Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source - PubMed (original) (raw)

Comparative Study

. 2005 Nov 1;102(44):16043-8.

doi: 10.1073/pnas.0503252102. Epub 2005 Oct 17.

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Comparative Study

Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source

Olivia L Champion et al. Proc Natl Acad Sci U S A. 2005.

Abstract

Campylobacter jejuni is the predominant cause of bacterial gastroenteritis worldwide, but traditional typing methods are unable to discriminate strains from different sources that cause disease in humans. We report the use of genomotyping (whole-genome comparisons of microbes using DNA microarrays) combined with Bayesian-based algorithms to model the phylogeny of this major food-borne pathogen. In this study 111 C. jejuni strains were examined by genomotyping isolates from humans with a spectrum of C. jejuni-associated disease (70 strains), chickens (17 strains), bovines (13 strains), ovines (5 strains), and the environment (6 strains). From these data, the Bayesian phylogeny of the isolates revealed two distinct clades unequivocally supported by Bayesian probabilities (P = 1); a livestock clade comprising 31/35 (88.6%) of the livestock isolates and a "nonlivestock" clade comprising further clades of environmental isolates. Several genes were identified as characteristic of strains in the livestock clade. The most prominent was a cluster of six genes (cj1321 to cj1326) within the flagellin glycosylation locus, which were confirmed by PCR analysis as genetic markers in six additional chicken-associated strains. Surprisingly these studies show that the majority (39/70, 55.7%) of C. jejuni human isolates were found in the nonlivestock clade, suggesting that most C. jejuni infections may be from nonlivestock (and possibly nonagricultural) sources. This study has provided insight into a previously unidentified reservoir of C. jejuni infection that may have implications in disease-control strategies. The comparative phylogenomics approach described provides a robust methodological prototype that should be applicable to other microbes.

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Figures

Fig. 1.

Fig. 1.

Phylogenomic relationship of strains associated with different ecological niches. P = 1.0 represents 100% of all phylogenies showing a given topology. Strains are designated at the end of branches and are colored according to the ecological niche from which the C. jejuni strain was isolated.

Fig. 2.

Fig. 2.

Phylogenomic relationship of strains associated with different clinical outcomes. Strains are designated at the end of branches and are colored according to the clinical outcome of the C. jejuni infection or livestock/environmental source.

Fig. 3.

Fig. 3.

Distribution of cj1321 among C. jejuni strains. Parsimony-based gene analysis for determining the distribution of individual CDS cj1321 throughout the phylogenetic tree. Strains in which cj1321 are absent are colored yellow; strains in which cj1321 are present are colored blue. Strains in the livestock clade all contain cj1321 with one exception. cj1321 is absent in strains in the nonlivestock clade with eight exceptions.

Fig. 4.

Fig. 4.

Detection of cj1321–cj1326 in additional chicken isolates B, 17M, and A. PCR products from DNA of chicken isolates B, 17M, and A were amplified with primers for genes cj1321 to cj1326 inclusive.

Fig. 5.

Fig. 5.

Distribution of cj1365 among C. jejuni strains. Parsimony-based gene analysis for determining the distribution of individual CDS cj1365 throughout the phylogenetic tree. Strains in which cj1365 are absent are colored yellow. Strains in which cj1365 are present are colored blue. cj1365 is absent from all six beach isolates, eight clinical isolates, and three livestock isolates.

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