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The genome sequence of the flesh-eating Clostridium perfringens
By Birgit Reinert


Japanese researchers have sequenced the genome of Clostridium perfringens, a bacterium whose toxic strains can cause disease in humans ranging from mild diarrhea to life-threatening infections. The sequencing revealed that the pathogen's virulence is closely linked to the nutrients and various materials it obtains from the host to grow and survive. Found in the environment and in the intestines of animals and humans alike, the bacterium is the most widely distributed pathogen in nature, according to the new study.

Clostridium perfringens bacteria on a blood agar plate.

The researchers sequenced a virulent type of C. perfringens strain 13 using a whole-genome shotgun strategy. This strain is known to cause gas gangrene, a rapidly progressive and often fatal infection causing painful swelling at wounds or surgical sites. Once the organism has entered the human body through an injury, it grows rapidly and produces various toxins that destroy the host's tissue.

The C. perfringens genome, which is over 3 million base pairs long, consists of a circular chromosome and a very small DNA structure called plasmid. Some 2,660 genes reside on the chromosome, of which 56 percent have obvious similarity to known genes in other organisms. The study was led by Tohru Shimizu, of the University of Tsukuba in Ibaraki, Japan.

Circular map of the C. perfringens chromosome. View larger

By comparing the C. perfringens sequence to the genome of Clostridium acetobutylicum, a nonpathogenic relative whose genome was sequenced last September, Shimizu's team found that the most distinct feature of C. perfringens is the existence of genes related to virulence. They newly identified twenty genes as potential disease-causing factors.

"The genome information of C. perfringens and the comparison with the C. acetobutylicum genome present us with a clear picture about its way of life as a pathogen," the researchers write in Proceedings of the National Academy of Sciences.

"The pathogenicity and nutritional acquisition must be highly coupled in C. perfringens infection, and this unique nutritional feature would be a possible target for the inhibition of growth and prevention of C. perfringens infection," the researchers conclude.

The complete genome sequence and annotation are available online at

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Shimizu, T. et al. Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc Natl Acad Sci USA 99, 996-1001 (January 22, 2002). Published online January 15, 2002.
Nolling, J. et al. Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J Bacteriol 183, 4823-4838 (August 2001).

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