Deciphering Antimicrobial Resistance Transmission Pathways in Healthcare Through Genomic Epidemiology

Antimicrobial resistance (AMR) in clinically relevant bacterial pathogens represents a major and growing challenge to infection prevention and control worldwide. The spread of resistance is facilitated by both high-risk clonal lineages and mobile genetic elements (MGEs), enabling the rapid dissemination of resistance determinants within hospitals and across healthcare networks. The adoption of whole-genome sequencing (WGS) and advanced analytic methodologies has revolutionized our ability to identify transmission clusters, trace dissemination routes, and characterize the evolutionary dynamics of resistance at an unprecedented resolution. Despite these advances, many investigations remain descriptive, often limiting their scope to cataloging resistance genes or profiling individual isolates, with limited integration of genomic data and epidemiological context. As a result, actionable evidence for designing and implementing targeted surveillance and control strategies is still lacking in many settings.This Research Topic seeks to showcase innovative studies that leverage genomics and advanced data-driven approaches to untangle the complex transmission networks underlying AMR in healthcare environments. The main objective is to generate actionable insights by integrating genomic, epidemiological, and experimental data, thus deepening our understanding of how resistant pathogens emerge, evolve, and spread in clinical contexts. We are particularly interested in research addressing clinically relevant bacterial pathogens such as Enterococcus spp., Staphylococcus spp., Enterobacterales, and Acinetobacter spp. Studies on fungi and viruses will only be considered if they are directly linked to antimicrobial pressure or mobile resistance elements. We invite Original Research, Reviews, and Methods articles focused on resistance mechanisms, genomic epidemiology, mobile genetic elements, transmission dynamics, and resistance evolution. Exclusively phenotypic studies without supporting genetic or genomic analysis are discouraged.We welcome contributions covering, but not limited to, the following themes:- Comparative genomic and population analyses of hospital- and community-acquired pathogens, focusing on resistomes and mobilomes.- WGS-based outbreak investigations and transmission reconstruction in hospitals and long-term care.- Resistance mechanisms in key clinical bacteria, including genes, regulatory pathways, and evolutionary context.- Roles of MGEs (plasmids, transposons, integrons) in the rapid spread of resistance, including plasmid tracking and long-read sequencing approaches.- Studies combining with in vitro experiments or animal models to validate resistance mechanisms, fitness costs, or long-term persistence-related phenotypes.- Applications of multi-omics, artificial intelligence, and computational biology in resistance prediction, transmission inference, and pathogen source tracing, with results validated by experiments or real-world datasets to ensure reliability. Topic editors: Yaming Shan, Qi Zhao, Weiliang Xie, Mark J. Lee Source: https://www.frontiersin.org/research-topics/77530/deciphering-antimicrobial-resistance-transmission-pathways-in-healthcare-through-genomic-epidemiology