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Originally published as Genetics Published Articles Ahead of Print on February 19, 2006.
Genetics, Vol. 172, 2081-2092, April 2006, Copyright © 2006
doi:10.1534/genetics.105.054601
Analysis of Core Housekeeping and Virulence Genes Reveals Cryptic Lineages of Clostridium perfringens That Are Associated With Distinct Disease Presentations
Alejandro P. Rooney*,1,
James L. Swezey*,
Robert Friedman
,
David W. Hecht
and
Carol W. Maddox
* Microbial Genomics Research Unit, National Center for Agricultural Utilization Research, U.S. Department of Agriculture–Agricultural Research Service, Peoria, Illinois 61604, Biotechnology and Bioservices Center, University of Connecticut, Storrs, Connecticut 06269, Division of Infectious Disease, Loyola University Medical Center, Maywood, Illinois 60126 and Veterinary Diagnostic Laboratory, University of Illinois, Urbana, Illinois 61802
1 Corresponding author: Microbial Genomics Research Unit, National Center for Agricultural Utilization Research, USDA–ARS, 1815 N. University St., Peoria, IL 61604.
E-mail: rooney{at}ncaur.usda.gov
Clostridium perfringens is an important human and animal pathogen that causes a number of diseases that vary in their etiology and severity. Differences between strains regarding toxin gene composition and toxin production partly explain why some strains cause radically different diseases than others. However, they do not provide a complete explanation. The purpose of this study was to determine if there is a phylogenetic component that explains the variance in C. perfringens strain virulence by assessing patterns of genetic polymorphism in genes (colA gyrA, plc, pfoS, and rplL) that form part of the core genome in 248 type A strains. We found that purifying selection plays a central role in shaping the patterns of nucleotide substitution and polymorphism in both housekeeping and virulence genes. In contrast, recombination was found to be a significant factor only for the virulence genes plc and colA and the housekeeping gene gyrA. Finally, we found that the strains grouped into five distinct evolutionary lineages that show evidence of host adaptation and the early stages of speciation. The discovery of these previously unknown lineages and their association with distinct disease presentations carries important implications for human and veterinary clostridial disease epidemiology and provides important insights into the pathways through which virulence has evolved in C. perfringens.
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