Molecular characterization of emerging multi-drug resistant Clostridium perfringens isolated from pork production chains in Korea

Clostridium perfringens is a common cause of foodborne illnesses and is involved in human and animal gastrointestinal diseases. Surveillance of C. perfringens in the pork production chain is crucial to manage the risk of pathogen transmission. This study aimed to investigate the prevalence, antimicrobial resistance profile, and genomic characteristics of C. perfringens in pork production chains in Korea. The overall prevalence of C. perfringens was 23.6% (330/1397), with 48.8 (178/365), 16.6 (138/832), and 7.0% (14/200) in pig farms, slaughterhouses, and retail markets, respectively. Toxinotyping revealed 98.9% type A and 1.1% type C isolates. Among them, 29.1% carried the beta-2 toxin gene. Antimicrobial susceptibility tests identified 20 multi-drug resistant isolates, with the highest resistance against tetracycline (65.1%). Whole-genome sequencing further revealed 17 antimicrobial resistance and 12 virulence genes. Subsequent phylogenetic analysis identified three clonal clusters, two of which revealed a clonal relationship with human clinical isolates reported in China. The ST408 isolate from the retail pork meat, IJCP45, harboured the optrA gene in a plasmid and was identical to known optrA-carrying plasmids in C. perfringens from livestock in China, suggesting the introduction and dissemination of optrA by the transmission of a specific plasmid in east Asian countries. To our knowledge, this is the first comprehensive study of C. perfringens in the pork meat production system as an “One Health” approach. The study findings provide baseline data for the distribution and genetic characteristics of pig-associated C. perfringens in Korea and indicate the zoonotic transmission potential of C. perfringens from pigs to humans.