Toxin gene profiles, antibiotic resistance, and genetic diversity of Clostridium perfringens from food-producing animals: a whole-genome sequencing study with implications for food safety

Clostridium perfringens is a significant zoonotic foodborne pathogen. To systematically assess the potential risks associated with food-producing animals as a reservoir of C. perfringens in the early stages of the food production chain, we conducted whole-genome sequencing (WGS) and phenotypic analysis of 91 clinical C. perfringens isolates collected from pigs, chickens, cows, ducks, and geese across different regions of China. The results revealed that the isolates harbored a rich repertoire of toxin genes, with 71.43% (65/91) carrying greater than or equal to 10 toxin genes. Besides the classic type A, type C, which causes animal enterotoxemia, was most prevalent in pigs (45.76%). Notably, the and necrotic B-like (NetB) toxin, typically associated with avian necrotic enteritis, was also detected in isolates from cows and geese, suggesting potential cross-host transmission of toxin types. Antimicrobial susceptibility testing revealed a severe resistance situation, particularly among porcine isolates, which showed the highest resistance rates to clindamycin, penicillin, and tetracycline, with widespread multidrug resistance (MDR). Genomic analysis further identified 14 types of antimicrobial resistance (AMR) genes. The tetracycline resistance gene tetA(P) had an extremely high carriage rate of 94.51%, and AMR genes were most enriched in porcine isolates. Multilocus sequence typing (MLST) identified 59 sequence types (STs), 42 of which were newly discovered, demonstrating high genetic diversity. Major clonal complexes (CCs) showed certain host and geographic clustering. Furthermore, while the restriction-modification (RM) system was present in all isolates, the distribution of other defense systems like CRISPR-Cas was strain-specific. This study revealed that C. perfringens from Chinese food-producing animals is characterized by high virulence, extensive antimicrobial resistance, and high genetic diversity. It highlighted that pigs may serve as a crucial reservoir and evolutionary hub for virulent MDR isolates, posing a continuous threat to food safety and public health, and underscored the necessity for enhanced monitoring at the farm level.