Genomic adaptation of <i>Clostridium perfringens</i> to human intestine

<i>Clostridium perfringens</i> is often associated with foodborne diseases, posing significant public health risks. However, genomic investigation of <i>C. perfringens</i> isolates from the human population has been lacking. This study aims to fill this knowledge gap by examining the genomic characteristics of <i>C. perfringens</i> isolates from 699 individuals at a provincial hospital in China. We further conducted evolutionary and pan-genomic analyses, incorporating isolates from humans and animals worldwide. The results reveal potential regional and transregional transmission of <i>C. perfringens</i> among individuals, along with the common transfer of small gene clusters during this process. Notably, the food poisoning-associated toxin gene <i>cpe</i> was identified in a fusion plasmid for the first time in an isolate, indicating fusion of pCP13-like and pCW3-like plasmids and the potential for transfer of <i>cpe</i> across genetic backgrounds. Moreover, we observed that the genomic characteristics of <i>C. perfringens</i> correlate with host species, with specific toxin genes, such as <i>pfoA</i> and <i>colA</i>, potentially influencing host selectivity. Through this comprehensive genomic analysis, we provide novel insights into the fusion of pCW3-like and pCP13-like plasmids, the genetic location of <i>cpe</i>, the transmission dynamics of <i>C. perfringens</i> strains, and the relationship between toxin genes and host relevance. These findings expand our understanding of <i>C. perfringens</i> and its implications for public health.