Global genomic insights into the antimicrobial resistance of Escherichia marmotae

Escherichia marmotae has recently emerged as a zoonotic pathogen of growing global significance due to its capacity to acquire and disseminate antimicrobial resistance (AMR). Despite increasing scientific attention, the global distribution, genomic diversity, and evolutionary dynamics of AMR within this species remain largely unknown. This study conducted the first comprehensive global assessment of E. marmotae population structure, distribution, phylogeny, and resistance profiles using 273 high-quality genomes spanning 1950–2025 from the National Center for Biotechnology Information (NCBI) database. Isolates originated from 21 countries, with a pronounced geographic skew toward New Zealand (52.0%), and were predominantly isolated from environmental (61.5%) and animal (30.8%) sources. Phylogenetic reconstruction uncovered extensive cross-species and transboundary transmission, with ST133 representing the most dominant lineage. The overall antimicrobial resistance gene (ARG) carriage rate was 11.7%, including clinically significant β-lactamases such as bla_KPC and bla_CTX-M. Resistance to aminoglycoside and β-lactam was most frequently observed. Plasmids were identified in 75.8% of isolates, particularly of the IncFIB and IncFII types. Notably, bla_KPC-2 was identified in E. marmotae for the first time, predominantly embedded within IS1182- bla_TEM-1B-bla_KPC-2-IS1182-associated plasmid structures, highlighting its high potential for interspecies gene exchange. This global genomic atlas of E. marmotae offers key insights into the geographic dissemination and interspecies dynamics of AMR within this emerging zoonotic bacterium.