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Letter

Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens

¹ The Institute for Genomic Research, Rockville, Maryland 20850, USA; ² Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton 3800, Australia; ³ Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24601, USA; ⁴ Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA; ⁵ Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, United Kingdom; ⁶ Department of Veterinary Science, University of Arizona, Tucson, Arizona 85721, USA

Clostridium perfringens is a Gram-positive, anaerobic spore-forming bacterium commonly found in soil, sediments, and the human gastrointestinal tract. C. perfringens is responsible for a wide spectrum of disease, including food poisoning, gas gangrene (clostridial myonecrosis), enteritis necroticans, and non-foodborne gastrointestinal infections. The complete genome sequences of Clostridium perfringens strain ATCC 13124, a gas gangrene isolate and the species type strain, and the enterotoxin-producing food poisoning strain SM101, were determined and compared with the published C. perfringens strain 13 genome. Comparison of the three genomes revealed considerable genomic diversity with >300 unique "genomic islands" identified, with the majority of these islands unusually clustered on one replichore. PCR-based analysis indicated that the large genomic islands are widely variable across a large collection of C. perfringens strains. These islands encode genes that correlate to differences in virulence and phenotypic characteristics of these strains. Significant differences between the strains include numerous novel mobile elements and genes encoding metabolic capabilities, strain-specific extracellular polysaccharide capsule, sporulation factors, toxins, and other secreted enzymes, providing substantial insight into this medically important bacterial pathogen.

⁸ Corresponding author.

E-mail ipaulsen{at}tigr.org; fax (301) 838-0208.

[Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GenBank under accession numbers CP000246 (C. perfringens ATCC 13124 chromosome) and CP000312, CP000313, CP000314, and CP000315 (C. perfringens SM101 chromosome, pSM101A, pSM101B, and SM101, respectively).]

Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.5238106

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