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Journal of Clinical Microbiology, October 2006, p. 3742-3751, Vol. 44, No. 10
0095-1137/06/$08.00+0     doi:10.1128/JCM.00618-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Novel Method To Identify Source-Associated Phylogenetic Clustering Shows that Listeria monocytogenes Includes Niche-Adapted Clonal Groups with Distinct Ecological Preferences

Department of Food Science, Cornell University, Ithaca, New York,¹ Department of Animal Sciences, Colorado State University, Fort Collins, Colorado,² Department of Biostatistics and Computational Biology, Cornell University, Ithaca, New York,³ Center for Bioinformatics and Institute of Biology, University of Copenhagen, Copenhagen, Denmark⁴

Received 22 March 2006/ Returned for modification 30 April 2006/ Accepted 27 May 2006

While phylogenetic and cluster analyses are often used to define clonal groups within bacterial species, the identification of clonal groups that are associated with specific ecological niches or host species remains a challenge. We used Listeria monocytogenes, which causes invasive disease in humans and different animal species and which can be isolated from a number of environments including food, as a model organism to develop and implement a two-step statistical approach to the identification of phylogenetic clades that are significantly associated with different source populations, including humans, animals, and food. If the null hypothesis that the genetic distances for isolates within and between source populations are identical can be rejected (SourceCluster test), then particular clades in the phylogenetic tree with significant overrepresentation of sequences from a given source population are identified (TreeStats test). Analysis of sequence data for 120 L. monocytogenes isolates revealed evidence of clustering between isolates from the same source, based on the phylogenies inferred from actA and inlA (P = 0.02 and P = 0.07, respectively; SourceCluster test). Overall, the TreeStats test identified 10 clades with significant (P < 0.05) or marginally significant (P < 0.10) associations with defined sources, including human-, animal-, and food-associated clusters. Epidemiological and virulence phenotype data supported the fact that the source-associated clonal groups identified here are biologically valid. Overall, our data show that (i) the SourceCluster and TreeStats tests can identify biologically meaningful source-associated phylogenetic clusters and (ii) L. monocytogenes includes clonal groups that have adapted to infect specific host species or colonize nonhost environments.

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