Clostridium perfringens is a Gram-positive anaerobic spore-forming bacterium found in soil, the intestines of humans and animals, and sewage. At temperatures between 10 and 60°C in anaerobic conditions and high moisture levels, toxins may be produced, and meat of any kind can be contaminated with spores. C. perfringens strains are classified into five groups (A-E) depending on their production of different toxins. The type A strain causes gas gangrene, necrotic enteritis, and mild diarrhea in humans. C. perfringens-induced diseases are among the most commonly reported food-borne illnesses.

After entry of vegetative cells or spores into the tissues, through a wound for example, rapid growth is observed, and toxins and degradative enzymes are produced, resulting in massive invasion and destruction of the tissues. Although toxin production and its regulation have been well studied, the pathogenesis and physiology of C. perfringens are not yet completely understood. A study of the entire genome sequence of C. perfringens reveals new insights in understanding the onset of the disease, and may contribute to the development of therapeutics to block C. perfringens invasion in humans.

Shimizu et al. determined the genome sequence of C. perfringens strain 13, classified as a type A strain. The genome contains 3,031,430 bp, has a remarkably low G+C content of 28.6% and contains 2,660 putative open reading frames (ORFs). A plasmid named pCP13 was also present and consists of 54,310 bp with a G+C content of 25.5% and 63 putative ORFs. Of the ORFs present in the genome, 56.1% showed similarity to functional genes in databases, 18.9% showed similarity to genes encoding unknown proteins, and 25.2% are unique to the C. perfringens genome. Comparison of the C. perfringens genome with the genome of the non-pathogenic C. acetobutylicum revealed interesting differences that may be related to their different lifestyles.For instance, genes encoding β- and α-galactosidases, β-mannosidase, and various virulence-associated proteins in C. perfringens were not found in C. acetobutylicum, whereas the latter contained genes encoding, for example, chemotaxis/flagella-related proteins, and nitrogen-fixation genes that were absent from C. perfringens. C. perfringens can metabolize a variety of carbohydrate sources, including fructose, mannose, galactose, glycogen, lactose, and starch, which is consistent with the presence of many genes for carbohydrate-degrading enzymes - for instance, sucrase, β-mannosidase, and β-amylase. The genome includes 211 genes encoding putative transport systems involved in import or export of amino acids, cations/anions, carbohydrates, and nucleosides/nucleotides. Many genes related to spore formation or germination were found, but over 80 Bacillus subtilis genes involved in spore formation had no homologs in C. perfringens, suggesting a different mechanism of spore formation. All genes encoding toxins - for instance, hemolysin, phospholipase C, collagenase, enterotoxin, hyaluronidase, sialidase, and perfringolysin O - were found on the chromosome, with the exception of two that were found on the plasmid. Surprisingly, none of these virulence-related genes was present in pathogenicity islands - distinct regions of the genome present in some pathogens in which virulence genes are clustered together. Furthermore, 48 genes encoding bacterial two-component systems were found. One of these is the VirR/VirS system, which is involved in regulating the production of certain toxins.