Prevalence, Antimicrobial Resistance, and Genomic Analysis of Yersinia enterocolitica from Livestock Farms in Qinghai, China

Introduction: Yersinia enterocolitica is a zoonotic foodborne pathogen that contaminates water, animal-derived food products, thereby posing a continuous threat to food safety and public health. Methods: In 2025, a total of 513 animal-derived and environmental samples were collected from five livestock farms in Qinghai, China. Isolates were characterized using biotyping, antimicrobial susceptibility testing, whole-genome sequencing, multilocus sequence typing (MLST), and analyses of resistance/virulence genes, plasmids, pan-genome, and phylogeny. For comparative purposes, genomic data of 60 Y. enterocolitica strains from other regions of China were retrieved from the NCBI database. Results: The overall isolation rate of Y. enterocolitica was 1.56%, with a higher detection rate in environmental water samples than in bovine feces or porcine anal swabs in Qinghai, China. Biotype 1A was predominant, followed by biotype 4. MLST identified six sequence types (ST5, ST18, ST3, ST404, ST278, and ST26). Antimicrobial susceptibility testing revealed high resistance rates to ampicillin (100%) and sulfisoxazole (87.5%), and most isolates exhibited multidrug resistance. Whole-genome analysis identified 116 virulence-related genes and 14 genes associated with antimicrobial or disinfectant resistance; crp, vatF, and y56_beta-lactamase were present in all isolates. Pan-genome and phylogenetic analyses demonstrated substantial genomic variability, and some isolates from Qinghai were closely related to strains from Ningxia, China. Conclusions: Y. enterocolitica isolates from livestock farms in Qinghai, China, exhibit a certain level of contamination and pose a risk of multidrug resistance. The high detection rate in environmental water suggests potential transmission from farm environments to the food chain. This study provides scientific evidence for regional epidemiological surveillance, food safety risk assessment, and the development of AMR control strategies in China.