Pathogenomic Characterization of Multidrug-Resistant Escherichia coli Strains Carrying Wide Efflux-Associated and Virulence Genes from the Dairy Farm Environment in Xinjiang, China

<b>Background/Objectives</b>: Livestock species, particularly dairy animals, can serve as important reservoirs of <i>E. coli</i>, carrying antibiotic resistance and virulence genes under constant selective pressure and their spread in the environment. In this study, we performed the pathogenomic analysis of seven multidrug resistant (MDR) <i>E. coli</i> strains carrying efflux-associated and virulence genes from the dairy farm environment in Xinjiang Province, China. <b>Methods</b>: First, we processed the samples using standard microbiological techniques followed by species identification with MALDI-TOF MS. Then, we performed whole genome sequencing (WGS) on the Illumina NovaSeq PE150 platform and conducted pathogenomic analysis using multiple bioinformatics tools. <b>Results</b>: WGS analysis revealed that the <i>E. coli</i> strains harbored diverse antibiotic efflux-associated genes, including conferring resistance to fluoroquinolones, aminoglycosides, aminocoumarins, macrolides, peptides, phosphonic acid, nitroimidazole, tetracyclines, disinfectants/antiseptics, and multidrug resistance. The phylogenetic analysis classified seven <i>E. coli</i> strains into B1 (<i>n</i> = 4), C (<i>n</i> = 2), and F (<i>n</i> = 1) phylogroups. PathogenFinder predicted all <i>E. coli</i> strains as potential human pathogens belonging to distinct serotypes and carrying broad virulence genes (ranging from 12 to 27), including the Shiga toxin-producing gene (<i>stx1</i>, <i>n</i> = 1). However, we found that a few of the virulence genes were associated with prophages and genomic islands in the <i>E. coli</i> strains. Moreover, all <i>E. coli</i> strains carried a diverse bacterial secretion systems and biofilm-associated genes. <b>Conclusions</b>: The present study highlights the need for large-scale genomic surveillance of antibiotic-resistant bacteria in dairy farm environments to identify AMR reservoir spillover and pathogenic risks to humans and design targeted interventions to further stop their spread under a One Health framework.