@article {pmid41768604,
year = {2026},
author = {Revilla-Guarinos, A and Camelo Castillo, A and Cebrián, R and Ferrer, MD and López-López, A and Adrados-Planell, A and Lahoz Oliva, S and Ledesma, L and Hols, P and Mira, Á},
title = {Streptococcus dentisani 7746 encodes a cocktail of 14 bacteriocins associated with Com and Blp-like quorum sensing regulatory systems.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2633915},
pmid = {41768604},
issn = {2000-2297},
abstract = {AIM: We explored in silico and in vitro the complete bacteriocin profile of the oral probiotic Streptococcus oralis subsp. dentisani strain 7746 with the primary objective of providing a descriptive analysis of bacteriocin genomic organization, regulatory context, and transcriptional expression.

METHODS: The recently closed genome of 7746 was subjected to genome mining searches for bacteriocin biosynthetic gene clusters with BAGEL4 and antiSMASH. Orthology conservation analyses were performed to distinguish between bacteriocin-like peptides (Blp) and competence (Com) related peptides. We assessed bacteriocins' transcription by non-quantitative cross-gene RT-PCR.

RESULTS: Three new bacteriocin-coding genes were identified, which increased to 14 the number of bacteriocins encoded by S. dentisani 7746. We proved that all 14 identified bacteriocins are transcriptionally expressed. We have assigned names to bacteriocins with unnamed orthologs in other species, proposing the name Denticins (from Denticin A to Denticin H). Our analysis led us to propose a model for competence and bacteriocin regulation in this strain, ruled by complete sets of Com and Blp-like quorum sensing systems.

CONCLUSION: Our results suggest that S. dentisani 7746 is the bacterial isolate with the largest repertoire of bacteriocin genes known to date and that part of its blp-like region might have been acquired by horizontal gene transfer from pneumococci.},
}

@article {pmid41765576,
year = {2026},
author = {Diniz, MN and Canellas, ALB and Brunelli, RC and Laport, MS},
title = {Hotspots of antimicrobial resistance and horizontal gene transfer among gram-negative bacteria in water and plastic samples from recreational waters.},
journal = {Journal of environmental sciences (China)},
volume = {162},
number = {},
pages = {754-762},
doi = {10.1016/j.jes.2025.08.007},
pmid = {41765576},
issn = {1001-0742},
abstract = {Antimicrobial resistance is a growing concern for global health and anthropogenic activities have accelerated the spread of resistant bacteria to alarming levels. This study aimed to isolate and identify bacteria from water and floating plastic collected in a polluted recreational estuary, the Bom Jesus Cove in Guanabara Bay, Rio de Janeiro (Brazil). Overall, 36 water samples and 10 plastic samples were collected over one year, among which potential pathogens such as Klebsiella pneumoniae and Escherichia coli were found. The presence of antimicrobial resistance genes, particularly those conferring resistance to beta-lactams and colistin, as well as integron-integrase genes was evaluated. The blaKPC gene, which encodes the K. pneumoniae carbapenemase (KPC), was detected in 7.6 % of the investigated strains, among which 70.6 % were also positive for the expression of carbapenemases and were submitted to antimicrobial susceptibility testing. Mobile colistin resistance genes, including mcr-9 and mcr-3, were detected in 9.0 % of the tested strains. Of great concern was the detection of mcr variants in extended-spectrum-β-lactamase- and carbapenemase-producing strains, thereby highlighting that resistance to last-resort antimicrobials circulates in the marine environment, notably within common pollutants like plastics. A strain of carbapenemase-producing Kluyvera ascorbata successfully transferred the blaKPC-2 gene to E. coli DH5α. This strain was selected for whole genome sequencing based on its extensive beta-lactam resistance profile, revealing further insights into the mobilization of this clinically relevant resistance gene. These results underscore the importance of unveiling the dynamics of antimicrobial resistance in aquatic environments, pointing to the emergence of high-risk phenotypes that pose a threat to human health.},
}

@article {pmid41765445,
year = {2026},
author = {Dao, DT and Suzuki, M and Kobayashi, Y and Hirabayashi, A and Kasuga, I and Tran, HH and Takemura, T and Abe, H and Hasebe, F and Shibayama, K},
title = {Characterization of Integrative and Conjugative Elements Carrying blaNDM-1 and blaKPC-2 in an Environmental Pseudomonas guariconensis Isolate.},
journal = {Japanese journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.7883/yoken.JJID.2025.255},
pmid = {41765445},
issn = {1884-2836},
abstract = {Urban wastewater is increasingly recognized as a major reservoir of antimicrobial resistance and horizontal gene transfer. From urban wastewater in Hanoi, Vietnam, we isolated a multidrug-resistant Pseudomonas guariconensis strain, KNHN1, resistant to most antimicrobials, including carbapenems and cephalosporins, but susceptible to cefiderocol; and intermediate to colistin. Whole-genome sequencing revealed two chromosomally integrated integrative and conjugative elements (ICEs): ICEPgKNHN1_KPC (131 kb) carrying blaKPC-2 and ICEPgKNHN1_NDM (108 kb), carrying blaNDM-1, both flanked by conserved 18-bp att sites in the tRNA[Gly] loci and encoding MOBH-type relaxases. Polymerase chain reaction and subsequent sequencing confirmed ICE excision from the chromosome and formation of circular intermediates. Conjugation to Pseudomonas putida KT2440 occurred at ~10[-2] frequency, producing transconjugants with ICEPgKNHN1_NDM (~85%), ICEPgKNHN1_KPC (~10%), or both, all showing broad range β-lactam resistance. Comparative analysis indicated that ICEPgKNHN1_NDM has a highly conserved backbone across multiple species and often co-carries blaPME-1 and other resistance genes. To our knowledge, this is the first report of chromosomally integrated blaNDM‑1 and blaKPC‑2 in P. guariconensis mediated by functional ICEs. These findings underscore the pivotal role of environmental bacteria as reservoirs of clinically significant resistance genes, and highlight ICEs as key drivers in the dissemination of carbapenem resistance.},
}

@article {pmid41764388,
year = {2026},
author = {Zhu, K and Amirali, A and Auch, B and Babler, KM and Biswas, P and Bowie, K and Choudhary, S and Currall, BB and Grills, GS and Healy, HG and Liachko, I and Lucaci, AG and Mason, CE and Sharkey, M and Shigeno Risse-Adams, O and Shukla, BS and Sisson, Z and Stevenson, M and Williams, SL and Zulli, A and Peccia, J and Solo-Gabriele, HM},
title = {Proof-of-concept of host attribution of antimicrobial resistance genes using wastewater Hi-C metagenome sequencing.},
journal = {Journal of water and health},
volume = {24},
number = {2},
pages = {148-159},
pmid = {41764388},
issn = {1477-8920},
support = {//4Catalyzer/ ; U01DA053941/DA/NIDA NIH HHS/United States ; P30AI073961/NH/NIH HHS/United States ; },
abstract = {The proliferation of antimicrobial resistance genes (ARGs) poses public health risks globally, with wastewater treatment plants (WWTPs) serving as dissemination hubs for horizontal gene transfer. In this study, we evaluated the potential of applying Hi-C sequencing coupled with metagenomic bioinformatics for surveillance of ARGs and other microbial fitness traits using samples from WWTPs. Hi-C sequencing has the advantage over other molecular approaches by directly associating genes conveying fitness to their host microbe, plus to their element type (in plasmids, phages, or within the core genome of its host microbe). Results from Hi-C analyses confirm results from more laborious approaches by showing that aminoglycoside resistance is disseminated by plasmids. Mercury resistance was found in Zoogloea bacteria. Resistance genes to quaternary ammonium compounds were found within bacteriophages. Results from this study provide proof-of-concept for the potential value of Hi-C metagenome sequencing in wastewater attribution studies by illustrating the breadth of information that can be obtained about the microbial community, the exchange of genes, and their interconnections. We believe that with further development, Hi-C sequencing can be integrated into routine monitoring of wastewater for the purpose of providing near-real-time information about the dissemination of fitness traits, including ARGs.},
}

@article {pmid41764382,
year = {2026},
author = {Vu, K},
title = {Plastics as vectors for pathogens and antibiotic resistance genes in aquatic systems.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {93},
number = {4},
pages = {552-568},
pmid = {41764382},
issn = {0273-1223},
abstract = {The increasing amount of plastics in aquatic systems poses risks to water quality and biodiversity by transporting pathogens and antibiotic resistance genes. This article reviews how plastics spread and persist as vectors for these contaminants. In addition, their attachment, transport, and release mechanisms on plastic surfaces are discussed, underscoring the need for advanced detection and monitoring methods. Future research should focus on developing practical mitigation strategies and policy interventions to address plastic-mediated microbial pollution. Ultimately, this article emphasizes the value of interdisciplinary work to protect aquatic ecosystems and public health from the adverse effects of plastic pollution and proposes potential solutions to address this global challenge.},
}

@article {pmid41762839,
year = {2026},
author = {Wang, C and Wang, P and Zhang, W and Peng, K and Wang, Y and Wang, Z and Li, R},
title = {Comprehensive evaluation of disinfectants on the horizontal transfer of antibiotic resistance genes mediated by SXT integrative conjugative elements.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141504},
doi = {10.1016/j.jhazmat.2026.141504},
pmid = {41762839},
issn = {1873-3336},
abstract = {The global spread of antimicrobial resistance (AMR) is primarily driven by horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) via mobile genetic elements. Disinfectants have been reported to accelerate this process, yet most studies focus on plasmid-mediated ARG dissemination, overlooking the role of integrative and conjugative elements (ICEs). Unlike plasmids, ICEs integrate into chromosomes while retaining transfer ability, making them critical for ARG persistence. Here, we established intraspecific and interspecific conjugation models to systematically evaluate the effects of various disinfectants on SXT ICE conjugative transfer. Phenolic and quaternary ammonium disinfectants showed variable effects across different models, whereas oxidants, guanidines, organic acids, and most halogen‑based disinfectants consistently promoted SXT ICE transfer. We further focused on potassium monopersulfate (PMS) and potassium ferrate (PF), which increased SXT ICE conjugation frequency by at least 1.28‑fold and 1.45‑fold, respectively, across all models. Moreover, PMS and PF enhanced the transfer of SXT ICE into environmentally relevant microbiota (derived from feces, soil, and water) by at least 1.75‑fold and 1.37‑fold, respectively, and altered the community structure of the resulting transconjugants. Mechanistic analysis revealed that PMS and PF triggered the SOS response, leading to the de-repression of SXT ICEs, while also enhancing energy metabolism and disrupting membrane homeostasis. These effects collectively promoted SXT ICE transfer. Our findings suggest that disinfectants could unintentionally accelerate AMR dissemination, underscoring the need for more cautious application strategies.},
}

@article {pmid41762158,
year = {2026},
author = {Wj, WJL and Cheang, R and Taracena, M and Ayub, MJ},
title = {Ancestral Wolbachia lineages are likely donors of ribotoxin genes in Aedes aegypti.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jeb/voag014},
pmid = {41762158},
issn = {1420-9101},
abstract = {Ribosome-inactivating proteins (RIPs) are enzymes that irreversibly inhibit protein synthesis by depurinating a specific adenine residue in the ribosomal RNA. Although members of this gene family are widespread in plants and bacteria, their occurrence in metazoans is rare and restricted to a few insect lineages, including Culicinae mosquitoes. Previous studies suggested that these genes were acquired by mosquitoes via horizontal gene transfer (HGT) from bacteria lineage, but the source lineage remained unidentified. Here, we report the discovery of RIP-encoding genes in two Wolbachia strains. Phylogenetic analyses confirmed the monophyletic relationship between Wolbachia and mosquito RIPs, implying Wolbachia as the donor of these genes. These results shed light on the evolutionary dynamics of RIPs and the dual role of Wolbachia as both a functional contributor and genetic donor. By bridging the gap between endosymbiont and host genomes, this work provides new evidence for HGT as a source of adaptive innovation in insects. The implications of these findings for the ongoing debate on HGT in metazoans are also discussed.},
}

@article {pmid41761781,
year = {2026},
author = {Collins, CF and Alston, BT and Hibdige, SGS and Raimondeau, P and Baker, ER and Sotelo, G and Papadopulos, AST and Christin, PA and Pereira, L and Dunning, LT},
title = {Regulatory features determine the evolutionary fate of laterally acquired genes in plants.},
journal = {Molecular biology and evolution},
volume = {43},
number = {2},
pages = {},
doi = {10.1093/molbev/msag042},
pmid = {41761781},
issn = {1537-1719},
support = {NE/V000012/1//Natural Environment Research Council/ ; NE/T011025/1//Natural Environment Research Council/ ; //University of Sheffield/ ; 947921//MAPAS/ ; URF\R\180022//Royal Society University Research/ ; },
abstract = {Lateral gene transfer (LGT) is widespread in eukaryotes, including in animals and plants where it can fuel adaptive evolution and innovation. However, the factors that influence the integration and long-term retention of transferred genes remain poorly understood. The pangenome of the grass Alloteropsis has a high turnover of laterally acquired genes, and here we combine expression, methylation, and genomic data to identify factors promoting their long-term persistence. Most transferred genes appear to be degenerating, showing lower expression levels and/or greater sequence truncation compared to their vertically inherited homologs. These degenerating genes also show significantly higher levels of DNA methylation, potentially indicating transcriptional silencing. The likelihood of a transferred gene being retained will be influenced by how easily it can be expressed in the recipient genome. In Alloteropsis, putatively functional laterally acquired genes had expression levels significantly more similar to their donor ortholog than to their vertically inherited homolog. Transferred genes carry cis-regulatory elements encoded on the fragment of DNA that moves between species, likely facilitating their expression in the new genomic context. Evolutionary novelty may also increase the likelihood that selection retains a transferred gene. However, only a significant difference in expression level, not sequence divergence, between donor orthologs and vertically inherited homologs is associated with successful lateral gene transfer. Overall, our results show that most transferred genes degrade over time. However, those capable of regulating their own expression are more likely to persist and contribute to long-term evolutionary innovation.},
}

@article {pmid41760775,
year = {2026},
author = {Jie, J and Gu, S and Li, D and Zhang, M and Luo, ZQ and Song, L},
title = {The type VI secretion system of Acinetobacter: mechanisms, biology and therapeutic potential.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {41760775},
issn = {2399-3642},
abstract = {The Type VI secretion system (T6SS) is widely recognized as a contractile nanomachine that mediates interbacterial antagonism, yet its biological roles and evolutionary logic vary substantially across bacterial lineages. In this Review, we synthesize recent advances in the Acinetobacter T6SS field and propose a unifying perspective in which the system functions as a context-dependent fitness module rather than a constitutive virulence weapon. We highlight how Acinetobacter has rewired a single T6SS platform through non-canonical structural solutions, multilayered regulatory integration, and an unusually expansive effector repertoire. Beyond microbial competition, emerging clinical and experimental evidence links T6SS activity to host immune amplification, disease severity, and the dynamics of horizontal gene transfer and antibiotic resistance. By integrating structural biology, regulatory logic, effector function, and clinical observations, this Review reframes the Acinetobacter T6SS as an adaptable system that balances aggression, persistence, and metabolic cost in polymicrobial and host-associated environments. This perspective not only advances conceptual understanding of T6SS diversity but also highlights translational opportunities for diagnostics, vaccines, and anti-virulence strategies targeting multidrug-resistant Acinetobacter infections.},
}

@article {pmid41759977,
year = {2026},
author = {Jing, K and Li, Y and Li, Y and Meng, Q and Zhang, J and Guan, Q},
title = {Migration of antibiotic resistance genes in process of biodegradation of sulfonamide antibiotics in biofilm-sediment: Mechanisms, microbial communities, and driving factors.},
journal = {Bioresource technology},
volume = {448},
number = {},
pages = {134286},
doi = {10.1016/j.biortech.2026.134286},
pmid = {41759977},
issn = {1873-2976},
abstract = {The main removal pathway of sulfonamide antibiotics (SAs) in biofilm-sediment system is biodegradation, which not only promotes the enrichment of drug-resistant bacteria, but its metabolic intermediates also promote the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Since the biofilm-sediment multiphase system is closer to characteristics of the natural aquatic environment, the study of the dynamic migration process of ARGs in this system can reveal the propagation patterns of ARGs more realistically. Therefore, this study investigated the migration characteristics of ARGs and their driving mechanisms during the biodegradation of SAs in the biofilm-sediment system. The results showed that the migration of ARGs exhibited obvious stratification characteristics: the abundance of ARGs in the surface biofilm fluctuated in synchrony with the degradation of SAs, the HGT mediated by mobile genetic elements (MGEs) in middle sediments enabled the cross-layer migration and accumulation of ARGs, while deep sediments were limited in migration due to hypoxia and pore barriers. Changes in the bacterial community also facilitated the migration of ARGs, with the proliferation of host bacteria dominating the surface layer and the formation of a composite transfer system of "host bacteria-ARGs-MGEs" in the middle layer. The multivariate statistical analysis model confirmed that the synergistic effects of bacterial abundance, MGEs and environmental factors contributed 95-99% to the migration of ARGs in the surface and middle layers, with pH being the strongest positive regulator. These results demonstrated that the migration of ARGs is closely related to the degradation process of pollutants.},
}

@article {pmid41759554,
year = {2026},
author = {Dai, X and Liu, H and Bai, X and Li, D and Wang, T and Zhong, H and Xu, H and Sun, J},
title = {Insights into antibiotic resistomes from gut metagenome-assembled genomes of the free-range pigs.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0240725},
doi = {10.1128/spectrum.02407-25},
pmid = {41759554},
issn = {2165-0497},
abstract = {The pig gut microbiome serves as a reservoir for antibiotic resistance genes (ARGs), which pose a threat to public health and environmental safety. To investigate the presence of ARGs carried by free-range pigs, which have frequent contact with humans and their environment, we characterized the resistome of the pig gut microbiome through metagenomic sequencing of fecal samples from 120 pigs across four provinces in China (Yunnan, Guizhou, Sichuan, and Jiangsu). By constructing metagenome-assembled genomes (MAGs) and gene catalogs, we explored the microbial community structure and ARG distribution. Our analysis revealed a highly diverse array of ARGs, particularly those conferring resistance to multidrug, glycopeptide, peptide, and tetracycline antibiotics. Bacillota A and Actinomycetota were the dominant phyla across samples. However, notable regional differences in microbiota composition and resistance profiles were observed. These differences were likely influenced by local farming practices and environmental conditions. Guizhou harbored 11 unique ARG types, followed by Sichuan (seven), which showed region-specific resistome signatures. Escherichia coli and other microbial taxa were closely linked with ARG abundance, suggesting potential vectors for horizontal gene transfer. Analysis of mobile genetic elements (MGEs) further supported this, revealing a strong linear correlation between MGE and ARG abundance, with transposase elements particularly associated with multidrug ARGs. These findings highlight the central role of MGEs in ARG dissemination and underscore the need for targeted strategies to curb antibiotic resistance in livestock systems. Regional variation in resistome profiles further emphasizes the influence of local agricultural practices on resistance dynamics.IMPORTANCEThe growing prevalence of antibiotic resistance poses a significant global health threat, making it imperative to trace the origins and transmission routes of ARGs. This study delivers a comprehensive genomic reference for the porcine gut microbiota and clarifies how regional farming practices shape distinct resistome profiles. Integrating these data with analyses of mobile genetic elements and microbial hosts reveals the complex interplay among host, microbiota, and environment, thereby extending current knowledge of the pig gut ecosystem. These findings provide an evidence-based foundation for targeted surveillance and intervention strategies to curb antibiotic resistance in livestock and safeguard public health.},
}

@article {pmid41759320,
year = {2026},
author = {Yin, Y and Wu, H and French, CE and Lu, Z},
title = {Triclosan induced restructuring of microbial communities and antibiotic resistance gene dynamics in activated sludge: insights and mitigation strategies.},
journal = {Water research},
volume = {296},
number = {},
pages = {125614},
doi = {10.1016/j.watres.2026.125614},
pmid = {41759320},
issn = {1879-2448},
abstract = {The widespread presence of emerging contaminants, such as triclosan (TCS), in environmental systems raises significant concerns regarding their ecological risks, particularly the propagation of antibiotic resistance genes (ARGs). In this study, sequencing batch reactors (SBRs) were exposed to a TCS concentration gradient to simulate the accumulation of TCS in activated sludge and to elucidate its effects on microbial community structure, ARG dissemination, and horizontal gene transfer (HGT). Using a multi-omics approach that integrated 16S rRNA amplicon sequencing, short- and long-read metagenomics, and genome-scale metabolic modeling, we demonstrated that increasing TCS concentrations progressively reduced microbial diversity and stability. At lower TCS concentrations (0-1.0 mg/L), ARG-carrying bacteria were enriched, whereas at higher concentrations (10 mg/L), TCS eliminated ARG-carrying bacteria and selected for strains rich in mobile genetic element (MGE). Notably, HGT led to genome expansion of Acidomonas methanolica (from 3.75 Mb to 7.13 Mb), disrupting the microbial interaction networks within the community. Additionally, the introduction of a triclosan-degrading hydrogel-magnetic biochar-engineered strain composite mitigated the destabilizing effects of TCS stress on the microbial community, enhanced its resilience, and facilitated TCS degradation, thus reducing associated environmental risks. Our findings highlight how gradient TCS exposure reshapes microbial communities, promotes the dominance of MGE-enriched taxa, and has profound implications for the ecological and evolutionary dynamics of microbial communities in aquatic ecosystems. This study provides novel insights into the role of emerging contaminants in the propagation of resistance and microbial adaptation.},
}

@article {pmid41758123,
year = {2026},
author = {Gharbi, M and Abbassi, MS},
title = {Ecology and antimicrobial resistance of Campylobacter in wildlife: insights into specialist and generalist lineages and zoonotic potential.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovag031},
pmid = {41758123},
issn = {1472-765X},
abstract = {Wildlife is a critical reservoir of Campylobacter species, particularly C. jejuni and C. coli, carrying diverse genetic lineages, virulence factors, and antimicrobial resistance (AMR) genes. Birds, especially migratory and synanthropic species, are the primary carriers, though mammals, reptiles, and other vertebrates also contribute to maintenance and dissemination. Wildlife-associated strains include both host-specific lineages and generalist clonal complexes (e.g. ST21, ST45, ST828) capable of crossing wildlife, livestock, humans, and environmental interfaces, reflecting high zoonotic potential. Virulence factors, including motility, adhesion and invasion proteins (CadF, CiaB), and cytolethal distending toxin (CDT), facilitate colonization and survival, while efflux pumps and stress-response genes enhance persistence under antibiotic pressure. AMR is widespread, with resistance to fluoroquinolones, macrolides, tetracyclines, and multidrug phenotypes, driven by anthropogenic contamination, environmental reservoirs, and horizontal gene transfer. Key resistance determinants include gyrA mutations, tet(O), erm(B), cmeABC efflux pumps, and β-lactamases. Despite advances, knowledge gaps remain, particularly for non-avian hosts, environmental reservoirs, and resistance mechanisms. A One Health approach integrating microbiology, genomics, ecology, and epidemiology is essential to map transmission pathways, monitor emerging resistance, and guide interventions to reduce the public health impact of zoonotic and antibiotic-resistant Campylobacter.},
}

@article {pmid41757979,
year = {2026},
author = {Zhang, X and Luo, Q and Gong, Z and Yang, H and Chen, X and Wang, B and Yuan, M and Chen, Y and Jia, Y and Guo, S},
title = {Nano-selenium mitigates antibiotic resistance in paddy ecosystems via microbiome remodeling and environmental filtering shifts.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0223125},
doi = {10.1128/aem.02231-25},
pmid = {41757979},
issn = {1098-5336},
abstract = {UNLABELLED: The dissemination of antibiotic resistance genes (ARGs) in paddy ecosystems poses a serious threat to environmental health. A pot experiment was conducted to assess the efficacy of alkyl glycoside-stabilized selenium nanoparticles (AG-SeNPs) in mitigating ARG abundance within the soil, phyllosphere, and rice grains. Functional prediction, null model analysis, variance partitioning, and structural equation modeling were employed to identify ARG hosts, key metabolic pathways, and environmental drivers of ARG dynamics. Results showed that foliar application of AG-SeNPs (30 g ha[-1]) reduced ARGs by 5.13 × 10[6] copies g[-1], 2.28 × 10[7] copies g[-1], and 1.25 × 10[6] copies g[-1] in the rhizosphere soil, phyllosphere, and grains, respectively. TetPA and tetGF were dominant ARGs, predominantly associated with Mariniphaga anaerophila, Sediminibacter magnilacihabitans, and Limnospira fusiformis. ARG attenuation was linked to enhanced ABC transporter activity and suppressed purine metabolism and ribosome function, thereby reducing intracellular antibiotic pressure and limiting ARG expression in soil microbes. In the phyllosphere, activation of two-component systems modulated stress responses and antimicrobial resistance pathways, constraining horizontal gene transfer. Nano-selenium increased heterogeneous selection in the phyllosphere, enhancing deterministic filtering of ARG hosts and restructuring microbial communities. Environmental factors explained 42.81% of ARG variation, wherein selenium accumulation in leaves directly reduced ARG abundance, and soil pH, electrical conductivity, and organic matter indirectly influenced ARG dynamics through microbial community restructuring. These findings highlight that AG-SeNPs mitigate ARGs through an environmentally mediated, microbially driven cascade, offering a promising strategy for antibiotic resistance control in agricultural systems.

IMPORTANCE: The dissemination of antibiotic resistance genes within agricultural soil-plant systems poses a severe threat to food safety and public health. This study demonstrates that foliar application of nano-selenium fertilizer effectively reduces ARG abundance in the soil, phyllosphere, and rice grains. We found that nano-selenium functions not by direct bactericidal action but by beneficially reshaping the microbial communities in both the leaves and soil, thereby suppressing the pathways for ARG transmission. Our findings provide a novel and sustainable strategy to mitigate antibiotic resistance in agricultural ecosystems, potentially reducing the risk of these genes entering the human food chain via rice.},
}

@article {pmid41754427,
year = {2026},
author = {Shah, K and Guo, Y and Adnan, M and Wu, H},
title = {Xanthomonas spp.: Devastating Plant Pathogens and Sustainable Management Strategies.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754427},
issn = {2076-0817},
support = {31960610//National Natural Science Foundation of China/ ; 32160723//National Natural Science Foundation of China/ ; 202304BI090030//Special Science and Technology Mission of Yunnan Province/ ; },
abstract = {The genus Xanthomonas comprises devastating plant pathogens responsible for significant yield losses in globally critical crops such as rice (Oryza sativa L.), citrus (Citrus L. spp.), cassava (Manihot esculenta Crantz), and tomato (Solanum lycopersicum L.). This review synthesizes current knowledge on the molecular mechanisms driving Xanthomonas pathogenicity, including the type III secretion system (T3SS) that translocates effector proteins, transcription activator-like effectors (TALEs) that reprogram host transcription, and extracellular polysaccharides (EPS) that promote biofilm formation and immune evasion, which collectively enable host colonization, immune suppression, and disease progression. Rapid adaptation through genomic plasticity and horizontal gene transfer (HGT) exacerbates challenges in disease management by facilitating evasion of host defenses and environmental stressors. Economically, Xanthomonas spp. inflict billions in annual losses through crop damage, trade restrictions, and eradication efforts, disproportionately affecting resource-limited regions. Emerging antibiotic resistance and climate-driven shifts in pathogen distribution further threaten food security. Sustainable strategies, such as CRISPR-based genome editing to disrupt susceptibility genes, biocontrol agents (e.g., Bacillus and Pseudomonas spp.), and nanotechnology-driven antimicrobials offer promising alternatives to conventional copper-based and chemical controls. This review underscores the urgent need for integrated, climate-resilient management approaches to mitigate the ecological and socioeconomic impacts of Xanthomonas diseases, bridging genomic insights with innovative control measures, to address escalating threats posed by these pathogens in a changing global climate.},
}

@article {pmid41753753,
year = {2026},
author = {Lerner, A and Lieber, AD and Nelson-Dooley, C and Leu, A and Perro, M and Koch, G and Benzvi, C and Smith, J},
title = {Genetically Modified Microorganisms: Risks and Regulatory Considerations for Human and Environmental Health.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753753},
issn = {2076-2607},
abstract = {Advances in affordable genetic engineering have accelerated the creation and large-scale environmental release of genetically modified microorganisms (GMMs). While beneficial applications exist, GMMs may present unique, long-term risks to human and environmental health. Unlike static chemicals, GMMs are biologically active, self-replicating entities capable of rapid mutation and global dispersal. Current regulatory frameworks place responsibility on each country to regulate GMMs, without a clear, coordinated international policy. This review details critical risk scenarios, including horizontal gene transfer to native species and the possible disruption of vital human microbiomes (gut, oral, and infant), which could increase resistance to degradation, promote traits that expand a microbe's range of hosts or ecological niches, and enhance the production of novel metabolites with unexpected biological activity. In soil, GMMs may support the emergence of "super bugs" or destabilize carbon sequestration cycles, potentially impacting climate resilience. Engineered microbial enzymes in the food supply may also act as environmental drivers of autoimmunity. Given the limited understanding of microbial ecology, we propose a decision-based biosafety workflow emphasizing pre-release risk assessment and continuous post-release monitoring. We urge national and international regulators to adopt the precautionary principle to better protect human health and the environment from the potential negative outcomes of GMMs.},
}

@article {pmid41753661,
year = {2026},
author = {Yi, S and Xu, X and Yin, L and He, Z and Wang, X},
title = {Site-Specific Nested Integration of Tn1806 into ICESa2603-Family Integrative and Conjugative Elements in Streptococcus agalactiae.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753661},
issn = {2076-2607},
support = {2025Y0054//the Clinical Research Special Program of Shanghai Municipal Health Commission/ ; },
abstract = {Composite integrative and conjugative elements (ICEs) frequently mediate the co-transfer of multiple antibiotic resistance genes during horizontal gene transfer, but their formation mechanisms remain unclear. This study investigated the site-specific integration of Tn1806 into ICESa2603-family ICEs in Streptococcus agalactiae by conjugation experiments. PCR screening of 161 S. agalactiae clinical isolates identified potential Tn1806-like ICE carriers; whole-genome sequencing was performed to further characterize the macrolide-resistance isolates from this group. PCR detection resulted in 24 carrying Tn1806-like ICEs being found, five of which were macrolide-resistant. Genomic analysis for these five revealed distinct Tn1806-like ICEs (ICESag16, ICESag57, ICESag139, ICESag167, and ICESag220), three of which were found nested within another ICE (ICESpy009, an ICESa2603-family ICE). Conjugation experiments confirmed ICESag167 could integrate into the snf2 (methyltransferase containing a SNF2 helicase domain) of ICESpy009 in recipient cells, generating a composite ICE. Re-conjugation verified the transferability of composite ICE at low frequencies (8.63 × 10[-8]), during which some nested ICESag167 were excised and transferred independently. This work provides first experimental evidence supporting Tn1806 nesting within another ICE as a mechanism for resistance accumulation and mobile element evolution in S. agalactiae. The spread of such composite ICEs may confer multiple forms of resistance to new hosts, challenging infection treatment and raising public health concerns.},
}

@article {pmid41750474,
year = {2026},
author = {Scrascia, M and Tempesta, AA and Cafiso, V and Pazzani, C and Mezzatesta, ML},
title = {Bloodstream Infections Due to Carbapenemase-Producing Escherichia coli: A Comprehensive Review.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41750474},
issn = {2079-6382},
support = {project number P2022RHYTM//This work was supported by the EU funding with the MUR PRIN 2022 PNRR, project number P2022RHYTM, title: "A snapshot of transferable plasmids based on omics and clonal epidemiology in hospital acquired carbapenem-resistant Enterobacterales: a pilot study"/ ; },
abstract = {Background/Objectives: Carbapenemase-producing Escherichia coli (CP-Ec) has emerged as an important contributor to the global crisis of antimicrobial resistance. Although less prevalent than carbapenemase-producing Klebsiella pneumoniae, CP-Ec exhibits marked genomic plasticity, efficient plasmid-mediated dissemination, and increasing involvement in bloodstream infections. This comprehensive review summarizes the global epidemiology, molecular features, treatment options, clonal structure and transmission dynamics of CP-Ec. Particular attention is given to the expanding repertoire of NDM, OXA-48-like, and KPC carbapenemases and their associated plasmid backbones. Key high-risk clones, including ST410, ST167 and ST131, are highlighted as drivers of international spread. Conclusions and Future Directions: CP-Ec bloodstream infections represent a growing clinical challenge, often associated with severe outcomes and limited therapeutic options, particularly for NDM producers. The emergence of treatment failures with last-resort agents further underscores the need for improved management strategies. Strengthened global surveillance, integration of genomic epidemiology, optimized antimicrobial stewardship, and targeted infection control measures are essential to limit the dissemination of CP-Ec and mitigate its impact on human health.},
}

@article {pmid41750413,
year = {2026},
author = {Martins, LB and Carneiro, MT and Vieira-Alcântara, K and Chagas, TPG and Zahner, V},
title = {Silent Waterborne Carriers of Carbapenem-Resistant Gram-Negative Bacilli and Antimicrobial Resistance Genes in Rio de Janeiro's Aquatic Ecosystems.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41750413},
issn = {2079-6382},
support = {E-26/210.982/2021//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ) - Postgraduate Support - Course and Postgraduate Studies/ ; E-26/210.228/2018//FAPERJ/ ; },
abstract = {Background/Objectives: Water pollution caused by human activities disrupts ecosystems and promotes the spread of antimicrobial resistance genes (ARGs), posing a public health threat. This study investigated the presence of resistant Gram-negative bacteria and resistance genes in water from two sites occasionally exposed to domestic and hospital effluents, the Carioca River (CR) and Rodrigo de Freitas Lagoon (RFL), both used for recreation. Methods: Physicochemical parameters and coliform levels were measured. Bacterial isolates were identified by Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) and tested for antimicrobial susceptibility using disk diffusion. The Minimum Inhibitory Concentration (MIC) was determined using the E-test[®] and broth microdilution methods. PCR was used to detect carbapenem resistance and other ARGs from the DNA of bacterial isolates obtained from water samples. Results: CR presented signs of environmental degradation, with low dissolved oxygen and high coliform counts. One Citrobacter braakii isolate showed resistance to all tested antimicrobials, raising concern for untreatable infections. Carbapenem-resistant isolates accounted for 49.4% of the total, harboring blaKPC (20%), blaTEM (5%), blaVIM (5%), and blaSPM (5%). The intl1 gene was found in 10% of isolates, indicating potential horizontal gene transfer. Conclusions: The findings from a one-day sampling reveal the presence of multidrug-resistant bacteria that carry antimicrobial resistance genes in polluted aquatic systems. These highlight the connection between water contamination and antimicrobial resistance. The evidence underscores the urgent need for environmental monitoring and effective management strategies to reduce public health risks.},
}

@article {pmid41749291,
year = {2026},
author = {Haro-Moreno, JM and Díaz-Arinero, E and Aldeguer-Riquelme, B and Rubio-Portillo, E},
title = {Effects of marine heatwaves on the dynamics of marine coastal microbial communities.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00861-3},
pmid = {41749291},
issn = {2524-6372},
support = {CIGE/2022/21//Generalitat Valenciana/ ; },
abstract = {BACKGROUND: Climate change is projected to intensify and prolong marine heatwaves, characterized by abnormally high sea surface temperatures. These events can profoundly alter ecosystem composition and functioning, sometimes triggering mass mortality events. The Mediterranean Sea, due to its semi-enclosed nature, is particularly susceptible to warming, with future climate scenarios predicting a temperature increase of up to 3.8 °C and at least one persistent heatwave annually by 2100. Despite this vulnerability, the effects of marine heatwaves on seawater microbial and viral communities remain poorly understood.

RESULTS: Using microcosm experiments, we examined microbial and viral dynamics under control conditions (20 °C) and two simulated marine heatwaves (MHWs) (23 °C and 25 °C). By the end of the experiment, microbial assemblages in all three conditions were dominated by metagenome-assembled genomes (MAGs) that were not detected in the initial natural sample, indicating the competitive success of rare biosphere taxa over initially abundant species. Virulence factors and antibiotic resistance genes increased in relative abundance throughout the incubation, but such increase was amplified under warming conditions. Temperature also shaped viral strategies, with heatwaves showing a higher percentage of integrated lysogenic viruses compared to control samples. This trend was consistent with observations from natural samples, where lysogenic viruses peaked during warmer months.

CONCLUSIONS: The shift toward lysogeny observed under elevated temperatures may enhance horizontal gene transfer, accelerating the spread of virulence and antibiotic resistance genes. In fact, we observed an increased abundance of these genes in samples under heat stress. These processes could weaken ecosystem resilience, disrupt microbial-driven biogeochemical cycles, and amplify risks to marine and human health. Our study underscores the need to integrate microbial and viral responses into predictions of ocean functioning in a rapidly warming world.},
}

@article {pmid41747947,
year = {2026},
author = {Wang, G and Yan, P and Zheng, B and Zeng, Q and Xing, Q and Hu, J and Wang, M},
title = {Screening and identification of bacterium-derived horizontally transferred genes in the genomes of three Penaeus species.},
journal = {Developmental and comparative immunology},
volume = {},
number = {},
pages = {105575},
doi = {10.1016/j.dci.2026.105575},
pmid = {41747947},
issn = {1879-0089},
abstract = {Horizontal gene transfer (HGT) is a major force shaping genome evolution in both prokaryotes and eukaryotes. In the past decade, numerous horizontally transferred genes from bacteria have been identified in eukaryotic lineages, with a substantial proportion found in arthropods. Shrimp, which are economically important cultured arthropods, maintain intimate associations with bacteria, providing an ideal platform for HGT research. In this study, we analyzed bacterium-derived HGT based on high-quality genomes of Penaeus monodon, Penaeus chinensis, and Penaeus japonicus via homology searches and phylogenetic analysis. Our analysis revealed 19 HGT genes, with 11 identified in P. monodon, 5 in P. chinensis, and 3 in P. japonicus. These candidates show features consistent with post-transfer assimilation in the host genome. Specifically, 84% of the candidates contain annotated introns, consistent with intron acquisition after genomic integration. In addition, most candidates exhibit GC content similar to their host genomes, consistent with post-transfer sequence amelioration. Functional annotation indicates their involvement in metabolism and catalytic activity. Notably, horizontally transferred candidates, such as chondroitinase-AC-like and lantibiotic transporter ATP-binding protein SrtF-like, can be used to test hypotheses regarding horizontally transferred genes' roles in host-microbe interfaces and shrimp immunity. The presence of glycosaminoglycan (GAG) lyase-encoding HGT genes in all three species is consistent with an early acquisition in the penaeid lineage. Collectively, our findings demonstrate that bacterium-derived horizontally transferred genes not only structurally integrate into penaeid shrimp genomes but also provide a curated resource for future comparative analyses and experimental validation relevant to shrimp-microbe interactions and aquaculture.},
}

@article {pmid41747697,
year = {2026},
author = {Jin, L and Li, C and Addou, AM and Zhang, S and Li, H},
title = {Global heavy metal-antibiotic co-pollution: Distribution, ARG co-selection, toxic synergism, and AOPs-mediated remediation with focus on non-radical pathways.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141601},
doi = {10.1016/j.jhazmat.2026.141601},
pmid = {41747697},
issn = {1873-3336},
abstract = {Heavy metal and antibiotic co-pollution has become a global environmental concern due to its persistence, bioaccumulation, and synergistic toxic effects. This review synthesizes key advances in its sources, distribution, toxicity, and remediation. Globally, six typical heavy metals and eight major classes of antibiotic resistance genes (ARGs) exhibit significant spatial heterogeneity: high pollution levels occur in industrialized regions (Asia, Europe, North America) and mineral-rich areas (South America, Africa), with heavy metals driving ARG dissemination via co-selection (reactive oxygen species-induced SOS response and horizontal gene transfer). Toxic interactions between antibiotics and heavy metals (e.g., complexation, sorption competition) further exacerbate ecological risks. Among remediation technologies, advanced oxidation processes (AOPs) stand out, particularly non-radical pathways mediated by Fe(IV)/Fe(V) species, which offer superior selectivity against inorganic interference and synchronous degradation/transformation of co-pollutants. Conventional techniques (adsorption, phytoremediation) are limited by poor adaptability to complex matrices, while AOPs (e.g., persulfate-, ferrate-based systems) show great potential for practical application. This review clarifies the environmental behavior of co-pollution and the core role of non-radical AOPs, providing a scientific basis for efficient pollution control.},
}

@article {pmid41747693,
year = {2026},
author = {Yang, T and Yuan, R and Wang, X and Zhai, L and Dong, X and Chen, H and Guo, Z and Jiao, H and Huang, LZ and Yang, Y and Jia, QQ},
title = {π-conjugated microplastics act as hazard amplifiers of antibiotic resistance through cross-kingdom network engineering.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141592},
doi = {10.1016/j.jhazmat.2026.141592},
pmid = {41747693},
issn = {1873-3336},
abstract = {Microplastics are recognized as environmental vectors for antibiotic resistance genes (ARGs), a role traditionally ascribed to physical mechanisms such as biofilm-enhanced horizontal gene transfer. Here, we uncover a chemistry-driven pathway that fundamentally surpasses the traditional passive vector model. We show that π‑conjugated polystyrene (PS) microplastics serve as powerful chemical hazard amplifyers by specifically concentrating the signaling molecule indole on their surfaces through π-π stacking and electrostatic interactions (binding energy = -128.56 kcal/mol), creating localized interfacial risk hotspots. These hotspots drive the reprogramming of soil microbiomes, as evidenced by distinct transformations in dissolved organic matter (DOM), and promote a cross-kingdom microbial alliance centered on the keystone fungus Pseudeurotium. This fungal hub transmits the amplified indole signal to bacterial degraders, markedly elevating the dissemination risk of clinically relevant ARGs (e.g., sul2). Through an integration of molecular simulations, multi-omics analyses, and causal modeling, our structural equation modeling (SEM) identifies the amplified indole signal as the primary direct driver of ARG abundance (path coefficient β = 0.47)-an effect 23.5 times greater than that of the PS polymer itself. Our findings establish "Chemical Interfacial-Driven Network Engineering (CIDNE)" as a pivotal mechanism, redefining how synthetic materials actively reshape microbial networks and escalate environmental resistome risk through molecular-scale interfacial interactions.},
}

@article {pmid41747516,
year = {2026},
author = {Hu, X and Yu, K and Chai, B and Tang, Q and Gao, X and Wang, J and Yan, Z and Li, Y and Zhang, L and Wang, C and Lei, X and Chen, B and He, L},
title = {Polyethylene microplastics specifically drive the dissemination of ARGs: Mechanisms involving microbial community restructuring and horizontal gene transfer.},
journal = {The Science of the total environment},
volume = {1021},
number = {},
pages = {181587},
doi = {10.1016/j.scitotenv.2026.181587},
pmid = {41747516},
issn = {1879-1026},
abstract = {As emerging contaminants, the impact of microplastics (MPs) on antibiotic resistance genes (ARGs), virulence factors (VFs), and host microbial communities in lakes remains unclear. To address this, we conducted a 28-day incubation experiment using water from Yiquan Lake, employing metagenomic sequencing to investigate the effects of different types of microplastics-polyethylene (PE), polystyrene (PS), polypropylene (PP), and a mixture (Mix), each at a concentration of 1 item/L-compared to a raw water control (RAW). Results showed significant enrichment of Proteobacteria and Bacteroidetes in PE and Mix groups. Genera such as Agrobacterium and Microbacterium increased in PE and PS groups, serving as major hosts of ARGs and VFs. Network analysis revealed positive correlations between Agrobacterium, Escherichia, and ARGs, suggesting horizontal gene transfer may facilitate the spread of resistance and virulence. Two-factor PS formed highly connected yet competitive networks, whereas Mix constructed modular and stable networks. Single-factor PE enhanced microbial connectivity but reduced ARGs connectivity, while Mix increased the modularity of both microbes and ARGs. PE elevated the abundance of ARGs, VFs, and mobile genetic elements, with multidrug resistance and efflux pumps as dominant mechanisms. Additionally, PE downregulated quorum sensing transporter genes while upregulating regulatory factors, significantly promoting RND efflux systems (AcrAB-TolC) to maintain resistome homeostasis. This study highlights the distinct environmental effects of different MPs, underscoring the need to prioritize PE-related risks in aquatic ecosystems. Improved management of plastic waste in and around lakes is recommended to mitigate MP-mediated ARG dissemination and preserve freshwater ecosystem services.},
}

@article {pmid41743627,
year = {2026},
author = {Bollini, R and Cento, V},
title = {PCNE: A Tool for Plasmid Copy Number Estimation.},
journal = {Bioinformatics and biology insights},
volume = {20},
number = {},
pages = {11779322251410037},
pmid = {41743627},
issn = {1177-9322},
abstract = {The identification of plasmids from assembled genomes is well supported by numerous different tools, yet very few incorporate a plasmid copy number estimation step. This limits a comprehensive plasmid analysis, often leaving researchers to perform copy number estimation independently, leading to a lack of standardization. Plasmid Copy Number Estimator (PCNE) addresses this by providing an accessible and versatile command-line tool for estimating plasmid copy numbers directly from short-read sequencing data. Starting from standard input data like raw reads and a genome assembly, PCNE allows to apply a flexible normalization strategy, including an optional GC-bias correction, and is designed to complement existing plasmid detection pipelines. By simplifying and standardizing copy number estimation, PCNE, through the integration of state-of-art methodologies, aims to empower researchers to gain deeper insights into plasmid biology, particularly in studies of antimicrobial resistance and horizontal gene transfer.},
}

@article {pmid41743511,
year = {2025},
author = {Cherbuin, JDR and Llodrá, J and Borcard, L and Kaessmeyer, S and Ramette, A and Fernandez, JE and Wagner, TM and Torres-Puig, S and Kuhnert, P and Turner, D and Labroussaa, F and Jores, J},
title = {Characterization of Phylogenetically Distinct Temperate Phages from Kenyan Mammaliicoccus sciuri.},
journal = {PHAGE (New Rochelle, N.Y.)},
volume = {6},
number = {4},
pages = {259-271},
pmid = {41743511},
issn = {2641-6549},
abstract = {BACKGROUND: Temperate bacteriophages are widespread in bacterial genomes and can play significant roles in bacterial evolution and pathogenicity. Despite their importance, they remain poorly characterized in nonclinical Staphylococcaceae, particularly Mammaliicoccus sciuri.

MATERIALS AND METHODS: We analyzed 26 M. sciuri strains isolated from the nasal cavities of East African dogs and camels. Prophages were induced using mitomycin C, and isolated phages were characterized by whole-genome sequencing, phylogenetic analysis, electron microscopy imaging, and host-range determination.

RESULTS: Eight novel siphoviruses were isolated. Phylogenomic analysis revealed two new families, each comprising two genera. Notably, phages from one of these families (with genomes >130 kbp) exhibit a broad host range, while the other family is related to previously described phages implicated in horizontal gene transfer.

CONCLUSION: Our findings reveal unexpected diversity of temperate phages in M. sciuri, expanding current knowledge of phage distribution in animal-associated opportunistic pathogens.},
}

@article {pmid41743354,
year = {2026},
author = {Lin, H and Huang, Z and Guo, Y},
title = {Co-evolution of resistance and virulence in Klebsiella pneumoniae liver abscess: PLA-specific mechanisms and therapeutic dilemmas.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1767477},
pmid = {41743354},
issn = {2235-2988},
abstract = {The co-evolution of resistance and virulence in Klebsiella pneumoniae poses a significant challenge in the management of pyogenic liver abscesses (PLA), particularly with the advent of carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP). This review specifically addresses PLA to consolidate current knowledge on how key virulence factors-such as the K1/K2 capsule, hypermucoviscosity, and aerobactin-contribute to hepatic infection. It also examines the molecular mechanisms, including plasmid fusion and horizontal gene transfer, that are believed to facilitate the convergence of hypervirulence and carbapenem resistance. Additionally, the review discusses the unique clinical challenges presented by CR-hvKP in the context of PLA, including diagnostic delays, antimicrobial treatment failures, and complications in drainage. Emerging countermeasures, such as rapid molecular diagnostics and novel anti-virulence strategies, are also explored. By integrating contemporary molecular insights with the specific clinical challenges of PLA management, this review provides an updated translational perspective aimed at bridging the gap between pathogenesis and therapeutic strategies for CR-hvKP-associated infections.},
}

@article {pmid41740706,
year = {2026},
author = {Asima, SP and Mayur, A and Sonalisha, S and Parashar, R and Batsya, I and Sinha, A and Raina, V and Suar, M and Verma, SK},
title = {Imperative implication of microplastics as vital agent for salmonellosis inducing biofilms, antibiotic resistance, and health risk.},
journal = {Environmental research},
volume = {297},
number = {},
pages = {124090},
doi = {10.1016/j.envres.2026.124090},
pmid = {41740706},
issn = {1096-0953},
abstract = {Microplastics (MPs) have emerged as dynamic microbial interfaces that reshape pathogen ecology, antibiotic resistance evolution, and disease transmission. This review examines how MPs function as reservoirs and vectors for Salmonella enterica, highlighting the plastisphere as a stable biofilm microhabitat that enhances bacterial adhesion, environmental persistence, stress tolerance, and virulence expression. We summarize evidence that MP surfaces especially weathered, hydrophobic polymers, promote dense biofilms that protect Salmonella from desiccation, UV exposure, sanitization, and antimicrobial agents. Within these structured communities, co-localization of Salmonella with antibiotic residues, heavy metals, and diverse microbial taxa accelerates horizontal gene transfer and co-selection of antibiotic resistance genes and virulence determinants. MPs thereby act as mobile genetic "incubators" that disseminate multidrug-resistant Salmonella across soil, aquatic systems, wastewater networks, food production environments, and host microbiomes. These interactions link environmental contamination with zoonotic and foodborne transmission pathways, constituting a critical One Health concern. We identify current methodological gaps and propose research priorities for mechanistic risk assessment, monitoring frameworks, and intervention strategies. Recognizing MPs as active ecological players rather than inert pollutants is essential for mitigating their role in the global spread of pathogenic and antimicrobial-resistant Salmonella.},
}

@article {pmid41739546,
year = {2026},
author = {McInerney, JO},
title = {Genomic Perplexity and the Evolution of Context-Dependent Function.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msag041},
pmid = {41739546},
issn = {1537-1719},
abstract = {The fundamental principle that selection acts on a gene's function often assumes implicitly that this function is fixed and intrinsic. However, empirical evidence from pangenomics, synthetic biology, and GWAS consistently demonstrates that organismal function is highly context-dependent, varying across genomic backgrounds and cellular states, even for core genes. Drawing a conceptual parallel with modern large language models (LLMs), I propose that genomes, like LLMs, do not encode fixed functions but rather probability distributions over functional and phenotypic outcomes. This framework draws a conceptual analogy between epistasis and transformer-style "attention mechanisms," suggesting that genomic context weights the influence of distant genetic elements. I also introduce the concept of genomic perplexity - an information-theoretic measure of the statistical unexpectedness and incompatibility of a genetic element within its host context. I demonstrate how perplexity serves as a quantifiable metric for the well-known fitness cost associated with inter-species gene flow (e.g. horizontal gene transfer (HGT) and introgression), where a new gene represents a high-perplexity token. This perspective formalizes longstanding observations of genomic fit and provides a testable framework for predicting the integration potential of accessory genes and directing future research in synthetic biology and evolutionary modelling.},
}

@article {pmid41738746,
year = {2026},
author = {Castellani, LG and Cabrera, MD and Luchetti, A and Nilsson, JF and Pérez-Giménez, J and Bañuelos-Vazquez, LA and Alva, A and Wibberg, D and Busche, T and Kalinowski, J and Schlüter, A and Pühler, A and Niehaus, K and Pistorio, M and Torres Tejerizo, G},
title = {Characterization of RcgA and RcgR, two rhizobial proteins involved in the modulation of plasmid transfer.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0324225},
doi = {10.1128/spectrum.03242-25},
pmid = {41738746},
issn = {2165-0497},
abstract = {UNLABELLED: Plasmid conjugative transfer (CT) is a major mechanism of horizontal gene transfer in bacteria, facilitating genome evolution and dissemination of adaptive traits. Due to the energetic cost of CT, its regulation becomes an important process to ensure energetic balance within cells. In Rhizobium favelukesii, the plasmid pLPU83a belongs to group I-C of rhizobial plasmids, which require the transcriptional regulator TraR for CT. In well-characterized systems, TraR typically activates conjugative genes in response to quorum-sensing (QS) signals such as acyl-homoserine lactones. However, pLPU83a does not respond to these signals, raising questions about how TraR is regulated in this system. This study addresses the function of RcgA and RcgR, two proteins encoded upstream of traR on pLPU83a, whose function has previously been associated with CT modulation. Through proteomic, transcriptomic, and microscopy approaches, we show that RcgR acts as a repressor of CT, inhibiting traR expression and, therefore, the transcription of genes involved in CT, thereby reducing plasmid transfer rate. In contrast, RcgA is essential for CT but does not affect the expression of CT genes; it is localized at the membrane and may play a structural role in the mating pair formation system. Functional assays revealed that the repression facilitated by RcgR is independent of the anti-activator TraM and that TraR is essential for transfer even in the absence of RcgR. These findings locate RcgA and RcgR as key elements of a new circuit that modulates rhizobial plasmid conjugation and propose a novel mechanism of TraR control in systems uncoupled from QS signaling.

IMPORTANCE: Plasmid transfer is a central mechanism of gene exchange in bacteria, enabling the spread of traits with ecological and evolutionary relevance. Rhizobium favelukesii is a soil bacterium that carries multiple plasmids, including pLPU83a, which serves as a model to study conjugative transfer. This plasmid requires the transcriptional regulator TraR for transfer but-unlike classical systems-lacks the cognate gene that encodes the AHL synthase typically involved in quorum-sensing regulation. In previous work, two novel proteins encoded on pLPU83a, RcgA and RcgR, were identified as key elements in this regulatory system. Here, we further characterized their roles: RcgR represses the transcription of traR and, consequently, that of all conjugative genes, while RcgA is essential for transfer and localizes to the membrane, suggesting a structural function. These results provide mechanistic insight into how plasmid transfer is regulated in systems uncoupled from quorum sensing, highlighting alternative layers of control in bacterial conjugation.},
}

@article {pmid41737956,
year = {2026},
author = {Zhang, B and Wang, X and Qi, X and Zhang, L and Pei, N and Tao, Z and Liu, J},
title = {Bacterial co-detection is associated with higher multidrug-resistant Pseudomonas aeruginosa risk: insights from the MIMIC-IV database and metagenomic analysis.},
journal = {JAC-antimicrobial resistance},
volume = {8},
number = {1},
pages = {dlag023},
pmid = {41737956},
issn = {2632-1823},
abstract = {BACKGROUND: Pseudomonas aeruginosa (PA) poses a significant clinical challenge due to its high antibiotic resistance. While microbial communities aid in spreading antibiotic resistance genes (ARGs), their role in the emergence of multidrug-resistant Pseudomonas aeruginosa (MDR-PA) is unclear. This study examines the impact of bacterial interactions on MDR-PA prevalence and underlying mechanisms.

METHODS: This retrospective cohort study analysed 2965 PA-positive culture patients from the Medical Information Mart for Intensive Care IV (MIMIC-IV version 3.1) database, stratified by bacterial co-detection with PA. Propensity score matching (PSM) and logistic regression were used. Metagenomic sequencing was performed on deep endotracheal secretions from 19 PA ventilator-associated pneumonia (VAP) patients, constructing an ARGs dissemination network within the lower respiratory tract (LRT) microbiota. Comparative analysis of LRT microbiota and ARGs profiles was conducted between PA-VAP survivors and non-survivors.

RESULTS: Patients with bacterial co-detection with PA had a significantly higher MDR-PA prevalence and mortality than those with PA-only detection. Logistic regression identified bacterial co-detection as an independent risk factor for MDR-PA (adjusted OR 2.14; 95% CI 1.64-2.83, P < 0.001) and subsequent mortality (adjusted OR 1.67; 95% CI 1.30-2.14, P < 0.001). Metagenomic analysis of 19 PA-VAP cases suggested that horizontal gene transfer (HGT) may facilitate inter-species dissemination of ARGs (e.g. eptB, smeE, ANT(4')-Ia) between PA and other co-colonizing LRT microbiota. Distinct ARG profiles were observed between PA-VAP survivors and non-survivors.

CONCLUSION: Our findings indicate that bacterial co-detection with PA elevates the risk of MDR-PA and worsens clinical outcomes, potentially driven by HGT-mediated ARG exchange within the host microbiota.},
}

@article {pmid41736799,
year = {2026},
author = {Zhao, Q and Wang, D and Lin, H and Zhou, T and Zhang, J and Shang, J and Cai, D and Sun, Y and Hu, Z and Zhang, J},
title = {Unraveling the activity of phage-carrying antibiotic resistance genes in constructed wetlands.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1764958},
pmid = {41736799},
issn = {2235-2988},
mesh = {*Wetlands ; *Bacteriophages/genetics ; *Bacteria/genetics/drug effects/virology ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Geologic Sediments/microbiology ; Gene Expression Profiling ; },
abstract = {Antimicrobial resistance (AMR) is a global public health challenge, and risk assessments based solely on gene abundance often underestimate the immediacy of resistance dissemination. This study presented a carrier-centric framework integrating metagenomic and metatranscriptomic profiling with deep learning-based identification of mobile genetic elements, applied to a full-scale constructed wetland (CW). CW overall reduced ARG burdens, with genomic abundance in plants, sediments, and water decreasing by 98.5%, 80.9%, and 88.8%, respectively. However, transcriptional activity showed an opposite trend, with sediments exhibiting the highest ARG expression, highlighting their pivotal role in the persistence and dissemination of resistance. In sediments, phage-mediated expression increased sharply from 4.0% to 92.5%, exceeding plasmid-associated levels by ~276-fold, revealing a low-abundance but high-activity residual risk pattern. Furthermore, 16 of the 310 recovered nonredundant MAGs were identified as phage hosts, 11 of which were potentially pathogenic, antibiotic-resistant bacteria (PARB) and were more active in sediments than in water or plants. These findings indicate that transduction within high-density, biofilm-associated niches constitutes a key terminal risk source. In addition, sediment acts as a high-risk reservoir where redox and ionic gradients, together with residual lomefloxacin and other antibiotics, enhance phage infectious activity and the accumulation of ARGs. Through cross-compartment transmission along the sediment-water interface, these phage-associated and PARB populations continuously seed the overlying water. It is recommended that ARG risk assessment shift from static abundance to an activity-aware, carrier- and host-resolved approach, prioritizing sediment-targeted transcript monitoring and phage transduction early warning to support risk mitigation in CW.},
}

*Wetlands
*Bacteriophages/genetics
*Bacteria/genetics/drug effects/virology
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Metagenomics
Geologic Sediments/microbiology
Gene Expression Profiling

@article {pmid41735391,
year = {2026},
author = {Kovács, ÁB and Wehmann, E and Bekő, K and Grózner, D and Bali, K and Kreizinger, Z and Sawicka, A and Bányai, K and Gyuranecz, M},
title = {Genome-wide association study of Mycoplasma anserisalpingitidis strains for antibiotic susceptibility.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-39804-w},
pmid = {41735391},
issn = {2045-2322},
abstract = {Mycoplasma anserisalpingitidis is a facultative pathogenic bacterium affecting waterfowl, predominantly geese and sporadically ducks. Understanding the molecular basis of antimicrobial resistance mechanisms is crucial in the preservation of antibiotic efficiency. This study aimed to elucidate the genetic background of antibiotic susceptibility profiles of 110 M. anserisalpingitidis strains against nine antimicrobial agents. Significant associations between k-mers and five (tylvalosin, tilmicosin, enrofloxacin, lincomycin, spectinomycin) of the nine antimicrobial agents were identified by pyseer. Significant associations were found in multiple coding sequences that encode various members of efflux pumps, epigenetic regulation and topoisomerases among many other groups of functions. Certain k-mers associated with genes found putative prophage-like sequences suggest potential horizontal gene transfer events that could facilitate the acquisition of novel resistance mechanisms. Based on our findings, the genetic background of antimicrobial resistance of M. anserisalpingitidis is composed of multiple factors. Our results not only correlated with the majority of known antibiotic resistance mechanisms (e.g. drug target modification, efflux pumps, methyltransferases) but also showed potentially novel genes that could play a significant role in antimicrobial resistance. The results may serve to expedite the diagnosis of M. anserisalpingitidis antibiotic susceptibility profiles and support the fight against the spreading of resistance.},
}

@article {pmid41733351,
year = {2026},
author = {Yin, Z and Chen, X and Xiao, J and Tian, X and Li, Z and Zhang, M and Jing, B and Li, D and Deng, X and Peng, L},
title = {Insights into novel diagnostic assay development, antimicrobial resistance, and pathogenicity in Proteus mirabilis through pan-genome analysis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0189825},
doi = {10.1128/aem.01898-25},
pmid = {41733351},
issn = {1098-5336},
abstract = {Proteus mirabilis, a significant pathogen associated with human urinary tract infections (UTIs), demonstrates escalating multidrug resistance (MDR) that complicates clinical management. Accurate identification and in-depth genomic analysis are essential for monitoring and controlling this pathogen. This study aimed to identify the species-specific gene repertoire, antimicrobial resistance (AMR), and virulence genetic profiles through pan-genome analysis to develop novel detection methods and better understand emerging public health threats. The genus Proteus exhibits an open pan-genome, with P. mirabilis harboring a distinct species-specific gene repertoire. Two species-specific core genes, PMI3020 and PMI3598, were identified as molecular targets. We developed conventional PCR and TaqMan probe-based real-time PCR assays, which demonstrated high specificity when tested against P. mirabilis and non-P. mirabilis isolates. The TaqMan probe-based real-time PCR demonstrated a sensitivity of 3.43 × 10[2] CFU/mL using serial dilutions of P. mirabilis DNA. Comparative genomic analysis revealed significant differences in AMR and pathogenicity-related gene repertoires between P. mirabilis and other Proteus spp. The higher prevalence of AMR phenotypes in P. mirabilis correlated with its greater abundance of AMR genes. Emerging AMR genes acquired through horizontal gene transfer (HGT) have increased MDR risks, particularly to carbapenems and cephalosporins. Additionally, P. mirabilis genomes contain more virulence genes mainly related to adherence and iron acquisition. Our findings establish pan-genome analysis as an effective tool for identifying specific genetic markers to detect pathogens accurately and provide a comprehensive genomic framework illuminating AMR dynamics and virulence in P. mirabilis, thereby providing a valuable foundation for future public health risk assessments.IMPORTANCEP. mirabilis is a major uropathogen with increasing AMR prevalence. The dissemination of AMR genes across healthcare and community settings poses critical challenges to infection control. This study conducted pan-genome analysis of Proteus to identify P. mirabilis-specific gene repertoire, of which species-specific core genes were used as molecular targets to develop highly sensitive PCR assays for accurate detection of this pathogen. Compared with other Proteus spp., P. mirabilis possesses a greater abundance of AMR genes, resulting in a higher prevalence of AMR phenotypes, including significant resistance to carbapenems and cephalosporins. This study establishes pan-genome analysis as an effective strategy for mining species-specific genetic markers, enabling the development of novel PCR assays for accurate pathogen detection. The comprehensive genomic framework enhances understanding of AMR dynamics and virulence mechanisms essential for public health risk assessment.},
}

@article {pmid41733349,
year = {2026},
author = {van den Broek, S and Nybom, I and Feola Conz, R and Sun, Y and Bucheli, TD and Doetterl, S and Hartmann, M and Garland, G},
title = {Soil microbial and plant responses to increasing antibiotic concentration: a case study of five antibiotics.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0158125},
doi = {10.1128/aem.01581-25},
pmid = {41733349},
issn = {1098-5336},
abstract = {UNLABELLED: Antibiotic contamination from biogenic waste in agricultural soils poses a significant threat to soil health and crop productivity. We investigated the effect of antibiotics on the soil microbial community, antibiotic resistance genes, and mobile genetic elements (MGEs) and plant productivity in a 6-week greenhouse trial. Here, Spinacia oleracea (spinach) and Raphanus sativus (radish) were grown from seeds, and a mix of five antibiotics, namely sulfamethoxazole, trimethoprim, enrofloxacin, clarithromycin, and chlortetracycline, was added to the soil at concentrations of 0, 0.1, 1, and 10 mg kg[-1] soil dry weight (c0, c0.1, c1, and c10, respectively). Overall, we found that the antibiotic treatments significantly impacted prokaryotic α-diversity and prokaryotic and fungal β-diversity. The relative abundance of human and plant pathogens did not increase under antibiotic exposure, but there was a significant reduction in plant growth-promoting bacteria. Moreover, the c10 treatment significantly increased the abundance of MGE intI1, indicative of horizontal gene transfer and sulfonamide resistance gene sul1, and significantly lowered radish biomass and nitrogen uptake, while spinach biomass and nitrogen uptake were unaffected. In summary, our study showed that antibiotic exposure significantly changed prokaryotic community diversity, while fungi remained largely unaffected. The reduction of plant growth-promoting bacteria may have a significant impact on soil nutrient cycling and crop productivity, but more research is needed to understand the long-term impact of these co-applied antibiotics on food production. Additionally, more studies are needed to understand the effect of antibiotics on realistic, field-scale conditions to fully understand the impact on environmental and human health.

IMPORTANCE: Agricultural soils are frequently contaminated with complex mixtures of antibiotics from various biogenic sources, yet we lack a clear understanding of their specific ecological impact. While many studies investigate antibiotics, they are often studied in pollution sources like manure, which contain confounding factors like heavy metals. To provide a mechanistic understanding of antibiotic-specific responses, we investigated the effects of a complex, five-antibiotic mixture on the soil-plant system, independent of other contaminants. As expected, antibiotics reduced prokaryotic diversity and increased the abundance of some genes related to antibiotic resistance. Additionally, antibiotic exposure reduced plant growth-promoting bacteria, which may have subsequent detrimental effects on plant and soil health. Moreover, we found that antibiotic exposure can reduce plant biomass and nitrogen uptake, but this is highly plant dependent. This research highlights the critical need to monitor antibiotic pollution due to its potential detrimental effect on plant health and alterations to the soil microbiome.},
}

@article {pmid41732174,
year = {2026},
author = {Eerden, SA and Abeel, T and van Loosdrecht, MCM and Roy, S},
title = {Phylogenetic analysis reveals diversity in glycan biosynthesis in "Candidatus Accumulibacter".},
journal = {Biofilm},
volume = {11},
number = {},
pages = {100350},
pmid = {41732174},
issn = {2590-2075},
abstract = {Although biofilms are widespread in nature, the ecological roles and compositional diversity of the extracellular polymeric substances (EPS) forming these structures remain poorly understood. Here, we apply a bottom-up genomic approach by investigating the biosynthetic potential for glycan precursors in the genus "Candidatus Accumulibacter", with a focus on assessing the intra-genus variability. Within a curated set of 61 "Ca. Accumulibacter" MAGs, our analysis revealed a dichotomy in glycan precursors between a conserved core group of 9 nucleotide-sugars and a variable accessory set of 12 nucleotide-sugars, out of 50 nucleotide-sugars tested. The core nucleotide-sugars in "Ca. Accumulibacter" are related to nucleotide-sugars also found to be widely distributed across the tree of life, whereas the accessory set is enriched in rare nucleotide-sugars. The accessory nucleotide-sugars show an irregular distribution across "Ca. Accumulibacter" phylogeny, and divergent evolutionary histories. This highlights the possibility that distinct evolutionary pressures act on different parts of the EPS-formation metabolism, leading to genotypic diversification driven by complex biological phenomena such as horizontal gene transfer that support the observed divergent evolutionary histories.},
}

@article {pmid41730359,
year = {2026},
author = {Britti, D},
title = {Molecular mimicry in the agroecosystem: A new paradigm for understanding how pesticide residues drive the emergence of antimicrobial resistance.},
journal = {Environmental toxicology and pharmacology},
volume = {123},
number = {},
pages = {104974},
doi = {10.1016/j.etap.2026.104974},
pmid = {41730359},
issn = {1872-7077},
abstract = {Antimicrobial resistance (AMR) is a mounting global crisis, with environmental dissemination of antibiotic resistance genes (ARGs) emerging as a critical driver. Agroecosystems, chronically exposed to complex mixtures of bioactive chemicals, including pesticides, represent an underrecognized hotspot for AMR evolution. This review synthesizes established mechanisms by which pesticides select for resistance and introduces a novel hypothesis: molecular mimicry as a hidden driver. Evidence highlights three key pathways: cross-resistance via multidrug efflux pumps; coselection on mobile genetic elements; and enhanced horizontal gene transfer under pesticide-induced stress. Structural similarities may cause bacterial defense systems to misidentify pesticide molecules as antimicrobial threats, triggering resistance responses analogous to endocrine disruption by xenoestrogens such as BPA and DDT. Case studies on macrolides and ivermectin illustrate this concept, as both share macrocyclic lactone scaffolds with insecticides like spinosyns. This framework positions pesticide pollution as a central contributor to AMR, underscoring the need for One Health-based regulatory reform.},
}

@article {pmid41726958,
year = {2026},
author = {Khanal, S and Walsh, S and Shehata, N and Ahearne, A and Belin, D and Larson, B and Tabor, B and Wall, D and Stevens, C},
title = {Predator avoidance promotes inter-bacterial symbiosis with myxobacteria in polymicrobial communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.12.705600},
pmid = {41726958},
issn = {2692-8205},
abstract = {Myxobacteria are predatory soil bacteria with the largest known bacterial genomes, rich in biosynthetic gene clusters for specialized metabolites. Despite their ecological importance as potential keystone taxa in soil food webs, there is a disconnect between laboratory-isolated myxobacteria and abundant Myxococcota detected in environmental metagenomic studies. Here, we report the isolation and characterization of stable myxobacterial swarm consortia from rhizospheric soil, consisting of myxobacteria associated with novel Microvirga species. Using metagenomic sequencing, we assembled metagenome-assembled genomes (MAGs) for four consortia, revealing phylogenetically distinct yet stably associated bacterial partnerships. Comparative genomics identified evidence of horizontal gene transfer, including acyl-homoserine lactone (AHL) synthases and ankyrin repeat (ANKYR) proteins shared between consortium members, and genome-scale metabolic modeling predicted complementary auxotrophies. Remarkably, time-lapse microscopy revealed that Archangium exhibited markedly reduced predation toward its Microvirga companion (0.7% predation rate) compared to non-symbiotic Myxococcus xanthus (14.9% predation rate), while maintaining robust predatory capacity against Escherichia coli prey. These findings indicate that predation avoidance and metabolic complementarity can drive stable inter-bacterial symbiosis in predatory myxobacterial communities, providing foundational insights into previously overlooked myxobacterial partnerships that may be prevalent in natural soil ecosystems.},
}

@article {pmid41724996,
year = {2026},
author = {Liu, Q and Jia, J and Chen, X and Wu, C},
title = {Stress-induced enrichment of Pseudomonas sp. stimulates the adaptive response of Auxenochlorella pyrenoidosa and antibiotic-resistant proliferation.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02335-7},
pmid = {41724996},
issn = {2049-2618},
support = {32401408//National Natural Science Foundation of China/ ; 42477426//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The phycosphere is an important ecological niche for bacteria and antibiotic resistance genes (ARGs). However, whether and how the interaction between microalgae and bacteria changed, and its further effect on the transmission of ARGs under pollutant stress remains enigmatic. Here, Auxenochlorella pyrenoidosa was co-cultured with bacteria screened from lake water to explore the algal-bacteria interaction and ARGs' transmission in the presence of florfenicol (FF) and polylactic acid microplastics (PLA MPs).

RESULTS: Our study demonstrated that the growth and metabolism of A. pyrenoidosa were promoted under FF treatment or co-treatment with PLA MPs, validated by phenotypic, transcriptome, and metabolome analyses. In contrast, the abundance of phycospheric bacteria was decreased as a result of niche competition. Nonetheless, the transmission of ARGs in the phycosphere was promoted due to the enrichment of antibiotic-resistant bacteria, especially Pseudomonas, rather than horizontal gene transfer. The algal-bacteria co-culture experiment further suggested that vitamin B6 secreted by Pseudomonas sp. likely contributes to underpinning A. pyrenoidosa' survival under FF and PLA MPs stress.

CONCLUSIONS: These findings underscore the dynamic interplay and co-evolution between algae and bacteria under pollutant exposure, and reveal a potential mechanism of vitamin B6-mediated mutualism. This study provides new insights into the assembly of phycospheric bacterial communities and the adaptive strategies of microalgae in contaminated aquatic environments. Video Abstract.},
}

@article {pmid41724873,
year = {2026},
author = {de Almeida, LN and Silva, MJFE and de Freitas Rodrigues Jesuino, B and Tupy, SM and Vieira, JHR and Xavier, GA and da Rocha, JPL and Gonçalves, OS and Santana, MF},
title = {Comparative genomic analyses reveal key traits for biocontrol and the promotion of plant growth in Paenibacillus strains.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {3},
pages = {},
pmid = {41724873},
issn = {1573-0972},
abstract = {UNLABELLED: Paenibacillus species have emerged as promising candidates for sustainable agriculture due to their functional versatility in plant growth promotion and biocontrol. We performed a comparative genomic analysis of 428 high-quality Paenibacillus genomes to assess their ecological adaptability and biotechnological potential. The analyzed strains originated from diverse environments, reflecting broad ecological distribution. Functional annotation revealed a widespread occurrence of plant growth-promoting traits (PGPTs), including phosphate and potassium solubilization, siderophore biosynthesis, nitrogen fixation, and phytohormone-related compounds. On average, the genomes contained 249 genes associated with biofertilization, 190 with phytohormone production, 97 linked to bioremediation, and around 322 involved in competitive exclusion. The open pan-genome configuration (b = 0.503) highlights notable genetic plasticity and ongoing gene acquisition. While the core genome was enriched in essential functions, accessory and unique fractions carried genes associated with environmental adaptation and niche specialization. Analysis of mobile genetic elements (MGEs) showed that some PGPT-related genes occur in mobile regions, suggesting horizontal gene transfer contributes to the dissemination of beneficial traits. Diverse BGCs, including those encoding Bacillopaline, Tridecaptin, Fusaricidin B, Paeninodin, and Polymyxin, were identified, many with antimicrobial potential. CAZyme profiling revealed abundant chitinases, supporting pathogen suppression capacity. No virulence factors were detected, and antibiotic resistance genes were rare, underscoring the genus’ low pathogenicity. Altogether, these findings position Paenibacillus as a genetically and functionally diverse group with strong potential as a safe, sustainable resource for developing biofertilizers and biopesticides.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11274-026-04811-6.},
}

@article {pmid41724454,
year = {2026},
author = {Ghasemian, A and Al-Marzoqi, AH and Ali, ZA and Nouruzi, F and Abdollahi, A and Montaseri, Z and Memariani, M and Zarenezhad, E},
title = {Engineered Bacteria as living detectors of tumor DNA: A new diagnostic frontier.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {586},
number = {},
pages = {120914},
doi = {10.1016/j.cca.2026.120914},
pmid = {41724454},
issn = {1873-3492},
abstract = {The identification of tumor-generated DNA must be accurate, minimally invasive, and precise, as it forms a fundamental aspect of effective cancer diagnosis, prognosis, and customized treatment plans. Recent advances in synthetic biology have pioneered the creation of genetically engineered bacteria as innovative biosensors capable of detecting tumor-derived DNA directly in situ. This review explores key developments in designing these microbial sentinels to pinpoint oncogenic DNA alterations, particularly emphasizing KRAS mutations that drive many cancers. By leveraging natural competence and horizontal gene transfer, in combination with CRISPR-Cas tools for selective targeting and integration of mutant DNA sequences, engineered bacteria can distinguish between tumor and wild-type DNA and produce observable reporter outputs. We further elaborate on various molecular engineering strategies using unique genetic circuits, homologous recombination, multiplexed CRISPR systems and safety circuits to improve specificity, sensitivity and biosafety. An additional perspective in the discussion incorporates diverse bacterial species and various cancer types, with a specific emphasis on colorectal and gastrointestinal cancers, while also considering possible applications to other solid tumors. Detection modalities encompass in vitro assays, organoid models, in vivo mouse models, and non-invasive stool sampling, offering an impressive range of platforms for validating biosensors. The positive aspects of these approaches, such as real-time detection, affordability, programmability, and reduced invasiveness, need to be balanced with their negative aspects concerning biosafety, colonization efficiency, and detection sensitivity limitations. Looking forward, this review delves into the translational potential of engineered bacterial biosensors for clinical cancer diagnostics, their integration with therapeutic delivery systems, and future directions that involve multiplexed detection and the incorporation of digital health. Indubitably, engineered bacterial tumor DNA biosensors represent a key fusion of microbiology, synthetic biology, and oncology, aimed at revolutionizing the diagnosis and management of cancers.},
}

@article {pmid41724354,
year = {2026},
author = {Wang, XQ and Xu, L and Du, MJ and Wang, HN and Lei, CW},
title = {Genomic Islands Associated with the Dissemination of Multidrug Resistance in Clinically Important Pathogenic Bacteria.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2026.02.007},
pmid = {41724354},
issn = {2213-7173},
abstract = {OBJECTIVES: To elucidate the role of genomic islands (GIs) as key vehicles of horizontal gene transfer in disseminating antibiotic-resistance genes (ARGs) across bacterial species and in fostering multidrug-resistant (MDR) strain emergence, and to provide a comprehensive overview of current knowledge.

METHODS: We integrated recent literature on mobile genomic islands (GIs), summarized their basic architecture and functional features, systematically catalogued the types/subtypes of resistance islands identified in major epidemic pathogens (Salmonella, Proteus mirabilis, Staphylococcus aureus, Acinetobacter baumannii, etc.), and delineated their horizontal transfer mechanisms.

RESULTS: (1) GIs can integrate into host chromosomes, excise under specific cues, and transfer to new recipients, thereby facilitating the spread of clinically important ARGs. (2) Diverse novel multidrug-resistant genomic islands have been characterized in the above pathogens.

CONCLUSIONS: GIs are one of the key vehicles that facilitate the dissemination of ARGs and the evolution of bacterial multidrug resistance. A systematic understanding of their structure, transfer mechanisms and core functions offers a reference framework for future surveillance of multidrug-resistant genomic islands and for developing countermeasures against antimicrobial resistance.},
}

@article {pmid41724083,
year = {2026},
author = {Zhang, G and Zhang, D and Li, W},
title = {Antagonistic effects of microplastic biofilms on antibiotic resistance gene horizontal transfer in water environments.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {293},
number = {},
pages = {107766},
doi = {10.1016/j.aquatox.2026.107766},
pmid = {41724083},
issn = {1879-1514},
abstract = {Emerging pollutants, microplastics, found in water environments, accumulate microorganisms on their surfaces, forming biofilms that concentrate antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Horizontal gene transfer (HGT) of ARGs is one of the primary ways bacteria acquire antibiotic resistance. Most studies reported that biofilm formation promoted the HGT of ARGs. However, this study found that microplastic biofilms might inhibit ARG conjugation. Previous research focused on the impact of environmental factors on ARG conjugation among suspended bacteria, but studies on microplastic biofilms were lacking. Therefore, this study selected environmental factors that have been extensively investigated and are recognized as significant facilitators and inhibitors of ARG conjugation, namely nano-alumina and free nitrous acid (FNA), to compare their effects on ARG conjugation in suspended bacteria and microplastic biofilms. The results showed that when the concentration of nano-alumina was 5.0 mmol/L, the ARG conjugation frequency in microplastic biofilms was significantly lower than in suspended bacteria. Nano-alumina could enhance cell membrane permeability and increase the bacteria's ability to transfer DNA, thereby promoting ARG conjugation. However, microplastic biofilms could reduce the promoting effect of nano-alumina, thereby inhibiting ARG conjugation. FNA could inhibit ARG conjugation among suspended bacteria. Microplastic biofilms could reduce the inhibitory effect of FNA, ultimately leading to a higher frequency of conjugation in microplastic biofilms compared to suspended bacteria. This study reveals the mechanisms by which microplastic biofilms promote or inhibit ARG conjugation, providing new insights for dialectically studying the effects of microplastic biofilms on ARG transmission.},
}

@article {pmid41723801,
year = {2026},
author = {Hetta, HF and Alatawi, Z and Bukhari, SQ and Barnawi, HIM and Algammal, AM and Eissa, EH and Al Masri, M and Ramadan, YN},
title = {Human infections caused by pathogenic Burkholderia: current clinical challenges and future perspectives.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41723801},
issn = {1439-0973},
abstract = {BACKGROUND AND OBJECTIVES: The genus Burkholderia comprises diverse environmental bacteria, although only a limited number of species are clinically significant. Among these, Burkholderia mallei, Burkholderia pseudomallei, and the Burkholderia cepacia complex (Bcc) are the primary human pathogens associated with severe infections. This review aims to synthesize current knowledge on these species, focusing on their epidemiology, pathogenicity, diagnostic approaches, and treatment challenges, while identifying key gaps and future research directions.

METHODS: A narrative synthesis of the literature was conducted, integrating findings from microbiological, clinical, and genomic studies addressing major pathogenic Burkholderia species and their management.

RESULTS: B. mallei causes glanders, a zoonotic infection transmitted through contact with infected animals. B. pseudomallei, an environmental organism endemic to tropical and subtropical regions, causes melioidosis, particularly in individuals with risk factors such as diabetes. The Bcc, comprising over 20 species, poses significant risks in patients with cystic fibrosis and chronic granulomatous disease, where it may lead to severe outcomes including "cepacia syndrome" and nosocomial outbreaks linked to contaminated medical products. Pathogenic Burkholderia species exhibit highly dynamic genomes shaped by horizontal gene transfer, contributing to virulence and intrinsic resistance to multiple antimicrobials, including polymyxins and many β-lactams. Advances in laboratory diagnosis include the use of molecular techniques, mass spectrometry, and whole-genome sequencing alongside conventional methods. Treatment remains challenging due to multidrug resistance, often requiring prolonged and intensive therapeutic regimens.

CONCLUSIONS: Clinically significant Burkholderia species present substantial diagnostic and therapeutic challenges due to their virulence and intrinsic antimicrobial resistance. Improved diagnostic strategies, optimized treatment protocols, and further research into prevention and control measures are essential to mitigate their clinical impact.},
}

@article {pmid41721206,
year = {2026},
author = {Michelioudakis, V and Zafranas, A and Myrisiotis, C and Makri, S and Katsoula, A and Campos, M and Vasileiadis, S and Karpouzas, DG},
title = {Comparative Genomic and Transcriptomic Analysis Reveals Why Paenarthrobacter Strains Are Specialists in the Degradation of the Fungicide Iprodione.},
journal = {Microbial biotechnology},
volume = {19},
number = {2},
pages = {e70319},
pmid = {41721206},
issn = {1751-7915},
support = {MIS 5002636//Omic-Engine RI project/ ; //Co-financed Greece and European Union/ ; //European Regional Development Fund/ ; },
mesh = {*Fungicides, Industrial/metabolism ; *Hydantoins/metabolism ; *Aminoimidazole Carboxamide/metabolism/analogs & derivatives ; Soil Microbiology ; Gene Expression Profiling ; Genomics ; Genome, Bacterial ; Amidohydrolases/genetics/metabolism ; Biodegradation, Environmental ; Phylogeny ; Metabolic Networks and Pathways/genetics ; },
abstract = {Paenarthrobacters degrade the fungicide iprodione through a pathway involving an amidase (IpaH), a deacetylase (DdaH) and a hydrolase (DuaH). We aimed to elucidate the mechanisms of this catabolic specialisation and its evolution in Paenarthrobacters. Two new iprodione-degrading Paenarthrobacter strains TA1.8 and C1 were sequenced, and their genomes were analysed comparatively to the iprodione-degrading Paenarthrobacter strains YJN-5 and YJN-D. We noted different gene organisation motifs amongst strains, suggesting different stages of pathway evolution in the studied strains depending on their prior exposure to iprodione. Strains derived from soils exposed to iprodione (TA1.8, YJN-5 and YJN-D) carry multiple copies of ipaH, ddaH and duaH. Conversely, strain C1, isolated from a pristine soil, carried one copy of the set. Comparative genomics and pangenome analysis of Paenarthrobacters suggested an evolution route of the iprodione transformation pathway which involves acquisition of ddaH through horizontal gene transfer, gene duplication of the chromosomally encoded ipaH and ddaH, and further genetic rearrangements for pathway optimisation, complementing duaH, a core gene in Paenarthrobacters. Transcriptomic analysis of TA1.8 verified the importance of all ipaH, ddaH and duaH homologues in iprodione transformation and pointed to hydantoinases as potential facilitators of the transformation of the hydantoin-containing intermediate N-(3,-5-dichlorophenyl)-2,4-dioxoimida-zolidine, a step mediated by DdaH.},
}

*Fungicides, Industrial/metabolism
*Hydantoins/metabolism
*Aminoimidazole Carboxamide/metabolism/analogs & derivatives
Soil Microbiology
Gene Expression Profiling
Genomics
Genome, Bacterial
Amidohydrolases/genetics/metabolism
Biodegradation, Environmental
Phylogeny
Metabolic Networks and Pathways/genetics

@article {pmid41719533,
year = {2026},
author = {Ippolito, I and Hug, L},
title = {Antimicrobial resistance gene diversity, prevalence, and mobility within four landfills.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2025-0226},
pmid = {41719533},
issn = {1480-3275},
abstract = {Antibiotics in landfills create selection pressures on the microorganisms present, selecting for antibiotic resistance genes (ARGs) and antibiotic resistant organisms (ARO). The aim of this study was to assess whether landfills are hot-spots of antimicrobial resistance and whether landfills may contribute to global ARO diversity through ARG lateral gene transfer. Genome resolved metagenomic sequencing combined with sequence-search-based and deep learning tools were used to determine ARG diversity and prevalence from four active municipal landfills and their adjacent ground or surface water systems. Comparison to pristine and anthropogenic environments highlighted that landfill microbial communities contain distinct ARG signatures, including a broader diversity of ARGs. Plasmids made up 4.1-8.4% of assembled scaffolds and carried 5.4-12.0% of the identified ARGs in assembled data, depending on the sample type. Enriched ARG resistance mechanisms on mobile elements included multidrug resistance and antibiotic inactivation. The results indicate that landfills house a high diversity of antimicrobial resistance mechanisms and drug classes, with a moderate fraction encoded on mobile elements. Landfills are thus likely mixing grounds for ARG transfer and evolution of novel or augmented ARO lineages.},
}

@article {pmid41717089,
year = {2025},
author = {Shi, S and Qi, J and Peng, W and Su, X and Chen, P and Xu, S and Li, S and Ma, L and Wang, W and Jiang, K and Liu, Z and Li, W and Xiong, H and Wang, Y},
title = {Convergent gut microbiome adaptation and pervasive antibiotic resistome in Qinghai-Tibet Plateau passerines.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1733974},
pmid = {41717089},
issn = {1664-302X},
abstract = {INTRODUCTION: The Qinghai-Tibet Plateau, an extreme high-altitude ecosystem, presents a unique model for studying host-microbe-environment coevolution under environmental stress. However, the role of resident wildlife, particularly non-migratory passerines, as reservoirs and vectors for cross-boundary antibiotic resistance gene (ARG) dissemination remains poorly understood.

METHODS: Here, through metagenomic analysis of two endemic passerines (Pseudopodoces humilis and Pyrgilauda ruficollis) and their habitats.

RESULTS: We reveal convergent adaptations in their gut microbiomes, dominated by Actinomycetota, Pseudomonadota and Bacillota. Functional enrichment in carbohydrate metabolism and genetic information processing underpins host energy optimization in extreme high-altitude environments. Critically, these birds constitute a major reservoir of ARGs, harboring 153 antibiotic resistance ontologies (AROs) with nearly universal resistance to clinical antibiotic classes. The core resistome-comprising glycopeptide (van clusters), fluoroquinolone, and tetracycline resistance genes-reflects anthropogenic contamination amplified by environmental persistence. Environmental transmission pathways were unequivocally demonstrated via 47 AROs shared between avian hosts and proximal matrices (soil/grass), coupled with livestock-derived antibiotic influx through excreta, establishing the plateau as a hotspot for resistance gene flux. Strikingly, "low-abundance-high-resistance" taxa (Pseudomonadota, Actinomycetota, and Bacillota; ≤30% abundance but >80% ARG contribution) drive resistome plasticity, potentially facilitated by horizontal gene transfer.

DISCUSSION: Our findings redefine resident passerines as sentinels of ecosystem health and bridges for cross-boundary antimicrobial resistance (AMR) spread. Mitigating global AMR thus necessitates interdisciplinary strategies targeting environmental reservoirs (e.g., regulating livestock antibiotic use) and monitoring avian-mediated gene flow.},
}

@article {pmid41715166,
year = {2026},
author = {Zhang, J and Xu, L and Ge, X and Zi, X and Chen, S and Liu, C and Wang, K and Zhou, J and Dou, T and Wong, JWC and Lin, Q and Kang, X and Cao, Z},
title = {Cross-kingdom genomic variation in chicken gut microbiomes: insights from China's diverse local breeds.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02347-3},
pmid = {41715166},
issn = {2049-2618},
support = {2024A1515140076//Guangdong Basic and Applied Basic Research Foundation/ ; 202401AU070079//Yunnan Fundamental Research Projects/ ; 221110133//Dongguan University of Technology Top Talent Professor Start Up Fund/ ; 202301BD070001-136//Key Project of Yunnan Province Agricultural Joint Special Project/ ; 202305AC160040//Yunnan Province Young and Middle-aged Academic and Technical Leader Reserve Talent Project/ ; },
abstract = {BACKGROUND: The gut microbiome possesses substantial genetic diversity that supports microbial adaptation, but the genomic variation patterns across its prokaryotic and viral populations remain incompletely characterized.

RESULTS: Through integrated metagenomic and metatranscriptomic analysis of ten indigenous chicken breeds from China, we recovered 1527 representative prokaryotic MAGs, 37,555 representative DNA viral contigs, and 1867 representative RNA viral contigs (primarily comprising Bacillota/Bacteroidota, Uroviricota, and Lenarviricota/Pisuviricota, respectively). By integrating complementary short-read and long-read metagenomics with metatranscriptomics, we identified structural variants (SVs) and single-nucleotide variants (SNVs) in these cross-kingdom genomes. Positive SV-SNV density correlations occurred consistently across all microbial groups, indicating coordinated mutational processes. DNA viruses exhibited the highest variant prevalence (86.9% SNVs, 47.7% SVs), with temperate phages accumulating significantly more variants than virulent phages. Functionally, prokaryotic variants accumulated in carbohydrate metabolism and amino acid metabolism, while viral variants demonstrated broad metabolic hijacking. Horizontal gene transfer (HGT) was characterized by a strong virus-associated signature (69.40% of 536 events) and marked by an asymmetric pattern, with phage-to-bacteria (P-to-B) flow alone constituting 37.50% of all events. Random forest analysis revealed a strong bidirectional predictive relationship between SV and SNV densities across prokaryotic, DNA viral, and RNA viral populations, suggesting coupled genomic instability. Niche breadth emerged as a major driver of SNVs across kingdoms and was positively correlated with variant density. In prokaryotes, HGT events significantly shaped variant patterns. For viruses, genomic GC content was an important factor and consistently showed a negative correlation with SNV density in both DNA and RNA viruses.

CONCLUSIONS: These findings demonstrate that coordinated mutational processes and kingdom-specific intrinsic factors drive genomic variation, with viruses serving as key genetic exchange vectors in chicken gut ecosystems. Video Abstract.},
}

@article {pmid41714151,
year = {2026},
author = {Labiak, PH and Kuo, LY and Fauskee, BD and Karol, KG},
title = {Evolutionary mobility and genetic dynamics of MORFFO genes: shuttling among ancient plant lineages.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70986},
pmid = {41714151},
issn = {1469-8137},
support = {303330/2022-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; NSTC 114-2621-B-007-001//National Science and Technology Council in Taiwan/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {Plastid genomes (plastomes) of land plants are characterized by their architectural and genic content stability. However, fern plastomes exhibit unexpected dynamism, characterized by the presence of mobile protein-coding genes (CDS) - Mobile Open Reading Frames in Fern Organelles (MORFFOs). We investigate the evolutionary dynamics of MORFFOs in 30 species of Anemiaceae (Schizaeales), an ancient lineage of ferns, focusing on their transposition, substitution patterns, codon usages, and RNA editing patterns. MORFFOs expand plastome size and occur in diverse intergenic regions, exhibiting dynamic locations, genealogies, and exceptionally high substitution rates compared with canonical plastid CDS. Sliding window and codon usage analyses demonstrate that MORFFOs are under purifying selection but exhibit distinct codon preferences that deviate from those of other plastid CDS, suggesting functional constraints. Phylogenetic incongruence between MORFFOs and other plastid CDS, along with their extraordinary substitution rates and mobility, implies their replication outside plastids. Our findings highlight that MORFFOs are dynamic, potentially selfish genetic elements capable of transcription, translation, and replication independently from plastomes, and fern plastomes might acquire these mobile CDS through frequent horizontal gene transfer and possibly intracellular gene transfer.},
}

@article {pmid41713669,
year = {2026},
author = {Khalifa, HO and Mohammed, T and Ramadan, H and Abdalla, A and Ghazawi, A and Al-Marzooq, F},
title = {Phylogenomic and population genomic insights into the dissemination of ESBL-producing Escherichia coli causing bloodstream infections in the United Arab Emirates.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {139},
number = {},
pages = {105905},
doi = {10.1016/j.meegid.2026.105905},
pmid = {41713669},
issn = {1567-7257},
abstract = {Extended-spectrum β-lactamase-producing Escherichia coli are globally disseminated pathogens whose success is driven by clonal expansion and horizontal gene transfer. However, the population structure and evolutionary relationships of these organisms in the United Arab Emirates remain insufficiently characterized. In this study, we applied a population genomic and phylogenomic approach to investigate ESBL-producing E. coli causing bloodstream infections and their genetic relatedness to strains from non-human reservoirs within a One Health framework. Forty-five ESBL-producing E. coli isolates recovered from bloodstream infections between 2021 and 2024 were analyzed, with whole-genome sequencing performed on 29 representative isolates. Genomic analyses revealed the predominance of internationally disseminated high-risk lineages, particularly sequence types ST131 and ST1193, largely associated with the ESBL gene blaCTX-M-15. Conserved genetic contexts of blaCTX-M-15 in these lineages suggested stable vertical inheritance, whereas greater diversity of mobile genetic elements was observed among non-ST131 isolates, indicating ongoing horizontal gene transfer. Additional resistance determinants, including blaDHA-1, blaSHV-12, and notably the carbapenemase gene blaNDM-5, contributed to multidrug-resistant genotypes, indicating the coexistence of ESBL and carbapenemase activity in a subset of isolates. Phylogenomic comparisons based on core genome variation demonstrated close genetic relatedness between clinical isolates and E. coli from food, poultry, and environmental sources in the United Arab Emirates. These findings indicate that bloodstream infections are associated with shared circulating ESBL-producing E. coli lineages exhibiting genetic relatedness across human and non-human reservoirs. The results highlight the evolutionary connectivity of E. coli populations and emphasize the importance of integrated genomic surveillance to track and limit the spread of multidrug-resistant pathogens.},
}

@article {pmid41713270,
year = {2026},
author = {Jiao, X and Ji, W and Zhang, X and Zhang, S and Dolfing, J and Yang, K and Xie, B and Zhang, Y and Feng, J and Wu, D},
title = {Microcystins 'steer' antibiotic resistome dynamics by synergetic metabolism and horizontal gene transfer in a megacity's water supply catchment microbiota.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141525},
doi = {10.1016/j.jhazmat.2026.141525},
pmid = {41713270},
issn = {1873-3336},
abstract = {The proliferation of Microcystis has been linked to the widespread occurrence of antibiotic resistance genes (ARGs). Yet, the underlying mechanisms driven by the proliferation-induced microbial metabolic interactions and elevated microcystins (MCs) levels remain unclear. Here, through a year-long field study conducted in Shanghai's largest drinking water supply catchment, we demonstrated that Microcystis proliferation significantly increased ARG relative abundance (by 0.28 ± 0.05 log10(RPKM+1), corresponding to an approximately 60 % increase in abundance; P < 0.05, n = 63) and markedly reshaped the resistome structure (PERMANOVA, P < 0.01). During the whole Microcystis biomass cycle, the MCs were identified as the most predominant driver of the dynamics of waterborne ARGs (SNPs-RDA > 0.6, P < 0.01). Metagenomic binning and metabolic network reconstruction revealed that MC enhanced metabolic cooperation between ARG hosts and surrounding microorganisms (iNAP, Student's T-test, P < 0.001), suggesting MC-involved and nutrient co-metabolism that facilitated persistence of ARGs and the associated bacteria. Furthermore, plasmid conjugation experiments indicated that MCs significantly elevated plasmid-mediated ARG-transfer efficiency by twofold (Wilcoxon test, P < 0.05), promoting the spread of multidrug-resistant genes such as MexB, which may enable MCs to efflux. To quantify these effects, an MC index (MI) and a physiochemical index (PI) were developed, co-explaining > 80 % of ARG variation and identifying dissemination thresholds (TITAN, MI > 0.490 and PI > -0.032) for dominant resistance types. Our findings highlight MC as a natural promoter of ARG transmission, and the proposed indices offer viable tools for monitoring and mitigating antibiotic resistance in drinking water sources.},
}

@article {pmid41712274,
year = {2026},
author = {Winkler, MA and Hetland, MAK and Kaspersen, HP and Bakksjø, RJ and Bernhoff, E and Fostervold, A and Hawkey, J and Lunestad, BT and Marathe, NP and Raffelsberger, N and Samuelsen, Ø and Sunde, M and Sundsfjord, A and Lam, MMC and Löhr, IH},
title = {A One Health study of Klebsiella pneumoniae species complex plasmids shows a highly diverse and ecologically adaptable plasmidome.},
journal = {Microbial genomics},
volume = {12},
number = {2},
pages = {},
pmid = {41712274},
issn = {2057-5858},
mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/isolation & purification/classification ; *Plasmids/genetics ; Humans ; Animals ; Gene Transfer, Horizontal ; Klebsiella Infections/microbiology ; Whole Genome Sequencing ; One Health ; Virulence/genetics ; Genetic Variation ; Norway ; Genome, Bacterial ; },
abstract = {Plasmids play a pivotal role in the horizontal gene transfer (HGT) of antimicrobial resistance (AMR) and virulence determinants among bacteria. Members of the Klebsiella pneumoniae species complex (KpSC) can colonize humans, animals and various environments and frequently cause nosocomial and community-acquired infections in humans. While plasmid-borne AMR genes are prevalent in clinical strains, the diversity, distribution and association of plasmids encoding AMR and virulence across ecological niches remain poorly characterized. Understanding the traits governing successful plasmid transmission within and between ecological niches is critical for developing effective AMR prevention strategies. Here, we identify ecological and structural factors shaping plasmid persistence and dissemination. We analysed the plasmidome (i.e. total genetic content attributable to plasmids) of 578 whole-genome sequenced KpSC isolates collected in Norway between 2001 and 2020 from human (n=453), animal (n=102) and marine (n=23) sources. Plasmids from complete hybrid assemblies were annotated and clustered to evaluate the plasmid diversity and content across niches. Additionally, the representativeness of this plasmid collection was determined by clustering with a global collection of 8,656 circularized KpSC plasmids. In total, 1,415 circularized plasmids were identified and grouped according to rearrangement distance using Pling, resulting in 130 clusters (≥2 plasmids each), of which 36% (n=47) contained plasmids from more than one niche. The plasmids exhibited significant diversity, as 37% (n=524) remained singletons after clustering. AMR and virulence genes existed across diverse clusters and singletons but predominantly resided on 120-250 kbp conjugative or mobilizable plasmids harbouring various transposable elements. Human isolates carried higher overall plasmid burdens and harboured most AMR-encoding plasmids, while animal isolates were significantly enriched for virulence plasmids (P<0.001), largely due to iuc3 plasmids in pigs. Plasmids from human, animal and marine isolates formed shared genetic clusters spanning ecological boundaries, revealing the existence of widely distributed backbones already primed for AMR gene acquisition. The extensive diversity of KpSC plasmids highlights the dynamic nature of plasmid evolution, driven by HGT and selective pressures. The presence of variable clusters, marked by high genetic diversity, indicates a dynamic plasmidome capable of rapid adaptation to environmental pressures through the acquisition and rearrangement of accessory genes.},
}

*Klebsiella pneumoniae/genetics/pathogenicity/isolation & purification/classification
*Plasmids/genetics
Humans
Animals
Gene Transfer, Horizontal
Klebsiella Infections/microbiology
Whole Genome Sequencing
One Health
Virulence/genetics
Genetic Variation
Norway
Genome, Bacterial

@article {pmid41710376,
year = {2026},
author = {Jiang, X and Liu, F and Chai, J and Li, X and Li, Y and Fu, S and Li, Y},
title = {A One Health Perspective on the Plasmid Backbone Preference and Evolutionary Adaptation of tmexCD-toprJ in Klebsiella spp.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {585632},
pmid = {41710376},
issn = {1178-6973},
abstract = {BACKGROUND: Antimicrobial resistance (AMR) poses a critical One Health challenge, linking human, animal, and environmental health through the movement of multidrug-resistant (MDR) bacteria and resistance determinants. The tmexCD-toprJ gene cluster, an efflux pump conferring high-level resistance to tigecycline and eravacycline. However, its plasmid backbone preferences and evolutionary trajectories in Klebsiella spp. remain insufficiently characterized.

METHODS: This study investigated the plasmid backbone preference and evolutionary characteristics of tmexCD-toprJ-harboring plasmids in Klebsiella spp. using whole-genome sequencing of three clinical strains carrying tmexCD-toprJ collected from 2018 to 2023. Conjugation assays, comparative genomics, and global epidemiological analysis were performed to assess plasmid mobility, genetic context, and evolutionary direction under the One Health framework.

RESULTS: All three isolates (K7, K36, and K307) exhibited MDR and harbored major resistance genes, including blaIMP-4, mcr-1.1, and blaNDM-1 , respectively. The plasmid from K36 was transferable to EC600 (frequency, 10[-7]), confirming cross-species mobility. Global database analysis revealed that tmexCD-toprJ-positive Klebsiella spp. isolates (n=92) originated mainly from humans (59.8%), followed by animals (37.0%) and environments (3.3%). Phylogenetic and plasmid analyses the tmexCD1-toprJ1 variant was mainly associated with these hybrid plasmids, frequently co-localizing with sul1, qnrB, and strA/B to form stable "tigecycline-aminoglycoside-sulfonamide" co-resistance modules. In contrast, tmexCD2-toprJ2 was more often inserted into classical resistant plasmids.

CONCLUSION: These findings demonstrate that tmexCD-toprJ has evolved as a highly mobile resistance determinant within Klebsiella spp. disseminating across the human-animal-environment interface via hybrid plasmids and horizontal gene transfer. This underscores the urgent need for integrated One Health surveillance and containment strategies to mitigate plasmid-mediated multidrug resistance and its global public health impact.},
}

@article {pmid41708296,
year = {2026},
author = {Huang, J and Zhang, J and Liang, H and Fang, P and Tang, A and Klümper, U and Guo, J and Berendonk, TU and Honda, R and Lin, L and Li, X and Li, B},
title = {Antibiotics or Heavy Metals in Livestock Wastewater: Which One Is the Main Driver for the Development and Spread of Antibiotic Resistance under Coexposure?.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06042},
pmid = {41708296},
issn = {1520-5851},
abstract = {Antibiotics and heavy metals are widely used in livestock farming to promote animal health and growth, leading to their frequent co-occurrence as contaminants in livestock wastewater. However, their relative contributions to shaping the antibiotic resistome in treatment systems remain unclear. In this study, we simulated an aerobic activated sludge process treating livestock wastewater containing enrofloxacin and heavy metals (Cu[2+] and Zn[2+]) to evaluate the development of antibiotic resistance using metagenomic and metatranscriptomic approaches. We observed a diverse and transcriptionally active resistome with over half of the detected antibiotic resistance genes (ARGs) showing expression. ARG profiles under coexposure to enrofloxacin and heavy metals more closely resembled those under heavy metal exposure alone than those under enrofloxacin exposure alone. Zn[2+] exposure resulted in the highest absolute ARG abundance, nearly double that of the control group. Both enrofloxacin and heavy metals significantly altered the abundance and phylogenetic composition of the antibiotic-resistant bacteria (ARB). The exposure to Zn[2+] enhanced the relative abundance and expression level of both metal resistance genes (MRGs)-carrying ARB and the ARGs-carrying plasmids. Phylogenetic analysis of ARG flanking sequences revealed high homology across various genetic contexts. Among mobile genetic elements, plasmids had a greater influence on ARG profiles than did phages or integrative and conjugative elements (ICEs). Transcriptional profiles of microbial physiological adaptations suggested that modulation of cell membrane permeability, promotion of conjugative transfer, and formation of biofilm might play roles in enhancing antibiotic resistance. These findings suggest at environmentally relevant concentrations, heavy metals such as Zn[2+] may present a stronger selective pressure than enrofloxacin for the propagation of antibiotic resistance in aerobic activated sludge process treating livestock wastewater.},
}

@article {pmid41707201,
year = {2026},
author = {Sudhakari, PA and Ramisetty, BCM},
title = {Toxin-antitoxin systems propagate through addictive selection during bacterial chromosome-plasmid conflicts.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnag021},
pmid = {41707201},
issn = {1574-6968},
abstract = {Plasmids are obligate genetic parasites that significantly influence bacterial host adaptation, ecology, and clinically relevant traits such as antibiotic resistance. They persist within host populations primarily through self-maintenance mechanisms, most notably Toxin-Antitoxin (TA) systems, which are autoregulated poison-antidote operons mediating genomic conflict. Plasmid-encoded TAs act as "addiction modules," promoting plasmid stability via post-segregational killing of daughter cells that fail to inherit the plasmid. However, the widespread and abundant presence of TAs on bacterial chromosomes remains an evolutionary puzzle. We conducted comprehensive bioinformatics analyses of 11,000 bacterial chromosomes and 1,300 plasmids, focusing on Type II TAs in Escherichia and Shigella species, to elucidate their prevalence, distribution, and ecological significance. Our results reveal distinct horizontal gene transfer patterns and strongly support the anti-addiction hypothesis, which posits that chromosomal TAs protect host cells by neutralizing TA-plasmid addiction effects. This neutralization allows for plasmid loss without the toxin-mediated lethal consequences, resulting in a pattern of mutual exclusivity between identical chromosomal and plasmid TAs. This study reinforces the view that chromosomal Type II toxin-antitoxin systems play a significant role in counteracting addiction processes within bacterial chromosomes.},
}

@article {pmid41706200,
year = {2026},
author = {Zhou, D and Fan, J and Zhang, D and Ma, X and Li, Y and Zhang, X and Zheng, S and Hou, Q and Li, S and Li, G and Han, H},
title = {Emergence of a KL239-OCL6-ST63 Carbapenem-Resistant Acinetobacter pittii Strain, Co-carrying blaNDM-1 and blaOXA-500.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {181},
pmid = {41706200},
issn = {1432-0991},
support = {no.202410201105//the Jilin Province's Training Program of Innovation and Entrepreneurship for Undergraduates/ ; },
mesh = {*beta-Lactamases/genetics/metabolism ; *Acinetobacter/genetics/drug effects/isolation & purification/enzymology/classification ; *Carbapenems/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Animals ; Plasmids/genetics ; *Acinetobacter Infections/microbiology ; Phylogeny ; Humans ; China ; *Bacterial Proteins/genetics/metabolism ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; Genome, Bacterial ; Moths/microbiology ; Whole Genome Sequencing ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {To characterize the genomic features, antimicrobial resistance mechanisms, and biological characteristics of a carbapenem-resistant Acinetobacter pittii strain co-harboring plasmid-borne blaNDM-1 and chromosomally located blaOXA-500. An A. pittii strain (L802) was isolated from an intestinal sample of a diarrhea outpatient in Hangzhou, Zhejiang Province, China. Whole-genome sequencing was performed using Illumina and Oxford Nanopore platforms, followed by comprehensive bioinformatics analysis. The localization of blaNDM-1 was determined by S1-PFGE and Southern blotting. Horizontal gene transfer potential was evaluated by conjugation and electrotransformation assays. Antimicrobial susceptibility testing, biofilm formation assays, virulence evaluation using a Galleria mellonella infection model, scanning electron microscopy, phylogenetic analysis, and RT-qPCR analysis of resistance gene expression under carbapenem induction were conducted. Strain L802 was identified as A. pittii ST63 and exhibited high-level resistance to carbapenems and multiple cephalosporins, while remaining susceptible to polymyxin B and tigecycline. Whole-genome analysis revealed a 3.86 Mb circular chromosome and four plasmids. The blaNDM-1 gene was located on a ~ 41 kb IncR-type plasmid (pL802-NDM-1) together with aph(3')-VI, sharing 99-100% sequence identity with plasmids from diverse Enterobacteriaceae species. Conjugation assays failed to yield transconjugants; however, electrotransformation confirmed that the blaNDM-1-carrying plasmid could be introduced into Escherichia coli DH5α under laboratory conditions. Importantly, blaOXA-500 was located on the chromosome, representing a rare genetic configuration that may contribute to enhanced stability compared with plasmid-borne resistance genes. Phenotypic assays showed weak biofilm formation and low virulence in the Galleria mellonella model. Phylogenetic analysis indicated that L802 clustered closely with other A. pittii strains isolated in China, suggesting possible regional dissemination. This study reports, for the first time in Zhejiang, China, an A. pittii strain co-harboring plasmid-borne blaNDM-1 and chromosomally located blaOXA-500. The coexistence of mobile and chromosomally encoded carbapenemase genes highlights a concerning resistance strategy and underscores the need for continuous surveillance and infection control measures against emerging multidrug-resistant Acinetobacter species.},
}

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

@article {pmid41704853,
year = {2025},
author = {Wang, Q and Wang, W and Qiu, Y and Dai, G and Li, B and Zhou, Y and Bai, Y and Zhang, J},
title = {Chromosomal dif sites and associated modules identified in Acinetobacter sp. drive the horizontal transfer of antibiotic resistance.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1708097},
pmid = {41704853},
issn = {1664-302X},
abstract = {INTRODUCTION: Modules containing antibiotic resistance genes (ARGs) flanked by Xer site-specific recombination sites have been identified in Acinetobacter plasmids and are considered mobile genetic elements (MGEs) that facilitate horizontal gene transfer via the XerCD site-specific recombination (XerCD SSR) system. Although additional dif-like sites have been identified on the Acinetobacter chromosome beyond the main locus, it remains unclear whether these sites are associated with chromosomal dif modules.

METHODS: MacConkey agar plates supplemented with meropenem were used to isolate the resistant strain. Whole-genome sequencing (WGS) was performed on the Oxford Nanopore platform, and the bacterial species was identified using Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (dDDH). Antimicrobial susceptibility testing was performed against 18 antibiotics. Identification of dif and pdif sites was performed using BLAST tools.

RESULTS: This study identified numerous Xer modules containing resistance genes, IS elements, and other functional genes within the chromosome and plasmid of strain M10 (Acinetobacter sp.) isolated from a farmer at a cattle farm in Guangxi, China. Genome analysis and antimicrobial susceptibility testing confirm the association between these modules carrying resistance genes and resistant phenotypes. Chromosomal dif sites and associated dif modules in the strain were highly similar (sequence identity >99%) to plasmid-carried pdif sites and associated pdif modules in the public database. These suggest that additional chromosomal dif-like sites facilitate dif module formation, and that gene flow occurs between the chromosomes and plasmids of Acinetobacter. Furthermore, most Xer sites clustered to form a linear multi-module array, termed chromosomal dif module island and plasmid-borne pdif module island. Similar configurations were frequently observed in public Acinetobacter plasmid genomes.

DISCUSSION: Additional dif-like sites are present in Acinetobacter chromosomes, which are unlikely to play a function in chromosomal dimer resolution, and the modules they form are functionally similar to pdif modules, both of which play an important role in horizontal gene transfer.},
}

@article {pmid41702340,
year = {2026},
author = {Asha, IJ and Gupta, SD and Munim, MA and Akter, NN and Tamanna, S and Rahman, A and Imran, A and Das, SC and Hossain, MM and Islam, MM and Barman, DN},
title = {Emerging zoonotic risks: whole-genome sequencing reveals antimicrobial resistance and genomic diversity in Providencia stuartii isolated from broiler chickens in Noakhali, Bangladesh.},
journal = {Poultry science},
volume = {105},
number = {5},
pages = {106602},
pmid = {41702340},
issn = {1525-3171},
abstract = {Providencia stuartii is emerging as an Extensively Drug-Resistant (XDR) pathogen commonly found in animals, insects, and in burned and immunocompromised conditions. The misuse of antibiotics in poultry feed causes the emergence of XDR bacteria in the poultry industry. The knowledge of zoonotic transmissibility of poultry-derived P. stuartii remains elusive in Noakhali, Bangladesh. Poultry fecal and rectal swab samples were collected from selected farms in Noakhali, Bangladesh. Bacterial isolation and identification were performed using MacConkey agar, biochemical tests, and 16S rRNA Sanger sequencing. Antimicrobial susceptibility was assessed by the Kirby-Bauer disk diffusion method, and isolates with high multiple antibiotic resistance (MAR) indices were selected for whole-genome sequencing (WGS). Quality control, genome assembly, annotation, gene identification, pan-genome analysis, pathogenicity profiling, and comparative proteome analyses were subsequently conducted. Antibiogram analysis showed that ps_nstu_001 and ps_nstu_002 were resistant to 17 and 13 tested antibiotics, respectively. Furthermore, whole-genome sequencing revealed that both strains harbored resistance determinants to aminoglycosides, tetracyclines, sulfonamides, cephalosporins, β-lactams, and carbapenems. Additionally, mobile genetic elements (MGEs) and plasmids were identified, which represent the horizontal gene transfer capability. Moreover, pangenome analysis revealed ongoing gene acquisition and substantial genomic diversity among the isolates. The isolate ps_nstu_001 was identified as a putative human pathogen and clustered closely with a clinical strain isolated in the United States. In contrast, ps_nstu_002 was predicted to be a non-human pathogen; however, it exhibited a clear evolutionary relationship with a clinical isolate obtained from a diarrheal patient in Bangladesh, suggesting potential pathogenic relevance. Global pathogenic potential of the studied strains and key proteomic similarities between pathogenic and non-pathogenic strains revealed by pathogenicity profiling and proteome comparison. To conclude, these XDR isolates indicate the potential for zoonotic transmission and the spread of resistant genes to other animals, posing a significant public health risk.},
}

@article {pmid41701335,
year = {2026},
author = {Chatterjee, J and Kayet, P and Ghosh, M and Dutta, S and Basak, S},
title = {Genetic Exchanges Shape the Evolutionary Diversification Among Shigella phages.},
journal = {Journal of molecular evolution},
volume = {},
number = {},
pages = {},
pmid = {41701335},
issn = {1432-1432},
support = {2021-10515//Indian Council of Medical Research/ ; },
abstract = {Shigella is a genus of bacteria that is a prevalent cause of bacterial diarrhoea (i.e., shigellosis). Shigella bacteriophages are shaping bacterial fitness. Bacteriophages can carry genes that contribute to Shigella virulence and antibiotic resistance, and these genes are frequently found on mobile genetic elements (MGEs). Horizontal gene transfer (HGT) of these components is a major driver of bacterial evolution. A comprehensive genomic analysis of these bacteriophages is required to deepen understanding of candidate genes for MGEs and HGTs. Through genetic exchange, phages acquire novel genetic features that confer selective advantages. In this study, we identified the weighted gene repertoire relatedness (wGRR) metric. We associated it with the infecting host species andgenetic exchanges among Shigella phages using the weighted gene repertoire relatedness (wGRR) metric. We associated them with the infecting host species and phage lifestyles to examine evolutionary constraints among phages. We observed that HGTs can affect genes' GC content, which, in turn, influences amino acid usage, thereby shaping the amino acid usage of the resulting proteins. Host-range expansion is also observed among Shigella phages. However, we also noted that Shigella phages do not have the propensity for genetic transfer with dissimilar lifestyles. The gene pool of bacteriophages, due to horizontal transfer, can broaden their host range, making them more suitable for applications in phage therapy against antibiotic-resistant bacteria. Horizontal gene transfer can expand the bacteriophage gene pool, thereby increasing host range and making them more suitable for phage therapy against antibiotic-resistant bacteria. Overall, this study provides deeper insight into MGEs and HGTs among Shigella phages and their evolutionary significance for infectivity.},
}

@article {pmid41700089,
year = {2026},
author = {Rezvykh, AP and Kulikova, DA and Zelentsova, ES and Protsenko, L and Bespalova, AV and Guseva, IO and Blumenstiel, JP and Evgen'ev, MB and Funikov, SY},
title = {Transposable elements as drivers of genome evolution in Drosophila virilis.},
journal = {Nucleic acids research},
volume = {54},
number = {4},
pages = {},
pmid = {41700089},
issn = {1362-4962},
support = {22-74-10050-P//Russian Science Foundation/ ; },
mesh = {Animals ; *Drosophila/genetics/classification ; *DNA Transposable Elements/genetics ; *Genome, Insect ; *Evolution, Molecular ; Heterochromatin/genetics ; Retroelements ; Epigenesis, Genetic ; Gene Transfer, Horizontal ; Euchromatin/genetics ; Phylogeny ; Histones/metabolism ; },
abstract = {Transposable elements (TEs) drive genomic innovation, but their dynamics in non-model species remain unclear. Here, we integrated multi-omics data to explore TE dynamics in Drosophila virilis, an important model for repetitive DNA research. By combining computational predictions with manual curation, we identified 100 TE families and delineated three temporal waves of TE mobilization: recent activity, speciation-associated, and ancient invasions. TEs in D. virilis dynamically colonise both euchromatin and heterochromatin, suggesting heterochromatin is not solely a repository for degenerate repeats. While most TEs are widespread across strains, some exhibit strain-specific expansions, indicating varied activity and silencing. We found substantial evidence for horizontal transfer of TEs among close relatives, demonstrating that the D. virilis species group functions effectively as a TE "ecosystem", allowing for recurrent invasion, loss, and re-invasion of TE lineages across the group. Epigenetic profiling revealed that H3K9me3 spreading from TEs represses adjacent genes in a distance-dependent manner, influenced by insertion length and genomic context, affecting developmental and metabolic genes. We also discovered the first spontaneous polymorphic inversion in D. virilis linked to retrotransposons. Our findings illuminate TEs as drivers of genomic innovation, influencing gene regulation and evolutionary trajectories, providing a framework for studying TE dynamics across animal species.},
}

Animals
*Drosophila/genetics/classification
*DNA Transposable Elements/genetics
*Genome, Insect
*Evolution, Molecular
Heterochromatin/genetics
Retroelements
Epigenesis, Genetic
Gene Transfer, Horizontal
Euchromatin/genetics
Phylogeny
Histones/metabolism

@article {pmid41699883,
year = {2026},
author = {Zeng, Z and Mansfield, JW and Vadillo-Dieguez, A and Connell, J and Irvine, J and Hulin, MT and Frutos, FD and Rabiey, M and Grinberg, NF and Harrison, RJ and Xu, X and Jackson, RW},
title = {Genomic Surveillance of Epiphytic Pseudomonas syringae Highlights Shared Reservoirs and Cross-Habitat Threats to Cherry Orchards and Nearby Woodland Plants.},
journal = {Molecular plant pathology},
volume = {27},
number = {2},
pages = {e70208},
pmid = {41699883},
issn = {1364-3703},
support = {BB/T010746/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //Jabbs Foundation/ ; },
mesh = {*Pseudomonas syringae/genetics/pathogenicity ; *Plant Diseases/microbiology ; *Prunus avium/microbiology ; Phylogeny ; *Ecosystem ; Genome, Bacterial/genetics ; Plant Leaves/microbiology ; Genomics ; Forests ; },
abstract = {Plant surfaces host diverse microbial communities acting as reservoirs for pathogenic lineages, yet the ecological dynamics and evolutionary consequences of such reservoirs remain underexplored. We conducted landscape-scale genomic surveillance of Pseudomonas syringae on symptomless leaves of cultivated cherry in orchards and wild plant species in adjacent woodlands across the UK, aiming to understand how phyllosphere populations contribute to the emergence of bacterial canker. Whole genome sequencing of 540 isolates collected over two years and across four regions revealed 10 diverse P. syringae phylogroups (PGs) on symptomless leaves. Both orchard and woodland environments harboured a similar range of PGs, but recovery frequency was very different. PG2d strains dominated cherry orchards, whereas PGs 2b and 13a were prevalent in woodlands. Certain PG2d subclades, recovered from both environments, caused disease on cultivated and wild cherry leaves. Additional strains were found to be pathogenic to Phaseolus bean pods. The pathogens of cherry were characterised by the presence of genes encoding the synthesis of the pathotoxin syringolin A and a subset of effector proteins including HopAW1, AvrRpm1 and HopAR1. Resolution of subclades within PG2d provided insights into the emergence of virulent epiphytic strains that have not yet reached the mostly northerly sampling sites but are threats to both cultivated and environmental Prunus spp. Fine-scale analysis of subclade PG2d-3 revealed potential divergence between orchard and woodland populations, with 49 genes exclusive to a woodland lineage. Thirty-eight of these genes were found within prophages, indicating the potential role of bacteriophage-mediated horizontal gene transfer in adaptation to non-agricultural reservoirs.},
}

*Pseudomonas syringae/genetics/pathogenicity
*Plant Diseases/microbiology
*Prunus avium/microbiology
Phylogeny
*Ecosystem
Genome, Bacterial/genetics
Plant Leaves/microbiology
Genomics
Forests

@article {pmid41699255,
year = {2026},
author = {Tao, H and Zhou, L and Zhou, Y and Wang, Y and Lv, H and Wang, T and Xu, C and Chu, Y and Wang, X and Song, T and Lin, J},
title = {Functional characterization of macrolide esterase from cyanobacteria and their potential dissemination risk.},
journal = {npj antimicrobials and resistance},
volume = {4},
number = {1},
pages = {10},
pmid = {41699255},
issn = {2731-8745},
support = {2023YFS0384;NO. FZBC2022003;ZSKHHZ [2021] No.320;Grant No.: 82372290;2023NSFSC1467//Sichuan key research and development program;Open Project Program of Irradiation Preservation Key Laboratory of Sichuan Province, Sichuan Institute of Atomic Energy;Zunyi Technology and Big data Bureau, Moutai institute Joint Science and Technology Research and Development Project;National Natural Science Foundation of China;Natural Science Foundation of Sichuan Province/ ; 2023YFS0384;NO. FZBC2022003;ZSKHHZ [2021] No.320;Grant No.: 82372290;2023NSFSC1467//Sichuan key research and development program;Open Project Program of Irradiation Preservation Key Laboratory of Sichuan Province, Sichuan Institute of Atomic Energy;Zunyi Technology and Big data Bureau, Moutai institute Joint Science and Technology Research and Development Project;National Natural Science Foundation of China;Natural Science Foundation of Sichuan Province/ ; 2023YFS0384;NO. FZBC2022003;ZSKHHZ [2021] No.320;Grant No.: 82372290;2023NSFSC1467//Sichuan key research and development program;Open Project Program of Irradiation Preservation Key Laboratory of Sichuan Province, Sichuan Institute of Atomic Energy;Zunyi Technology and Big data Bureau, Moutai institute Joint Science and Technology Research and Development Project;National Natural Science Foundation of China;Natural Science Foundation of Sichuan Province/ ; 2023YFS0384;NO. FZBC2022003;ZSKHHZ [2021] No.320;Grant No.: 82372290;2023NSFSC1467//Sichuan key research and development program;Open Project Program of Irradiation Preservation Key Laboratory of Sichuan Province, Sichuan Institute of Atomic Energy;Zunyi Technology and Big data Bureau, Moutai institute Joint Science and Technology Research and Development Project;National Natural Science Foundation of China;Natural Science Foundation of Sichuan Province/ ; 2023YFS0384;NO. FZBC2022003;ZSKHHZ [2021] No.320;Grant No.: 82372290;2023NSFSC1467//Sichuan key research and development program;Open Project Program of Irradiation Preservation Key Laboratory of Sichuan Province, Sichuan Institute of Atomic Energy;Zunyi Technology and Big data Bureau, Moutai institute Joint Science and Technology Research and Development Project;National Natural Science Foundation of China;Natural Science Foundation of Sichuan Province/ ; 2023YFS0384;NO. FZBC2022003;ZSKHHZ [2021] No.320;Grant No.: 82372290;2023NSFSC1467//Sichuan key research and development program;Open Project Program of Irradiation Preservation Key Laboratory of Sichuan Province, Sichuan Institute of Atomic Energy;Zunyi Technology and Big data Bureau, Moutai institute Joint Science and Technology Research and Development Project;National Natural Science Foundation of China;Natural Science Foundation of Sichuan Province/ ; 2023YFS0384;NO. FZBC2022003;ZSKHHZ [2021] No.320;Grant No.: 82372290;2023NSFSC1467//Sichuan key research and development program;Open Project Program of Irradiation Preservation Key Laboratory of Sichuan Province, Sichuan Institute of Atomic Energy;Zunyi Technology and Big data Bureau, Moutai institute Joint Science and Technology Research and Development Project;National Natural Science Foundation of China;Natural Science Foundation of Sichuan Province/ ; 2023YFS0384;NO. FZBC2022003;ZSKHHZ [2021] No.320;Grant No.: 82372290;2023NSFSC1467//Sichuan key research and development program;Open Project Program of Irradiation Preservation Key Laboratory of Sichuan Province, Sichuan Institute of Atomic Energy;Zunyi Technology and Big data Bureau, Moutai institute Joint Science and Technology Research and Development Project;National Natural Science Foundation of China;Natural Science Foundation of Sichuan Province/ ; 2023YFS0384;NO. FZBC2022003;ZSKHHZ [2021] No.320;Grant No.: 82372290;2023NSFSC1467//Sichuan key research and development program;Open Project Program of Irradiation Preservation Key Laboratory of Sichuan Province, Sichuan Institute of Atomic Energy;Zunyi Technology and Big data Bureau, Moutai institute Joint Science and Technology Research and Development Project;National Natural Science Foundation of China;Natural Science Foundation of Sichuan Province/ ; 2023YFS0384;NO. FZBC2022003;ZSKHHZ [2021] No.320;Grant No.: 82372290;2023NSFSC1467//Sichuan key research and development program;Open Project Program of Irradiation Preservation Key Laboratory of Sichuan Province, Sichuan Institute of Atomic Energy;Zunyi Technology and Big data Bureau, Moutai institute Joint Science and Technology Research and Development Project;National Natural Science Foundation of China;Natural Science Foundation of Sichuan Province/ ; 2023YFS0384;NO. FZBC2022003;ZSKHHZ [2021] No.320;Grant No.: 82372290;2023NSFSC1467//Sichuan key research and development program;Open Project Program of Irradiation Preservation Key Laboratory of Sichuan Province, Sichuan Institute of Atomic Energy;Zunyi Technology and Big data Bureau, Moutai institute Joint Science and Technology Research and Development Project;National Natural Science Foundation of China;Natural Science Foundation of Sichuan Province/ ; },
abstract = {The global dissemination of antibiotic resistance genes (ARGs) across diverse environments has emerged as a critical challenge to public health. As essential primary producers, Cyanobacteria colonize extreme and heterogeneous habitats, coexisting with gut microbiota in wastewater, marine ecosystems, and reservoirs, where they may potentiate the proliferation and transmission of ARGs under antibiotic selective pressures. In this study, three macrolide esterases (NOD-1, OCA-1, and OCB-1) of Cyanobacterial origin were identified through mining of local genomic repositories. These enzymes, classified as serine-dependent alpha/beta -hydrolases, were experimentally validated through antimicrobial susceptibility testing and zone of inhibition assays to inactivate specific 16-membered macrolide antibiotics. Comparative analysis of genomic regions flanking these resistance determinants revealed the presence of mobile genetic elements (MGEs) and co-localized multidrug resistance genes, strongly suggesting the likelihood of horizontal gene transfer (HGT) within Cyanobacterial populations. Such genetic mobility may exacerbate antibiotic resistance dissemination in aquatic ecosystems, underscoring the ecological risks posed by Cyanobacteria as reservoirs and vectors of ARGs.},
}

@article {pmid41698534,
year = {2026},
author = {Jaffer, YD and Abdolahpur Monikh, F and Nguyen, NHA and Sevcu, A and Abdulkadir, N and Raha, J and Katsumiti, A and Bilbao, A and Altman, K and Grossart, HP},
title = {Bio-based microplastics increase the horizontal transfer of antibiotic resistance genes in aquatic environments.},
journal = {NanoImpact},
volume = {41},
number = {},
pages = {100613},
doi = {10.1016/j.impact.2026.100613},
pmid = {41698534},
issn = {2452-0748},
abstract = {The role of microplastics as vectors for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) is increasingly recognized. This study investigated whether bio-based microplastics, often promoted as environmentally friendly alternatives, exhibit similar or enhanced HGT potential compared to conventional plastics. We examined the HGT rates of the trimethoprim resistance gene (dfrA1) and tetracycline resistance gene (tetA), carried on a broad-host-range plasmid, among Escherichia coli (donor) and Vibrio parahaemolyticus, Pseudomonas sp., or a natural lake microbial community (recipients). Four bio-based polymer types-polylactic acid (PLA) granules, commercial PLA, high-density polyethylene (HDPE) granules, and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV)- were compared with two conventional microplastics, polyethylene terephthalate (PET) and bottle-derived HDPE. The bio-based microplastics exhibited significantly higher HGT frequencies, with a 21-48-fold increase compared to control chitosan in single-strain experiments and a 13-fold increase within the lake microbial community. 16S rRNA amplicon sequencing revealed distinct bacterial community compositions colonizing different microplastic types in the lake water. The transconjugant communities, indicative of successful HGT events, were strongly influenced by microplastic type. While Nannocystis was generally dominant, the PLA (granule) microplastic exhibited a unique profile dominated by Candidatus Megaira and Niveispirillum. Additionally, Flavobacterium and Fluviicola were uniquely detected as transconjugants on HDPE (granule). These findings demonstrate that bioplastics have a significant influence on the selective enrichment of specific transconjugant genera, suggesting a prominent role of microplastics, particularly bio-based plastics, in shaping ARG dissemination within complex microbial ecosystems. We recommend a comprehensive risk assessment of bio-based plastics, particularly their potential to enhance the spread of ARGs, before their widespread implementation in consumer products.},
}

@article {pmid41697036,
year = {2026},
author = {Reva, ON and Sifuna, A and Orata, F and Omolo, C and Iramiot, JS and Enright, MC and Mutshembele, A and Zhou, J and Shivoga, WA},
title = {From Lake Victoria to the Tap: Antibiotic Resistance and Pathogenic Contamination of Kisumu City Water Supply and Wastewater Network.},
journal = {Tropical medicine & international health : TM & IH},
volume = {},
number = {},
pages = {},
doi = {10.1111/tmi.70105},
pmid = {41697036},
issn = {1365-3156},
support = {GCRFNGR8\1143//UK Global Challenges Research Fund Networking/ ; NIHR163838//UK National Institute for Health and Care Research/ ; },
abstract = {Waterborne diseases and antimicrobial resistance (AMR) pose mounting public health threats across sub-Saharan Africa, particularly in rapidly urbanising regions dependent on untreated or poorly treated surface waters. This study applied shotgun metagenomic sequencing to characterise microbial communities, virulence factors and antibiotic resistance genes (ARGs) in water samples collected from Lake Victoria, River Wigwa, Dunga Water Treatment Plant, Nyalenda Wastewater Stabilisation Ponds and the tap water outlet in post-treatment supply pipe in Kisumu city (Kenya). Bacterial taxa dominated all metagenomes, with 121 classes represented. Cyanobacteria, particularly Planktothrix, were highly abundant in lake and tap water, whereas wastewater and river samples exhibited greater taxonomic diversity. Major human pathogens, including Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii and Bacillus cereus/anthracis, were detected in nearly all samples, with unexpectedly high prevalence in tap water. Viral indicators of faecal contamination (adenoviruses, enteroviruses and torque teno viruses) corroborated widespread wastewater influence. Functional gene profiling revealed a rich resistome comprising aminoglycoside-modifying enzymes, β-lactamases, vancomycin-resistance operons and disinfectant-resistance determinants. The highest ARG and virulence gene frequencies occurred in tap and treatment-plant water, suggesting that incomplete disinfection and biofilm persistence promote the proliferation and exchange of ARGs between environmental and pathogenic taxa. In contrast, Lake Victoria water exhibited lower ARG abundance, reflecting natural self-purification processes. These findings underscore the inadequate water treatment and open wastewater systems create ecological 'hotspots' for ARG selection and horizontal gene transfer. Metagenomic surveillance integrated into One Health frameworks can enhance risk forecasting and guide interventions to mitigate AMR emergence and dissemination in freshwater systems serving over 35 million people across the Lake Victoria basin.},
}

@article {pmid41692309,
year = {2026},
author = {Hao, X and Jiang, L and Chen, M and Liu, S and Zhu, L and Jiang, D and Bai, L},
title = {Antibiotic sensitivity as a key Determinant: B. Subtilis Reshapes the Microecology to mitigate antibiotic resistance genes during composting.},
journal = {Bioresource technology},
volume = {447},
number = {},
pages = {134222},
doi = {10.1016/j.biortech.2026.134222},
pmid = {41692309},
issn = {1873-2976},
abstract = {This study aimed to investigate the role of inoculant antibiotic susceptibility in controlling antibiotic resistance genes (ARGs) during aerobic composting. A systematic comparison was conducted using Bacillus subtilis strains (sensitive, S; resistant, R) to assess ARG dynamics, microbial community evolution, and the underlying ecological mechanisms. Results demonstrated that the sensitive strain significantly enhanced composting efficiency, achieving a higher and longer-lasting secondary thermophilic phase (58.4°C for 4 days) and superior maturity indices compared to the resistant strain. Crucially, the R strain counteracted the ARG-removal effect of high temperatures, increasing total ARG abundance by 28.40% by day 6 and resulting in a final ARG burden 2.74 times higher than the S treatment.Microecological mechanism analysis revealed that the sensitive strain fostered a specialized, modular microbial network with reduced niche breadth, enhancing community stability and functioning as a genetic firewall to restrict ARG dissemination. In contrast, the resistant strain created a fragile, hyper-connected network with higher mobility of mobile genetic elements (MGEs), which facilitated horizontal gene transfer.Host identification analysis confirmed this mechanism, showing the S treatment effectively reduced potential ARG hosts to only two genera (PseudomonasandMoheibacter), significantly fewer than the 11 and 7 hosts identified in the control and R treatments, respectively. Partial least squares path modeling (PLS-PM) revealed that the sensitive strain uniquely reduced the influence of MGEs while enhancing temperature's role in ARG reduction. The findings establish that employing antibiotic-sensitive functional strains is a reliable strategy to mitigate environmental antibiotic resistance risks.},
}

@article {pmid41691814,
year = {2026},
author = {Guo, H and Liu, Q and Han, H and Xu, W and Shi, W and Zhao, M and Xiao, X and Liu, J and Li, T},
title = {Unveiling the adaptive evolution of halotolerant aceticlastic methanogenesis: Multi-scale responses and energy partition.},
journal = {Water research},
volume = {294},
number = {},
pages = {125552},
doi = {10.1016/j.watres.2026.125552},
pmid = {41691814},
issn = {1879-2448},
abstract = {The high concentration of salt ions in saline organic wastewater poses significant challenges for wastewater treatment technologies, particularly impacting the stability of anaerobic digesters. Aceticlastic methanogenesis is a crucial pathway for converting acetate into methane through methanoarchaea whose metabolism is adversely impacted by salt stress. To address this, long-term adaptive laboratory evolution (ALE) was conducted to cultivate halotolerant aceticlastic methanoarchaea, incorporating metagenomics, metatranscriptomic sequencing, metabolomics, and metabolic modeling to delineate genetic and metabolic responses. The evolved microbiome achieved a substantial increase in methanogenic activity at 5 % sodium chloride, reaching 82.25 % theoretical conversion of acetate to methane, significantly outperforming the original microbiome. This ALE process overcame the natural scarcity of aceticlastic methanogens in hypersaline environments. Key adaptation mechanisms were confirmed at the transcriptional level, primarily involving the upregulation of genes for inorganic ion transport, compatible solute uptake, and de novo biosynthesis. Horizontal gene transfer also contributed significantly through the transfer of osmoregulation genes, particularly those for compatible solute transport, suggesting an energy-efficient adaptation strategy of accumulating rather than synthesizing solutes. Metabolic flux analysis revealed that adjustments in energy distribution under salt stress are driven by the energetic cost of synthesizing compatible solutes, which highlights the importance of solute transporters for energy conservation. This study elucidates the complex interplay between metabolic reprogramming and gene transfer in enhancing microbial resilience under salt stress, thereby deepening our understanding of microbial adaptations in extreme environments and advancing biotechnological approaches for saline wastewater treatment.},
}

@article {pmid41690916,
year = {2026},
author = {Raoelijaona, F and Szczepaniak, J and Schahl, A and Bray, JE and Zhou, JC and Baker, L and El Omari, K and Lowe, E and Low, YS and Rodriguez, CM and Landsberg, MJ and Lott, JS and Kleanthous, C and Chavent, M and Maiden, MC and Seiradake, E},
title = {Ancestral neuronal receptors are bacterial accessory toxins.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-69246-x},
pmid = {41690916},
issn = {2041-1723},
support = {202827/Z/16/Z//Wellcome Trust (Wellcome)/ ; 226647/Z/22/Z//Wellcome Trust (Wellcome)/ ; 218205/Z/19/Z//Wellcome Trust (Wellcome)/ ; EMBO Young Investigator Programme//European Molecular Biology Organization (EMBO)/ ; },
abstract = {Horizontal gene transfer events were crucial in the emergence of multicellular life. A striking example is the acquisition of Teneurins, putative surface-exposed toxins in bacteria that function as cell adhesion receptors in metazoan neuronal development. Here, we demonstrate the evolutionary relationships between metazoan and bacterial Teneurins. We use cryogenic electron microscopy and bioinformatic analysis to show that bacterial Teneurins harbour a toxic protein in a proteinaceous shell. They are rare but widely distributed across bacterial taxa and are predominantly seen in species with complex social behaviours, suggesting roles in cell-to-cell interaction. This work confirms that metazoan Teneurins are repurposed bacterial toxins that have evolved to be essential mediators of intercellular communication in all advanced nervous systems. Their acquisition was a key event in the evolution of metazoans.},
}

@article {pmid41689363,
year = {2026},
author = {Valenzuela, M and Vásconez, IN and Méndez, V and Fuentes, B and Altimira, F and Valdés, F and Montenegro, I and Besoain, X and Seeger, M},
title = {Copper resistance and genetic determinants in Chilean strains of Clavibacter michiganensis the causal agent of bacterial canker of tomato.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70665},
pmid = {41689363},
issn = {1526-4998},
support = {//Universidad Técnica Federico Santa María/ ; //Agencia Nacional de Investigación y Desarrollo/ ; //GORE & CORE Region de O'Higgins/ ; },
abstract = {BACKGROUND: The control of Clavibacter michiganensis, the causal agent of bacterial canker in tomato, remains a significant challenge for crop cultivation. While copper-based products are the most commonly used bactericides, their efficacy against this pathogen is often inefficient. Therefore, the objective of this study was to determine the copper susceptibility of five Chilean Clavibacter michiganensis strains and to characterize their associated copper resistance gene repertoire.

RESULTS: Chilean strains VQ28, VQ143, and VL527 showed moderate copper resistance, being able to grow at a concentration ≤ 0.32 mm of copper in CYEG medium. In contrast, strains OP3 and MSF322 showed higher copper resistance, growing at a copper-concentration ≤ 0.4 mm. The search for genes associated with copper resistance revealed the presence of the copA, copC, copD, copZ, ycnI and ycnJ genes and the csoR1 regulator gene in the chromosomes of all the strains analyzed. The presence and location of the csoR2 and csoR3 regulators genes varied among the strains. Strains MSF322 and OP3, shown to be more tolerant to copper, possess a copB gene located in a plasmid which was not found in other Chilean strains. Notably, strain OP3, isolated in 2015 - years after the other strains - harbors copper resistance genes on plasmids highly similar to those in other Chilean strains, suggesting recent horizontal gene transfer.

CONCLUSION: Chilean strains of Clavibacter michiganensis exhibit moderate tolerance to copper, and the acquisition of new genes through horizontal gene transfer could play a crucial role in Clavibacter michiganensis copper resistance. © 2026 Society of Chemical Industry.},
}

@article {pmid41686637,
year = {2026},
author = {Gorzynski, J and Harling-Lee, JD and Figueroa, W and Alves, J and Yebra, G and Freeman, T and Penadés, JR and Fitzgerald, JR},
title = {Bacterial defense systems and host ecology drive the evolution of intra-species lineages.},
journal = {Cell reports},
volume = {45},
number = {2},
pages = {116957},
doi = {10.1016/j.celrep.2026.116957},
pmid = {41686637},
issn = {2211-1247},
abstract = {Horizontal gene transfer (HGT) is a major driver of diversity in bacterial populations. However, our understanding of its impact on the evolution of intra-species lineages is limited. The multi-host bacterial pathogen Staphylococcus aureus is differentiated into genetic lineages known as clonal complexes (CC) with variable host and disease tropisms. Here, we demonstrate that CCs exhibit extensive variation in pangenome size, structure, and gene flow, influenced by both genetic and ecological barriers to HGT. Examination of pangenome openness for each CC revealed remarkable variation that correlated strongly with host-species promiscuity. Notably, CCs were defined by horizontally acquired defense systems, and genetic subpopulations have diverged by changes to their type I restriction-modification (R-M) system repertoire, suggesting a role in lineage emergence. Overall, our data indicate a key role of HGT of defense systems in promoting the differentiation of S. aureus into lineages, with host ecology as a major driver of accessory genome variation.},
}

@article {pmid41684701,
year = {2026},
author = {Rao, YZ and Li, YX and Li, ZW and Qu, YN and Hedlund, BP and Williams, TA and Qi, YL and Xie, QJ and Yang, HL and Zhang, YQ and Jiang, HC and Palmer, M and Shi, M and Shu, WS and Hua, ZS and Li, WJ},
title = {Horizontal gene transfer and gene loss drove the divergent evolution of host dependency in Micrarchaeota.},
journal = {National science review},
volume = {13},
number = {4},
pages = {nwaf542},
pmid = {41684701},
issn = {2053-714X},
abstract = {The DPANN superphylum is a deep-branching radiation of archaea with small cell and genome sizes. Most DPANN lineages are predicted or validated to be host-dependent. However, certain lineages have substantial biosynthetic capacities and are potentially less dependent on hosts, or even free-living. Here, we reconstructed 163 Micrarchaeota genomes, comprising 48 assigned to previously undescribed orders and 115 affiliated with known orders. Investigation of their genetic repertoire revealed substantial metabolic capacity in Norongarragalinales-, Anstonellales- and the newly proposed Wunengiarchaeales-associated lineages, including complete or near-complete glycolysis and de novo biosynthetic pathways for nucleotides, amino acids, cofactors and cell envelopes. We classified genes related to the central metabolism but which are uncommon in DPANN archaea as putative free-living associated genes (pFLAGs). The extensive presence of pFLAGs in Norongarragalinales suggests a potential host-independent lifestyle. Reconstruction of evolutionary history revealed that these pFLAGs were not ancestral within the DPANN superphylum. Instead, we suggest that less-host-dependent organisms evolved from symbionts through the gradual acquisition of pFLAGs through horizontal gene transfer, whereas other Micrarchaeota lineages with streamlined genomes experienced reductive evolution due to thermal adaptation. Our analyses demonstrate that host dependency is not always an evolutionary dead end, but can be reversed through the acquisition of new metabolic capabilities by horizontal transfer.},
}

@article {pmid41684676,
year = {2026},
author = {Chukwujindu, C and Kolton, M and Fasakin, O and Pathak, A and Seaman, J and Chauhan, A},
title = {Microbial community structure and functional potential in a long-term uranium-nickel contaminated ecosystem.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1741152},
pmid = {41684676},
issn = {1664-302X},
abstract = {This study examined the microbial community structure, functional potential, and resistance determinants in uranium (U)- and nickel (Ni)-contaminated soils from the Savannah River Site (SRS), a former nuclear materials production and waste collection facility operated by the U. S. Department of Energy (DOE). Soil cores were collected from the Steed Pond area, where long-term discharge of acidic wastewater resulted in spatially variable contamination levels. Concentrations of U and Ni in the collected samples ranged from 0.22-10.44 g kg[-1] and 0.79-2.28 g kg[-1], respectively. Shotgun metagenomic and high-throughput quantitative PCR (HT-qPCR) analyses revealed bacterial communities dominated by Pseudomonadota, Actinomycetota, and Acidobacteriota, with enrichment of taxa affiliated with genera known to include diazotrophic members (e.g., Bradyrhizobium and Burkholderia), alongside increased abundance of nitrogen fixation-related functional genes. Carbon and nitrogen cycle genes were generally well represented across samples, with selective shifts observed in acetate assimilation genes (acsA/acsE) and comparatively low abundance of hydrazine oxidoreductase (hzo), indicating pathway-specific variation rather than broad metabolic suppression. A total of 117 resistance-associated genes were identified, comprising 93 antibiotic-resistance genes (ARGs), 3 metal-resistance genes (MRGs), and 21 mobile genetic elements (MGEs). Strong positive correlations among ARGs, MRGs, and MGEs indicate co-selection and horizontal gene transfer, forming a genetically mobile resistome. Collectively, these findings demonstrate that long-term U-Ni contamination selects for metabolically versatile, diazotroph-enriched, and genetically mobile microbiomes. Such communities exhibit both resistance proliferation and bioremediation potential, providing key insights into microbial adaptation and ecosystem recovery in legacy nuclear-contaminated soils.},
}

@article {pmid41684385,
year = {2026},
author = {Andres-Lasheras, S and Zaheer, R and Ortega-Polo, R and Schwinghamer, T and Abeysekara, S and Zovoilis, A and Zaidi, SE and Jelinski, M and McAllister, TA},
title = {Integrative and conjugative elements in Mycoplasmopsis bovis from Western Canadian feedlot cattle: characterization and conjugative transfer.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1719776},
pmid = {41684385},
issn = {2297-1769},
abstract = {INTRODUCTION: Bovine respiratory disease (BRD) is the most significant disease affecting North American feedlot cattle. It is a multifactorial disease influenced by bacterial and viral pathogens, as well as management and environmental factors. Mycoplasmopsis bovis is among the most pathogenic bovine mycoplasmas and is associated with chronic BRD that often fails to respond to antimicrobial therapy. Integrative and conjugative elements (ICE) facilitate horizontal gene transfer among mycoplasmas and may contribute to the spread of antimicrobial resistance in M. bovis.

METHODS: We identified mycoplasma ICEs (MICE) in the genomes of sequenced M. bovis isolates from western Canadian feedlot cattle (n = 124) and in vitro mating experiments to assess conjugation.

RESULTS AND DISCUSSION: Of these isolates, 33.1% harbored the array of MICE genes required for conjugation. M. bovis isolates conjugated at frequencies of 10-7-10-8 when cultured in SP4 broth under orbital agitation. Since MICE circularization is the initial step in conjugation, the presence of circular MICE (cMICE) was used as a proxy for conjugation capability (n = 451). Interestingly, 25.7% of the isolates were cMICE-positive, with a higher prevalence observed in M. bovis isolated from dairy as compared to beef feedlot cattle. Additionally, calves classified as high-risk for BRD were more likely to harbor cMICE-positive M. bovis in both cattle types. Backgrounded dairy cattle had a higher likelihood of carrying cMICE-positive M. bovis than those originating from ranches. These findings lay the groundwork for assessing cattle source as a determinant of cMICE-positive M. bovis and for developing targeted strategies to mitigate antimicrobial resistance.},
}

@article {pmid41679514,
year = {2026},
author = {Huang, WC and Huang, YT and Ko, WC and Shih, WA and Teng, CH and Wang, JL},
title = {Tet(X4)-Producing Escherichia coli Isolates in Taiwan.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2026.01.014},
pmid = {41679514},
issn = {2213-7173},
abstract = {BACKGROUND: Plasmid-mediated tet(X4), linked to high-level tigecycline resistance, was first identified in China with Escherichia coli (E. coli) as a major reservoir. No confirmed cases had been reported in Taiwan.

METHODS: We examined 81 tigecycline-resistant E. coli isolates (MIC ≥ 4 mg/L) collected in Taiwan from 2015-2022, including 71.6% carbapenem-resistant and 28.4% carbapenem-susceptible strains. Thirty-six underwent whole-genome sequencing to investigate resistance mechanisms.

RESULTS: Two isolates (2.5%) carried tet(X4) on novel plasmids (pEC1360-1 and pEC1638-1). Both plasmids contained the ISVsa3-estT-tet(X4)-ISVsa3 (IETI) element, a mobile unit capable of transposon-mediated transfer without a fixed integration hotspot. The tet(X4)-positive strains showed distinct evolutionary divergence from the first reported Chinese strain (LHM10-1). Tet(X4) was located on different Inc-type plasmids, including a 66.8 kb IncR and a 159.3 kb IncR/IncFIB(K)/IncFIA(HI1) plasmid, across various sequence types. No tet(X4) was detected in carbapenem-resistant isolates. Other resistance genes, such as cmlA1 and floR, were more prevalent in carbapenem-susceptible isolates (66.7% vs. 25.9%, P = 0.077).

CONCLUSION: This study reports the first tet(X4)-positive E. coli isolates in Taiwan, both from carbapenem-susceptible strains. The presence of novel mobile plasmids underscores the potential for horizontal gene transfer. Continuous surveillance of tet(X) and other last-line antibiotic resistance mechanisms is essential to mitigate the risk of further spread.},
}

@article {pmid41679041,
year = {2026},
author = {Jia, J and Ao, H and Xiong, X and Wang, S and Xi, X and Chen, K and Wu, C},
title = {Cladophora drives the evolution of its epiphytic communities and antibiotic resistome in the littoral zone of Qinghai Lake.},
journal = {Water research},
volume = {294},
number = {},
pages = {125530},
doi = {10.1016/j.watres.2026.125530},
pmid = {41679041},
issn = {1879-2448},
abstract = {Cladophora blooms, exacerbated by climate change and littoral eutrophication, pose a significant ecological threat. Of particular concern is their potential to disrupt phytoplankton and bacterial assemblages, triggering a cascade of effects that may include shifts in nutrient cycling and the dissemination of resistomes. However, the mechanistic links between Cladophora's life-stage-dependent dissolved organic matter (DOM) release, its role in restructuring epiphytic communities, and its promotion of resistome dissemination in natural, oligotrophic lakes remain poorly understood. To address this, this study integrates field and laboratory investigations of Cladophora qinghaiensis sp. nov.. The algal phycosphere functions as a dynamic "gene incubator", driven by chemical shifts in algal‑derived DOM. During decay under low‑oxygen conditions, DOM composition transitions from tyrosine‑like proteins to recalcitrant fulvic‑acid‑like compounds, selectively enriching competitive, intrinsically resistant taxa such as Halomonas and Phacus. Microbes such as Acinetobacter drive nutrient cycling (e.g., nitrogen metabolism) and serve as hotspots for resistomes within the phycosphere. Contrary to the expectation that high cell density favors horizontal gene transfer (HGT), genomic analyses show that vertical gene transfer (VGT) dominates antibiotic resistance gene (ARG) proliferation in this niche, a pattern explained by strong DOM‑mediated host selection and subsequent propagation. In contrast, the resistome in the surrounding water is more diverse and primarily shaped by HGT via mobile genetic elements. These results establish a mechanistic link between life‑stage‑specific algal DOM components, selective epiphytic communities enrichment, and divergent pathways of resistome evolution, positioning the phycosphere as a key source of ARGs that amplifies ecological risk in nearshore environments.},
}

@article {pmid41677891,
year = {2026},
author = {Mehmood, MS and Marakkalage, UKRK and Arif, T and Javaid, F and Abid, MA and Shahid, M and Parvez, A and Saddique, MN and Ali, S},
title = {mcr gene family evolution and structural mechanisms of colistin resistance: from mcr-1 to emerging variants.},
journal = {Archives of microbiology},
volume = {208},
number = {4},
pages = {186},
pmid = {41677891},
issn = {1432-072X},
mesh = {*Colistin/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Drug Resistance, Bacterial/genetics ; Evolution, Molecular ; Animals ; *Gram-Negative Bacteria/genetics/drug effects ; *Bacterial Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Plasmids/genetics ; Multigene Family ; Escherichia coli Proteins ; },
abstract = {The mcr gene family, responsible for plasmid-mediated resistance to colistin, poses a growing threat to public health by reducing the efficacy of colistin, a critical last-resort antibiotic for multidrug-resistant Gram-negative bacteria. The mcr-1 gene, discovered in 2015, marked a significant shift in understanding colistin resistance, and subsequent mcr variants (mcr-2 to mcr-10) have emerged globally. These genes alter lipid A in bacterial cell membranes, decreasing colistin's binding and efficacy. The mcr genes are typically located on mobile plasmids, facilitating horizontal gene transfer across bacterial species. Our review examines the evolution, genetic mechanisms, and structural characteristics of the mcr gene family, discussing their spread across human, animal, and environmental contexts. In this review, we highlight the clinical implications of mcr-mediated resistance, noting the co-occurrence of mcr with other antimicrobial resistance determinants, which complicates treatment options. Additionally, it explores detection methods, global epidemiology, and potential strategies to combat mcr resistance, including the development of inhibitors and CRISPR-based gene editing. Our review concludes that combating mcr-mediated colistin resistance requires global surveillance, coordination across sectors, and continued research to stop its spread and impact.},
}

*Colistin/pharmacology
*Anti-Bacterial Agents/pharmacology
Humans
*Drug Resistance, Bacterial/genetics
Evolution, Molecular
Animals
*Gram-Negative Bacteria/genetics/drug effects
*Bacterial Proteins/genetics/metabolism
Gene Transfer, Horizontal
Plasmids/genetics
Multigene Family
Escherichia coli Proteins

@article {pmid41677413,
year = {2026},
author = {Shi, J and Xie, Q and Yu, F},
title = {Parasitic Plant-Host Interactions: Molecular Mechanisms and Agricultural Resistance Strategies.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e19030},
doi = {10.1002/advs.202519030},
pmid = {41677413},
issn = {2198-3844},
support = {2023YFF1001400//National Key Research and Development Program of China/ ; 32525045//National Natural Science Foundation of China/ ; 32222010//National Natural Science Foundation of China/ ; 32401872//National Natural Science Foundation of China/ ; 20240484588//Beijing Nova Program/ ; 2024BBF02001//Ningxia Hui Autonomous Region Key R&D Program/ ; PC2024B01004//Pinduoduo-China Agricultural University Research Fund/ ; 1201-15055009//Chinese Universities Scientific Fund/ ; },
abstract = {Obligate parasitic plants, particularly members of the Orobanchaceae family, including Striga and Orobanche, greatly devastate crop production. Here, we synthesize recent advances in understanding the molecular and ecological dynamics underlying parasitic plant-host interactions, focusing on critical stages of parasitism: germination, host detection, haustorium formation, and resource extraction. Orobanchaceous parasites exploit host-derived strigolactones (SLs) to break seed dormancy, whereas Cuscuta species do not rely on SLs for germination. Instead, chemotropic responses to host-exuded compounds and light signals guide the directional growth of their seedlings. Haustorium morphogenesis, initiated through host lignin-derived quinones and redox-sensitive compounds, establishes vascular connectivity enabling nutrient diversion. Meanwhile, host organisms employ sophisticated multi-tier defense strategies encompassing SL biosynthesis, lignin deposition enhancement, hypersensitive cellular responses, and hormone-coordinated immunity. Key discoveries, such as receptor kinases and horizontal gene transfer events, highlight evolutionary arms races between parasites and hosts. Emerging technologies like CRISPR offer promising avenues for engineering resistant crops by disrupting parasitic signaling or enhancing host immunity. This review underscores the importance of integrating molecular insights with agricultural innovation to mitigate yield losses and addresses future challenges, including climate-driven parasite spread and the need for sustainable, genomics-driven solutions. By deciphering the silent dialogue between parasites and hosts, this work provides foundations for transformative strategies to safeguard global food security.},
}

@article {pmid41676731,
year = {2026},
author = {Tran, E and Xu, PN and Assis, R},
title = {Ecological context structures duplication and mobilization of antibiotic and metal resistance genes in bacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41676731},
issn = {2692-8205},
support = {R35 GM142438/GM/NIGMS NIH HHS/United States ; },
abstract = {Antibiotic resistance is a global challenge driven by the persistence and spread of resistance genes across ecological contexts. While mobile genetic elements (MGEs) facilitate horizontal gene transfer, gene duplication represents an additional mechanism through which resistance genes can be amplified, diversified, and maintained under selection. How these processes interact across environments remains poorly understood. Here, we examined genome-level patterns of resistance gene abundance, duplication, and mobilization across clinical, agricultural, and wastewater settings, focusing on both antibiotic resistance genes (ARGs) and metal resistance genes (MRGs). Resistance gene profiles were strongly structured by environment, with distinct duplication patterns emerging across sources. Duplicate genes were frequently associated with MGEs, although the strength of this relationship varied by resistance type and ecological context. Despite frequent co-occurrence of ARGs and MRGs, their duplication and mobilization dynamics were not uniformly coupled at the genome level. Together, these findings highlight gene duplication as a context-dependent contributor to resistance evolution and underscore the importance of ecological setting in shaping how resistance genes persist and spread across microbial communities.},
}

@article {pmid41675707,
year = {2025},
author = {Wu, J and Yang, X and Zhao, L and Li, Z and Zhao, G and Zhang, L},
title = {Systematic characterization of horizontally transferred biosynthetic gene clusters in the human gut microbiota using HTBGC-Finder.},
journal = {iMetaOmics},
volume = {2},
number = {1},
pages = {e62},
pmid = {41675707},
issn = {2996-9514},
abstract = {The human gut microbiota contains biosynthetic gene clusters (BGCs) that encode bioactive secondary metabolites, which play pivotal roles in microbe-microbe and host-microbe interactions and serve as a rich source of pharmaceutical lead compounds. Understanding the horizontal transfer of BGCs can reveal insights into microbial adaptation, resource utilization, and evolutionary mechanisms, thereby advancing biotechnological applications. Despite its importance, horizontal transfer of BGCs within the gut microbiota remains poorly understood. In this study, we introduce a novel tool, the Horizontally Transferred Biosynthetic Gene Clusters Finder (HTBGC-Finder), designed to systematically identify potential horizontally transferred BGCs (HTBGCs) within the extensive human gut microbiota. Using HTBGC-Finder, we identified 81 potential HTBGCs, underscoring the prevalence and significance of horizontal gene transfer in shaping the genetic landscape of the gut microbiome. Remarkably, ribosomally synthesized and post-translationally modified peptides (RiPPs) constituted the majority of these HTBGCs (76 out of 81, 93.83%), exhibiting a significantly higher transfer rate compared to non-RiPPs (Chi-squared test, p < 0.001). Upon detailed examination of BGCs, cyclic-lactone-autoinducer (CLA) and RiPP recognition element (RRE)-containing BGCs were predominant, representing nearly three-quarters of the total (45, or 55.56%, and 14, or 17.28%, respectively). Notably, CLA BGCs also demonstrated a higher transfer rate than non-CLA BGCs (Chi-squared test, p < 0.001). Taxonomy profiling revealed that horizontal BGC transfer occurred exclusively in the phyla Bacteroidota (synonym Bacteroidetes) and Bacillota (synonym Firmicutes), with 50 and 31 instances, respectively. Furthermore, cross-phylum transfer events were observed, highlighting the complex interactions between the gut microbiota and host health. These findings offer valuable insights into the horizontal transfer dynamics of BGCs within the gut microbiome and their potential implications for host-microbiota interactions.},
}

@article {pmid41673559,
year = {2026},
author = {Vargas, D and Merle, R and Friese, A and Roesler, U and Robé, C},
title = {Conjugation frequency of ESBL- and pAmpC- E. coli in broiler chickens in vivo and in vitro.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04822-1},
pmid = {41673559},
issn = {1471-2180},
abstract = {BACKGROUND: Plasmid-mediated conjugation is a major form of horizontal gene transfer (HGT), facilitating dissemination of antimicrobial resistance (AMR) and the emergence of multi-drug-resistant (MDR) strains. In poultry, Escherichia coli producing extended-spectrum β-lactamases (ESBL) and plasmid-mediated AmpC β-lactamase (pAmpC) enzymes are common and contribute to antibiotic resistance. Additionally, plasmid-mediated colistin resistance gene mcr-1 in poultry requires attention, as it is a last-resort antibiotic in human medicine. Although plasmid-mediated conjugation is known to play a role in spreading antimicrobial resistance, its specific impact on resistance transmission within the broiler microbiota is still not well understood. We assessed conjugation dynamics of the mcr-1 gene from a pAmpC- E. coli to an ESBL- E. coli observed in an in vivo broiler chicken trial and compared them to conjugation frequencies under different in vitro conditions (LB broth, intestinal chicken cells in DMEM/F-12 medium, and DMEM/F-12 medium alone), with two initial bacterial loads.

RESULTS: From in vivo trial, among 138 broiler chickens sampled after a 49-day fattening period, transconjugants were detected in the cecal content of 35 broilers. The median conjugation frequency observed was of -5.02 log10 transconjugants/donor. Median conjugation frequencies across all in vitro conditions varied by less than one log unit (between - 6.8 and - 6.0 log10 transconjugants/donor), and no significant differences in conjugation efficiency were observed between initial bacterial concentrations.

CONCLUSIONS: We confirmed bacterial conjugation between pAmpC-producing E. coli carrying the mcr-1 gene and ESBL-producing E. coli both in vitro and in vivo. The similar conjugation efficiencies observed across different in vitro methods suggest that experimental conditions have minimal influence under controlled settings. In contrast, the in vivo results underscore the significance of the host's physiological environment in HGT. The presence of transconjugants after a 49-day fattening period indicates that intestinal bacteria function as reservoirs for resistance plasmids and could facilitate their spread throughout the broiler production chain. However, limitations like the possibility of plasmid transfer to other bacteria, unknown persistence of the plasmid in the gut, and potential modulations of transfer efficiency under antibiotic selection must be considered when interpreting the results.},
}

@article {pmid41672331,
year = {2026},
author = {Yu, J and Allela, OQB and Alkhazali, WH and Bishoyi, AK and Oweis, R and Varma, P and Kashyap, A and Panigrahi, R and Chauhan, AS and Sameer, HN and Yaseen, A and Athab, ZH and Adil, M},
title = {The Gut Microbiome as a Modulator of Antibiotic Resistance: Mechanisms, Dynamics, and Therapeutic Interventions.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108357},
doi = {10.1016/j.micpath.2026.108357},
pmid = {41672331},
issn = {1096-1208},
abstract = {The gut microbiome is increasingly recognized as a critical factor in the dynamics of antibiotic resistance, influencing the acquisition, persistence, and dissemination of antibiotic resistance genes (ARGs) among both commensal and pathogenic bacteria. This research focuses on elucidating the mechanisms by which the gut microbiome modulates the horizontal gene transfer (HGT) of ARGs, a key driver of the global antibiotic resistance crisis. By employing advanced metagenomic sequencing and functional assays, this study aims to identify specific microbial species, genetic elements, and metabolic pathways that either facilitate or inhibit the transfer of ARGs within the gut environment. Particular attention is given to the role of microbial metabolites, interspecies interactions, and environmental factors that shape the resistome the collection of all resistance genes within the microbiome. Additionally, this research explores innovative microbiome-based interventions, such as the use of probiotics, prebiotics, and bacteriophage therapy, to disrupt the transmission of ARGs and restore microbial balance. These interventions are designed to target the gut microbiome as a reservoir of resistance genes, offering a novel approach to curbing the spread of antibiotic resistance. The significance of this work lies in its potential to provide actionable insights into microbiome-mediated resistance mechanisms and to develop targeted strategies that complement traditional antibiotic therapies. By addressing the gut microbiome as a modifiable factor in the resistance landscape, this research could contribute to mitigating the global burden of antibiotic resistance, preserving the efficacy of existing treatments, and improving public health outcomes in the face of this pressing challenge.},
}

@article {pmid41672316,
year = {2026},
author = {Wang, J and Gao, X and Wei, N and Ma, R and Yang, Y and Li, G and Tian, Y and Yuan, J},
title = {Persulfates radical-driven advanced oxidation: promising approach to regulate antibiotic resistance genes in composting systems.},
journal = {Bioresource technology},
volume = {446},
number = {},
pages = {134190},
doi = {10.1016/j.biortech.2026.134190},
pmid = {41672316},
issn = {1873-2976},
mesh = {Oxidation-Reduction ; *Composting/methods ; *Sulfates/pharmacology/chemistry ; *Drug Resistance, Microbial/genetics/drug effects ; Bacteria/genetics/drug effects ; Manure/microbiology ; *Genes, Bacterial/genetics ; Soil Microbiology ; },
abstract = {Composting serves as a pivotal technology for recycling livestock manure and reducing antibiotic resistance genes (ARGs). However, optimizing only its physicochemical properties or microbial community yields limited success in ARG removal. In contrast, persulfate radical-driven advanced oxidation processes (AOPs) have proven highly effective in eliminating ARGs. This study demonstrates that the biological heat generated during composting can activates persulfate, not only boosting the ARGs removal rate to 96% but also effectively suppressing the rebound and re-enrichment of ARGs during the compost maturation stage, maintaining a removal rate of 55%. Specifically, this approach reduces the abundances of mobile genetic elements (MGEs, e.g., intI2, IncQ-oriV) and target ARGs (tetA, tetQ, strA, sul3). The mechanisms underlying ARG removal involve two key aspects: First, strong oxidative radicals produced by persulfate activation directly oxidize and damage resistant bacteria, thereby decreasing the abundances of ARGs and MGEs. Second, persulfate primarily inhibits ARGs transmission by reshaping the bacterial community structure. In traditional composting, non-host core bacteria act as "bridges" connecting distinct microbial modules, directly facilitating inter-modular ARGs transmission. Dominant genera such as Bacillus, norank_f__Limnochordaceae, Marinimicrobium, and Tepidimicrobium mainly carry key MGEs (intI2, Tn916/1545, tnpA, IS613), which further amplify the risk of ARGs dissemination. In contrast, following persulfate addition, only Truepera is detected as a non-host core bacterium, significantly reducing cross-module ARGs transmission pathways. This study offers a promising regulation strategy for mitigating ARG-related risks during composting.},
}

Oxidation-Reduction
*Composting/methods
*Sulfates/pharmacology/chemistry
*Drug Resistance, Microbial/genetics/drug effects
Bacteria/genetics/drug effects
Manure/microbiology
*Genes, Bacterial/genetics
Soil Microbiology

@article {pmid41671169,
year = {2026},
author = {Saati-Santamaría, Z and Pérez-Mendoza, D and Khashi U Rahman, M and de Sousa, BFS and Montero-Calasanz, MDC and Rey, L and Roy, S and Sanjuán, J and García-Fraile, P},
title = {Evolutionary mechanisms underlying bacterial adaptation to the plant environment.},
journal = {FEMS microbiology reviews},
volume = {50},
number = {},
pages = {},
pmid = {41671169},
issn = {1574-6976},
support = {PID2023-150384NB-I00//Agencia Estatal de Investigación/ ; PCI2022-132990//Agencia Estatal de Investigación/ ; RED2022-134667-T//Ministerio de Ciencia e Innovación/ ; PID2021-124344OB-I00//Ministerio de Ciencia e Innovación/ ; //Consejería de Educación de Castilla y León/ ; //FEDER/ ; 101090267//Horizon Europe/ ; RYC2023-045204-I//Horizon Europe/ ; //ESF/ ; //NextGenerationEU/ ; //US Department of Agriculture/ ; 2022-38821-37353//National Institute of Food and Agriculture/ ; 2217830//National Science Foundation/ ; RYC2019-028468-I//Ramón y Cajal/ ; //European Social Fund/ ; PID2021-1059124344OB-I00//CNPq/ ; 101034371//H2020 Marie Skłodowska-Curie Actions/ ; },
abstract = {Plants and bacteria have coevolved over hundreds of millions of years, forming complex associations ranging from mutualism to pathogenicity that are essential for plant survival and ecosystem function. Bacterial adaptation to plant environments involves dynamic evolutionary mechanisms including horizontal gene transfer, gene regulation, and metabolic specialization, enabling bacteria to persist and specialize within diverse plant-associated niches. Here we review how evolutionary forces such as selection, drift, and gene flow shape bacterial genomes, regulatory networks, and ecological strategies in response to plant-imposed pressures, underpinning both beneficial and pathogenic lifestyles. Understanding these processes provides a unified evolutionary framework for bacterial adaptation to plants and highlights their implications for sustainable agriculture and microbiome-based innovations.},
}

@article {pmid41670362,
year = {2026},
author = {Campbell, P},
title = {The Influence of National Antibiotic Consumption on Neisseria gonorrhoeae Antibiotic Resistance in Norway, 2003-2024.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag076},
pmid = {41670362},
issn = {1537-6613},
abstract = {OBJECTIVES: To investigate whether national population-level antibiotic consumption influences antimicrobial resistance (AMR) in Norwegian Neisseria gonorrhoeae isolates. To explore metrics suitable for ecological AMR studies.

METHODS: Longitudinal Norwegian gonococcal susceptibility data (2003-2024) were analysed alongside national antibiotic consumption. Temporal trends were examined graphically and associations assessed using one-tailed Spearman rank correlations. Novel metrics - The 'Susceptible Isolate Pressure Indicator' (SIPI) and 'Wild-Type Isolate Pressure Indicator' (WIPI) ratios were introduced to characterise shifts in minimum inhibitory concentration (MIC) distributions within susceptible or wild-type ranges.

RESULTS: Strong positive, significant correlations were observed between consumption of the most widely used antibiotic classes in Norway - betalactamase-sensitive penicillins and tetracyclines - and gonococcal geometric mean MIC for benzylpenicillin (ρ=0.776, p<0.001) and tetracycline (ρ = 0.841, p<0.001). Penicillin-class consumption was also significantly associated with betalactamase plasmid carriage (ρ = 0.637, p = 0.013), consistent with horizontal gene transfer from commensal flora.

CONCLUSIONS: Even in a low-consumption European context, Norwegian antibiotic use appears to shape gonococcal resistance, possibly partly via gene uptake from commensal Neisseria. The SIPI and WIPI ratios describe susceptible-range MIC histogram shapes, and offer utility for AMR surveillance by capturing isolate flux.},
}

@article {pmid41668896,
year = {2026},
author = {Eskandar, K},
title = {The role of uropathogenic Escherichia coli biofilms in antibiotic-resistant urinary tract infections: Nanoparticle-based, phage therapy, and quorum-sensing inhibitor approaches.},
journal = {Current urology},
volume = {20},
number = {2},
pages = {82-88},
pmid = {41668896},
issn = {1661-7649},
abstract = {BACKGROUND: Urinary tract infections (UTIs) caused by uropathogenic E. coli (UPEC) pose a global health challenge, largely due to UPEC biofilms that drive persistent infections and antibiotic resistance.

MATERIALS AND METHODS: To explore the role of UPEC biofilms in antibiotic-resistant UTIs and summarize emerging therapeutic strategies, this study conducted a systematic review adhering to PRISMA guidelines and registered in PROSPERO (CRD420251040212). A structured search of PubMed, Google Scholar, Scopus, and Web of Science identified English-language studies published up to 2024, with 57 eligible studies selected after three-stage screening and analyzed via thematic synthesis.

RESULTS: This study explored UPEC biofilms enhance resistance through extracellular matrix barriers, persister cell formation, efflux pump upregulation, and horizontal gene transfer; emerging therapies including bacteriophage therapy, quorum-sensing inhibitors, and nanoparticle-based drug delivery effectively target biofilms by penetration, signaling disruption, and improved drug efficacy. Additional approaches such as antibiofilm peptides, probiotics, and immunotherapy also demonstrate potential.

CONCLUSIONS: The UPEC biofilms are key to chronic UTIs, and novel targeted therapies offer promising solutions, but clinical validation, regulatory hurdles, and combination therapy optimization are critical for translation to clinical practice.},
}

@article {pmid41668884,
year = {2026},
author = {Lee, SY and Choi, HJ and Lee, S and Choi, J and Kwak, JS and Kang, YJ and Hong, SC},
title = {Genome-based characterization of AHPND and non-AHPND Vibrio campbellii isolates from Republic of Korea.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1724818},
pmid = {41668884},
issn = {1664-302X},
abstract = {With mounting evidence that Vibrio campbellii can act as a causative agent, acute hepatopancreatic necrosis disease (AHPND) represents a serious threat to global shrimp aquaculture. In this study, we present a comparative genomic analysis of 101 V. campbellii strains, including the recently isolated pathogenic and non-pathogenic strains, V. campbellii HJ-2023 and V. campbellii HJ-2023n, from the Republic of Korea. Whole-genome sequencing revealed that the pathogenic strain harbors three plasmids and carries the canonical AHPND toxin genes pirA and pirB, along with an expanded repertoire of virulence and secretion system genes. Pan-genome and insertion sequence analyses showed that pathogenic strains tend to cluster based on shared mobile genetic elements, particularly transposases located near toxin genes, underscoring the role of horizontal gene transfer in virulence acquisition. Although all strains displayed a broad distribution of antibiotic-resistance genes, pathogenicity did not consistently correlate with their presence. Similarly, carbohydrate-active enzyme (CAZyme) profiles were largely conserved, although certain enzymes, such as chitinases, may contribute accessory functions in host invasion. Notably, the AHPND-associated V. campbellii HJ-2023 strain contained multiple copies of key T6SS and T1SS genes, suggesting an increased potential for toxin delivery. These findings suggest that pathogenic potential in V. campbellii likely arises not only from the presence of toxins but also from the complex interplay of mobile elements, secretion systems, and genomic architecture. This study provides an essential genomic framework for understanding the emergence of AHPND in V. campbellii and offers insights to enhance molecular diagnostics, strengthen biosecurity, and improve disease control strategies in shrimp aquaculture.},
}

@article {pmid41666926,
year = {2026},
author = {Kim, CY and Podlesny, D and Schiller, J and Khedkar, S and Fullam, A and Orakov, A and Schudoma, C and Robbani, SM and Grekova, A and Kuhn, M and Bork, P},
title = {Planetary microbiome structure and generalist-driven gene flow across disparate habitats.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.12.051},
pmid = {41666926},
issn = {1097-4172},
abstract = {Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersal, driven by natural processes and human activities, interconnects microbiomes across habitats, yet most comparative studies focus on specific ecosystems. To study planetary microbiome structure, function, and inter-habitat interactions, we systematically integrated 85,604 public metagenomes spanning diverse habitats worldwide. Using species-based unsupervised clustering and parameter modeling, we delineated 40 habitat clusters and quantified their ecological similarity. Our framework identified key drivers shaping microbiome structure, such as ocean temperature and host lifestyle. Regardless of biogeography, microbiomes were structured primarily by host-associated or environmental conditions, also reflected in genomic and functional traits inferred from 2,065,975 genomes. Generalists emerged as vehicles thriving and facilitating gene flow across ecologically disparate habitat types, illustrated by generalist-mediated horizontal transfer of an antibiotic resistance island across human gut and wastewater, further dispersing to environmental habitats, exemplifying human impact on the planetary microbiome.},
}

@article {pmid41666847,
year = {2026},
author = {Matijašević, D and Kljajević, N and Malešević, M and Gardijan, L and Stanovčić, S and Jovčić, B and Novović, K},
title = {Heating-season dynamics of the airborne microbiome, resistome and mobilome in Belgrade, Serbia.},
journal = {Environment international},
volume = {208},
number = {},
pages = {110114},
doi = {10.1016/j.envint.2026.110114},
pmid = {41666847},
issn = {1873-6750},
mesh = {Serbia ; *Microbiota ; Seasons ; *Air Microbiology ; Environmental Monitoring ; Air Pollution/statistics & numerical data ; *Drug Resistance, Microbial/genetics ; *Air Pollutants/analysis ; },
abstract = {Antimicrobial resistance (AMR) and air pollution are critical global health challenges, but their interplay remains poorly understood, particularly in Europe. Serbia, characterized by extensive antibiotic use, high prevalence of multidrug-resistant isolates and severe air pollution, provides a relevant model to study airborne AMR dissemination. During the heating season, air samples were collected at eight locations in Belgrade, representing industrial, traffic loaded and background environments. Shotgun metagenomics, co-occurrence networks and NMDS ordinations were applied to investigate the relationships between atmospheric pollutants, antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs) and mobile genetic elements (MGEs). Autumn microbiomes were dominated by Lactococcus spp., whereas winter lacked such dominance. ARGs associated with antibiotic inactivation accounted for > 50% in autumn and > 75% in winter, with β-lactam resistance (blaTEM) predominating in both seasons. Winter resistomes also showed more consistent patterns of BRGs and MRGs, with multibiocide/acid and multimetal resistance prevailing. Integron analysis revealed predominance of class 1 integrons (intI1) commonly associated with Escherichia coli. Plasmid-related contigs were most similar to sequences reported in Acinetobacter baumannii and E. coli, while plasmid signatures related to Lactococcus lactis were also detected in autumn. Crucially, the network analysis revealed a seasonal restructuring of the airborne resistome. Autumn networks displayed fragmented structure, showing antagonism between Lactococcus and Escherichia, whereas winter networks coalesced into a densely interconnected superhub that could facilitate horizontal gene transfer and co-selection of resistance determinants. These findings suggest that prolonged air pollution and seasonality jointly shape airborne resistomes, reinforcing the need for integrated environmental and AMR surveillance in highly polluted urban areas.},
}

Serbia
*Microbiota
Seasons
*Air Microbiology
Environmental Monitoring
Air Pollution/statistics & numerical data
*Drug Resistance, Microbial/genetics
*Air Pollutants/analysis

@article {pmid41665349,
year = {2026},
author = {Gong, H and Wu, Q and Xu, M and Meng, W and Wang, Y and Ju, C and Fu, Y},
title = {Host adaptation in Salmonella enterica serovar Typhimurium: population structure, pathovariants, and genomic mechanisms.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0220125},
doi = {10.1128/aem.02201-25},
pmid = {41665349},
issn = {1098-5336},
abstract = {Salmonella enterica serovar Typhimurium is a major zoonotic pathogen of global concern to human and animal health. With its broad host range, this serovar can colonize humans as well as domesticated and wild animals. Although historically considered a model host-generalist pathogen, whole-genome sequencing (WGS) has uncovered substantial genetic diversity and the emergence of multiple host-adapted pathovariants within this serovar. In this minireview, we delineate the population structure of S. Typhimurium across diverse host species and identify the lineages/pathovariants specifically adapted to avian hosts (e.g., passerines, pigeons, ducks, geese, larids, and water birds) and those adapted to non-avian hosts (e.g., humans). We further discuss the genetic mechanisms underlying host adaptation of S. Typhimurium pathovariants, including genome degradation through point mutations and insertions/deletions, as well as the acquisition of prophages or antimicrobial resistance genes via horizontal gene transfer. The ongoing emergence of host-adapted pathovariants in zoonotic pathogens such as S. Typhimurium underscores the importance of high-resolution, WGS-based subtyping approaches for precise pathogen identification and source attribution. Moreover, elucidating the genetic mechanisms driving host adaptation of zoonotic pathogens at the strain level is essential for informing targeted strategies for surveillance, prevention, and control.},
}

@article {pmid41660861,
year = {2026},
author = {Ilchenko, K and Bonnin, RA and Rocha, EPC and Pfeifer, E},
title = {Efficient detection and typing of phage-plasmids.},
journal = {mBio},
volume = {},
number = {},
pages = {e0300025},
doi = {10.1128/mbio.03000-25},
pmid = {41660861},
issn = {2150-7511},
abstract = {UNLABELLED: Phage-plasmids (P-Ps) are temperate phages that replicate as plasmids during lysogeny. Despite their high diversity, they carry genes similar to phages and plasmids. This leads to gene exchanges and to the formation of hybrid or defective elements, which limits accurate detection of P-Ps. To address this challenge, we developed tyPPing, an easy-to-use method that efficiently detects and types P-Ps with high accuracy. It searches for distinct frequencies and sets of conserved proteins to separate P-Ps from plasmids and phages. tyPPing's strength comes from both its precise predictions and its ability to systematically type P-Ps, including the assignment of confidence levels. We tested tyPPing on several databases and a collection of incomplete (draft) genomes. While predictions rely on the quality of assemblies, we detected high-quality P-Ps and experimentally proved them to be functional. Compared to other classification methods, tyPPing is designed to detect distinct P-P types and surpasses other tools in terms of sensitivity and scalability. P-Ps are highly diverse, making the systematic identification of new types a difficult task. By combining tyPPing with other tools, however, we show a valuable foundation for addressing this challenge. How to use tyPPing and other approaches is documented in our GitHub repository: github.com/EpfeiferNutri/Phage-plasmids/.

IMPORTANCE: Mobile genetic elements, such as phages and plasmids, are diverse and drive bacterial evolution through horizontal gene transfer. Phage-plasmids, of which many carry antibiotic resistance genes or virulence factors, are both phages and plasmids and have life cycles of temperate phages and plasmids. This makes accurate classification difficult as current computational tools typically classify them as one or the other. We addressed this problem by developing tyPPing, a new and highly precise method, to systematically identify, separate, and catalog phage-plasmids. We demonstrated that tyPPing is highly accurate and broadly compatible. It provides a reliable foundation for all future studies involving phages and plasmids, ranging from agriculture environments to pathogenic strains of clinical settings.},
}

@article {pmid41657901,
year = {2026},
author = {Farinas, LMF and Dela Peña, LBRO and Rivera, WL},
title = {Shotgun metagenomics reveals the prevalence and mobility of antibiotic resistance genes in the West Bay of the human-impacted Laguna Lake.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1742578},
pmid = {41657901},
issn = {1664-302X},
abstract = {Laguna Lake, the largest freshwater lake in the Philippines, has been reported to harbor antibiotic-resistant bacteria, posing health risks to the millions who depend on it. However, limited knowledge of antibiotic resistance genes (ARGs) in the lake highlights the need for a comprehensive assessment of its resistome. In line with this, we characterized ARGs in the West Bay of Laguna Lake using shotgun metagenomic sequencing based on six metagenomes collected from three stations across two sampling months at a single depth. ARGs were quantified from short reads, and assembled contigs containing these genes-antibiotic-resistant contigs (ARCs)-were analyzed to assess mobility through associations with plasmids and mobile genetic elements (MGEs). β-lactam resistance genes (0.023-0.048 copies per cell) were the most prevalent, corroborating previous reports. Meanwhile, the detection of bacitracin (0.013-0.028 cpc) and polymyxin (0.009-0.011 cpc) resistance genes raises new concerns, as resistance to these antibiotic classes has not been previously reported in the lake. Furthermore, 44.8 and 30.4% of ARCs were associated with plasmids and MGEs, respectively. ARCs carrying genes for resistance to β-lactams, chloramphenicol, and tetracyclines were frequently identified as mobile, indicating a high potential for horizontal gene transfer and suggesting possible antibiotic contamination in the lake. Overall, this study provides the first metagenomic insight into the resistome of Laguna Lake using short-read sequencing and highlights its role as an environmental reservoir of mobile ARGs. The findings underscore the need for expanded ARG surveillance to improve antimicrobial resistance risk prediction.},
}

@article {pmid41654982,
year = {2026},
author = {Park, SH and Ji, SK and Shin, S and Park, C and Shin, JI and Jung, SH and Choi, JH and Lee, DG},
title = {Outbreak investigation and genomic analysis reveal hidden transmission networks of KPC-2-producing Enterobacterales in a South Korean hospital.},
journal = {Antimicrobial resistance and infection control},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13756-026-01706-x},
pmid = {41654982},
issn = {2047-2994},
support = {2021R1A2C1009867//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: We investigated a KPC-2-producing Enterobacterales (KPC-2 CPE) outbreak in a Korean hospital from July to September 2019, which subsided following enhanced surveillance and strict infection control. The study aimed to elucidate transmission dynamics using epidemiological and genomic methods.

METHODS: The study period covered the outbreak and a 9-month post-outbreak observation. Investigations included a matched case-control study and whole-genome sequencing (WGS) of isolates, including long-read sequencing for two isolates. Single nucleotide polymorphism (SNP) analysis (≤ 6 SNPs for clonality, ≤ 15 for relatedness) was used to construct transmission networks.

RESULTS: A total of 42 KPC-2 CPE cases were identified: 34 Klebsiella pneumoniae, 4 Escherichia coli, 1 Enterobacter asburiae, and 3 cases co-colonized with K. pneumoniae and E. coli. Among these, 33 were hospital-linked and 9 were imported. Retrospective tracing indicated that covert transmission began a month before the outbreak, and 13 hospital wards were identified as potential acquisition sites. Genomic analysis revealed all but one K. pneumoniae belonged to ST307, cgMLST 439, which grouped into three clades. Clade 1 was linked to a specific hospital ward, supported by the case-control study (adjusted odds ratio, 3.63; 95% confidence interval, 1.36-9.63); Clade 2 was spread between wards via a haemodialysis unit and shared healthcare personnel. Imported cases had the same clones as early hospital-linked cases, suggesting undetected introduction before enhanced surveillance. Additionally, an IncX3 plasmid carrying blaKPC-2 was found in both K. pneumoniae and E. coli, indicating horizontal gene transfer.

CONCLUSION: This study demonstrates that clonal spread of KPC-2 CPE can remain undetected without enhanced active surveillance, underscoring the need for early detection. Genomic analysis clarified ST307 K. pneumoniae transmission through unrecognised epidemiological links and horizontal blaKPC-2 transfer to E. coli.},
}

@article {pmid41649927,
year = {2026},
author = {Zhen, J and Wei, W and Duan, H and Hou, Y and Chen, X and Liu, Y and Ni, SQ and Ni, BJ},
title = {Micro- and nanoplastics facilitate the propagation of antimicrobial resistance in mixed microbial consortia.},
journal = {Cell reports},
volume = {45},
number = {2},
pages = {116946},
doi = {10.1016/j.celrep.2026.116946},
pmid = {41649927},
issn = {2211-1247},
abstract = {Navigating the emerging pollutant crisis appears increasingly daunting, with the interaction between micro- and nanoplastics (M/NPs) and antimicrobial resistance (AMR) in complex microbial consortia remaining poorly understood. Here, mixed-culture microcosms are subjected to polymer- and size-resolved plastic exposures, and resistome and mobilome dynamics are quantified using phenotyping and multi-omics. M/NP exposure increases AMR gene abundance and reshapes resistance profiles in a polymer-dependent manner, dominated by efflux and target alteration. Particle miniaturization amplifies resistome diversity and gene mobility, and nanoplastics show the highest horizontal gene transfer activity and strongest co-localization of AMR genes with mobile genetic elements, forming dense cross-phylum transfer networks. Mechanistically, nanoplastics elevate ROS and membrane damage, activate the SOS response, and upregulate conjugation, competence, and transposase functions. Increased ATP generation and efflux activity sustain stress tolerance and energy-intensive DNA exchange, turning nanoplastics into hotspots of transferable resistance with implications for microbial evolution and ecological resilience.},
}

@article {pmid41649717,
year = {2026},
author = {Yusuf, AG and Bello, TT and Anifiwoshe, SO},
title = {Molecular mimicry and trafficking of peptide effectors in sedentary nematodes: emerging drivers of feeding site formation and host signaling hijack.},
journal = {Crop health},
volume = {4},
number = {1},
pages = {1},
pmid = {41649717},
issn = {2948-1945},
abstract = {Despite significant advances in understanding the biology of plant-parasitic nematodes, the emergence of peptide hormone mimicry as a virulence strategy presents a complex facet of nematode parasitism. This review integrates recent advances on how nematode effectors, such as CLEs, CEPs, RALFs, IDA, and PSYs, are processed, post-translationally modified, and trafficked to hijack host signaling and developmental programs. By linking structural mimicry with receptor engagement and subcellular targeting, we highlight how these effectors reprogram plant transcriptional and immune responses to drive the formation of nematode feeding sites. We further explore the evolutionary origins of these effectors, emphasizing how processes such as horizontal gene transfer, neofunctionalization, and convergent selection have shaped peptide effectors into lineage-specific virulence factors. Finally, we outline critical research gaps focusing on structural and computational analyses of effector-receptor interfaces, functional genomics of trafficking and activation and translational opportunities for engineering durable host resistance. Together, these insights underscore the influence of molecular mimicry on nematode virulence and position effector biology as a frontier for translational innovation in crop protection.},
}

@article {pmid41649278,
year = {2026},
author = {Selleri, E and Tarracchini, C and Petraro, S and Mancabelli, L and Milani, C and Turroni, F and Shao, Y and Browne, HP and Lawley, TD and van Sinderen, D and Ventura, M and Lugli, GA},
title = {Assessment of genome evolution in Bifidobacterium adolescentis indicates genetic adaptation to the human gut.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0117325},
doi = {10.1128/msystems.01173-25},
pmid = {41649278},
issn = {2379-5077},
abstract = {UNLABELLED: Bifidobacterium adolescentis is one of the most frequently encountered bifidobacterial species present in the adult human gut microbiota, with a prevalence of approximately 60%. Despite its high prevalence, B. adolescentis has not been extensively studied and characterized, and our understanding of its physiological traits, genetic diversity, and potential interactions with other members of the human gut microbiota or with its host is therefore fragmentary. In the current study, a data set comprising 1,682 B. adolescentis genomes was compiled by combining publicly available data and metagenome assemblies from 131 projects to uncover the unique genetic characteristics of this species. A pangenome analysis of B. adolescentis identified 203 clusters of orthologous genes absent from the other five human-associated Bifidobacterium species, six of which were in silico predicted to encode functions unique to this taxon. Furthermore, 2,597 genes were predicted to have been acquired by horizontal gene transfer, including genes encoding extracellular structures involved in interaction with the host and other microorganisms, and phage defense mechanisms against bacteriophages. Detailed phylogenetic analysis revealed seven clusters within the B. adolescentis species, each partially associated with the origin of strain isolation, suggesting phylogenetic differentiation shaped by geographical strain origin. Moreover, a large-scale metagenomic analysis of over 10,000 human gut metagenomes from healthy adults revealed that B. adolescentis co-occurs with 36 putative beneficial commensals and butyrate-producing taxa, highlighting its role as a key bifidobacterial species involved in microbial networking within the adult human gut microbiota.

IMPORTANCE: To comprehensively explore the biodiversity within a microbial species, the reconstruction of a substantial number of genomes is essential. In this study, we successfully uncovered the genetic diversity of Bifidobacterium adolescentis by retrieving a large number of genomes from human gut metagenomic samples. The complete overview of the B. adolescentis pangenome enabled us to investigate the genetic features that distinguish this gut commensal from other bifidobacterial species residing in the human intestinal microbiota.},
}

@article {pmid41649272,
year = {2026},
author = {Leonard, SP and Halvorsen, TM and Lim, B and McCall, NA and Park, DM and Jiao, Y and Yung, MC and Ricci, DP},
title = {Synthetic overlapping genes stabilize genetic systems.},
journal = {mBio},
volume = {},
number = {},
pages = {e0272525},
doi = {10.1128/mbio.02725-25},
pmid = {41649272},
issn = {2150-7511},
abstract = {UNLABELLED: Overlapping genes-wherein two different proteins are translated from alternative reading frames of the same DNA sequence-provide a means to stabilize an engineered gene by directly linking its evolutionary fate with that of an overlapping gene. However, creating overlapping gene pairs is challenging, as it requires redesigning both protein products to accommodate overlap constraints. Here, we present a new "overlapping, alternate-frame insertion" (OAFI) method for creating synthetic overlapping genes by inserting an "inner" gene, encoded in an alternate frame, into a flexible region of an "outer" gene. Using OAFI, we create new overlapping gene pairs of genetic reporters and bacterial toxins within an antibiotic resistance gene. We show that both the inner and outer genes retain function despite redesign, with translation of the inner gene influenced by its overlap position in the outer gene. Importantly, we show that, despite these inner gene sequences not contributing to outer gene function, selection for the outer gene alters the permitted inactivating mutations in the inner gene, and that overlapping toxins can restrict horizontal gene transfer of the antibiotic resistance gene. Overall, OAFI offers a versatile tool for synthetic biology, expanding the applications of overlapping genes in gene stabilization and biocontainment.

IMPORTANCE: Genetically engineered microbes promise to improve human health and help solve global climate crises. However, the widespread adoption of these microbes is often hindered by genetic instability caused by mutations and by the unpredictable spread of synthetic genes in the environment. We present a simple but effective method for creating synthetic overlapping genes to stabilize genes against mutations and prevent their spread in the environment. This method is broadly useful for constructing stable genetically engineered microbes and studying how they evolve in the environment.},
}

@article {pmid41648637,
year = {2026},
author = {Chetrit, D and Roy, CR and Karatekin, E},
title = {Type IV Secretion System Drives Lipid Mixing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41648637},
issn = {2692-8205},
support = {R01 NS122388/NS/NINDS NIH HHS/United States ; R37 AI041699/AI/NIAID NIH HHS/United States ; },
abstract = {Type IV secretion systems (T4SSs) are versatile molecular machines used by bacteria to secrete protein effectors into host cells, promoting pathogenesis, and to transfer DNA between bacteria through conjugation, driving horizontal gene transfer. Most, like Dot/Icm of the pathogen Legionella pneumophila (L. pneumophila) or Escherichia coli (E. coli) RK2, are primed for substrate delivery only upon contact with a target membrane, but mechanisms are unknown. A pilus could bind a receptor to initiate priming, but many T4SSs, especially those that deliver effectors, lack a pilus. Here, we present evidence that T4SSs are primed by direct contact with target membrane lipids. Combining fluorescence assays with genetics and biochemistry, we found that Dot/Icm drives lipid exchange between bacterial cells and between bacteria and synthetic membranes containing only lipids. Lipid exchange requires membrane contact but does not require ATP hydrolysis or even full complex assembly. Minimally, the outer membrane core complex protein DotG needs to be present in at least one of the apposed membranes. We similarly observed lipid mixing with the simpler E. coli RK2 T4SS, where we could follow lipid mixing and plasmid transfer simultaneously. We found that lipid mixing always preceded or accompanied plasmid transfer, suggesting it may be part of the contact-dependent priming mechanism. Lipid mixing was inhibited or promoted by lipids that inhibit or promote membrane fusion, respectively. Lipids inhibiting lipid mixing also inhibited substrate transfer. Together, our results suggest that initial contact between DotG outer segments and target membrane lipids promotes lipid mixing as part of the mechanism that primes T4SS for substrate translocation.},
}

@article {pmid41648574,
year = {2026},
author = {Hullinger, AC and Callahan, VE and Dalia, AB},
title = {Low affinity DNA-binding promotes cooperative activation of natural transformation in Vibrio cholerae.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.21.700895},
pmid = {41648574},
issn = {2692-8205},
abstract = {UNLABELLED: DNA-binding transcriptional regulators control gene expression in response to environmental cues. A subset of these proteins, called transmembrane transcriptional regulators (TTRs), directly bind DNA to regulate transcription while remaining anchored in the cytoplasmic membrane. Prior work has shown that in the presence of the polysaccharide chitin, two TTRs, TfoS and ChiS, coordinate to induce the expression of TfoR, a small RNA that is critical for natural transformation in Vibrio cholerae . Specifically, it was shown that ChiS recruits the P tfoR locus to the membrane, which allows for the subsequent activation of this promoter by TfoS. However, it was also shown that increasing TfoS protein levels bypasses this coordination, allowing TfoS to activate the promoter independently. It therefore remains unclear what molecular mechanisms drive the requirement for ChiS in native conditions. Here, we show that ChiS binds P tfoR with a higher affinity than TfoS. We hypothesized that the low affinity of TfoS for P tfoR helps reinforce its dependence on ChiS for activation. To test this, we isolated a mutant allele of the TfoS DNA-binding domain that has a higher affinity for P tfoR . We show that this high-affinity TfoS allele promotes ChiS-independent activation of P tfoR . These results demonstrate that the relative DNA-binding affinity of TTRs is a critical feature that drives their coordination.

IMPORTANCE: DNA-binding transmembrane transcriptional regulators (TTRs) are critical for some bacterial species to properly sense and respond to their environments. Recent work highlights that pairs of TTRs can coordinate their activities to regulate gene expression, allowing them to sensitively control behaviors like virulence and horizontal gene transfer. However, the mechanisms that enable this coordination remain poorly understood. Here, we show that the relative DNA-binding affinity of paired TTRs is a critical feature that can drive their coordination.},
}

@article {pmid41648278,
year = {2026},
author = {Sarkis, AW and Sørensen, JL and Sondergaard, TE and Nielsen, KL and Frisvad, JC and Theobald, DL and Hedstrom, L},
title = {An activity-resistance tradeoff constrains enzyme evolution.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.19.700455},
pmid = {41648278},
issn = {2692-8205},
abstract = {UNLABELLED: The presence of self-resistance genes in antibiotic-producing organisms poses a paradox: how can resistance evolve before the antibiotic exists, and how can an antibiotic producer arise without first evolving resistance? Here we examine the evolutionary origins of self-resistance to mycophenolic acid (MPA), an inhibitor of inosine monophosphate dehydrogenase (IMPDH). The MPA biosynthetic gene cluster (BGC) includes a resistant IMPDH-B. Homologs of IMPDH-B occur not only in MPA producers but also in many non-producing fungi, where remnants of the MPA BGC remain detectable. The phylogeny of IMPDH-B is incongruent with the fungal species tree, consistent with multiple horizontal gene transfer events between Aspergillus and Sordariomycetes. We characterized eleven extant IMPDH-Bs, five from MPA producers and six from nonproducers, along with seven resurrected ancestral enzymes (Anc1-Anc7). MPA resistance appeared between Anc2 and Anc3 and coincided with a loss of catalytic efficiency. Across both ancestral and extant enzymes, MPA resistance correlated strongly with reduced activity, revealing a robust activity-resistance trade-off that has persisted for millions of years. Unexpectedly, both the IMPDH-Bs and ancestral enzymes Anc3-Anc7 were also resistant to ribavirin-5'-monophosphate (RVP), an IMP-competitive inhibitor. Because MPA and RVP bind to similar enzyme conformations, the activity-resistance trade-off likely reflects a design constraint imposed by the need to maintain resistance to multiple inhibitors. Intriguingly, although Anc1 and Anc2 are equally sensitive to MPA, Anc2 shows reduced susceptibility to RVP. This pattern suggests that pre-existing resistance to another IMPDH inhibitor may have created a permissive background for the later evolution of MPA biosynthesis.

SIGNIFICANCE: Antibiotic producers must be resistant to the toxins that they produce, but how such self-resistance develops is a mystery. The mycophenolic acid (MPA) biosynthetic gene cluster (BGC) encodes a resistant variant of the MPA target IMPDH (IMPDH-B). Many fungi retain IMPDH-B although they have lost the ability to produce MPA. The IMPDH-B and species phylogenies are incongruent, suggesting evolution of the BGC was complicated. MPA resistance correlates with low catalytic efficiency in modern and ancestral IMPDHs, revealing a robust design constraint tradeoff. Surprisingly, IMPDH-Bs are also resistant to an IMP-competitive inhibitor (RVP). RVP resistance appears to have emerged before MPA resistance. Perhaps resistance to RVP created a background that permitted the genesis of a new toxin.},
}

@article {pmid41648272,
year = {2026},
author = {Christman, ND and Dalia, TN and Chlebek, JL and Dalia, AB},
title = {The stoichiometry of minor-to-major pilins regulates the dynamic activity of the type IVa competence pilus in Vibrio cholerae.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.17.700090},
pmid = {41648272},
issn = {2692-8205},
abstract = {UNLABELLED: Type IVa pili (T4aP) are bacterial surface appendages that perform various functions including twitching motility, surface attachment, cell-cell interactions, and DNA uptake for natural transformation. Pivotal to each of these functions is the ability of T4aP to be dynamically extended and retracted from the cell surface. However, the factors that regulate this dynamic activity remain poorly understood. To address this question, we employ the competence T4aP from Vibrio cholerae as a model system. T4aP are composed of major and minor pilin subunits, named based on their relative abundance in the pilus filament. Prior work has established that minor pilins form a complex that initiates T4aP assembly. This allows for the subsequent addition of major pilins to the filament, which promotes T4aP extension. Here, we uncover that the stoichiometry of minor-to-major pilins is a crucial determinant of T4aP dynamic activity. Specifically, we show that either (1) overexpressing minor pilins or (2) underexpressing the major pilin results is a dramatic increase in the frequency of T4aP dynamics. These results indicate that the stoichiometry of major-to-minor pilins, not their absolute abundance, is one mechanism that regulates T4aP dynamic activity.

AUTHOR SUMMARY: Type IVa pili (T4aP) are a broadly conserved family of filamentous bacterial appendages that help bacteria colonize surfaces, move towards or away from stimuli, and gain new traits through a mechanism of horizontal gene transfer called natural transformation. T4aP are primarily composed of protein subunits called major and minor pilins, named based on their relative abundance in the pilus filament. Bacteria can dynamically extend and retract pilus filaments from their surface through polymerization and depolymerization of these pilins. This dynamic activity is critical for the activities that T4aP carry out. However, the factors that regulate this dynamic activity remain incompletely understood. Here, we find that the ratio of minor-to-major pilins is one factor that regulates the frequency of dynamic activity. Minor pilins are a universally conserved feature of T4aP. So, the minor-to-major pilin ratio may be a broadly conserved mechanism for controlling dynamic T4aP activity in diverse bacterial species.},
}

@article {pmid41644585,
year = {2026},
author = {Zhou, Y and Liu, K and Gong, P and Wu, J and Ren, Z and Jin, E},
title = {Integrated metagenomic and 16S rRNA analysis reveals temporal associations between resistance genes and microbial communities during dairy manure composting.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41644585},
issn = {2045-2322},
mesh = {*Manure/microbiology ; *Composting/methods ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Animals ; *Microbiota/genetics ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Dairying ; Metagenome ; *Drug Resistance, Bacterial/genetics ; Soil Microbiology ; Cattle ; Genes, Bacterial ; },
abstract = {Dairy manure composting is widely applied to stabilize organic waste and reduce environmental pollution, yet the behavior of resistance determinants during this process remains insufficiently resolved. In this study, shotgun metagenomic sequencing was used to characterize temporal changes in antibiotic resistance genes (ARGs), metal resistance genes (MRGs), biocide resistance genes (BRGs), mobile genetic elements (MGEs), and microbial community composition during dairy manure composting. Rather than inferring direct mechanistic causation, our analyses focused on identifying statistically supported trends, associations, and co-occurrence patterns across composting stages. We observed a rapid decline in the relative abundance of ARGs compared with MRGs and BRGs during the thermophilic phase, coinciding with increasing temperature, while specific genes such as sul2 persisted throughout the process. Shifts in microbial community composition, particularly changes in the relative dominance of Actinobacteria and Proteobacteria, were significantly associated with variations in resistome profiles. Correlation and network analyses further revealed strong associations among ARGs, MRGs, BRGs, and MGEs, suggesting potential co-selection and horizontal gene transfer linkages without implying direct causal mechanisms. In addition, several opportunistic bacterial genera showed positive associations with aminoglycoside- and macrolide-lincosamide-streptogramin-type ARGs, indicating possible dissemination risks following compost application. Overall, this study provides an integrated, association-based overview of resistome and microbial community dynamics during dairy manure composting and highlights the importance of considering multiple resistance determinants when evaluating composting as a manure management strategy.},
}

*Manure/microbiology
*Composting/methods
*RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
Animals
*Microbiota/genetics
*Drug Resistance, Microbial/genetics
Bacteria/genetics
Dairying
Metagenome
*Drug Resistance, Bacterial/genetics
Soil Microbiology
Cattle
Genes, Bacterial