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Clostridium perfringens  causes a variety of human and animal enteric diseases including food poisoning, antibiotic-associated diarrhea, and necrotic enteritis. Yet, the reservoirs of enteropathogenic enterotoxin-producing strains remain unknown. We conducted a genomic comparison of 290 strains and a heat resistance phenotyping of 30  C. perfringens  strains to elucidate the population structure and ecology of this pathogen.  C. perfringens  genomes shared a conserved genetic backbone with more than half of the genes of an average genome conserved in >95% of strains. The c pe -carrying isolates were found to share genetic context: the  cpe -carrying plasmids had different distribution patterns within the genetic lineages and the estimated pan genome of  cpe -carrying isolates had a larger core genome and a smaller accessory genome compared to that of 290 strains. We characterize  cpe -negative strains related to chromosomal  cpe- carrying strains elucidating the origin of these strains and disclose two distinct groups of chromosomal  cpe -carrying strains with different virulence characteristics, spore heat resistance properties, and, presumably, ecological niche. Finally, an antibiotic-associated diarrhea isolate carrying two copies of the enterotoxin  cpe  gene and the associated genetic lineage with the potential for the emergence of similar strains are outlined. With  C. perfringens  as an example, implications of input genome quality for pan genome analysis are discussed. Our study furthers the understanding of genome epidemiology and population structure of enteropathogenic  C. perfringens  and brings new insight into this important pathogen and its reservoirs.

frontiers in microbiology

Comparative Genome Analysis and Spore Heat Resistance Assay Reveal a New Component to Population Structure and Genome Epidemiology Within Clostridium perfringens Enterotoxin-Carrying Isolates