Prevalence, Phylogenetic Distribution, Antimicrobial Resistance, and Genetic Relatedness of Extraintestinal Pathogenic E. coli (ExPEC) Strains Isolated from Beef Cattle and Slaughterhouse Environment

Escherichia coli is a commensal bacterium found in the gastrointestinal tracts of animals, and they might serve as a vehicle for transmitting extraintestinal pathogenic Escherichia coli (ExPEC) to the environment and human. This study aimed to investigate the prevalence, phylogenetic distribution, antimicrobial resistance, and genetic relatedness of ExPEC in beef cattle, slaughterhouse environment, and workers involved in the evisceration process during slaughter. A total of 447 samples were collected from two slaughterhouses located in the Diyarbakir and Batman cities of the Southeast Anatolia Region of Turkiye. The samples included swabs from beef carcasses (n = 133), rectal samples (n = 133), hides (n = 133), knives (n = 18), holding pens (n = 12), water (n = 6), and workers’ hands (n = 12). The samples were analyzed for the presence of ExPEC, and then isolates were screened for antimicrobial susceptibility, phylogenetic groups, and genetic relatedness. A total of 36 out of 447 samples were confirmed to be ExPEC-positive, yielding a prevalence rate of 8.80%. The contamination rates for carcasses, hides, rectal, knives, holding pens, water, and workers’ hands were 10.5%, 6.06%, 6.5%, 5.5%, 8.3%, 0%, and 25%, respectively. The ExPEC isolates were classified into phylogroups D (38.8%), B1 (25.0%), B2 (25.0%), and A (5.5%). Of the isolates, 55.55% (20/36) exhibited resistance to at least one antimicrobial agent from three or more, with the highest resistance observed against ampicillin (61.1%). ERIC-PCR analysis revealed that 35 of the isolates formed 19 distinct clusters, indicating a high level of genetic diversity among the ExPEC isolates. The results of this study demonstrate that beef cattle, the slaughterhouse environment, and workers’ hands can serve as sources of ExPEC contamination.