Whole genome sequencing based characteristics and transmission risk analysis of Shiga toxin producing Escherichia coli from goats, breeding environment and raw mutton in Zigong, Sichuan

ObjectiveTo investigate the prevalence and molecular characteristics of Shiga toxin-producing Escherichia coli （STEC） in goat’s feace， breeding environments， and retail raw mutton in Zigong， Sichuan Province， and to provide support for risk assessment， traceability investigation， and scientific prevention and control strategies for STEC infections.MethodsSamples of goat feces， farm environment sewage， and retail raw mutton were collected from four districts and two counties in Zigong for STEC isolation. Whole genome sequencing was performed， and multilocus sequence typing （MLST）， serotyping， Shiga toxin subtyping， antibiotic resistance genes were analyzed， and core genome single nucleotide polymorphism （cgSNP） phylogenetic analysis were conducted based on the whole genome sequences.ResultsFrom May to July 2024， a total of 466 samples were collected， and 74 STEC strains were isolated， including 67 from goat feces （67/431， 15.55%）， 4 from environmental sewage （4/6， 66.67%）， and 3 from raw mutton （3/29， 10.34%）. The 74 STEC strains were classified into 20 different serotypes， 21 MLST types， and 5 Shiga toxin subtypes. Sixty-four （64/74， 86.49%） strains carried more than 5 antibiotic resistance genes. cgSNP phylogenetic analysis revealed that strains of serotypes O38：H26 and O12：H25 persisted in goats across different regions of Zigong and showed high genetic relatedness with strains from the environment and raw mutton.ConclusionThe high carriage rate of STEC in goats in Zigong， along with the diverse molecular characteristics of the strains， indicates potential transmission pathways through environmental contamination and raw mutton. The potential risk of human infection should be closely monitored.