Comparative genomic analysis of food-animal-derived and human-derived Clostridium perfringens isolates from markets in Shandong, China

<i>Clostridium perfringens</i> (<i>C. perfringens</i>) is a foodborne pathogen that poses a significant threat to both animal husbandry and public health. In this study, 27 <i>C. perfringens</i> strains were isolated from animal samples and animal-derived food products. Antibiotics resistances among the isolates were phenotypically and genotypically analyzed and Whole genome sequencing (WGS). In combination with the genomes of 141 human-derived <i>C. perfringens</i> strains from public databases, this study conducted comprehensive analyses of antibiotic resistance genes, virulence genes, multilocus sequence typing (MLST), prophage detection, and pan-genome analysis for a total of 168 strains of <i>C. perfringens</i>. Antibiotics resistances among the isolates were phenotypically and genotypically analyzed and found 24 of them (88.9%, 24/27) were identified as multidrug-resistant (MDR). WGS analysis revealed that 13 strains belonged to known sequence types (ST), and the remaining strains represented 10 new STs. By analysis in combination with data of 141 <i>C. perfringens</i> isolates from the database, it was implied that ST221, ST72 and ST370 were present in both animal-derived and human-derived <i>C. perfringens</i>. It is worth noting that 108 out of 168 strains of <i>C. perfringens</i> (64.3%, 108/168) were found to carry prophages, which were found more prevalent in human-derived <i>C. perfringens</i> isolates. Pan-genome and phylogenetic analysis of 168 <i>C. perfringens</i> strains indicated that <i>C. perfringens</i> possesses an open pan-genome with genetic diversity. This study provides genomic insights into <i>C. perfringens</i> from food animals and humans, shedding light on the importance for monitoring the <i>C. perfringens</i> in livestock in China for better public health.