Whole-Genome Sequencing–Based Characterization and Antimicrobial Resistance Analysis of Shiga Toxin–Producing Escherichia coli Isolated from Retail Meat Products

Shiga toxin–producing Escherichia coli (STEC), a zoonotic foodborne pathogen, has become a critical global public health issue. This study investigates molecular traits and antimicrobial resistance (AMR) mechanisms of STEC strains derived from retail meat products sourced from domestic production in Liaocheng city, Shandong province, China, to inform health risk assessment. Using quantitative real-time polymerase chain reaction (qPCR), phenotypic AMR testing, and whole-genome sequencing (WGS), 38 STEC isolates were identified from 400 retail meat products, with an isolation rate of 9.5%. Significant differences in STEC isolation rates were detected among different meat types, and mutton exhibited a relatively high isolation rate of 26.09%. Genomic virulence analysis showed that there were higher proportions of single stx 2 (58.33%) and dual stx 1 /stx 2 genotypes (33.33%) in mutton isolates than in beef ( stx 2 : 48.00%, dual stx 1 /stx 2 : 12.00%), and only the stx 2 gene was found in pork isolates. STEC isolates exhibited marked serotypic diversity, including O128ac:H2, O168:H7, O178:H7, O2:H25, and O6:H10. Multilocus sequence typing analysis revealed heterogeneous sequence type (ST) distributions among isolates, with ST10 , ST25 , and ST2722 as dominant STs, suggesting diverse contamination sources. STEC isolates exhibited high phenotypic resistance to tetracycline (TET) (68.42%), which corresponded to the highest detection rate of the TET resistance gene tet(A) at the genomic level. All isolates were susceptible to ertapenem, meropenem, ceftazidime, ceftazidime-avibactam, ciprofloxacin, and amikacin. Multidrug resistance (MDR) analysis indicated that 16 STEC isolates were MDR strains, with beef-derived isolates having relatively high MDR rates. This study verifies the occurrence of STEC in retail meat, highlighting prevalent AMR and substantial genetic heterogeneity among isolates. The findings underscore the necessity of systematic surveillance to limit STEC transmission along the meat supply chain and facilitate targeted food safety interventions.