Commensal Bacteria as the Reservoir of Antimicrobial Resistance Genes

Antimicrobial resistance (AMR) is widely recognized as a major global health threat, yet its ecological foundations remain insufficiently explored. While clinical pathogens are the primary focus of surveillance efforts, increasing evidence highlights the critical role of commensal bacteria as reservoirs of antimicrobial resistance genes (ARGs). This silent reservoir plays a critical role in the evolution and spread of antimicrobial resistance (AMR), often preceding its emergence in clinically relevant pathogens. These microorganisms, which inhabit humans, animals, and environmental niches, constitute a vast and dynamic resistome that can be mobilized under selective pressure. Through mechanisms such as horizontal gene transfer mediated by plasmids, transposons, bacteriophages and outer membrane vesicles (OMV), commensals contribute to the emergence and dissemination of resistance traits across ecological boundaries. Understanding the structure, function, and dynamics of commensal resistomes is therefore essential to fully elucidate AMR evolution within the One Health framework.This Research Topic aims to advance current knowledge on the role of commensal bacteria in the maintenance, evolution, and transmission of antimicrobial resistance. We seek to move beyond a pathogen-centric perspective by integrating ecological, genomic, and functional approaches to characterize commensal reservoirs across human, animal, and environmental compartments. Emphasis is placed on identifying the drivers that shape resistome composition, including antimicrobial usage, host-associated factors, and environmental pressures. Contributions exploring the mobilization potential of ARGs, especially through mobile genetic elements and plasmid-mediated transfer, are highly encouraged. Studies addressing the interface between commensals and opportunistic pathogens, as well as those investigating the transition from harmless colonization to clinically relevant resistance dissemination, are of particular interest. Additionally, this Research Topic welcomes work leveraging high-resolution methodologies, such as metagenomics, long-read sequencing, and genome-resolved analyses, to uncover hidden reservoirs and transmission pathways. By fostering interdisciplinary perspectives, this collection aims to provide a more comprehensive understanding of AMR ecology and inform strategies for surveillance, risk assessment, and mitigation.We welcome studies addressing the diversity, dynamics, and functional relevance of antimicrobial resistance within commensal bacterial communities. Submissions may include, but are not limited to, the following sub-topics:• Resistome characterization in human gut and oral microbiota, focusing on relevant commensal taxa• Mobile genetic elements in ARG dissemination and overlap between ARG gene pools in commensal and pathogenic microbiota• Horizontal gene transfer mechanisms within commensal bacterial communities• Effects of antimicrobial use and co-selection pressures on resistome dynamics in human or livestock hosts• Functional characterization of resistance determinants from commensal organisms, including fitness trade-off assessments• Risk frameworks linking ARG transmission from commensal reservoirs to clinical outcomesStudies integrating One Health approaches, combining data across multiple ecosystems, are particularly encouraged. Methodological contributions and standardized approaches for resistome analysis are also within scope. All submissions should provide clear insights into the ecological and functional role of commensal bacteria in AMR emergence and spread.This Research Topic welcomes the following article types: FAIR² DATA Direct Submission, FAIR² Data, Hypothesis and Theory, Methods, Mini Review, Opinion, Original Research, Perspective, Review, Systematic Review, and Technology and Code articles. Topic editors: Teresa Semedo-Lemsaddek, Pablo Power, Taru Singh, Mohammad Tahir Siddiqui Source: https://www.frontiersin.org/research-topics/80000/commensal-bacteria-as-the-reservoir-of-antimicrobial-resistance-genes