Global genomic insights into antimicrobial resistance of Escherichia marmotae

Escherichia marmotae is an emerging zoonotic bacterium of increasing significance in global public health due to its antimicrobial resistance (AMR) potential. In recent years, research on E. marmotae has been increasing, demonstrating a trend toward greater depth and systematic investigation. However, the global distribution and underlying evolutionary drivers of AMR in E. marmotae strains remain largely unknown. Therefore, a comprehensive global analysis of the longitudinal trends and driving factors of AMR in E. marmotae is essential. In this study, we provide a global genomic and AMR characterization of E. marmotae. We analyzed 273 high-quality E. marmotae genomes spanning 1950-2025 from the National Center for Biotechnology Information (NCBI) genome database, focusing on their global distribution, phylogeny, and antimicrobial resistance profiles. Analysis of E. marmotae isolates from 21 countries revealed that the majority were from New Zealand (52.0%), with most strains originating from the environment (61.5%) and animals (30.8%). Phylogenetic analysis revealed extensive cross-country, cross-species, with ST133 being the most prevalent sequence type. The antimicrobial resistance gene (ARG) carriage rate was 11.7%, including the high-risk resistance genes, such as blaKPC and blaCTX-M. Aminoglycoside and beta-lactam resistance is the most common. Also, 75.8% of isolates carried plasmids, primarily of IncFIB and IncFII types. For the first time, blaKPC-2 was identified in E. marmotae, primarily within ISKpn6, ISKpn7, and IS1182-associated plasmids, suggesting high interspecies transmission potential. In summary, we present a global genetic atlas of E. marmotae, which provides valuable insights for understanding the transmission dynamics of AMR in this species.