Characteristics of Isolates of Clostridium perfringens from U.S. Foodborne Outbreaks

Introduction: It is estimated that one in six Americans or 50 million people acquire a foodborne illness each year in the United States. Of these, Clostridium perfringens is estimated to be responsible for 1 million. This pathogen induces foodborne illness by expression of the C. perfringens enterotoxin gene, cpe.

Purpose: The purpose of this study was to evaluate the presence/absence of enterotoxin genes and genetic characteristics of C. perfringens recovered from foodborne outbreaks in the US.

Methods: We evaluated 90 isolates from 18 outbreaks representing 13 states and one cruise ship. Isolates were genotyped for the cpe gene by PCR and draft genome sequences from representative isolates were generated using the Ion Torrent PGM. Draft genomes were compared using reference-free SNP analysis.

Results: Of 90 isolates, 56 (62%) harbored the cpe gene indicating potential to cause diarrheal illness; however, 34 (38%) of the isolates did not carry the gene and were incorrectly identified as the causative agent of the outbreak. Based on SNP analysis, the genome sequences of 25 cpe-positive isolates shared more SNPs with each other than the genomes of 5 cpe-negative isolates; moreover, the sequences of cpe-positive and cpe-negative strains isolated in these outbreaks did not cluster together. Among the cpe-positive strains, those food and stool isolates from outbreak related strains clustered together.

Significance: Toxin-negative C. perfringens is commonly misattributed as the etiology of foodborne illness, and therefore we suggest that all isolates be screened for the cpe gene. Furthermore, genome sequencing of C. perfringens isolated from food and individuals with foodborne illness can be used to rapidly establish epidemiologic associations.