Phenotypic and Molecular Characterization of Carbapenem-Resistant Escherichia coli Isolated from Retail Meats in Hat Yai, Thailand

(1) Background: Carbapenem-resistant Escherichia coli (CREC) is widespread and resistant to almost all available antimicrobial agents. In this study, we aimed to assess the phenotypic and molecular characteristics of CREC isolated from retail meats in Hat Yai, Songkhla, Thailand. (2) Methods: A total of 155 retail meat samples were randomly collected, and 412 presumptive carbapenem-non-susceptible isolates were screened via culturing on imipenem-containing eosin methylene blue (EMB) agar. Susceptibility to imipenem and meropenem was tested using the disk diffusion method, and carbapenemase and virulence genes in CREC isolates were detected using PCR. Phylogenetic groups and genetic relatedness of carbapenemase-positive CREC isolates were analyzed using gene markers and BOX-PCR, respectively. (3) Results: The results revealed a high prevalence of presumptive carbapenem-non-susceptible E. coli (CNSEC) isolates in beef samples. Over 89% of the CNSEC isolates from all meat types were identified as CREC. Of these, only 4.8% of the isolates from beef samples were positive for the blaNDM gene, and one was also positive for the blaVIM gene. These isolates carried only the fimH gene as a virulence factor. The blaNDM-positive CREC isolates were classified in phylogenetic Group D. (4) Conclusions: Identifying antimicrobial-resistant pathogens, particularly CREC, in food-producing animals is critical due to potential risks to public health.