exhibited heterogeneous distribution of resistance genes across lineages, indicating potential role of both clonal dissemination and horizontal gene transfer.

CONCLUSION: This study provides an overall genomic architecture of CRAB integrating comparative genomics, PanGWAS, and phylogenomics approaches. The findings underscore the complex interplay between ARGs, VFs, and MGEs in the genomic evolution of CRAB, expanding current understanding of CRAB adaptation and may contribute toward enhanced surveillance, antimicrobial stewardship, and exploration of alternative therapeutic targets.},
}

*Acinetobacter baumannii/genetics/drug effects/classification/enzymology/isolation & purification
*Carbapenems/pharmacology
*beta-Lactamases/genetics
*Genomics/methods
*Bacterial Proteins/genetics
Humans
*Anti-Bacterial Agents/pharmacology
Genome, Bacterial
Acinetobacter Infections/microbiology
Interspersed Repetitive Sequences
Genotype
Microbial Sensitivity Tests
Gene Transfer, Horizontal
Virulence Factors/genetics
Computer Simulation
Plasmids/genetics
Phylogeny

@article {pmid42656759,
year = {2026},
author = {Alejo, MA and Lozano Gamboa, MS and Muñoz Gomez, B and Hernández Magro Gil, KG and García-Contreras, R and Whitaker, RJ and Palacios Marmolejo, A and Ceapă, CD},
title = {Resistome, virulome, mobilome, and biosynthetic gene clusters adaptations of Acinetobacter baumannii Mexican strains before and during the COVID-19 pandemic: insights from whole-genome sequencing.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1830880},
pmid = {42656759},
issn = {2296-2565},
mesh = {Mexico/epidemiology ; *Acinetobacter baumannii/genetics/pathogenicity/drug effects ; Whole Genome Sequencing ; *COVID-19/epidemiology ; Multigene Family ; Humans ; Genome, Bacterial ; Phylogeny ; *Drug Resistance, Multiple, Bacterial/genetics ; *Acinetobacter Infections/epidemiology/microbiology ; SARS-CoV-2 ; },
abstract = {BACKGROUND: Acinetobacter baumannii is a critical multidrug-resistant pathogen whose genomic landscape in Mexico has been reshaped by the COVID-19 pandemic. While global studies have highlighted distinctive sequence type distributions, systematic analyses in Mexico remain limited.

METHODS: We analyzed 194 genomes, including 47 newly sequenced post-COVID isolates (MIQ), alongside 147 publicly available genomes (HPG). Whole-genome sequencing was combined with phylogenetic reconstruction, resistome and virulome profiling based on gene presence and absence, mobilome analysis, and biosynthetic gene cluster (BGC) characterization.

RESULTS: Two major clades dominated by Oxford STs 758, 208, 417, and 369 were identified. Resistome profiling uncovered 128 distinct resistome profiles (combinations of genes) and 44 emerging antimicrobial resistance genes (ARGs), with an increased number of resistance genes in the strains obtained during the pandemic. Virulome analysis revealed enrichment of metabolic adaptation genes (argG, carA, ilvC) in MIQ strains. Mobilome profiling demonstrated enrichment of ISAbA1 and ISAbA3 elements, known to mobilize carbapenemase genes. Mobilome profiling demonstrated enrichment of ISAba1 and ISAba3 elements, including novel associations such as bla OXA-72 with ISAba27 and bla OXA-66 with ISAba1. BGC analysis showed conserved siderophores involved in virulence, alongside diversification of the secondary metabolite repertoires in MIQ genomes. Additional observations included geographic mixing of clades across Jalisco, Aguascalientes, and Mexico City and referral bias toward carbapenemase-positive isolates. Because post-COVID isolates were enriched for referred high-risk cases, resistance estimates likely reflect a worst-case hospital scenario rather than community prevalence.

CONCLUSION: The genomic landscape of A. baumannii in Mexico has diversified post-COVID, with evidence of inter-regional transmission, virulome expansion, mobilome-driven ARG dissemination, and metabolic adaptation. These findings underscore the urgent need for coordinated genomic surveillance, functional and clinical validation of adaptation signals, and regionally integrated infection control strategies to mitigate resistance trajectories.},
}

Mexico/epidemiology
*Acinetobacter baumannii/genetics/pathogenicity/drug effects
Whole Genome Sequencing
*COVID-19/epidemiology
Multigene Family
Humans
Genome, Bacterial
Phylogeny
*Drug Resistance, Multiple, Bacterial/genetics
*Acinetobacter Infections/epidemiology/microbiology
SARS-CoV-2

@article {pmid42657294,
year = {2026},
author = {Lynch, J and Bradshaw, D and Hawkins, R and Howlin, R and Pavitt, S and Do, T},
title = {Oral dysbiosis: methodological evolution, the mobile resistome and the future of machine learning in dentistry.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2717773},
pmid = {42657294},
issn = {2000-2297},
abstract = {The oral microbiome acts as a significant, yet often overlooked, reservoir for antimicrobial resistance genes (ARGs). This review examines the role of the human resistome in oral health, evaluating current knowledge on the composition, function and dissemination of ARGs within the oral cavity. By comparing conventional culture-based methodologies against recent whole-genome sequencing (WGS) studies, we assess the critical role of the oral‒gut axis in resistance dissemination. The current literature indicates that horizontal gene transfer (HGT) facilitates the spread of mobile genetic elements within oral biofilms. Crucially, oral commensals, such as Fusobacterium spp., demonstrate the capacity to disseminate systemically, potentially transferring ARGs to pathogenic species. Recent WGS data further indicates a higher prevalence of ARGs in healthy individuals compared to those with dental caries, alongside an increased potential for ARG mobilisation with age. Ultimately, the dynamic oral resistome plays a vital role in both local and systemic health. Advanced methodologies, including WGS and machine learning, are essential for accurate resistome profiling and predicting antimicrobial susceptibility, which will guide prudent antibiotic prescribing in dentistry and mitigate the spread of antimicrobial resistance.},
}

@article {pmid42657744,
year = {2026},
author = {Mahelka, V and Caklová, P and Čegan, R and Villanueva-Corrales, S and Josefiová, J and Kneřová, J and Kopecký, D and Nagy-Nejedlá, M and Szecówka, M and Krak, K},
title = {The afterlife of a horizontally transferred gene: Expansion and functional diversification of a C1A peptidase in wild Hordeum species.},
journal = {The plant genome},
volume = {19},
number = {3},
pages = {e70242},
pmid = {42657744},
issn = {1940-3372},
support = {22-02469S//Czech Science Foundation/ ; RVO 67985939//Czech Academy of Sciences/ ; },
mesh = {*Hordeum/genetics/enzymology ; *Gene Transfer, Horizontal ; Phylogeny ; *Plant Proteins/genetics ; Evolution, Molecular ; DNA Copy Number Variations ; Genes, Plant ; },
abstract = {Horizontal gene transfer (HGT) can accelerate plant adaptation, but the evolutionary fate of newly acquired nuclear genes is often unclear. Here, we analyzed a papain-like cysteine peptidase horizontally transferred from Panicoideae to wild Hordeum (Poaceae). Using chromosome-level assemblies of 21 diploid Hordeum species, we assessed presence/absence, copy-number variation, coding diversity, selection, predicted protein functionality, and expression. To infer donor relationships, we screened 77 Panicoideae accessions (48 species, 20 genera) by polymerase chain reaction and sequenced positive amplicons with Nanopore. The transferred locus, likely acquired as part of a larger panicoid DNA segment, is retained across Hordeum sect. Stenostachys but shows strong post-transfer diversification, with 1-8 copies per species, extensive transposable-element insertions, and numerous coding-sequence variants. Close homologs in Panicoideae were rare and restricted to Panicum and Paspalum; gene trees identified Panicum bergii as the closest sampled relative. Selection analyses indicated heterogeneous constraints and episodic positive selection in some Hordeum lineages. Only a minority of copies retained an intact catalytic triad, whereas most were predicted to be pseudopeptidases. Transcripts were detected across species and tissues. These results indicate that an HGT-derived DNA block can persist, amplify, and diversify in recipient genomes, generating raw material for later functional evolution.},
}

*Hordeum/genetics/enzymology
*Gene Transfer, Horizontal
Phylogeny
*Plant Proteins/genetics
Evolution, Molecular
DNA Copy Number Variations
Genes, Plant

@article {pmid42658964,
year = {2026},
author = {Chen, T and Wang, X and Xiong, L and Lou, Z and Lu, P and He, Z and Ge, Q and Wu, H and Luo, Q and Shen, P and Chen, Y and Ding, H and Geng, Y and Liang, K and Yang, B and Xiao, T and Yu, W and Xiao, Y},
title = {Elevated wzc Mutation Frequency Promotes Carbapenem Resistance Evolution in Hypervirulent Klebsiella pneumoniae ST23.},
journal = {Emerging microbes & infections},
volume = {},
number = {},
pages = {2726043},
doi = {10.1080/22221751.2026.2726043},
pmid = {42658964},
issn = {2222-1751},
abstract = {AbstractThe worldwide expansion of carbapenemase-producing hypervirulent K. pneumoniae (CP-hvKP) raises serious concerns about potentially untreatable invasive infections. ST23, an archetypal hvKP clone, has been highlighted due to the rising prevalence of carbapenem resistance largely driven by horizontal plasmid transfer. However, the factors facilitating carbapenemase acquisition in this lineage remained unclear. We characterized 1159 ST23 isolates across 49 countries, including nine clinical carbapenemase-producing strains from China's national bloodstream infection surveillance network. Global phylogenetic analysis revealed two distinct sublineages, namely the globally distributed, hypervirulent ST23-I and the geographically restricted, multidrug-resistant ST23-II. Temporal analysis showed that ST23-I concurrently accumulated virulence and antimicrobial resistance traits. Among ST23-I isolates, carbapenemase plasmids exhibited notable genetic diversity and clear geographic segregation, with IncL-blaOXA-48 dominated in Europe and IncFII-blaKPC-2 in Asia. Conjugation assays revealed that IncFIIK34-blaKPC-2 and IncL-blaOXA-48 plasmids transferred more efficiently than IncX3-blaNDM-1 and IncFIIK2-blaNDM-1 plasmids, contributing to their high prevalence. Non-synonymous mutations in the capsular polysaccharide synthesis locus, particularly in wzc, were accumulated in ST23-KL1 CP-hvKP. Isogenic mutants carrying two identified wzc mutations (either wzc[2042A] [>] [G] or wzc[1738T] [>] [A]) exhibited partially reduced capsule production and enhanced conjugation efficiency of carbapenemase plasmids, confirming the functional impact of these mutations. Collectively, these findings demonstrate that an elevated wzc mutation frequency represents an adaptive evolutionary pathway that facilitates carbapenemase acquisition in hvKP ST23. The interplay between capsule-associated chromosomal mutations and plasmid-mediated horizontal gene transfer may shape the evolutionary adaptation of resistance in this clinically important pathogen.},
}

@article {pmid42643409,
year = {2026},
author = {Wang, Q and Cyriaque, V and Madsen, JS},
title = {Cooperative antibiotic resistance in bacteria: beyond biofilms.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1906606},
pmid = {42643409},
issn = {1664-302X},
abstract = {Cooperative behaviors among microorganisms, such as biofilm formation, are widespread and play a key role in the emergence and evolution of antibiotic resistance by promoting genetic exchange and environmental adaptability. Bacterial cooperation can involve the secretion of metabolically costly "public goods" that benefit neighboring cells. These include β-lactamases, chloramphenicol acetyltransferase, outer membrane vesicles, metabolites, and signaling molecules, which can protect susceptible bacteria by reducing local antibiotic concentrations and thereby attenuating selection pressure. Importantly, genes encoding these extracellular products are often subject to horizontal gene transfer, facilitating cooperative interactions across species within microbial communities. In this review, we summarize current knowledge of these extracellular products, highlight their roles in the development and evolution of cooperative antibiotic resistance, examine their potential implications for antibiotic therapy, and identify key gaps in current research. We also examine future research directions and consider how integrating microbial social interactions and community dynamics in antimicrobial strategies could offer new ways to reduce the emergence and spread of antibiotic resistance.},
}

@article {pmid42643892,
year = {2026},
author = {Chen, A and Li, H and Wang, Y and Hu, X and Li, T and Sun, L and Zuo, Y and Huang, P and Xi, Y and Wang, Y and Liu, Y and Zhang, Y and Wang, S},
title = {Genomic epidemiology and antimicrobial resistance of non-typhoidal Salmonella from retail meats in Beijing, China: implications for foodborne transmission and phage susceptibility.},
journal = {JAC-antimicrobial resistance},
volume = {8},
number = {4},
pages = {dlag182},
pmid = {42643892},
issn = {2632-1823},
abstract = {OBJECTIVES: To investigate the prevalence, antimicrobial resistance (AMR) profiles, genomic characteristics and phage susceptibility of non-typhoidal Salmonella (NTS) isolated from retail meats in Beijing, China, and to assess the potential for foodborne transmission and risks associated with phage application.

METHODS: A total of 583 retail meat samples (pork, chicken, beef, mutton) were collected across Beijing (2021-2022). NTS isolates were identified by serotyping and MALDI-TOF. Antimicrobial susceptibility was tested by broth microdilution. Whole-genome sequencing was performed on 153 isolates for resistome, virulome, plasmid typing and core-genome MLST (cgMLST). Phage lysis assays used 46 phages against representative isolates, and prophages were predicted in silico.

RESULTS: NTS prevalence was highest in pork (52.4%) and chicken (43.8%). Dominant serotypes were S. London and S. Enteritidis. Resistance rates were high for sulfisoxazole (74.6%), ampicillin (68.6%) and tetracycline (68.6%); 64.4% of isolates were multidrug-resistant (MDR). Genomic analysis revealed widespread resistance genes (e.g. bla CTX-M-55, sul, mph(A)) associated with mobile genetic elements (ISEcp1, IS91). cgMLST showed high genetic similarity between foodborne isolates and contemporaneous human clinical isolates from multiple provinces. Phage lysis was highly effective against S. Enteritidis (83.3%) but limited against S. Kentucky; 34.0% of isolates carried prophages containing transposons.

CONCLUSIONS: Retail meats in Beijing, particularly pork and chicken, represent an important reservoir of multidrug-resistant NTS. Comparative genomic analysis revealed close genomic relatedness between retail meat isolates and human clinical isolates, suggesting the potential for foodborne transmission along the food chain. In vitro phage lysis assays demonstrated serotype-dependent susceptibility patterns, highlighting the potential of phage-based control strategies for specific Salmonella serotypes. However, prophages containing transposon-associated sequences were identified in a subset of isolates, and their contribution to horizontal gene transfer warrants further investigation. Enhanced surveillance integrating food, animal, environmental and human clinical Salmonella monitoring, together with serotype-targeted intervention strategies, is needed to support a One Health approach to foodborne disease control.},
}

@article {pmid42644155,
year = {2026},
author = {Chandrashekar, C and Patel, M and Jandwa, H and Jadeja, A and Javvaji, CK},
title = {Management of Multidrug-Resistant Infections in ICUs: A Narrative Review of Pharmacological and Non-pharmacological Interventions.},
journal = {Cureus},
volume = {18},
number = {7},
pages = {e113404},
pmid = {42644155},
issn = {2168-8184},
abstract = {Multidrug-resistant (MDR) infections in ICUs are a growing global health challenge associated with increased morbidity, mortality, prolonged hospitalization, and rising healthcare costs. Critically ill patients are particularly vulnerable because of immune dysfunction, invasive procedures, prolonged ICU stays, and frequent exposure to broad-spectrum antibiotics, all of which increase susceptibility to MDR infections and antimicrobial selection pressure. Common MDR pathogens in ICU settings include Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE), and carbapenem-resistant Enterobacterales. Major resistance mechanisms include β-lactamase and carbapenemase production, efflux pump overexpression, reduced membrane permeability, target modification, biofilm formation, and horizontal gene transfer. Effective management of MDR infections in ICUs requires an integrated, evidence-based approach combining early recognition, microbiological diagnosis, optimized antimicrobial therapy, and strict infection-prevention strategies. Pharmacological management relies on appropriate empiric therapy, antimicrobial stewardship, therapeutic drug monitoring, and pharmacokinetic/pharmacodynamic optimization to improve treatment efficacy while minimizing toxicity and resistance development. Newer antimicrobial agents, including β-lactam/β-lactamase inhibitor combinations and cefiderocol, have expanded treatment options for resistant resistant Gram-negative infections. Non-pharmacological interventions such as hand hygiene, environmental disinfection, surveillance cultures where indicated, contact precautions, and multidisciplinary infection-control programs remain essential in reducing transmission. Emerging innovations, including artificial intelligence-guided antimicrobial selection, rapid diagnostic technologies, microbiome-based therapies, and bacteriophage therapy, show promise for future management. A multidisciplinary strategy integrating prevention, stewardship, and ongoing research is essential to reduce the MDR burden in ICUs and preserve antimicrobial effectiveness.},
}

@article {pmid42644988,
year = {2026},
author = {Hernández-Hernández, NG and González-Lara, IA and Usme-Duque, LK and Martínez-Berlanga, LA and Ortíz-Hernández, GD and León-Campos, MI and Puente-Urbina, B and Medina-Morales, MA and Loredo-Alcalá, EI and Ríos-González, LJ and Morales-Martínez, TK and Arredondo-Valdés, R and Romero-Galarza, A and Cano-Salazar, LF and Betancourt-Galindo, R and González-Díaz, MO and Rodríguez-Fuentes, N and Enríquez-Medrano, J and Soriano-Corral, F and Rosales-Ibáñez, R and Rodríguez-Navarrete, A and Cabrera-Munguía, DA and Claudio-Rizo, JA},
title = {Bioactive Hydrogel-MOF Composites as Resistance-Modulating Wound Interfaces: Molecular Mechanisms and Rational Design for Chronic Wound Management.},
journal = {Gels (Basel, Switzerland)},
volume = {12},
number = {8},
pages = {},
pmid = {42644988},
issn = {2310-2861},
support = {FORDECYT/PRONACES/6660//Secretaría de Ciencia Tecnología e Innovación/ ; },
abstract = {Chronic wounds are complex environments marked by persistent inflammation, oxidative stress, hypoxia, and conditions that favor antimicrobial resistance (AMR). Conventional antibiotics often fail due to bacterial persistence and the physicochemical barriers of the wound milieu. Biofilm-associated extracellular polymeric substances (EPS), efflux pump activity, quorum sensing (QS), and horizontal gene transfer (HGT) collectively drive antimicrobial tolerance and resistance dissemination, turning chronic wounds into reservoirs of multidrug-resistant pathogens. Consequently, emerging wound therapies demand multifunctional strategies that modulate the wound microenvironment while interfering with resistance-associated phenotypes. Hydrogel-metal-organic framework (MOF) composites have been explored as multifunctional interfaces that combine extracellular matrix-mimetic properties, tunable porosity, stimuli-responsiveness, and controlled therapeutic delivery with the bioactive functions of MOFs. Depending on their composition and architecture, these systems may exert antimicrobial and antibiofilm effects through ionic, electrostatic, osmotic, catalytic, and oxidative mechanisms, while also influencing ROS levels, inflammation, angiogenesis, and local drug transport. However, antimicrobial activity alone does not equate to resistance modulation. Evidence for direct effects on efflux systems, resistance phenotypes, or HGT remains inconsistent across reported platforms. This review critically examines representative hydrogel-MOF systems for chronic wound applications, comparing their composition, physicochemical properties, biological functions, proposed resistance-related mechanisms, advantages, limitations, and current level of evidence. We emphasize distinguishing experimentally demonstrated resistance-modulating effects from mechanistically proposed functions, and identifying design trade-offs and evidence gaps that must be addressed to develop wound interfaces capable of both supporting tissue regeneration and improving infection control.},
}

@article {pmid42645040,
year = {2026},
author = {Amanzholova, M and Akimbekova, A and Shaizadinova, A and Sutimbekova, N and Bissenova, N and Tarlykov, P and Abeldenov, S},
title = {Multiplex RPA-CRISPR/Cas12a Assay for Rapid Detection of Class D OXA-Type Carbapenem-Resistant Acinetobacter baumannii.},
journal = {Biosensors},
volume = {16},
number = {8},
pages = {},
pmid = {42645040},
issn = {2079-6374},
support = {BR24992881//Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {*Acinetobacter baumannii/genetics/isolation & purification/drug effects ; Carbapenems/pharmacology ; *beta-Lactamases/genetics ; Humans ; CRISPR-Cas Systems ; Bacterial Proteins/genetics ; Rapid Diagnostic Tests ; },
abstract = {Acinetobacter baumannii is a critical WHO priority pathogen due to its multidrug resistance and high mortality in carbapenem-resistant infections. Resistance is predominantly mediated by class D carbapenemase genes blaOXA-23 and blaOXA-40, which spread rapidly via horizontal gene transfer in healthcare settings. To address the lack of a rapid assay capable of detecting both blaOXA-23 and blaOXA-40 in a single analytical workflow, we developed a multiplex two-step RPA-CRISPR/Cas12a assay. Since infections caused by strains harboring either gene require identical therapeutic management, their co-detection in a single reaction is clinically justified. Although simultaneous use of two crRNAs within a single CRISPR/Cas12a reaction is often considered technically challenging due to potential inter-crRNA competition, here it advantageously enables dual-target coverage without compromising sensitivity. The assay demonstrated high specificity with no cross-reactivity against a panel of clinically relevant bacterial species, including closely related Acinetobacter spp. Evaluation using genomic DNA extracted from 63 cultured clinical A. baumannii isolates revealed blaOXA-23 in 19 isolates (30.2%), blaOXA-40 in 28 (44.4%), and co-carriage of both genes in 9 (14.3%), with at least one resistance gene detected in 60.3% of isolates. The complete workflow was accomplished within 45 min without specialized equipment, offering a rapid, sensitive, and cost-effective solution for point-of-care molecular surveillance of carbapenem-resistant A. baumannii in clinical and resource-limited settings.},
}

*Acinetobacter baumannii/genetics/isolation & purification/drug effects
Carbapenems/pharmacology
*beta-Lactamases/genetics
Humans
CRISPR-Cas Systems
Bacterial Proteins/genetics
Rapid Diagnostic Tests

@article {pmid42647273,
year = {2026},
author = {Jones, GH},
title = {Distribution of poly(A) polymerase I in bacteria: an expanded role for horizontal gene transfer.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {8},
pages = {},
pmid = {42647273},
issn = {1465-2080},
mesh = {*Gene Transfer, Horizontal ; *Polynucleotide Adenylyltransferase/genetics/metabolism ; *Bacteria/genetics/enzymology/classification ; Phylogeny ; Polyadenylation ; Escherichia coli Proteins/genetics/metabolism ; Escherichia coli/genetics ; },
abstract = {Poly(A) polymerase I (PAP I), the product of the pcnB gene, catalyses the polyadenylation of RNA 3'-ends in Escherichia coli. PAP I and pcnB were initially thought to be present only in the β, γ-Proteobacteria and a few other bacterial species. In the present study, blast searches using bacterial proteins bearing the PAP I signature sequence as queries have revealed the presence of proteins containing that signature sequence in a wide range of additional bacterial classes and phyla. Phylogenetic studies indicate that the pcnB genes in most of these newly identified species were not inherited by horizontal gene transfer (HGT) from β, γ-proteobacterial donors. Nevertheless, the present studies reveal a larger role for HGT in the inheritance of pcnB genes than was documented in previous studies. Together with the other studies cited here, the results presented below strongly suggest that the significant metabolic role for the polyadenylation of RNA 3'-ends in the domain Bacteria.},
}

*Gene Transfer, Horizontal
*Polynucleotide Adenylyltransferase/genetics/metabolism
*Bacteria/genetics/enzymology/classification
Phylogeny
Polyadenylation
Escherichia coli Proteins/genetics/metabolism
Escherichia coli/genetics

@article {pmid42648689,
year = {2026},
author = {Zhou, L and Xie, J and Zhang, L and Kong, L and Deng, P and Huang, J and Wang, W and Wu, S and He, S and Cheng, S},
title = {Substrate filling ratio affects nitrogen removal and antibiotic resistance risk in modular moving bed constructed wetland: Biofilm-mediated microbial community succession and resistome profiles reshaping.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125574},
doi = {10.1016/j.envres.2026.125574},
pmid = {42648689},
issn = {1096-0953},
abstract = {Constructed wetlands (CWs) are widely used for advanced treatment of wastewater treatment plant effluents and their nitrogen (N) removal performance is often inhibited by antibiotics. Biofilms on CW substrates play a fundamental role in pollutant biodegradation, microbial community stability and antibiotic resistance gene (ARG) dissemination. This study investigated the effects of substrate filling ratios (90% and 60%) in modular moving bed constructed wetlands (MMB-CWs) on operational performance, biofilm properties and antibiotic resistance risks. The MMB-CW with higher substrate filling ratio exhibited a better N removal efficiency of 83.7% and a significant reduction of nitrous oxide emission by 72.6%. The higher substrate filling ratio increased the protein/polysaccharide ratio of extracellular polymeric substances (EPS), potentially forming a hydrophobic barrier and structured a highly modular microbial network with pronounced niche differentiation. Genome-centric analysis revealed that core taxa carrying denitrification and anammox genes (narG, narH, nirS, nosZ, hzs, hdh) enriched by 1.5- to 12.6-fold in abundance in the MMB-CW with 90% substrate filling ratio. Notably, Desulfobacillus increased by 1.7-fold in abundance, which served as a keystone species driving denitrification, EPS construction, oxidative stress adaptation and energy production. The elevated abundances of enzymes catalyzing key electron- and energy-generating steps in the tricarboxylic acid cycle and denitrification enzymes drove a more complete denitrification process. The highly modular network restricted horizontal gene transfer of ARGs, mitigated the enrichment of pathogenic antibiotic-resistant bacteria (PARBs) and occurrence of high-risk ARGs in MMB-CW. The findings provide an optimization strategy for MMB-CW in view of treatment performance and ecological risk.},
}

@article {pmid42650670,
year = {2026},
author = {Shitada, C and Takahashi, M and Kuroda, M},
title = {Multiple Independent Origins of Tn916-Mediated Tetracycline Resistance in Clostridium tetani from a Confined Geographic Area.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/antibiotics15080745},
pmid = {42650670},
issn = {2079-6382},
support = {JP24fk0108666//Japan Agency for Medical Research and Development/ ; JP25K10353//Japan Society for the Promotion of Science/ ; },
abstract = {Background/Objectives: Tetracycline resistance in Gram-positive bacteria has increased globally through horizontal gene transfer. Antimicrobial resistance genes in Clostridium tetani, the causative agent of tetanus, are rarely reported. Previously, we identified tetracycline resistance gene tet(M)-positive C. tetani strains in Japan, but their evolutionary origin and acquisition mechanism remain unclear. This study aimed to elucidate the evolutionary origin of tet(M)-positive C. tetani and clarify the mechanism of horizontal resistance gene acquisition. Methods: Complete genome sequences of six tet(M)-positive C. tetani strains were determined using hybrid assembly of short-read (Illumina) and long-read (Oxford Nanopore) sequencing. Core genome single-nucleotide variant (SNV) analysis was performed to determine phylogenetic relationships. Tn916 element analysis of the tet(M) gene identified the origin of resistance genes and potential donor bacteria. Results: Based on core genome SNV analysis, all six tet(M)-positive strains belonged to Clade 1-2. The Tn916 element was approximately 18 kb and highly conserved; however, insertion sites differed significantly among strains. Phylogenetic analysis of the tet(M) gene revealed at least three distinct variants with different origins. Conclusions: Multiple independent acquisitions of Tn916-mediated tet(M), rather than clonal propagation, drove resistance emergence in geographically confined C. tetani populations. These findings support the notion that tetracycline resistance emerged through multiple independent horizontal transfer events involving Tn916. This pattern suggests that persistent environmental selective pressure, rather than clonal expansion, has shaped resistance dissemination, highlighting the importance of genomic surveillance and systematic monitoring to track the emergence of antimicrobial resistance in environmental and clinical settings.},
}

@article {pmid42650676,
year = {2026},
author = {de Sousa, T and Silva, C and Pereira, JE and Igrejas, G and Poeta, P},
title = {Clinical and Epidemiological Landscape of Antimicrobial Resistance and Virulence in Streptococcus Species.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/antibiotics15080751},
pmid = {42650676},
issn = {2079-6382},
support = {LA/P/0059/2020//Fundação para a Ciência e Tecnologia/ ; UIDB/CVT/00772/2020//Fundação para a Ciência e Tecnologia/ ; UID/50006/2025//Fundação para a Ciência e Tecnologia/ ; },
abstract = {Species of the genus Streptococcus constitute important pathogens in human and veterinary medicine, being responsible for a wide spectrum of infections ranging from mild illnesses to severe invasive pathologies. Although β-lactams continue to be effective against most species, the global increase in resistance to macrolides, lincosamides, tetracyclines, and, in some cases, reduced susceptibility to penicillin represents a growing challenge for antimicrobial therapy. This review synthesizes the clinical and epidemiological landscape of antimicrobial resistance in the main Streptococcus species, including Streptococcus pyogenes, Streptococcus agalactiae, Streptococcus pneumoniae, Streptococcus dysgalactiae, and other species of clinical and veterinary relevance, addressing their epidemiological profiles, molecular mechanisms of resistance, and virulence factors. The main genetic determinants involved in resistance are discussed, namely the erm, mef, and tet genes, as well as the impact of alterations in penicillin-binding proteins, horizontal gene transfer, and biofilm formation on the persistence of infections and decreased therapeutic efficacy. Simultaneously, the main virulence factors are analyzed, including polysaccharide capsules, adhesins, toxins, extracellular enzymes, and immune response evasion mechanisms that contribute to the colonization, dissemination, and severity of infections. The importance of epidemiological and genomic surveillance, particularly through whole-genome sequencing, in monitoring the spread of resistant clones and identifying determinants of resistance and virulence is also highlighted. Taken together, the data highlight the need to strengthen programs for the rational use of antimicrobials, to promote integrated surveillance strategies from a One Health perspective, and to deepen knowledge about the interaction between antimicrobial resistance and virulence, in order to improve strategies for the prevention, diagnosis, and treatment of infections caused by Streptococcus spp.},
}

@article {pmid42650690,
year = {2026},
author = {Kuan, NL and Yeh, KS},
title = {Genomic Characterization of Colistin and Fluoroquinolone Resistance in Multidrug-Resistant Escherichia coli from Diseased Food-Producing Animals in Taiwan.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/antibiotics15080765},
pmid = {42650690},
issn = {2079-6382},
support = {113AS-5.1.1-VI-04; 114AS-5.1.1-VI-04//Veterinary Research Institute, Ministry of Agriculture, Taiwan/ ; },
abstract = {Background: The global spread of antimicrobial resistance in Escherichia coli (E. coli) from food-producing animals is a critical concern within the One Health framework, particularly because of the potential transmission of clinically relevant resistance determinants across the animal-environment-human interface. Although extended-spectrum β-lactamase (ESBL)-producing E. coli strains have been widely characterized, the genomic mechanisms underlying resistance to the last-resort and critically important antimicrobials colistin and fluoroquinolones remain incompletely understood in animal-associated populations. This study characterized these resistance mechanisms in multidrug-resistant (MDR) E. coli from diseased food-producing animals. Methods: We used whole-genome sequencing (WGS) to characterize 77 MDR E. coli isolates from diseased livestock and poultry in Taiwan and analyzed the underlying resistance mechanisms and their co-occurrence. Results: Plasmid-mediated colistin resistance genes, including mcr-1.1, mcr-3.1, and mcr-3.5, were identified alongside chromosomal mutations, such as pmrB substitutions, indicating multiple evolutionary pathways to colistin resistance. Fluoroquinolone resistance was driven by both chromosomal mutations in quinolone resistance-determining regions and plasmid-mediated quinolone resistance genes, including qnr variants and aac(6')-Ib-cr. Notably, the frequent co-occurrence of resistance determinants targeting multiple antimicrobial classes suggests the presence of mobile genetic elements facilitating horizontal gene transfer. Conclusions: Although a subset of isolates overlapped with those reported in our previous ESBL-focused study, the present work presents a comprehensive genomic dissection of resistance mechanisms beyond β-lactamases. The convergence of colistin, fluoroquinolone, and ESBL-associated resistance determinants within individual isolates highlights the potential role of food-producing animals as reservoirs of multidrug resistance, with potential implications for cross-sectoral transmission. These findings underscore the importance of integrated surveillance strategies addressing potential zoonotic transmission under the One Health framework.},
}

@article {pmid42650708,
year = {2026},
author = {Goroftei, L and Popescu, CM and Profir, I and Jalba, GA and Gurau, G},
title = {Biofilm-Mediated Antimicrobial Resistance in Pediatric Klebsiella pneumoniae Urinary Tract Infections: A Narrative Review of Mechanisms, Clinical Challenges, and Therapeutic Strategies.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/antibiotics15080783},
pmid = {42650708},
issn = {2079-6382},
abstract = {Urinary tract infections (UTIs) caused by Klebsiella pneumoniae are an increasing challenge in pediatric practice due to the combined effects of biofilm formation, multidrug resistance (MDR), and limited therapeutic options for children. Biofilm development promotes bacterial persistence by impairing antibiotic penetration, enabling metabolic adaptation, promoting persister-cell formation, facilitating horizontal gene transfer (HGT), and inducing stress-induced mutagenesis, thereby reducing the effectiveness of conventional antimicrobial therapy. These mechanisms are further compounded by pediatric-specific challenges, including age-dependent pharmacokinetic variability, congenital urinary tract abnormalities, device-associated infections, and the limited availability of validated diagnostic tools for biofilm-associated infections. This narrative review integrates current knowledge of the molecular mechanisms underlying biofilm-mediated antimicrobial resistance with the unique diagnostic, pharmacological, and therapeutic challenges encountered in pediatric patients with K. pneumoniae UTIs. Emerging therapeutic strategies, such as optimized antibiotic combination therapy, bacteriophages, biofilm matrix-degrading enzymes, quorum-sensing inhibitors (QSIs), antimicrobial peptides (AMPs), and microbiome-directed approaches are critically evaluated with particular emphasis on their potential applicability in children. Although several anti-biofilm strategies have demonstrated encouraging results in experimental models, robust pediatric clinical evidence remains scarce. Current international guidelines continue to rely primarily on planktonic antimicrobial susceptibility testing without addressing biofilm-specific therapeutic considerations. In the absence of validated biofilm diagnostics, catheter stewardship and dosing optimization remain the most defensible clinical interventions available today. Broader translation of anti-biofilm strategies into pediatric practice will require dedicated pharmacokinetic studies, standardized biofilm diagnostics, and prospective clinical trials.},
}

@article {pmid42652351,
year = {2026},
author = {Makkaew, P and Bumyut, A and Megasari, NLA and Precha, N},
title = {Antibiotic Resistance Genes in Dust from Kindergarten Environments: A Systematic Review of Occurrence, Diversity, Determinants, and Exposure Implications.},
journal = {International journal of environmental research and public health},
volume = {23},
number = {8},
pages = {},
doi = {10.3390/ijerph23081036},
pmid = {42652351},
issn = {1660-4601},
mesh = {*Dust/analysis ; *Drug Resistance, Microbial/genetics ; *Schools ; *Genes, Bacterial ; Humans ; Child, Preschool ; *Environmental Exposure ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Kindergarten environments combine high microbial exposure with increased immunological vulnerability, yet antibiotic resistance genes (ARGs) in kindergarten dust remain poorly characterized. This systematic review synthesized evidence on the occurrence and potential health relevance of ARGs in kindergarten dust. Following PRISMA 2020 guidelines, PubMed, Scopus, and Web of Science were searched. Four studies from China, Hong Kong, and Norway (2018-2024) met the inclusion criteria. ARGs were detected in all kindergarten dust samples, indicating that dust is a consistent reservoir of antibiotic resistance determinants. A consensus resistome (classes detected in ≥2 studies) encompassed sulfonamide, macrolide-lincosamide-streptogramin B (MLSB), tetracycline, beta-lactam, aminoglycoside, and multidrug resistance genes; beta-lactam resistance genes were the only class reported in all four studies. Clinically important ARGs associated with last-resort antibiotics, including mecA, vanA, blaNDM, and mcr-5, were reported in three studies. Class 1 integron-integrase genes (intI1) frequently co-occurred with ARGs, suggesting potential horizontal gene transfer. Limited evidence indicated higher ARG abundance in urban and winter samples. One study reported antibiotic-resistant bacteria carrying resistance markers concordant with those in kindergarten dust in the urine of children attending the same facilities; however, this cross-sectional, single-site evidence is consistent with, but not sufficient to establish, a dust-to-child exposure pathway. The available evidence supports the plausibility that kindergarten dust may contribute to children's exposure to ARGs and ARG-carrying bacteria, but current studies do not establish causal transmission from dust to child colonization or infection. Standardized monitoring and longitudinal studies are needed to assess health risks and guide mitigation strategies in early childhood educational settings.},
}

*Dust/analysis
*Drug Resistance, Microbial/genetics
*Schools
*Genes, Bacterial
Humans
Child, Preschool
*Environmental Exposure
Anti-Bacterial Agents/pharmacology

@article {pmid42654749,
year = {2026},
author = {Martínez-Álvarez, S and Herrera-Espejo, S and Zarazaga, M and Höfle, U and Pachón-Ibáñez, ME and Torres, C},
title = {Virulence and Invasion Profiles of Escherichia coli Across One Health Reservoirs: Genomic Insights into High-Risk Clones and Their Defense Systems.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/pathogens15080812},
pmid = {42654749},
issn = {2076-0817},
support = {PID2022-139591OB-I00//MICIU/AEI/10.13039/501100011033 and ERDF/ EU/ ; },
mesh = {Humans ; Virulence ; Animals ; *Escherichia coli Infections/microbiology/veterinary ; *Escherichia coli/genetics/pathogenicity/classification/isolation & purification ; Bacterial Adhesion ; *One Health ; HEK293 Cells ; Genomics ; *Disease Reservoirs/microbiology ; Genome, Bacterial ; CRISPR-Cas Systems ; Virulence Factors/genetics ; Biofilms/growth & development ; Phenotype ; },
abstract = {Escherichia coli is a genetically diverse species encompassing both commensal and pathogenic lineages capable of transitioning among various hosts. Within a One Health framework, we conducted a targeted screening of 38 E. coli strains isolated from wildlife, livestock, and food reservoirs to characterize their pathogenic potential by integrating genomic and phenotypic approaches. In vitro functional assays, including biofilm formation, surface motility, and adherence and invasion of HEK-293 epithelial cells, were statistically evaluated using the non-parametric Mann-Whitney U test. Phenotypic analyses revealed that extraintestinal pathogenic (ExPEC) and uropathogenic E. coli (UPEC) strains, particularly those belonging to the high-risk ST117 clone, exhibited significantly enhanced adherence and internalization capacities. These virulent phenotypes strongly correlated with specific genetic signatures involved in iron acquisition and epithelial invasion (chuA, fyuA, vat, and tia), underscoring that the convergence of ExPEC/UPEC determinants drives increased colonization potential. Genomic characterization further revealed that despite high virulence and widespread antimicrobial resistance, the CRISPR/Cas subtype I-E system was highly prevalent (93.8%), displaying structural variations frequently driven by insertion sequences. Spacer analyses identified limited homology to plasmids and phages, suggesting past mobilome interactions rather than active restriction of current horizontal gene transfer. Overall, these findings illustrate how phenotypic traits of high-risk clones match their genomic virulence platforms. The convergence of multidrug resistance and pathogenic fitness across human, animal, and environmental interfaces underscores the need for integrated molecular surveillance in a One Health context.},
}

Humans
Virulence
Animals
*Escherichia coli Infections/microbiology/veterinary
*Escherichia coli/genetics/pathogenicity/classification/isolation & purification
Bacterial Adhesion
*One Health
HEK293 Cells
Genomics
*Disease Reservoirs/microbiology
Genome, Bacterial
CRISPR-Cas Systems
Virulence Factors/genetics
Biofilms/growth & development
Phenotype

@article {pmid42654900,
year = {2026},
author = {Liu, R and Huang, L and Mu, J and Lu, T and Zhang, Y and Deng, K and Xu, D},
title = {Structural Variation and Its Roles in Plant Genomes.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {16},
pages = {},
doi = {10.3390/plants15162498},
pmid = {42654900},
issn = {2223-7747},
support = {32260089//National Natural Science Foundation of China/ ; },
abstract = {Plant genomes exhibit extensive structural diversity generated by large-scale genomic alterations, collectively known as structural variations (SVs). Unlike single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels), SVs can reshape genome architecture through changes in sequence content, gene dosage, regulatory landscapes, and chromosome organization. Recent advances in long-read sequencing (LRS), pan-genome construction, and multi-omics technologies have greatly expanded our ability to identify and interpret SVs across plant species. In this review, we summarize recent progress in understanding the formation mechanisms, classification, and functional consequences of plant SVs. We discuss major sources of SV generation, including transposable element activity, non-allelic homologous recombination (NAHR), horizontal gene transfer (HGT), and genome restructuring following polyploidization. We further highlight how LRS and graph-based pan-genomes overcome limitations of traditional linear reference genomes and enable more comprehensive characterization of genetic diversity. Beyond variant discovery, we emphasize the importance of integrating genomic, transcriptomic, epigenomic, proteomic, metabolomic, and spatial omics datasets to decipher how SVs influence gene regulation and complex agronomic traits. We also discuss current challenges, including repetitive genomes, polyploidy, computational complexity, and translation of SV knowledge into practical breeding applications. Together, these advances establish SV-centered genomics as a critical framework for understanding plant genome evolution and accelerating precision crop improvement.},
}

@article {pmid42466908,
year = {2026},
author = {Fairusya, N and Wang, R and Honda, R},
title = {Plasmid-mediated antimicrobial resistance across One Health sectors: transmission dynamics and surveillance needs.},
journal = {mSphere},
volume = {11},
number = {8},
pages = {e0019226},
doi = {10.1128/msphere.00192-26},
pmid = {42466908},
issn = {2379-5042},
support = {JP24jm0210113h0001//Japan Agency for Medical Research and Development/ ; JPMEERF25S21211//Environmental Restoration and Conservation Agency/ ; 23H01535//Japan Society for the Promotion of Science/ ; },
mesh = {*Plasmids/genetics ; Humans ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Animals ; *One Health ; Anti-Bacterial Agents/pharmacology ; Interspersed Repetitive Sequences ; },
abstract = {Antimicrobial resistance (AMR) is increasingly recognized as a One Health challenge driven by the continuous exchange of resistant bacteria and resistance determinants across human, animal, and environmental sectors. While genomic surveillance has substantially improved detection of antimicrobial resistance genes (ARGs), most monitoring frameworks remain gene- or isolate-centric, limiting insight into the mechanisms that govern resistance transmission and persistence. Recent evidence indicates that plasmids, self-replicating mobile genetic elements (MGEs) capable of horizontal transfer across bacterial species, play an important role in disseminating clinically relevant resistance determinants across sectors. In this mini-review, we synthesize genomic and ecological evidence demonstrating that a limited number of plasmid incompatibility (Inc) groups recur across human, animal, and environmental reservoirs, often independent of bacterial host lineages. We highlight how plasmid transmission dynamics are shaped by host-independent mobility, ecological generalism, co-selection with accessory traits, and persistence in engineered and natural environments. We further examine why current AMR surveillance approaches, including ARG-centric metagenomics and isolate-based monitoring, systematically overlook these plasmid-mediated processes. Furthermore, we propose that plasmid-resolved analysis represents a critical and currently underutilized complementary layer for One Health AMR surveillance. Integrating plasmid classification and genomic reconstruction into wastewater-based epidemiology and cross-sector monitoring frameworks can improve attribution of transmission pathways, enhance early detection of high-risk resistance, and provide a mechanistic foundation for risk-informed intervention strategies.},
}

*Plasmids/genetics
Humans
*Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal
*Bacteria/genetics/drug effects
Animals
*One Health
Anti-Bacterial Agents/pharmacology
Interspersed Repetitive Sequences

@article {pmid42634926,
year = {2026},
author = {Dabravolski, SA and Vatlin, AA and Erbaeva, AZ and Herrera, C and Pavshintsev, VV and Mitkin, NA},
title = {The black soldier fly bioreactor: host-microbiome synergy in pathogen neutralization, xenobiotic remediation, and downstream feed safety.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70995},
pmid = {42634926},
issn = {1097-0010},
support = {//RUDN University Scientific Projects Grant System, project № 080536-2-000/ ; },
abstract = {Black soldier fly larvae (BSFL) are critical to the circular economy, transforming hazardous organic wastes into sustainable agricultural feed. However, processing high-bioburden substrates presents severe biosafety challenges. This review synthesizes recent advancements (2021-2026) regarding the multidimensional role of the BSFL gut bioreactor in waste sanitization and xenobiotic remediation. Pathogen neutralization is driven by a synergistic, tripartite defense system: host-derived antimicrobial peptides (AMPs), biophysical lipid interactions (e.g., lauric acid), and microbiome-mediated competitive exclusion. Concurrently, the gut microbiota deploys novel enzymatic pathways to actively degrade veterinary pharmaceuticals. Despite these sanitization capabilities, a profound biosafety paradox exists: while live, culturable vegetative pathogens and parent chemical antibiotics are eradicated, the intensive selective pressure within the gut environment facilitates horizontal gene transfer, leading to the amplification of antimicrobial resistance genes (ARGs). This study critically evaluates industrial interventions - including chemical pre-treatments, abiotic stress modulation, and probiotic bioaugmentation - designed to engineer the bioreactor and mitigate these genetic and horizontal transfer risks. Finally, the study explores the downstream impacts of BSFL biomass as a functional substitute for antibiotic growth promoters in livestock, highlighting its prebiotic capacity to positively modulate animal microbiomes. Overcoming current methodological and regulatory limitations via multi-omics will cement BSFL as a biosecure pillar of sustainable agriculture. © 2026 Society of Chemical Industry.},
}

@article {pmid42635434,
year = {2026},
author = {Sakdinan, B and Sinha, A and Qadri, F and Khan, AI and Nelson, EJ and Shapiro, BJ},
title = {Species-specific prophage induction by ciprofloxacin in human gut metagenomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0030326},
doi = {10.1128/msystems.00303-26},
pmid = {42635434},
issn = {2379-5077},
abstract = {Antibiotics are known to trigger prophage induction in controlled laboratory settings, but it remains unclear whether this also occurs within microbiomes in nature. Current methods investigating the link between antibiotics and prophage induction within the human gut rely on in vitro culturing of human gut bacterial isolates. Using a metagenomic approach, we aimed to measure prophage induction, and whether it is associated with antibiotic exposure. In two independent human cohorts, we compared prophage to bacterial host read depth ratios (P:H) across known or measured antibiotic exposures. We found that induction is not broadly associated with antibiotic exposures at the level of the overall microbiome, but that ciprofloxacin increases P:H ratios in certain bacterial species. We documented heterogeneous trajectories of P:H ratios over the course of antibiotic exposure, sometimes increasing and remaining high, or returning to baseline. This study complements experimental models by providing in vivo evidence of induction in the human gut.IMPORTANCEBacteriophages are viruses that infect a bacterial host. The lytic and lysogenic cycles are the two classic outcomes of phage infection. In the lytic cycle, the phage immediately replicates and lyses its host cell to release new viral particles. In the lysogenic cycle, the phage, now called a prophage, integrates its genome into that of its host without killing it. Prophages can switch to the lytic cycle in a process called induction, in which the viral genome is replicated, the host cell is lysed, and viral particles are released. The most immediate consequence of induction is host cell death, which can impact bacterial populations and communities. Since prophages are mobile genetic elements that can move between bacteria, they are also an important vehicle for horizontal gene transfer. While induction has been well studied in vitro, whether and how induction occurs within the complex microbial ecosystem in humans is less well characterized. Understanding prophage induction in vivo is therefore critical in corroborating in vitro observations.},
}

@article {pmid42636436,
year = {2026},
author = {Song, S},
title = {Epigenetically silenced cryptic foodborne pathogens: a silent food safety hazard triggered by host gut signals.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-6},
doi = {10.1080/10408398.2026.2722087},
pmid = {42636436},
issn = {1549-7852},
abstract = {Approximately 30-32% of global foodborne outbreaks lack an identified causative agent, a critical surveillance gap driven by traditional taxonomic-based monitoring that fails to detect epigenetically silenced cryptic pathogens. These foodborne commensal strains acquire functional virulence gene clusters via horizontal gene transfer, maintain stable, heritable virulence silencing in food matrices to evade routine detection, and undergo rapid virulence activation upon exposure to host gut-specific signals, triggering unexplained gastrointestinal infections. This critical Mini Review focuses on the unique "silent in food, virulent in host" phenotype, clarifies core prokaryotic epigenetic regulatory mechanisms, dissects unresolved controversies blocking translational application, and proposes actionable research priorities. We emphasize an urgent paradigm shift from taxonomic identification to functional epigenetic risk assessment to mitigate this hidden food safety threat. Unlike existing broad reviews, this work provides phenotype-specific critical analysis to fill a key literature gap for food safety regulation and industrial practice.},
}

@article {pmid42636903,
year = {2026},
author = {Wu, W and Wang, Y and Yang, TB and Zhang, XK and Wu, BD and Zhuang, JL and Cao, QY and Song, S and Li, W and Huang, TY and Xu, XY},
title = {Metagenomic insights into suppressing antibiotic-resistant bacteria in mesocosm-scale constructed wetlands: calamus-biochar alleviates selective pressure and disrupts genetic co-occurrence network.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135710},
doi = {10.1016/j.biortech.2026.135710},
pmid = {42636903},
issn = {1873-2976},
abstract = {As a mainstream technology for the advanced treatment of wastewater treatment plant effluents, constructed wetlands (CWs) exhibit limited efficiency in antibiotic removal and may instead serve as reservoirs for antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). To address this, a mesocosm-scale CW amended with 4.0% calamus-biochar (PBC) filler was developed, achieving average antibiotic removal efficiencies above 92.7%. Compared with the blank system, the average ARGs removal efficiency increased by 54.2% and the proliferation of ARB was suppressed by an average of 65.1%. Furthermore, we found that the PBC filler adsorbed 41.8% of antibiotics while associating with only 1.4% of total culturable microorganisms, which may alleviate antibiotic selection pressure. Metagenomic analysis revealed that PBC filler reduced the normalized abundance (copies per cell) of mobile genetic elements (MGEs) by 0.68-5.98 cpc, accounting for 24.7-56.1%, weakened ARG-MGE co-occurrence and decreased the abundance of ARG-MGE co-localized contigs. Metagenome-assembled genome (MAG) analysis identified that Pseudomonadota was the dominant ARB phylum, predominantly harboring multidrug resistance genes and transposases, with a 56.7% reduction in relative abundance compared to the blank system. Batch experiments further confirmed that the PBC filler inhibited the potential for horizontal gene transfer (HGT) by sequestering ARGs. This study developed a CW system supplied with PBC filler for efficient removal of antibiotics, ARGs and ARB. It further elucidated the underlying mechanisms, with the PBC filler potentially decreasing antibiotic bioavailability and the potential for HGT of ARGs, thereby suppressing ARB proliferation.},
}

@article {pmid42639686,
year = {2026},
author = {Quilliam, RS and Ormsby, MJ},
title = {The 'Lifeboat Hypothesis': Aquatic Microplastics in a Warming World-Climate-Resilient Refugia for Bacterial Pathogens.},
journal = {Global change biology},
volume = {32},
number = {8},
pages = {e71078},
pmid = {42639686},
issn = {1365-2486},
mesh = {*Microplastics ; Biofilms ; *Climate Change ; *Bacteria ; Ecosystem ; Global Warming ; },
abstract = {The Lifeboat hypothesis proposes that microplastics act as mobile microbial refugia, buffering environmental stress and enabling persistence, adaptation and dispersal of microorganisms, including pathogens and antimicrobial resistance (AMR) determinants. Microplastic-associated biofilms (the plastisphere) mitigate UV radiation, osmotic stress and environmental fluctuations, while promoting stress responses and horizontal gene transfer. Ocean circulation then facilitates long-range transport of these communities, linking distant ecosystems. Climate-driven cryosphere thaw may further introduce ancient microorganisms into the contemporary plastisphere ('paleo-plastisphere'), where they are captured and redistributed. In parallel, ingestion by marine organisms provides a biological bypass that enhances microbial survival and accelerates trophic transfer. Collectively, these processes position microplastics as dynamic vectors of microbial connectivity, with implications for infectious disease exposure, biosecurity leakage and transboundary AMR dissemination under global environmental change.},
}

*Microplastics
Biofilms
*Climate Change
*Bacteria
Ecosystem
Global Warming

@article {pmid42640968,
year = {2026},
author = {Ham, JH and Lee, YJ and Kim, HY},
title = {AI-assisted MALDI-TOF MS for identifying carbapenem resistance in clinical Acinetobacter baumannii isolates.},
journal = {Emerging microbes & infections},
volume = {15},
number = {1},
pages = {2716498},
doi = {10.1080/22221751.2026.2716498},
pmid = {42640968},
issn = {2222-1751},
mesh = {*Acinetobacter baumannii/drug effects/isolation & purification/genetics/chemistry ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; *Carbapenems/pharmacology ; Humans ; *Acinetobacter Infections/microbiology ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Artificial Intelligence ; *beta-Lactam Resistance ; },
abstract = {Carbapenem-resistant Acinetobacter baumannii (CRAB) is one of the most critical public health threats worldwide due to its high infection rates, substantial mortality, and limited therapeutic choices. As CRAB infections are frequently multidrug-resistant, rapid and accurate determination of carbapenem susceptibility is essential for appropriate therapeutic decision-making. We established an integrated framework combining matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) with artificial intelligence (AI) to enable rapid prediction of carbapenem resistance in A. baumannii. A total of 191 clinical and surveillance isolates, including CRAB and carbapenem-susceptible A. baumannii (CSAB), were recovered from hospitalized patients and phenotypically characterized by standard minimum inhibitory concentration testing. MALDI-TOF MS spectra were subsequently acquired, and six AI models were developed and systematically investigated for predictive performance, among which the eXtreme Gradient Boosting (XGBoost) model achieved the highest discriminatory performance, distinguishing CRAB from CSAB with an accuracy of 96.36% and robust overall performance. Feature importance analysis of the XGBoost model revealed that its high predictive performance was driven partially by spectral features associated with horizontal gene transfer-related elements and membrane and transport-associated proteins, providing candidate molecular correlates of carbapenem resistance. Overall, these results show that AI-assisted MALDI-TOF MS enables rapid and accurate prediction of carbapenem resistance in A. baumannii and provides insights into the molecular features associated with resistance acquisition.},
}

*Acinetobacter baumannii/drug effects/isolation & purification/genetics/chemistry
*Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
*Carbapenems/pharmacology
Humans
*Acinetobacter Infections/microbiology
*Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
*Artificial Intelligence
*beta-Lactam Resistance

@article {pmid42641584,
year = {2026},
author = {Godson, A},
title = {Carbon-Driven Metabolic Activation (CDMA): A conceptual framework linking biodegradable plastic degradation to resistome dynamics-A perspective requiring empirical validation.},
journal = {The Science of the total environment},
volume = {1050},
number = {},
pages = {182194},
doi = {10.1016/j.scitotenv.2026.182194},
pmid = {42641584},
issn = {1879-1026},
abstract = {Biodegradable plastics are increasingly promoted as environmentally sustainable alternatives to conventional plastics, yet their unintended microbiological consequences remain insufficiently explored. Here, we propose the Carbon-Driven Metabolic Activation (CDMA) framework as a conceptual hypothesis (not an established mechanism) to explain how polymer degradation may influence resistome dynamics through localized release of bioavailable carbon. During biodegradation, enzymatic depolymerization generates dissolved organic carbon that may transiently alleviate microbial carbon limitation, stimulating metabolic activity, biofilm formation, and horizontal gene transfer (HGT) under favourable environmental conditions. We distinguish CDMA from existing microbial ecological concepts by emphasizing polymer-specific degradation kinetics and temporally dynamic carbon release unique to biodegradable polymers. We critically synthesize recent experimental evidence (2022-2026), including both supporting and contradictory findings, demonstrating that the ecological consequences of biodegradable plastics vary substantially among polymer types and environmental compartments. Notably, the extremely slow hydrolysis of polylactic acid (PLA) outside industrial composting (half-life >5 years in marine environments) suggests that CDMA is unlikely to operate in many natural settings. We further introduce the Degradation-Risk Temporal Mismatch concept, whereby biodegradable plastics may generate transient ARG enrichment during active degradation, whereas conventional plastics act as persistent long-term reservoirs. We emphasize that CDMA is a testable conceptual framework requiring rigorous empirical validation before informing environmental risk assessment or regulatory decision-making. This perspective aims to stimulate mechanistic research on biodegradable plastic-resistome interactions within a One Health framework.},
}

@article {pmid42643317,
year = {2026},
author = {Shittu, AO and Perovic, O and Layer-Nicolaou, F and Strommenger, B and Adesoji, TO and Sulayman, TA and Afolayan, AO and Mellmann, A and Schaumburg, F},
title = {Molecular characterization of mupirocin-resistant MRSA from Germany and South Africa.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1865925},
pmid = {42643317},
issn = {2235-2988},
mesh = {*Methicillin-Resistant Staphylococcus aureus/genetics/drug effects/classification/isolation & purification ; *Mupirocin/pharmacology ; South Africa/epidemiology ; Humans ; *Anti-Bacterial Agents/pharmacology ; Germany/epidemiology ; *Staphylococcal Infections/microbiology/epidemiology ; Plasmids/analysis/genetics ; *Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Phylogeny ; Bacterial Proteins/genetics ; Genetic Variation ; Whole Genome Sequencing ; Virulence Factors/genetics ; Leukocidins/genetics ; Bacterial Toxins/genetics ; Exotoxins ; Nuclear Proteins ; },
abstract = {INTRODUCTION: Methicillin-resistant Staphylococcus aureus (MRSA) is a human pathogen of global public health importance. A key element of MRSA decolonization strategies is the administration of mupirocin, an antibiotic also used to treat superficial skin infections. However, the emergence and global increase of mupirocin-resistant (mupR)-MRSA highlight the need for active surveillance to support evidence-based MRSA control measures. This study investigated the antibiotic resistance, genetic diversity, and plasmid profiles of mupR-MRSA from Germany and South Africa.

METHODS: Phenotypic identification of mupR-MRSA strains was verified by molecular methods. Characterization of all strains included PCR detection of Panton-Valentine leucocidin, immune evasion cluster genes, and staphylococcal protein A typing. Representative strains from each spa type were selected for whole-genome sequencing to determine their clonal lineages and relationships, including antibiotic and virulence gene content. Comparative analysis, phylogeny and classification of mupA-carrying plasmids were determined.

RESULTS: Eighty-two mupR-MRSA were characterized, comprising 32 strains that exhibited high-level mupirocin resistance (HmupR) and 50 strains with low-level mupirocin resistance (LmupR). The plasmid-mediated mupA gene and the V588F mutation in the bacterial isoleucyl-tRNA synthetase gene were identified in strains that demonstrated HmupR and LmupR, respectively. However, mupA and the V588F mutation were detected in two strains from Germany. The mupR-MRSA from Germany were assigned to CC1, CC5, CC8, CC22, CC30, and ST59, while those from South Africa were grouped into CC8, CC22, and CC30. The strains harboured different SCCmec types (IIa, III, IVa, IVj, and V). Notably, mupR CC22-MRSA-IVj and tst-positive CC30-MRSA-IIa strains were identified in both countries. The mupA-positive plasmids formed four distinct communities, including two singletons. The mupA-positive plasmids from the strains in Germany often carried the aminoglycoside (aac(6')-Ie/aph(2'')-Ia) resistance genes. However, the β-lactam (blaZ), arsenic (arsB, arsC, arsR), and copper (mco) resistance genes were primarily identified on mupA-positive plasmids from strains obtained in South Africa.

DISCUSSION: This study highlights the genetic diversity and potential for horizontal gene transfer among mupA-positive MRSA lineages in the two countries, further supported by the regional clustering of mupA plasmids. Integrating genomic surveillance of chromosomal- and plasmid-mediated resistance with antimicrobial use and clinical data is needed for targeted MRSA infection prevention and control.},
}

*Methicillin-Resistant Staphylococcus aureus/genetics/drug effects/classification/isolation & purification
*Mupirocin/pharmacology
South Africa/epidemiology
Humans
*Anti-Bacterial Agents/pharmacology
Germany/epidemiology
*Staphylococcal Infections/microbiology/epidemiology
Plasmids/analysis/genetics
*Drug Resistance, Bacterial/genetics
Microbial Sensitivity Tests
Phylogeny
Bacterial Proteins/genetics
Genetic Variation
Whole Genome Sequencing
Virulence Factors/genetics
Leukocidins/genetics
Bacterial Toxins/genetics
Exotoxins
Nuclear Proteins

@article {pmid42630487,
year = {2026},
author = {Rajamohan, G and Mullany, P},
title = {Editorial: Mobilome manipulation: engineering microbiomes to counteract antimicrobial resistance.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1938991},
pmid = {42630487},
issn = {1664-302X},
}

@article {pmid42632239,
year = {2026},
author = {Majumdar, A and Johnson, DR and Kolb, S},
title = {Soil erosion and landscape elevation as unnoticed determinants of environmental antibiotic resistance distribution.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143361},
doi = {10.1016/j.jhazmat.2026.143361},
pmid = {42632239},
issn = {1873-3336},
abstract = {Climate change is reshaping the global antibiotic resistance gene (ARG) landscape through geomorphological processes that remain largely overlooked in the One Health framework. This critical review synthesises evidence on how soil erosion and landscape elevation gradients redistribute, select for, and disseminate ARGs across terrestrial and aquatic ecosystems. Erosion physically removes and transports ARG-bearing microbes, depletes nutrients, and co-selects for resistance via heavy metal exposure and horizontal gene transfer, creating source-sink dynamics that connect eroding hillslopes to downstream water bodies and food systems. Elevation gradients impose abiotic stressors-declining temperature, elevated UV radiation, and shifting pH-that drive microbial community reassembly through environmental selection and dispersal limitation, with emerging evidence linking bacterial competition at high altitude to enhanced multidrug efflux and resistome complexity. The review identifies critical knowledge gaps, including unquantified ARG mass fluxes across erosion-deposition gradients, unresolved dispersal-versus-selection mechanisms along elevation transects, and the absence of integrated One Health surveillance linking environmental ARG reservoirs to clinical outcomes. A synthesis of global case studies illustrates how these processes converge across diverse landscapes. The review concludes with a mechanistic research agenda-including reciprocal transplant experiments, landscape connectivity modelling, and cross-sectoral surveillance-needed to translate these emerging drivers into actionable climate-AMR mitigation policy.},
}

@article {pmid42632386,
year = {2026},
author = {Kang, Y and Qin, Y and Chen, N and Wen, S},
title = {Pollution characteristics, risk assessment, and environmental associations of microplastics and antibiotic resistance genes in tropical marine aquaculture: A comparative study across different farming systems in Hainan.},
journal = {Marine pollution bulletin},
volume = {233},
number = {Pt 2},
pages = {120282},
doi = {10.1016/j.marpolbul.2026.120282},
pmid = {42632386},
issn = {1879-3363},
abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) were compared across four marine aquaculture systems in Hainan (fish, shrimp, fish-shrimp mixed, and snail farms). MPs averaged 4.90 ± 5.50 items·L[-1], with polyethylene, rayon, polypropylene-polyethylene copolymer, and polystyrene as dominant polymers. Fibers (58.90%) and 100-500 μm particles prevailed. Snail farms showed the highest MP concentration (6.62 ± 1.68 items·L[-1]), while others ranged from 2.02 to 2.90 items·L[-1]. The Pollution Load Index indicated low contamination overall, but snail farms posed the highest potential ecological risk. A total of 130 ARGs belonging to 11 classes and 13 MGEs belonging to 6 classes were detected, with fish farms showing higher ARG abundance and fish-shrimp mixed systems showing higher MGE abundance. MGEs showed strong correlations with ARGs, indicating potential associations with ARG mobility rather than direct evidence of horizontal gene transfer. Salinity and specific conductance showed potential associations with ARG distribution, but these relationships should be interpreted as exploratory rather than statistically confirmed drivers. Risk Quotient (RQ) analysis revealed the highest combined ARG risks in shrimp and mixed farms, followed by fish, then snail farms. Tetracycline resistance genes dominated risk, reaching an RQ of 1772.14 in shrimp farms. The study provides system-specific insights into MP and ARG pollution and risks, supporting targeted monitoring and management in tropical marine aquaculture.},
}

@article {pmid42627103,
year = {2026},
author = {Wang, Y and Wang, X and Zhao, J and Zeng, J and Hu, S and Ji, F and Dong, G and He, H and Wang, C},
title = {Evolutionary and Epidemiological Characterization of Multidrug-Resistant Escherichia coli Isolated From Pangolins in China.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70161},
pmid = {42627103},
issn = {1749-4877},
support = {//Introduction of Leading Talents Program of the Guangdong Academy of Sciences/ ; },
abstract = {Malayan pangolin populations have fallen to a critically endangered level, and illegal trafficking of wild pangolins is a global problem. Little is known about antimicrobial-resistant bacteria (MDRB) harbored by pangolins, although pangolins are frequently consumed as food or used in traditional medicine. In this study, we report for the first time that strains of multidrug-resistant Escherichia coli were found in a captured Malayan pangolin in Shenzhen, China (December 2018). Antibiotic resistance genes (ARGs) were found in great diversity and abundance on conjugative plasmids, according to genomic analysis. IncX1-type replicon plasmids carrying numerous ARGs and conserved mobile genetic elements predominated in MDR E. coli isolates. Their ability to transport genes horizontally was further strengthened by structural characteristics such class 1 integron-like gene clusters, IS26, and Tn1721, which may have made cross-species dissemination easier. Overall, our findings suggest that illegal transboundary trafficking of Malayan pangolins may contribute to the dissemination of MDRB and highlight the potential public health risks associated with uncontrolled wildlife trade.},
}

@article {pmid42627158,
year = {2026},
author = {Edwards, S and Rice, D and Palomino, P and Newton, I and Mellies, JL},
title = {Ancestral hydrocarbon metabolism enables PET degradation by a natural bacterial consortium.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0082926},
doi = {10.1128/msystems.00829-26},
pmid = {42627158},
issn = {2379-5077},
abstract = {UNLABELLED: Plastic biodegradation in natural environments is increasingly recognized as a multi-organism process; however, the mechanisms enabling coordinated depolymerization and metabolism of polyethylene terephthalate (PET) remain poorly understood. Previously, we demonstrated that a full consortium containing three Pseudomonas and two Bacillus strains isolated from hydrocarbon-rich coastal soils of Galveston Bay, Texas, can synergistically depolymerize PET plastic and utilize it as a sole carbon source, a capacity not observed in individual isolates. In this report, using integrated comparative genomics, proteomics, and chemical analyses, we show that PET degradation in this system reflects exaptation of hydrocarbon metabolism, reinforced by metabolic division of labor. Within this naturally occurring consortium, Bacillus strains persist under environmental stress, establish biofilms, and perform essential secondary hydrolysis, while Pseudomonas strains catabolize aromatic monomers and buffer oxidative stress. Genes supporting these functions are enriched within the accessory genomes of the consortium strains, indicating consortium-enriched horizontal gene transfer. In addition to the canonical two-step hydrolytic pathway well documented in PET biodegradation, we identify a secondary methylation- and redox-associated process, mechanisms where the full consortium acts on the oligomer mono(2-hydroxyethyl) terephthalate (MHET), yielding nearly complete conversion to terephthalic acid and methylated MHET. Together, these findings support a model in which PET degradation is driven by pre-existing hydrocarbon metabolic traits distributed across the native consortium, particularly stress-response and redox pathways, aromatic catabolism, and alcohol catabolism.

IMPORTANCE: Environmental plastic degradation is rarely accomplished by a single organism; however, the microbial mechanisms enabling community-level polyethylene terephthalate (PET) plastic breakdown remain poorly understood. This study shows that a bacterial consortium isolated from crude petroleum-contaminated coastal soils degrades PET by coordinating older hydrocarbon, aromatic, stress-response, and redox-associated metabolisms rather than by acquiring a dedicated PET pathway. Predicted horizontal gene transfer events were linked mainly to survival, biofilm formation, and metabolic flexibility, not PET depolymerization itself. These findings shift the focus from searching for single PET-degrading organisms toward understanding how microbial communities combine pre-existing metabolic tools to process synthetic polymers and manage the chemical stress created during biodegradation.},
}

@article {pmid42627299,
year = {2026},
author = {Liao, KJ and Luo, Y and Zhuang, Q and Wei, HL},
title = {Type III secretion system diversity in the Pseudomonas fluorescens species complex.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71510},
pmid = {42627299},
issn = {1469-8137},
support = {Y2026PT03//Central Public-interest Scientific Institution Basal Research Fund/ ; G2026-05-10//Special Project of State Key Laboratory of Efficient Utilization of Arable Land in China/ ; },
abstract = {Type III secretion systems (T3SSs) play important roles in mediating interactions between bacteria and eukaryotic hosts by delivering effectors into host cells, yet their genetic diversity and evolutionary dynamics among rhizosphere-associated members of Pseudomonas fluorescens species complex (PFSC) remain poorly understood. We conducted a genome-based evolutionary analysis of T3SSs across a global collection of PFSC strains to investigate their phylogenetic evolution and diversity. The 88 T3SS-carrying strains were assigned to seven PFSC subgroups and clustered into six phylogenetically distinct T3SS categories, with 19 strains representing 13 previously undescribed species, highlighting substantial taxonomic diversity. Phylogenetic reconstructions showed that T3SSs formed a monophyletic clade sister to flagellar systems, suggesting a shared evolutionary origin, whereas variable GC content, the presence of mobile genetic elements, and incongruence between T3SS and species phylogenies suggested that horizontal gene transfer (HGT) has played an important role in T3SS evolution within the PFSC. T3SS-harboring strains possessed diverse genomic features, including genes previously associated with plant-growth-promoting functions and encoded atypical T3SS-associated proteins, while representative Rsp I and Rsp II strains retained partial effector translocation activity. Together, these findings reveal extensive diversification of T3SSs in rhizosphere-associated PFSC strains through HGT and provide a phylogenomic framework for future functional studies.},
}

@article {pmid42628965,
year = {2026},
author = {Lindahl, O and Berruga-Fernández, T and Soekhoe, J and Huseby, DL and Hughes, D},
title = {The evolutionary maintenance of amino acid prototrophy in Escherichia coli.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evag209},
pmid = {42628965},
issn = {1759-6653},
abstract = {Escherichia coli is a prototroph and can synthesize all twenty proteinogenic amino acids when required to grow in minimal medium. There are approximately sixty protein-coding genes individually essential for amino acid synthesis. This is a large mutational target for the accumulation of detrimental mutations. E. coli can rewire biosynthetic pathways in response to mutational damage, but the limits of this capacity are poorly understood. Here, to address evolutionary robustness, we asked whether and how the phenotypes of irreversible mutations causing auxotrophy could be suppressed or bypassed in the absence of horizontal gene transfer (HGT). Spontaneous suppressors could be selected for only ten of fifty-nine mutants tested (detection limit ∼7x10-11). Mechanisms of suppression included: regional amplifications; mutations increasing gene or operon expression; mutations relaxing enzyme specificity; and mutations causing biochemical pathway diversions. Overall, the data show that spontaneous suppression of auxotrophy caused by an irreversible mutation is an evolutionary survival mechanism relevant only to a minority of the genes essential for amino acid synthesis. As a consequence, the essential genetic foundations for amino acid prototrophy are expected to be degraded over time by mutations (Muller's ratchet) and metabolic rewiring alone will be insufficient to counteract this effect. This implies that maintaining phenotypes, including prototrophy in E. coli, and potentially other bacterial species, is likely to be reliant on HGT of housekeeping genes to counteract the effects of inevitable mutational inactivation. Accordingly, chromosomal HGT in bacteria may be critical for survival across diverse environmental niches.},
}

@article {pmid42623874,
year = {2026},
author = {Zhou, R and Ma, Z and Kou, S and Ni, Y and Huang, X and Wei, H and Jin, Q and Xu, H and Ding, Z},
title = {Microplastics as vectors for microbial pollutants: Biofilm-associated transfer of pathogens and antibiotic resistance genes in zebrafish intestine.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143329},
doi = {10.1016/j.jhazmat.2026.143329},
pmid = {42623874},
issn = {1873-3336},
abstract = {As composite carriers of microorganisms and pollutants, biofilm-attached microplastics (MPs) serve as potential vectors for the environmental migration and biotransmission of antibiotic resistance genes (ARGs) and pathogens. In this study, traditional polypropylene (PP) and biodegradable polylactic acid (PLA) MPs were used to investigate the interference effects of biofilms-attached MPs on gut microbiota and ARGs transmission, through a combination of laboratory biofilm cultivation, zebrafish (Danio rerio) exposure simulations, metagenomic sequencing, and metabolomic profiling. Results showed that MP biofilms likely induced gut dysbiosis and were associated with altered diversity and abundance of pathogens and ARGs. At the phylum level, Nitrospira was transferred from PP biofilms to the gut. At the genus level, 23 genera were transferred from MP biofilms, with PLA (23 genera) showing higher transfer capacity than PP (4 genera). Notably, two human pathogens, one opportunistic pathogen, and two ARGs (adeF and oqxB) were specifically transferred from PLA biofilms, highlighting the unique dissemination risk of biodegradable MPs. Mechanistically, MPs may activate mobile genetic elements (e.g., Tn916 transposon) through metabolic remodeling and quorum sensing, thereby promoting horizontal gene transfer and ARGs dissemination within the gut. Our findings highlight the potential role of MPs as carriers of microorganisms and ARGs, underscoring the biotransmission risks of antibiotic resistance caused by composite pollution.},
}

@article {pmid42624328,
year = {2026},
author = {da Silva, JC and Santos, ICO and da Conceição-Neto, OC and Silveira, MC and Sued-Karam, BR and Rodrigues, DCS and da Silva, GA and Dimas, SM and Gonzalez, IHL and Pribul, BR and D'Alincourt Carvalho-Assef, AP and Rocha-de-Souza, CM},
title = {Genomic Characterisation of ST233 Pseudomonas aeruginosa Co-producing KPC-2 and VIM-2 in Northeastern Brazil During the COVID-19 Pandemic: Evidence of Independent Horizontal Acquisition Events.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2026.08.014},
pmid = {42624328},
issn = {2213-7173},
abstract = {BACKGROUND: Dual-carbapenemase-producing Pseudomonas aeruginosa poses a major therapeutic and epidemiological challenge worldwide, yet systematic data on KPC and VIM co-production in Brazil remain limited. The COVID-19 pandemic intensified antimicrobial use, a period temporally associated with increased carbapenemase detection globally.

OBJECTIVES: To characterise the molecular epidemiology and resistance profiles of KPC and VIM co-producing P. aeruginosa isolates from Brazil (2019-2023).

METHODS: Between 2019 and 2023, 1,489 multidrug-resistant P. aeruginosa isolates were screened by multiplex PCR for carbapenemase-encoding genes. Co-producing isolates underwent pulsed-field gel electrophoresis (PFGE) for clonal profiling, followed by whole-genome sequencing (WGS) for high-resolution phylogenomic analysis. Antimicrobial susceptibility testing and plasmid characterisation using next-generation sequencing platforms were also performed.

RESULTS: Forty-two isolates (2.8%) harboured both blaKPC-2 and blaVIM-2, with detection occurring exclusively between 2020 and 2023, temporally coinciding with the COVID-19 pandemic. PFGE identified eight distinct clonal groups, providing evidence for independent horizontal gene transfer (HGT) events, whilst WGS confirmed all isolates as the high-risk ST233 lineage. Chromosomally integrated blaVIM-2 within class 1 integrons predominated; two isolates carried dual chromosomal copies. Plasmid-borne blaKPC-2 was identified across heterogeneous replicons (43.3-430.1 kb), suggesting multiple independent acquisition events. All co-producing isolates displayed extensive drug resistance, retaining in vitro susceptibility only to cefiderocol and colistin.

CONCLUSIONS: ST233 co-producing KPC and VIM, represents a high-risk resistance phenotype of epidemiological significance. Divergent genomic architectures suggest active horizontal dissemination across diverse genetic backgrounds rather than clonal expansion, highlighting the need for enhanced surveillance and infection control strategies.},
}

@article {pmid42626150,
year = {2026},
author = {Tjampakasari, CR and Sjatha, F and Yasmon, A and Syahrurachman, A and Guntari, N},
title = {Mutation analysis of dihydrofolate reductase (dfr) and dihydropteroate synthase (sul) genes in trimethoprim-sulfamethoxazole-resistant Escherichia coli from urinary tract infections.},
journal = {Iranian journal of microbiology},
volume = {18},
number = {4},
pages = {544-552},
pmid = {42626150},
issn = {2008-3289},
abstract = {BACKGROUND AND OBJECTIVES: Escherichia coli is the leading cause of urinary tract infections (UTIs) and has shown increasing resistance to trimethoprim-sulfamethoxazole (TMP-SMX). Resistance to TMP-SMX is commonly associated with the acquisition of resistance genes such as dfr and sul, often mediated by horizontal gene transfer. This study aimed to characterize the presence of dfr (dfrA1, dfrA5, dfrA7/17) and sul (sul1 and sul2) genes and to describe sequence variations in selected E. coli isolates.

MATERIALS AND METHODS: Urine culture samples were obtained from 678 patients suspected of having UTIs, and 21 samples yielded positive culture results. This study further analyzed 11 E. coli isolates, consisting of eight TMP-SMX-resistant isolates, two susceptible isolates, and one E. coli ATCC 25922 strain as a control. The clinical isolates were provided by the Clinical Microbiology Laboratory, Faculty of Medicine, Universitas Indonesia. PCR amplification and agarose gel electrophoresis were used to identify dfr and sul genes, followed by Sanger sequencing of selected amplicons. Sequence data were analyzed with BioEdit software and aligned against reference sequences from NCBI.

RESULTS: The distribution of resistance genes varies among resistant isolates. Some isolates carry the dfrA5 gene, while dfrA1 was detected in one isolate. The sul2 gene was present in a number of resistant isolates, while sul1 was identified but showed no differences from the reference sequence. Further sequence analysis revealed amino acid changes in the dfrA1, dfrA5, and sul2 genes, although these changes were not consistently found in all isolates.

CONCLUSION: This study characterizes the distribution of dfr and sul genes and their sequence variations in a limited number of E. coli isolates. The results suggest that TMP-SMX-resistant isolates may contain diverse genetic determinants associated with resistance. Nevertheless, the limited isolate number restricts the broader interpretation of these findings. Larger-scale studies, supported by functional analyses, are required to determine the contribution of these genes and their sequence variations to antibiotic resistance.},
}

@article {pmid42620617,
year = {2026},
author = {Rao, P and Aswathanarayan, JB and Madhunapantula, SV and Vittal, RR},
title = {Therapeutic strategies against biofilm-associated multidrug-resistant Klebsiella pneumoniae and Acinetobacter baumannii in ventilator-associated pneumonia.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1904655},
pmid = {42620617},
issn = {1664-302X},
abstract = {Ventilator-associated pneumonia remains one of the most common and severe healthcare associated infections in critically ill patients receiving mechanical ventilation. Among the predominant causative pathogens, multidrug-resistant Klebsiella pneumoniae and Acinetobacter baumannii pose a major clinical challenge due to their extensive antimicrobial resistance, environmental persistence, and ability to form biofilms on endotracheal tubes and other medical devices. Biofilm formation is central to VAP pathogenesis, facilitating bacterial adhesion, immune evasion, reduced antimicrobial penetration, and protective niches that support metabolic dormancy, persister-cell formation, and horizontal gene transfer. These mechanisms promote bacterial survival, recurrent infection, prolonged hospitalization, increased healthcare costs, and mortality. Resistance in K. pneumoniae and A. baumannii is mediated by multiple mechanisms, including β-lactamase production, efflux pump overexpression, reduced outer membrane permeability, target-site modification, and acquisition of mobile resistance determinants. The interaction between AMR and biofilm- associated persistence substantially compromises antimicrobial efficacy, particularly against carbapenem-resistant strains. Although recent advances have expanded treatment options, outcomes remain suboptimal in established biofilm-associated infections. This review examines the epidemiology, clinical burden, resistance mechanisms, biofilm mediated persistence, and host-pathogen interactions underlying MDR K. pneumoniae and A. baumannii associated VAP. Particular emphasis is placed on current therapeutic approaches and emerging anti-biofilm strategies, including antimicrobial-coated devices, nanotechnology-based interventions, matrix-disrupting enzymes, antimicrobial peptides, and anti-virulence approaches targeting quorum sensing and biofilm maturation. Understanding the interplay between AMR, biofilm persistence, and therapeutic failure is critical for developing more effective strategies to prevent and manage MDR-VAP.},
}

@article {pmid42622299,
year = {2026},
author = {Kaur, P and Roy, A and Bhattacharjee, S and Hallan, V},
title = {Plant Viruses as Master Manipulators: Exploiting Host Plants and Insect Vectors for Enhanced Transmission.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70829},
pmid = {42622299},
issn = {1365-3040},
abstract = {Plant viruses are evolutionarily endowed with traits that enhance their survival and dissemination attributes both in host plants and insect vectors. This review highlights current understanding of these multifaceted interactions, positioning plant viruses as master regulators of the intricate tripartite interactions. Direct viral effects on vector physiology and behaviour, highlighting evidence that viral infection may contribute to changes in olfactory systems, epigenetic modifications, involvement of salivary effectors, and horizontal gene transfer events that may vary vector competence, were summarised. The indirect mechanisms mediated through virus-induced alterations in host plant responses, including changes in volatile emissions, the development of visually and chemically attractive symptoms, and modulation of host immune defences that may influence vector attraction and feeding behaviour, were discussed. These viral infections have profound ecological and agricultural consequences, reflecting the fine balance these pathogens maintain between preserving host viability and maximising transmission. In intensively managed agro-ecosystems, environmental and biological conditions can strengthen these interactions, potentially promoting epidemic spread and altering vector behaviour. Deciphering these evolutionary strategies deepens our understanding of the dynamics governing pathogen-host-vector systems and opens new possibilities for designing targeted, sustainable interventions to disrupt viral transmission in crops.},
}

@article {pmid42622360,
year = {2026},
author = {Becerra-Rodríguez, C and Devillers, H and Legras, JL and Galeote, V and Bigey, F and Dequin, S and Marsit, S},
title = {Genomic Tales of Wine Yeasts: From Domestication to Functional Innovation.},
journal = {FEMS yeast research},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsyr/foag039},
pmid = {42622360},
issn = {1567-1364},
abstract = {Over the last decades, the yeast Saccharomyces cerevisiae has emerged as a key model for studying microbial domestication, particularly in the context of winemaking. The recent surge of population genomic data, encompassing thousands of genomes, has profoundly reshaped our understanding of the evolutionary history and adaptive potential of wine yeasts. Despite arising from a domestication bottleneck, wine yeasts form a well-structured population and display striking genome dynamism. Extensive variation in heterozygosity, aneuploidy, structural variations and gene content may provide a reservoir of genomic variation that contributes to adaptive potential in the harsh winemaking environment. While some genetic variation and genome restructuring contribute to adaptation, gene flow through hybridization, introgression and especially horizontal gene transfer has emerged as a major driver of functional innovation. These findings establish wine yeasts as a powerful model to link genome evolution with adaptation to anthropogenic environments. They also provide a foundation for the rational improvement of industrial strains through approaches such as quantitative trait locus mapping, adaptive laboratory evolution and genome-wide association studies. Extending these frameworks to non-Saccharomyces species and integrating genomic, functional and ecological data will be key to understanding and engineering microbial communities, to face the modern winemaking challenges.},
}

@article {pmid42622944,
year = {2026},
author = {Katiyar, P and Singh, P},
title = {The plastisphere paradox: microplastics as engines of antimicrobial resistance and hosts for polymer degraders.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {9},
pages = {},
pmid = {42622944},
issn = {1573-0972},
mesh = {Biodegradation, Environmental ; *Bacteria/genetics/drug effects/metabolism ; Gene Transfer, Horizontal ; Biofilms ; *Microplastics/metabolism ; *Drug Resistance, Bacterial/genetics ; Polymers/metabolism ; Biosurfactants ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; },
abstract = {Microplastics (MPs) have emerged as serious ecological pollutants that harbor diverse microbial communities in their biofilm ecosystem termed as plastisphere. This community serves as a reservoir for antibiotic resistance genes (ARGs), antimicrobial resistant bacteria (ARB) as well as other microorganisms involved in pollutant degradation. However, the dynamic interactions between antimicrobial resistance (AMR) and bioremediation in the plastisphere community are not well deciphered. This review examines the dual role of MPs as ARG vectors as well as emerging platforms for microplastic and other pollutant bioremediation. Plastisphere biofilms act as a hub for horizontal gene transfer (HGT), driven by active microbial interfaces, extracellular polymeric matrices, and co-selection pressures exerted due to antibiotics, heavy metals, and biocides. Metagenomics and metatranscriptomics approaches reveal the cohabitation of functional genes associated with both AMR and microplastic degradation, mediated by enzymes and multifunctional molecules such as biosurfactants. However, bioaugmentation using plastisphere derived microbial population risks HGT of ARGs or virulence factors to non-native and indigenous microorganisms. Hence, such applications call for stringent biosafety assessments to prevent inadvertent and unwanted ARG dissemination. By integrating ecological perils with advanced biotechnological opportunities, this review underlines the plastisphere paradox and highlights the demand for multiomics-driven One Health approaches to bring forth the interconnected challenges of MPs pollution, AMR, and bioremediation. This exploration yields promising avenues for developing integrated strategies that can address both persistent microplastic pollution and AMR spread concomitantly.},
}

Biodegradation, Environmental
*Bacteria/genetics/drug effects/metabolism
Gene Transfer, Horizontal
Biofilms
*Microplastics/metabolism
*Drug Resistance, Bacterial/genetics
Polymers/metabolism
Biosurfactants
Anti-Bacterial Agents/pharmacology
Drug Resistance, Microbial/genetics

@article {pmid42623751,
year = {2026},
author = {Ranjan, K and Gupta, N and Al-Mustapha, AI and Keenum, I and Shaheryar, M and Bose, D and Sharma, G and Tiwari, A},
title = {Environmental occurrence, ecotoxicity, and management perspectives of β-lactam antibiotics.},
journal = {Ecotoxicology and environmental safety},
volume = {323},
number = {},
pages = {120671},
doi = {10.1016/j.ecoenv.2026.120671},
pmid = {42623751},
issn = {1090-2414},
abstract = {β-Lactams are the most widely prescribed antibiotic class globally, comprising penicillins, cephalosporins, carbapenems, and monobactams. Their continual release to the environment raises concerns about both direct ecotoxicity and potential indirect effects on ecosystem function. This review highlights three key findings; 1) environmental concentrations can exceed predicted no-effect concentrations for resistance selection; for example ceftriaxone had been reported 6160 µg/L in wastewater influent and 4150 µg/L in effluent in India, indicating that many β-lactams have removal efficiency below 33%, 2) ecotoxicity data show that cyanobacteria (e.g. Microcystis aeruginosa, EC50 0.0037 mg/L for amoxicillin) are ≥ 1,000-fold more sensitive than macrofauna, and that chronic exposure at ng-µg/L levels may promote selection of antimicrobial resistance and facilitate horizontal gene transfer of these genes and 3). β-lactam resistance genes (blaCTX-M, blaNDM, blaOXA) are ubiquitous in wastewater and manure-amended soils and can persist even after the degradation of the parent compounds. Collectively, these finding indicates that β-lactam antibiotics pose significant risks to aquatic and soil ecosystems by contributing to the proliferation and maintenance of antimicrobial resistance in environmental reservoirs. The widespread environmental occurrence and persistence of β-lactams, along with associated resistance determinants, represent emerging One Health concerns. This narrative review synthesizes current literature on the ecotoxicological effects of β-lactam antibiotics, focusing on their major environmental sources, distribution across environmental matrices, impacts on non-target organisms, and emerging strategies to mitigate their environmental burdens. We further emphasize cross-disciplinary solutions spanning engineering, microbial ecology, policy, identify critical research gaps, and propose pragmatic pathways to reduce environmental selection pressure from β-lactams.},
}

@article {pmid42609526,
year = {2026},
author = {Yang, JM and Hou, PF and Jia, SY},
title = {Lactobacillus in autoimmune thyroid diseases: benefit or risk?.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1905146},
pmid = {42609526},
issn = {1664-3224},
mesh = {Humans ; Animals ; *Lactobacillus/immunology/physiology ; *Probiotics/therapeutic use/adverse effects ; *Gastrointestinal Microbiome/immunology ; *Autoimmune Diseases/microbiology/immunology/therapy ; *Thyroid Diseases/immunology/microbiology/therapy ; },
abstract = {Autoimmune thyroid diseases (AITDs), mainly Hashimoto's thyroiditis and Graves' disease, are common organ-specific autoimmune disorders driven by complex interactions among genetic susceptibility, immune dysregulation, environmental exposure, and microbial factors. Increasing evidence supports the relevance of the gut-thyroid axis, in which gut microbiota may influence thyroid hormone metabolism, intestinal barrier integrity, systemic inflammation, and thyroid-directed autoimmunity. Among gut commensals, Lactobacillus-related taxa have attracted attention because selected strains can modulate cytokine production, Treg/Th17 balance, short-chain fatty acid metabolism, epithelial barrier function, and inflammatory signaling pathways such as TLR4/NF-κB, AhR, and PPARδ-related pathways. However, most mechanistic evidence is derived from non-AITD animal, cellular, or metabolic disease models, and direct validation in AITD patients remains limited. This review summarizes current evidence on Lactobacillus-related strains in AITDs, emphasizing strain-specific effects, updated taxonomy, mechanistic plausibility, clinical heterogeneity, and translational limitations. We also discuss inconsistent microbial signatures, neutral or inconclusive clinical findings, and safety concerns, including probiotic-associated infection, antibiotic resistance genes, horizontal gene transfer, and potential pro-autoimmune effects. Overall, Lactobacillus-related interventions remain investigational, and future studies should prioritize standardized strain identification, disease-specific mechanisms, long-term safety, and well-designed clinical trials.},
}

Humans
Animals
*Lactobacillus/immunology/physiology
*Probiotics/therapeutic use/adverse effects
*Gastrointestinal Microbiome/immunology
*Autoimmune Diseases/microbiology/immunology/therapy
*Thyroid Diseases/immunology/microbiology/therapy

@article {pmid42611360,
year = {2026},
author = {Musini, A and Owais, M and Joshika, R},
title = {Genetic architecture and functional dynamics of integrons in Staphylococcus aureus resistance.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {},
pmid = {42611360},
issn = {1678-4405},
mesh = {*Integrons/genetics ; Anti-Bacterial Agents/pharmacology ; Humans ; *Staphylococcus aureus/genetics/drug effects ; *Staphylococcal Infections/microbiology ; *Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; },
abstract = {Staphylococcus aureus is a major opportunistic pathogen and a leading cause of community and hospital-acquired infections worldwide, with a growing capacity to develop multidrug resistance (MDR). Among the genetic mechanisms driving this resistance, integrons play a critical role by capturing, rearranging, and expressing antimicrobial resistance gene cassettes through site-specific recombination. Although integrons are traditionally associated with Gram-negative bacteria, increasing evidence highlights their significant contribution to resistance dissemination in S. aureus, particularly in methicillin-resistant S. aureus (MRSA) strains. This review focuses on current knowledge on the structure, function, and types of integrons, and their role in prevalence and mechanistic role in S. aureus. Integrons interact with other mobile genetic elements like transposons and plasmids to enable horizontal gene transfer across strains and species. Among the four recognized classes of integrons, class 1 is the most prevalent in S. aureus frequently associated with plasmids and transposons and show resistance to β-lactams, aminoglycosides, fluoroquinolones, and tetracyclines. Class 2 integrons occur less commonly and exhibit limited cassette diversity, while class 3 integrons remain rare. Epidemiological studies report class 1 integron prevalence ranging from 40 to 70% in clinical isolates across different regions, often correlating with resistance to β-lactams, aminoglycosides, fluoroquinolones, tetracyclines, and rifampicin, and co-occurring with SCCmec elements in MRSA. Integron-mediated resistance is further enhanced by stress-induced integrase activity and biofilm formation, promoting persistence in healthcare settings. Molecular detection methods, particularly multiplex PCR targeting integrase genes, are essential for surveillance. Understanding integron dynamics in S. aureus is crucial for informing antimicrobial stewardship, infection control strategies, and future interventions aimed at limiting the spread of MDR pathogens.},
}

*Integrons/genetics
Anti-Bacterial Agents/pharmacology
Humans
*Staphylococcus aureus/genetics/drug effects
*Staphylococcal Infections/microbiology
*Drug Resistance, Multiple, Bacterial/genetics
Gene Transfer, Horizontal

@article {pmid42611921,
year = {2026},
author = {Poudyal, P and Sy, B and Mediati, DG and Payne, M and Nandel, V and Norris, D and McAteer, S and Ullah, A and Li, S and Menz, L and Alquethamy, S and Scadden, J and Ridone, P and Waters, S and Dallman, TJ and Baker, M and Lan, R and Gally, D and Tree, JJ},
title = {Phage-encoded sRNA counteracts xenogeneic silencing in pathogenic E. coli.},
journal = {PLoS pathogens},
volume = {22},
number = {8},
pages = {e1014486},
doi = {10.1371/journal.ppat.1014486},
pmid = {42611921},
issn = {1553-7374},
abstract = {Horizontal gene transfer introduces foreign DNA that can disrupt cellular processes and is therefore subject to xenogeneic silencing by nucleoid-associated proteins such as H-NS and Hha. In Enterohaemorrhagic Escherichia coli (EHEC), prophages make up a large fraction of the accessory genome and encode many virulence factors, yet their expression must overcome this silencing. We identify a prophage-encoded small RNA (sRNA), HnrS, that functions as an anti-silencing factor by targeting the H-NS paralogue Hha. HnrS is a short (66-nt) sRNA that is enriched in the locus of enterocyte effacement (LEE[+]) E. coli strains and present in up to nine copies in EHEC and Enteropathogenic Escherichia coli (EPEC) genomes. HnrS base-pairs with the hha ribosome-binding site to inhibit translation, thereby modulating Hha-H-NS repression of virulence loci including the LEE type III secretion system. Loss of HnrS alters motility, T3SS expression, and a subset of Hha-regulated genes. These findings reveal an RNA-based counter-silencing strategy encoded by prophage to relieve xenogenic silencing.},
}

@article {pmid42612534,
year = {2026},
author = {Li, B and You, Y and Fan, Y and Wu, J and Lv, X and Ji, J and Zhang, M},
title = {Mechanism exploration of divergent partial denitrification performance under tetracycline stress: Insights from functional gene, electron transport and molecular docking.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143220},
doi = {10.1016/j.jhazmat.2026.143220},
pmid = {42612534},
issn = {1873-3336},
abstract = {Nitrates and antibiotics like tetracycline (TC) coexist in wastewater and inhibit nitrite (NO2[-]-N) accumulation during partial denitrification (PD), restricting anammox coupling. A moving bed biofilm reactor (PD-MBBR) and a sequencing batch reactor (PD-SBR) were compared under TC stress (0-8 mg/L). The PD-MBBR proved more robust, sustaining a high nitrate transformation ratio (NTR) of 95.11% and ∼53% TC removal. Metagenomic sequencing, quantitative polymerase chain reaction (qPCR), and molecular docking revealed this tolerance stemmed from physical shielding and metabolic compensation. Carrier-attached growth promoted extracellular polymeric substances (EPS) overproduction, forming a dense barrier preventing TC from binding to key denitrifying enzymes. The biofilm maintained stable nitrate reductase (NAR) activity via high narG and napA gene abundances, while nitrite reductase (NIR) was inhibited, ensuring efficient NO2[-]-N accumulation. This was supported by hyperactivated electron transport chain components, with complex III relative abundance increasing 15.08% and peak enzymatic activity reaching 149.02%. While IntI1-mediated horizontal gene transfer fortified community defense, concentrated antibiotic resistance genes (ARGs) within the biofilm pose a secondary dissemination risk. Thus, PD-MBBR provides an efficient pretreatment strategy for anammox, though downstream ARGs management is warranted.},
}

@article {pmid42614212,
year = {2026},
author = {Stekel, DJ and Cook, R and Ibrahim, DR and Jones, MA and Levine, DT and Hudson, CD and Kreft, JU and Hobman, JL},
title = {Interdisciplinary insights on selection, surveillance and mitigations of antimicrobial resistance dynamics on a UK dairy farm with relevance to other one health sectors.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1829030},
pmid = {42614212},
issn = {2297-1769},
abstract = {Antibiotic use in agriculture is a global driver for antimicrobial resistance (AMR). Dairy farming, one of the largest producers of agricultural waste, represents a critical opportunity for mitigating AMR impacts. We review, synthesize and generalize from results of 10 years of interdisciplinary study of AMR in the waste from a single, medium-sized intensive UK dairy farm and related One Health AMR work. Resistance patterns reflect a combination of (i) short-term stability with (ii) long-term change associated with altered antibiotic use. These dynamics were driven by clonal expansion and contraction characterized by chromosomal carriage of resistance, and co-selection by environmentally stable antimicrobials including copper, zinc and tetracycline, rather than horizontal gene transfer. We outline 10 considerations for study, surveillance and mitigation: (i) the need for long-term longitudinal sampling; (ii) the value of intense focus on representative sites; (iii) inclusion of both Gram-positive and Gram-negative sentinels; (iv) adoption of shared standards for measurement and reporting; (v) use of precise language for AMR hazards to enable appropriate study site selection; (vi) reduction of overall antibiotic use, e.g., through infection control; (vii) continued avoidance of veterinary use of internationally recognized critical human antibiotics; (viii) avoidance of environmentally stable antibiotics such as some tetracyclines; (ix) reduction of co-selection pressure via recovery of metals such as copper and zinc; and (x) mitigation of resistance through storage of slurry without further additions, e.g., through the use of two-tank systems. We propose that these considerations are relevant beyond dairy, applicable in wider livestock, environmental and One Health settings.},
}

@article {pmid42614264,
year = {2026},
author = {Keerthi, V and Ravindran, P and Kaliyur, S and Tuttagunta, SUS and Mathpal, S and Joshi, T and Ramaiah, S and Anbarasu, A},
title = {A comprehensive review of emerging therapeutic strategies against methicillin-resistant Staphylococcus aureus.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1815573},
pmid = {42614264},
issn = {1664-302X},
abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) remains one of the most significant multidrug-resistant bacterial pathogens responsible for a broad spectrum of infections ranging from mild skin infections to severe invasive diseases, including bacteremia, pneumonia, endocarditis, osteomyelitis, and sepsis. The rapid global dissemination of MRSA is primarily driven by the acquisition of the mecA gene encoding penicillin-binding protein 2a, which confers resistance to β-lactam antibiotics. In addition to β-lactam resistance, MRSA exhibits resistance to multiple antimicrobial classes through diverse mechanisms, including target-site mutations, efflux pumps, biofilm formation, horizontal gene transfer, and adaptive phenotypic variations. The virulence and persistence of MRSA is further enhanced by numerous virulence factors such as adhesins, toxins, immune evasion proteins, and extracellular enzymes that facilitate colonization, persistence, and host tissue damage. Biofilm formation additionally contributes to chronic infection and antibiotic tolerance. Despite the availability of conventional agents such as vancomycin, linezolid, and daptomycin, the emergence of resistant strains including vancomycin-resistant Staphylococcus aureus has significantly limited current therapeutic options. Consequently, there is an urgent need for innovative therapeutic strategies. This review comprehensively summarizes the evolution, pathogenesis, virulence mechanisms, biofilm biology, and antibiotic resistance mechanisms of MRSA, with particular emphasis on emerging therapeutic approaches. Novel strategies including antimicrobial peptides, nanomedicine, bacteriophage therapy, CRISPR-Cas systems, biomimetic nano-NETs, probiotics, monoclonal antibodies and plant-derived compounds are discussed as promising alternatives or adjuncts to conventional antibiotics. Collectively, these advances highlight the evolving landscape of MRSA management and the potential for next-generation therapeutics to overcome antimicrobial resistance challenges.},
}

@article {pmid42616439,
year = {2026},
author = {Ge, H and Liu, Y and Dai, X and Chen, Y and Huang, C and Zheng, C and Shan, M and Zhang, L and Yu, Y and Qiu, M and Fang, H},
title = {Enantioselectivity of Antibiotic Resistance Genes in the Gut of Earthworms Exposed to Metalaxyl.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {32},
pages = {25089-25101},
doi = {10.1021/acs.jafc.6c06342},
pmid = {42616439},
issn = {1520-5118},
support = {42177252//National Natural Science Foundation of China/ ; 1102021010152 (LS-12)//China National Tobacco Corporation/ ; 2023YFD1902903//National Key Research and Development Program of China/ ; 2023C02039-01//"Leading Goose" R&D Program of Zhejiang Province of China/ ; },
mesh = {Animals ; *Oligochaeta/microbiology/drug effects/genetics/metabolism ; *Alanine/analogs & derivatives/chemistry/pharmacology/metabolism ; *Bacteria/genetics/drug effects/isolation & purification/classification/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Fungicides, Industrial/chemistry/pharmacology/metabolism ; *Bacterial Proteins/genetics/metabolism ; *Soil Pollutants/chemistry/pharmacology/metabolism ; Stereoisomerism ; *Drug Resistance, Microbial ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Chiral pesticides often exhibit an enantioselective environmental behavior and ecological effects. Using a soil-earthworm microcosm, we investigated the dissipation and bioaccumulation of metalaxyl enantiomers and their effects on gut microbiota and antibiotic resistance genes (ARGs). R-metalaxyl dissipated rapidly (half-life 7-9 d), whereas S-metalaxyl persisted much longer (about 90 d), imposing prolonged selective pressure. Earthworms preferentially accumulated R-metalaxyl, with a maximum bioaccumulation factor of 0.42. High-concentration S-metalaxyl increased the total ARG abundance in earthworm guts by approximately 35% relative to the control. Antioxidant enzyme activities showed an enantioselective pattern of initial stimulation followed by decline over time. Metalaxyl increased Streptococcus abundance by 1-3% and reduced sensitive genera, while R-metalaxyl selectively enriched rifamycin-, multidrug-, and glycopeptide-resistance genes. Over 60% of ARGs co-occurred with plasmids, indicating an elevated horizontal gene transfer risk. These results confirm significant enantioselective effects of metalaxyl on dissipation, enrichment, microbiome structure, and antibiotic resistance transmission in earthworm guts.},
}

Animals
*Oligochaeta/microbiology/drug effects/genetics/metabolism
*Alanine/analogs & derivatives/chemistry/pharmacology/metabolism
*Bacteria/genetics/drug effects/isolation & purification/classification/metabolism
*Gastrointestinal Microbiome/drug effects
*Fungicides, Industrial/chemistry/pharmacology/metabolism
*Bacterial Proteins/genetics/metabolism
*Soil Pollutants/chemistry/pharmacology/metabolism
Stereoisomerism
*Drug Resistance, Microbial
Anti-Bacterial Agents/pharmacology

@article {pmid42619180,
year = {2026},
author = {Wang, J and Wu, B and Shen, J and Zhang, S and Cai, X and Pirhonen, M},
title = {A Novel Plant Secondary Metabolite-Binding Gene Family Required for Full Virulence in Pectobacterium parvum.},
journal = {Molecular plant pathology},
volume = {27},
number = {8},
pages = {e70328},
doi = {10.1111/mpp.70328},
pmid = {42619180},
issn = {1364-3703},
support = {C2026204045//the Natural Science Foundation of Hebei Province/ ; HBCT2024130210//the Earmarked Fund for Hebei Agriculture Research System, China/ ; },
mesh = {Virulence/genetics ; *Pectobacterium/pathogenicity/genetics/metabolism ; Bacterial Proteins/metabolism/genetics/chemistry ; Solanum tuberosum/microbiology ; *Multigene Family ; Phylogeny ; Plant Diseases/microbiology ; *Secondary Metabolism/genetics ; },
abstract = {Pectobacterium parvum is an emerging phytopathogen causing aerial stem rot of potato. P. parvum has a broad host range, with Chinese cabbage as one of its important hosts. Through multi-omics analysis, we discovered a previously uncharacterized gene family highly expressed during in planta infection, designated the plant secondary metabolite-binding (PSMB) family. This family likely originated via horizontal gene transfer and underwent lineage-specific expansion in P. parvum, forming a four-paralog pathogenicity island. Structural modelling revealed that PSMB proteins resemble the rhizobial RhiA protein, though their function in phytopathogens has not been established. Biochemical assays demonstrated that the representative member, PSMB1a, binds defensive plant secondary metabolites (PSMs) with high affinity. PSMB1a binds the solanidine with submicromolar affinity (Kd = 0.103 μM) and exhibited approximately 100-fold higher affinity over salicylic acid (Kd = 9.23 ± 2.35 μM), indicating selectivity for specific PSMs. Functional studies demonstrated that PSMB1a enhances tolerance to defensive PSMs and contributes to virulence. Heterologous expression of PSMB1a in sister species P. polare enhanced PSM tolerance and virulence on Chinese cabbage, but suppressed bacterial proliferation under non-stress conditions. Conversely, deletion of the entire PSMB pathogenicity island in P. parvum attenuated virulence on potato stems, Chinese cabbage, and radish while increasing in vitro growth, confirming a trade-off between virulence contribution and basal fitness. These findings identify the PSMB family as a new class of virulence factors in Pectobacterium and reveal a specialized adaptive strategy in P. parvum that involves the binding of defensive PSMs to facilitate infection.},
}

Virulence/genetics
*Pectobacterium/pathogenicity/genetics/metabolism
Bacterial Proteins/metabolism/genetics/chemistry
Solanum tuberosum/microbiology
*Multigene Family
Phylogeny
Plant Diseases/microbiology
*Secondary Metabolism/genetics

@article {pmid42620174,
year = {2026},
author = {Duarte, TDS and Floyd, HEE and Thamlikitkul, V and Trang, VD and Thach, PN and Abboud, C and Gales, AC and Dos Santos, FF and Ojok, D and Aryal, G and Chaudhary, MK and Ettu, AO and Adams, A and Hassan, MA and Omar, AM and Sarwar, Y and Morrissey, I and Alm, R and Sen, T and Elliott, AG and Cooper, M and Blaskovich, MB and Zuegg, J},
title = {Mapping the resistance landscape: A large-scale study of polymyxin-resistant pathogens circulating in low-and middle-income countries.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {42620174},
issn = {2693-5015},
abstract = {The increasing prevalence of antimicrobial resistance is a major public health challenge, particularly in low- and middle-income countries (LMICs). Polymyxins are last-resort antibiotics used for treating highly drug-resistant infections, however, the rise of polymyxin-resistant bacterial strains is further reducing treatment options in LMICs, where the burden is exacerbated by limited diagnostic capacity, poor antimicrobial stewardship, and limited surveillance infrastructure. There is a lack of comprehensive population-based surveillance of the emerging polymyxin resistance and a need to comprehend what genetic determinants are associated with this resistance. In this study, we collected 634 clinical isolates of polymyxin-resistant bacteria from 28 LMICs, then used whole genome sequencing, phylogenetic and bioinformatic analyses to identify species, sequence types and antibiotic resistance gene profiles. We found 12 bacterial species and focussed downstream analyses on 4 high priority pathogens: K. pneumoniae, E. coli, A. baumannii, and P. aeruginosa.. The analysis revealed clonal expansion of high-risk lineages across geographically dispersed LMIC settings. Phenotypic antimicrobial susceptibility testing using both VITEK 2 automated systems and broth microdilution (BMD) assays against an expanded panel of 44 antibiotics allowed us to correlate the bioinformatic analyses to the resistance profiles. These findings show clonal spread and horizontal gene transfer feature in the propagation of antimicrobial resistance and highlight that enhanced genomic surveillance is essential to inform treatment strategies and mitigate the spread of resistance to last-line antimicrobials.},
}

@article {pmid42606503,
year = {2026},
author = {Liu, H and Wang, W and Li, J and He, Y and Cao, S and Hu, Z and Liu, Y and Hao, J and Yan, Y and Otten, L and Chen, K},
title = {Embryophyte-wide detection of natural Agrobacterium-mediated horizontal gene transfer reveals an ancient role for mini T-DNAs.},
journal = {The Plant journal : for cell and molecular biology},
volume = {127},
number = {4},
pages = {e71087},
pmid = {42606503},
issn = {1365-313X},
support = {32370382//National Natural Science Foundation of China/ ; G262408//Special fund for scientific research of Shanghai landscaping and city appearance administrative bureau/ ; G242406//Special fund for scientific research of Shanghai landscaping and city appearance administrative bureau/ ; 2026//Special fund for scientific research of national botanical gardens to benefit sustainable development/ ; },
mesh = {*DNA, Bacterial/genetics ; *Gene Transfer, Horizontal/genetics ; *Agrobacterium/genetics ; Genome, Plant/genetics ; Plants, Genetically Modified/genetics ; Bryophyta/genetics ; },
abstract = {Agrobacterium transfers DNA into plant cells, leading to tumors, hairy roots (HR), and natural genetically modified organisms (nGMOs). Transferred DNAs (T-DNAs) from agrobacteria and T-DNA-derived cellular T-DNAs (cT-DNAs) from nGMOs vary considerably and may carry up to 15 different genes. Among these, opine synthase (ops) genes encode the synthesis of opines used as nutrients by the agrobacteria. Earlier studies predicted large numbers of naturally transformed plant species, but only few have been identified and studied so far. We therefore developed a general method to detect cT-DNAs in all publicly available whole genome sequences (WGS) and Sequence Read Archive (SRA) data from land plants. To avoid false positives, we only retained DNA sequences coding for T-DNA proteins. A total of 2614 nGMO species were identified, most are eudicots. However, cT-DNAs were also found in 82 mosses and 75 ferns, showing that Agrobacterium can also generate natural transformants among the early land plants. Analysis of 149 cT-DNA maps revealed different types of T-DNAs. Most notably, these included small T-DNAs (mini T-DNAs) with a single opine synthase gene. Mini T-DNAs are not expected to induce tumors or HRs. The predominance of mini cT-DNAs in mosses and ferns, and the presence of more complex cT-DNAs in spermatophytes, indicate that mini T-DNAs represent the earliest types of T-DNA. Our study also detected unusual T-DNA integration patterns, with multiple copies spread out over several hundreds of kilobases.},
}

*DNA, Bacterial/genetics
*Gene Transfer, Horizontal/genetics
*Agrobacterium/genetics
Genome, Plant/genetics
Plants, Genetically Modified/genetics
Bryophyta/genetics

@article {pmid42606832,
year = {2026},
author = {Coello-Delgado, Y and Gómez Baltazar, A and Redondo-Solano, M and Godínez Oviedo, A and Pacheco Aguilar, J and Hernández Iturriaga, M},
title = {Horizontal transfer of QAC resistance genes between Listeria innocua and Listeria monocytogenes strains isolated from a food production environment.},
journal = {Canadian journal of microbiology},
volume = {72},
number = {},
pages = {1-9},
doi = {10.1139/cjm-2025-0315},
pmid = {42606832},
issn = {1480-3275},
mesh = {*Listeria/genetics/drug effects/isolation & purification ; *Gene Transfer, Horizontal ; *Listeria monocytogenes/genetics/drug effects/isolation & purification ; *Drug Resistance, Bacterial/genetics ; *Quaternary Ammonium Compounds/pharmacology ; Food Microbiology ; *Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Temperature ; },
abstract = {The objective of this study was to determine the presence of quaternary ammonium compound (QAC) resistance genes in Listeria spp. strains and to evaluate the effect of temperature and substrate on interspecies gene transfer. A total of 23 L. monocytogenes strains, four L. innocua and 37 Listeria spp. isolates (excluding L. grayi, L. ivanovii, L. seeligeri, and L. welshimeri) were recovered from surfaces in a frozen vegetable processing facility. The presence of the bcrABC gene was assessed by endpoint PCR. The bcrABC gene was detected in 73.91% (17/23) of L. monocytogenes isolates, in 50.00% (2/4) of L. innocua strains and was not detected in the other Listeria species (0/37). Two L. innocua strains carrying the bcrABC gene and two L. monocytogenes strains lacking it were selected for mixed culture experiments. Four co-cultures were prepared, inoculated into tryptic soy broth and spinach extract, and incubated at 4, 25, and 36 °C for 10 days. Horizontal transfer of the bcrABC gene was observed in 7.87% (17/216) of reactions in tryptic soy broth and spinach extract, with higher frequencies at 25 °C (10/216, 4.63%) and 36 °C (6/216, 2.78%) and lower frequencies at 4 °C (1/216, 0.46%). Recipient L. monocytogenes strains revealed increased resistance to QACs (500 μg/mL).},
}

*Listeria/genetics/drug effects/isolation & purification
*Gene Transfer, Horizontal
*Listeria monocytogenes/genetics/drug effects/isolation & purification
*Drug Resistance, Bacterial/genetics
*Quaternary Ammonium Compounds/pharmacology
Food Microbiology
*Anti-Bacterial Agents/pharmacology
Bacterial Proteins/genetics
Temperature

@article {pmid42607351,
year = {2026},
author = {Hinrichs, R},
title = {Putative gatekeepers of incoming DNA: 3' exonucleases in natural transformation and bacterial evolution.},
journal = {Biochimica et biophysica acta. Molecular cell research},
volume = {1873},
number = {7},
pages = {120210},
doi = {10.1016/j.bbamcr.2026.120210},
pmid = {42607351},
issn = {1879-2596},
abstract = {Natural transformation is a key mechanism of bacterial adaptation in which exogenous DNA (eDNA) is taken up, processed into single-stranded DNA (ssDNA), and integrated into the genome. While earlier studies primarily focused on uptake mechanisms, transport proteins, and recombination processes, exonucleases were long regarded as merely nonspecific degradation enzymes in DNA uptake. However, recent studies show that nucleases, partly related to the SOS response, play a key role in processing uptake ssDNA. They affect the imported DNA, thereby promoting efficient recombination. This review highlights the interactions between nucleases and taken-up ssDNA, discusses the functional link between natural competence and the bacterial SOS damage response, and demonstrates that key components of these processes have been conserved in bacteria. This suggests a possible universal principle in which ssDNA-specific nucleases serve as switches between the DNA damage response, competence, and horizontal gene transfer.},
}

@article {pmid42599095,
year = {2026},
author = {Nagabhyru, P and Florea, S and Liu, H and Kachroo, P and Calie, PJ and Young, CA and Schardl, CL},
title = {Chemotypic diversity of the fungus Epichloë brachyelytri symbiotic with the wild forest grass Brachyelytrum erectum.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0075426},
doi = {10.1128/aem.00754-26},
pmid = {42599095},
issn = {1098-5336},
abstract = {Many cool-season grasses (Poaceae subfam. Poöideae) host seed-transmissible symbionts (endophytes) in the fungal genus Epichloë, which can produce diverse alkaloids that protect against invertebrate and, in some cases, vertebrate herbivores. Rarely have population surveys been conducted to assess comprehensive alkaloid profiles and diversity of Epichloë in wild grasses. In this study, we surveyed Brachyelytrum erectum, which is a woodland grass in an early-diverging lineage of Poöideae, and commonly symbiotic with Epichloë brachyelytri. Analytical methods based on high-resolution UHPLC-MS/MS were refined to provide rapid, comprehensive detection, and quantitation of E. brachyelytri alkaloids, for six B. erectum populations in Kentucky. Chemotypes were identified with two or three of the alkaloids exo-1-acetamidopyrrolizidine (1), chanoclavine (2), and peramine (3). Both 1 and 2 are known as intermediates in biosynthetic pathways to more complex alkaloids, and chemotypes having both 1 and 2 as pathway end-products are novel. Such chemotypes were also identified in other species, and phylogenetic analysis indicated their multiple origins by a combination of convergent evolution, possible horizontal gene transfer, and interspecific hybridization. Alkaloid levels were comparable between most populations and at most plant developmental stages. Levels of 3 were compared between E. brachyelytri variants with and without 1, providing evidence for competition between the pathways in young shoots, but not in older leaves or seeds. Furthermore, levels of 1 and 2 were moderate to high compared with their respective alkaloid classes in other grass-Epichloë symbiotic systems. We conclude that production of the alkaloids likely represents an important metabolic investment by E. brachyelytri.IMPORTANCEDefensive mutualisms, symbioses of hosts with organisms that defend them against parasites or predators, play important ecological roles. A widespread example is protection of cool-season grasses by symbiotic Epichloë species, which are fungi that transmit in seeds and produce several kinds of anti-insect alkaloids. Profiles of alkaloids evolve due to shifting balances of their benefits and the costs of producing them. In this study, Epichloë brachyelytri symbiotic with the wild forest grass Brachyelytrum erectum produced three alkaloids, of which two have been rarely reported. Furthermore, variations in its alkaloid profiles and quantities of each alkaloid at different plant growth stages and tissues suggested that occasional loss of its most abundant alkaloid can be adaptive due to the metabolic load of producing it. Although rare, similar alkaloid profiles were identified in several other species in which they arose by a combination of convergent evolution, possible horizontal gene transfer, and interspecific hybridization.},
}

@article {pmid42599638,
year = {2026},
author = {Abd-Alazeez, RA and Al-Janabi, SS and Mashaan, AO},
title = {Adaptive Evolution in Aminoacyl-tRNA Synthetases Drives Antibiotic Tolerance and Resistance in Clinical Klebsiella pneumoniae Isolates.},
journal = {Molecular biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42599638},
issn = {1559-0305},
abstract = {Klebsiella pneumoniae is a major global health threat due to the rapid spread of antimicrobial resistance (AMR), which severely limits treatment options. Although horizontal gene transfer of mobile genetic elements is a key driver of multidrug resistance, this study explores how adaptive evolution within the core genome may also contribute to the clinical success of resistant strains. Using whole-genome sequencing-based pangenome analysis of clinically relevant classical K. pneumoniae isolates, we identified 3159 variants distributed across 414 core genes, indicating that even highly conserved cellular functions accumulate mutations in clinical environments. Functional enrichment analysis revealed a significant concentration of mutations in the aminoacyl-tRNA synthetase (aaRS) pathway, a central component of protein synthesis and a known antibiotic target. Multiple missense variants were detected in eight aaRS genes, with the Asn366Asp mutation in metG present in all analyzed isolates. We hypothesize that this conserved, recurrent mutation may contribute to bacterial adaptation, potentially by modulating protein synthesis, although this proposed mechanism remains speculative and requires experimental validation. Recurrent mutations were also observed in ileS and leuS, both targets of existing antimicrobials, while a Ser480Pro mutation in pyrG (CTP synthase) was identified in several isolates. Overall, these findings highlight core genome variation as a potential contributor to antimicrobial resistance in K. pneumoniae and suggest that conserved mutations such as metG Asn366Asp may represent candidate genomic biomarkers warranting further investigation. Because this study is based solely on comparative genomics, the proposed functional and mechanistic interpretations should be regarded as hypotheses for future experimental testing.},
}

@article {pmid42603017,
year = {2026},
author = {DeZoysa, AR and Edison, LK and Denagamage, T and Pellissery, AJ and Bommineni, YR and Satharasinghe, D and Coiner, D and Simon, D and Tomson, K and Kariyawasam, S},
title = {Cross-species genomic analysis of Salmonella enterica subspecies enterica serovar Dublin isolated from dairy cattle, dogs, and humans in Florida from 2019 to 2024.},
journal = {One health (Amsterdam, Netherlands)},
volume = {23},
number = {},
pages = {101536},
pmid = {42603017},
issn = {2352-7714},
abstract = {Salmonella enterica serovar Dublin (S. Dublin) is a cattle-adapted pathogen that can cause severe systemic infections in humans and animals. Understanding genomic relatedness across host species is essential for assessing the zoonotic potential and dissemination of antimicrobial resistance (AMR). In this study, 78 clinical S. Dublin strains, isolated in Florida between 2019 and 2024, were subjected to comparative genomic analysis. These included 19 animal-derived isolates (17 from dairy cattle and two from dogs) and 59 human-derived isolates. AMR gene profiling revealed widespread multidrug resistance, with genes conferring resistance to aminoglycoside (aac(6')-Iaa, aph(6)-Id), tetracycline (tetA), and sulfonamide (sul2) detected in all isolates. Beta-lactamase genes, particularly bla TEM variants, were detected more frequently in human- and dog-derived isolates than in cattle-derived isolates. In contrast, rare bla CMY variants (bla CMY-61, bla CMY-130, bla CMY-153, and bla CMY-2b) were detected in only one cattle isolate. Plasmid analysis revealed that IncX1, IncFII(S), and IncC replicons were common among the isolates, highlighting their potential role in facilitating AMR dissemination via horizontal gene transfer. Virulence gene profiling revealed conserved Salmonella pathogenicity islands, type III and type VI secretion systems, and the spv operon across S. Dublin isolates from all host species. Multilocus sequence typing (MLST) confirmed that all isolates belonged to sequence type (ST) 10, and most harbored the Gifsy-2 prophage. The SNP-based phylogeny revealed distinct host-associated clades as well as mixed-host clusters, demonstrating close genomic relatedness among isolates from different host species and suggesting possible cross-species transmission, exposure to shared sources, or circulation of closely related lineages. These findings illustrate the interconnectedness of animal and human S. Dublin infections, emphasize the importance of responsible antimicrobial use, and highlight the value of genomic surveillance for detecting and controlling S. Dublin infections. Collectively, this study provides a genomic framework for assessing cross-species relatedness, virulence characteristics, and AMR patterns of S. Dublin.},
}

@article {pmid42605760,
year = {2026},
author = {Wang, R and Xu, Y},
title = {Prevalence and Molecular Characterization of Aminoglycoside Resistance Genes Among Drug-Resistant Pseudomonas aeruginosa Clinical Isolates in Chinese Hospital.},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {10766294261478179},
doi = {10.1177/10766294261478179},
pmid = {42605760},
issn = {1931-8448},
abstract = {BACKGROUND: Pseudomonas aeruginosa is a major cause of nosocomial infections, with increasing multidrug resistance complicating treatment outcomes. Aminoglycosides remain a cornerstone for managing P. aeruginosa infections, but resistance is escalating globally. This study investigates the prevalence of aminoglycoside resistance and the molecular basis of resistance, focusing on aminoglycoside-modifying enzyme (AME) and 16S rRNA methylase genes in P. aeruginosa clinical isolates from Anhui, China.

METHODS: A total of 354 non-duplicate P. aeruginosa isolates were collected from three tertiary hospitals between January 2023 and December 2024. Antimicrobial susceptibility was determined using the agar dilution method. Whole-genome sequencing and polymerase chain reaction (PCR) were employed to identify AMEs and 16S rRNA methylase genes. Statistical analyses assessed resistance profiles and gene-phenotype associations.

RESULTS: Aminoglycoside resistance was observed in 63% (222/354) of isolates, with resistance rates highest for streptomycin (60.2%), amikacin (56.1%), kanamycin (55.3%), and tobramycin (45.3%). The most prevalent AME gene was aac(6')-Ib9 (32.3%), followed by aph(3')-IIb (25.5%), aac(6')-IIa (20.8%), and ant(2″)-Ia (11.2%). The 16S rRNA methylase genes rmtB (4.4%) and armA (5.1%) were detected. Resistance genes were often associated with mobile genetic elements, suggesting horizontal gene transfer.

CONCLUSION: The high prevalence of aminoglycoside resistance, driven by diverse AMEs and 16S rRNA methylase genes, highlights the urgent need for enhanced antimicrobial stewardship, molecular surveillance, and infection control measures in Chinese hospitals to mitigate the spread of resistant P. aeruginosa.},
}

@article {pmid42595271,
year = {2026},
author = {Domingues, CPF and Rebelo, JS and Dionisio, F and Nogueira, T},
title = {Drivers of antimicrobial resistance gene clustering in plasmids: distribution, host clinical relevance, and plasmid mobility.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107964},
doi = {10.1016/j.ijantimicag.2026.107964},
pmid = {42595271},
issn = {1872-7913},
abstract = {Plasmids play a central role in the dissemination of antimicrobial resistance genes (ARGs) through horizontal gene transfer. However, the extent to which different resistance determinants are associated and how these associations vary with plasmid mobility and bacterial host context remains poorly understood. Here, we analysed more than 52,000 complete bacterial plasmids to investigate pairwise co-occurrence patterns among ARGs conferring resistance to 28 antibiotic classes. We found that non-random ARG associations are widespread, with more than half of all detected resistance-class combinations occurring more frequently than expected. Conjugative plasmids exhibited substantially more co-occurrences than mobilizable or non-transmissible plasmids, consistent with their prominent role in horizontal gene transfer. Although most ARG combinations are present in plasmids from both ESKAPEE pathogens and non-ESKAPEE species, several associations differed significantly in prevalence between the two groups. Among all resistance classes, tetracycline resistance genes showed the broadest spectrum of associations, whereas nitroimidazole resistance genes occurred exclusively in isolation. Together, these findings reveal that ARG co-occurrence in plasmids is structured rather than random and is strongly associated with both plasmid mobility and host context, providing new insights into the evolutionary organization of multidrug resistance.},
}

@article {pmid42595398,
year = {2026},
author = {Yin, Z and Li, J},
title = {Co-application of pan-genomics and machine learning uncovers novel insights into the maintenance and evolution of microcystins production trait in Microcystis.},
journal = {Harmful algae},
volume = {158},
number = {},
pages = {103128},
doi = {10.1016/j.hal.2026.103128},
pmid = {42595398},
issn = {1878-1470},
mesh = {*Microcystins/genetics/biosynthesis/metabolism ; *Microcystis/genetics/metabolism ; *Machine Learning ; Genomics ; Phylogeny ; Evolution, Molecular ; Genome, Bacterial ; Gene Transfer, Horizontal ; Multigene Family ; },
abstract = {Microcystins (MCs), the potent hepatotoxins produced by toxic strains of Microcystis and other cyanobacteria, pose a major threat to freshwater ecosystems worldwide. However, the regulatory mechanisms, evolutionary origin, and maintenance of this energy-intensive toxigenicity remain largely unresolved. Based on 132 non-redundant Microcystis strains, this study combined pan-genomics analysis, phylogenetic reconstruction, pan-genome-wide association analysis and machine learning approaches to investigate the regulatory and evolutionary basis of MCs production. Results suggest that MCs production likely originated as an ancestral trait in Microcystis, while secondary horizontal gene transfer (HGT) and homologous recombination across the MCs biosynthesis-related (mcy) gene cluster and its flanking regions might have contributed to its distribution among polyphyletic lineages. Enrichment analysis further indicated distinct metabolic strategies between toxic and non-toxic Microcystis strains. Toxic strains are enriched in secondary metabolism, whereas non-toxic strains prioritize core metabolic pathways. Through co-occurrence analysis and multi-method screening, this study identified a candidate type II toxin-antitoxin (TA) system (TumE-TumA) that may be synergistically associated with mcy gene cluster. Structural and energetic analyses predicted a potential interaction between the TumE-family toxin protein and mcyA RNA (ΔiG= -44.6 kcal/mol), suggesting its potential regulatory role in MCs biosynthesis. Taken together, these findings support a proposed co-evolutionary framework in which secondary HGT may contribute to the phylogenetic distribution of mcy gene cluster, while the TA system may form a synergistic network with mcy gene cluster, contributing to the maintenance and evolution of MCs production by balancing metabolic costs with ecological benefits. While these in silico predictions require experimental validation, they provide new insights into the adaptive evolution of cyanobacterial toxigenicity and inform future strategies for managing harmful algal blooms.},
}

*Microcystins/genetics/biosynthesis/metabolism
*Microcystis/genetics/metabolism
*Machine Learning
Genomics
Phylogeny
Evolution, Molecular
Genome, Bacterial
Gene Transfer, Horizontal
Multigene Family

@article {pmid42597922,
year = {2026},
author = {Rahman, MS and Wakeman, CA},
title = {Antibiotic resistance in Pseudomonas aeruginosa: mechanisms, diagnostic challenges, and omics-based diagnostic solutions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1791577},
pmid = {42597922},
issn = {1664-302X},
support = {R01 AI173686/AI/NIAID NIH HHS/United States ; },
abstract = {Pseudomonas aeruginosa is considered a multidrug resistant opportunistic pathogen associated with severe infections in immunocompromised patients. Owing to its diverse intrinsic and adaptive resistance strategies, as well as its capacity for horizontal gene transfer, P. aeruginosa represents a major contributor to the global antimicrobial resistance burden. Its remarkable ability to evade antibiotics arises from a wide range of mechanisms, including efflux pumps overexpression, porin modification, enzymatic inactivation and target site modifications, alongside phenotypic adaptations such as biofilm and persister cell formation. These complex resistance strategies of the organism have fueled the global emergence of multidrug resistant, extensively drug resistant and even pan drug resistant strains. These strains significantly complicate the treatment strategies. Conventional culture-based diagnostics are still considered the gold standard, yet their delays and limitations in detecting heteroresistance and biofilm-associated tolerance hinder timely therapeutic intervention. Recent advances in omics-based approaches, including genomics, epigenomics, transcriptomics, proteomics, lipidomics, metabolomics, and phenomics, provide powerful alternatives for rapid and precise identification of resistant P. aeruginosa. In parallel, innovative diagnostic platforms such as microfluidic lab on chip systems and machine learning driven artificial intelligence further enhance diagnostic resolution. Therefore, multi omics integration, coupled with advanced platforms would be a revolutionary strategy to deliver comprehensive and rapid resistance profiling in precision diagnostics. To convert this potential into practice, proper planning, standardized protocols, clinical validation and cost-effective implementation are urgently needed. Together, these advancements pave the way toward outpacing resistance in P. aeruginosa and reducing the global burden of antimicrobial resistance.},
}

@article {pmid42597927,
year = {2026},
author = {Agboola, OE and Agboola, SS and Olasehinde, OR and Aribigbola, TC and Shaleye, AB and Adefolake Alebiosu, I and Oyinloye, BE and Omotuyi, IO and Oyebamiji, AK and Fakoyede, OT},
title = {PlasmidRiskNet: An explainable machine-learning framework for antimicrobial resistance plasmid risk stratification.},
journal = {New microbes and new infections},
volume = {73},
number = {},
pages = {101823},
pmid = {42597927},
issn = {2052-2975},
abstract = {BACKGROUND: Plasmids are the principal vehicles of horizontal antimicrobial resistance (AMR) gene transfer, yet risk analyses rarely combine gene content, mobility, and network topology. We asked whether explainable machine learning over these dimensions can stratify plasmid dissemination risk, and tested rigorously where it succeeds and fails.

METHODS: From 72,556 PLSDB 2025 plasmids we integrated 251,138 AMRFinderPlus gene records with CARD v3 ontology and MOBsuite typing, built a co-resistance network, and derived a composite PlasmidRisk score from five features. Three classifiers were evaluated by five-fold cross-validation; external validation used WHO and ECDC 2024 to 2025 carbapenemase designations as a feature-independent reference. We added length- and host-adjusted burden models, phylum-normalized enrichment, and feature-category ablation.

RESULTS: AMR genes occurred in 41.0% of plasmids across 85 drug classes. The network (29,758 nodes) was heterogeneous rather than scale-free. Internal cross-validation AUCs exceeded 0.999, but because labels derived from the scored features this reflects internal consistency, not generalization. The feature-independent external AUC was modest (0.607): strong for the metallo-beta-lactamases bla NDM, bla VIM, and bla IMP (0.72 to 0.73) but at or below chance for bla KPC and bla OXA-48 (0.45 to 0.51). The conjugative burden advantage did not survive adjustment for length and host phylum (adjusted incidence rate ratio 0.93), with length dominant.

CONCLUSIONS: PlasmidRiskNet offers a useful pre-screening layer for MBL-bearing plasmids but not for the compact serine-carbapenemase backbones (bla KPC, bla OXA-48), which require replicon typing. Honest external and confounder-adjusted evaluation, not internal metrics, defines its class-specific surveillance value.},
}

@article {pmid42594086,
year = {2026},
author = {Nemidkanam, V and Ahmed, R and Chaichanawongsaroj, N},
title = {Identification of high-risk extended-spectrum β-lactamase-producing Escherichia coli clones harboring tet(X4) along the pork supply chain in central Thailand.},
journal = {PloS one},
volume = {21},
number = {8},
pages = {e0355459},
pmid = {42594086},
issn = {1932-6203},
mesh = {Animals ; *Escherichia coli/genetics/isolation & purification/drug effects/enzymology ; Thailand ; *beta-Lactamases/genetics/metabolism ; Swine ; Phylogeny ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli Infections/microbiology ; Whole Genome Sequencing ; Polymorphism, Single Nucleotide ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The global dissemination of antimicrobial-resistant (AMR) bacteria along the pork supply chain is a critical concern, as pigs are significant reservoirs for multidrug-resistant (MDR) Escherichia coli, a WHO-listed priority pathogen. This study investigated the genomic characteristics of extended-spectrum β-lactamase (ESBL)-producing E. coli across the pork production chain in Central Thailand, specifically focusing on the emergence of the last-resort tigecycline resistance gene, tet(X4). ESBL-producing E. coli isolates from a slaughterhouse pig cecum (n = 14) and retail market pork (n = 26) in central Thailand were collected. Whole-genome sequencing (WGS) was employed to analyze the resistome, virulome, and phylogenomic relationships. Analysis included non-metric multidimensional scaling (NMDS) of resistance and virulence gene determinants, single-nucleotide polymorphism (SNP) phylogeny, and core genome MLST (cgMLST). Resistome, virulome, and NMDS analysis demonstrated a shared clustering of antimicrobial resistance genes (ARGs) and virulence factors (VF) genes between cecum and pork isolates. Most isolates possessed extraintestinal pathogenic E. coli (ExPEC)-associated VF genes, underscoring the widespread pathogenic risk. tet(X4) was predominantly found in the dominant ST48 clone and these tet(X4) adjacent to ISCR2, providing evidence of horizontal gene transfer (HGT). cgMLST further demonstrated that these tet(X4) isolates are genetically related to global human, animal, and environmental strains. This study provides the first genomic evidence of tet(X4) circulation in ESBL-producing E. coli population across the slaughterhouse-to-retail continuum in central Thailand. Our findings suggest that the dissemination of tet(X4) in the pork supply chain is primarily via HGT. The implementation of firm food safety policies and enhanced hygiene practices is urgently required to inhibit the transmission of these high-risk strains to consumers.},
}

Animals
*Escherichia coli/genetics/isolation & purification/drug effects/enzymology
Thailand
*beta-Lactamases/genetics/metabolism
Swine
Phylogeny
Drug Resistance, Multiple, Bacterial/genetics
Escherichia coli Infections/microbiology
Whole Genome Sequencing
Polymorphism, Single Nucleotide
Anti-Bacterial Agents/pharmacology

@article {pmid42584072,
year = {2026},
author = {Eiler, A},
title = {Rethinking evolutionary inference in metagenomic time series.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0069326},
doi = {10.1128/msystems.00693-26},
pmid = {42584072},
issn = {2379-5077},
abstract = {As ecologists increasingly use metagenomic time series to track evolution in the wild, there is a risk of misinterpreting ecological dynamics as rapid adaptation. This Perspective identifies methodological limitations that generate misleading signatures of microbial evolution. A primary issue is confusing evolutionary change (driven by de novo mutation or horizontal gene transfer) with ecological lineage turnover, such as seasonal oscillations or the reactivation of dormant lineages. Current metagenome-assembled genomes can collapse micro-diverse lineages and decouple adaptive mobile elements, creating inaccurate genomic signatures of sweeps or stasis. To address these issues, I propose a framework integrating long-read sequencing, pangenome graph theory, and forward-time simulations to model populations as temporal genetic networks and better resolve microbial evolutionary dynamics.},
}

@article {pmid42584101,
year = {2026},
author = {Yu, D and Zhang, L and Agu, D and Gao, N and Xiao, Y and Zhang, M and Zhang, J and Yan, J},
title = {Temporal succession of microbiomes and resistomes during buried rat carcass decomposition.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0043726},
doi = {10.1128/msphere.00437-26},
pmid = {42584101},
issn = {2379-5042},
abstract = {Burial is a prevalent approach for disposing of human and animal carcass. Carcass decomposition is a key natural disturbance that reshapes microbial communities and modulates biogeochemical cycles. Animal intestines serve as critical natural reservoirs of antibiotic resistance genes (ARGs), and carcass decomposition concurrently remodels intestinal bacterial assemblages and resistome profiles. Most previous studies have characterized microbial succession in surface-exposed carcasses, yet the coordinated temporal shifts of intestinal microbiota, resistomes, and horizontal gene transfer (HGT) signatures within buried carcasses remain underexplored. We established a buried rat carcass model and performed metagenomic sequencing to characterize temporal dynamics of intestinal bacteria, ARGs, mobile genetic elements (MGEs), and HGT events. Bacterial communities underwent directional succession accompanied by reduced α-diversity and stage-specific β-diversity. Proteobacteria gradually outcompeted Firmicutes and Bacteroidetes to become dominant taxa. The resistome followed regular temporal changes: tetracycline and macrolide-lincosamide-streptogramin (MLS) ARGs prevailed in early decomposition, while multidrug, β-lactam, polymyxin, and quinolone ARGs accumulated in mid-late stages, with ARG richness peaking on day 28. Approximately 83% of temporally dynamic ARG subtypes were positively correlated with decomposition duration. Procrustes analysis (R[2] = 0.859) revealed strong correlations between bacterial succession and resistome dynamics, with Proteobacteria as potential multidrug-resistant hosts and major HGT donors. This study identifies a correlative cascade of microbial succession that drives MGE functional shift, which in turn increased HGT potential and ultimately leads to resistome accumulation in buried carcass intestinal habitats. These findings expand the theoretical framework of disturbance-driven microbial-resistome co-succession and offer insights into drivers of antibiotic resistance propagation in terrestrial cadaver systems.IMPORTANCEAnimal carcass burial is a ubiquitous natural terrestrial disturbance, and carcass intestinal contents represent a major endogenous reservoir of environmental antibiotic resistance genes (ARGs). Although extensive research has characterized microbial succession of exposed carcasses, the co-occurrence patterns of gut microbiome and resistome together with associated horizontal gene transfer (HGT) under buried conditions remain underexplored. Using metagenomic profiling of decomposing rat intestinal feces, this study explores a potential correlative cascade spanning bacterial succession, mobile genetic element (MGE) functional shifts, increased HGT potential, and gradual ARG enrichment. Our findings expand the ecological data set focused on subsurface buried carcass habitats and advance mechanistic knowledge of coupled microbiome-resistome succession driven by postmortem decomposition.},
}

@article {pmid42586007,
year = {2026},
author = {López-Cañizares, J and Truchado, P and Macrì, M and Cobo-Díaz, JF and Álvarez-Ordóñez, A and Bonetta, S and Allende, A},
title = {Water reuse within a circular economy: Long-read metagenomics reveals distinct residual resistome profiles across full-scale wastewater-reclamation systems in Murcia, Spain.},
journal = {Chemosphere},
volume = {411},
number = {},
pages = {145063},
doi = {10.1016/j.chemosphere.2026.145063},
pmid = {42586007},
issn = {1879-1298},
abstract = {Water reuse is a key pillar of circular economy strategies, particularly in water-scarce regions, by preserving freshwater resources and supporting agricultural production. Current regulations promote the use of reclaimed water for irrigation, placing wastewater treatment plants (WWTPs) at the center of this transition. However, emerging risks related to antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) challenge the safety of reuse as these determinants may persist after treatment. This study evaluated the effectiveness of ozonation, sodium hypochlorite, UV-C irradiation, and membrane bioreactor (MBR) systems in reducing ARGs in effluents from the Region of Murcia (Spain) across five sampling campaigns between 2023 and 2024. Metagenomic sequencing identified ARGs associated with 17 antibiotic classes, with macrolide-, β-lactam-, and tetracycline-ARGs dominating. Total ARG abundance was lower in treated effluents than in influents, with the greatest percentage reduction in MBR system, although based on only two effluent samples. Selected macrolide-, sulfonamide-, tetracycline- and β-lactam-ARGs nevertheless remained detectable after treatment, with distinct gene-specific profiles among the wastewater-reclamation systems. Effluent samples differed in the taxonomic composition of ARG-carrying reads and in the detection of ARGs putatively co-localized on mobilome associated contigs. These findings show that total ARG reduction alone does not fully characterize wastewater-reclamation performance because substantial decreases in total ARG burden were accompanied by different residual resistome profiles. Combining ARG abundance, identity, potential hosts, and genomic context enables a fuller assessment of reclaimed-water treatment. These metagenomic associations indicate potential persistence and mobility but do not constitute direct evidence of horizontal gene transfer or quantitative environmental risk.},
}

@article {pmid42589394,
year = {2026},
author = {Wiser, MF},
title = {Origins and Molecular Features of a Chimeric Type-P4A ATPase-Guanylate Cyclase from Stramenopiles and Alveolates.},
journal = {International journal of molecular sciences},
volume = {27},
number = {15},
pages = {},
pmid = {42589394},
issn = {1422-0067},
mesh = {*Guanylate Cyclase/genetics/chemistry/metabolism ; Phylogeny ; Evolution, Molecular ; Amino Acid Sequence ; *Adenosine Triphosphatases/genetics/chemistry/metabolism ; Models, Molecular ; Sequence Alignment ; },
abstract = {A chimeric protein produced from the fusion of a type-P4 ATPase, also called flippase, and a guanylate cyclase (P4GC) was originally described in ciliates and malaria parasites. An extensive search for P4GC homologs was carried out, and the protein's structural features were determined by sequence alignments and homology modeling. P4GC is found in all alveolate lineages and in some stramenopile lineages. This suggests that the gene fusion event occurred in a common ancestor of stramenopiles and alveolates after the divergence of rhizarians, although alternative evolutionary scenarios cannot be excluded. This scenario necessitates the subsequent loss of P4GC in some stramenopile lineages. Alternatively, the gene fusion may have arisen in an early alveolate lineage and subsequently been transferred horizontally to an ancestor of oomycetes and bicosoecids, or vice versa. The sequence homology of the flippase module is not well preserved in some lineages, whereas the structure and sequence homology of the cyclase module is highly conserved in all lineages. These findings suggest that the cyclase module has been subject to stronger evolutionary constraints than the flippase module, while the latter may have undergone lineage-specific functional diversification. However, despite sequence divergence, homology modeling indicates that the predicted 3-dimensional structures of the flippase modules are highly conserved across all lineages, suggesting that structural constraints have preserved its functional role(s) within P4GC. Together, these findings indicate that P4GC has undergone lineage-specific functional diversification while maintaining a highly conserved guanylate cyclase module throughout alveolate and stramenopile evolution.},
}