Comparative Genome Analysis of Clostridium difficile Using DNA Microarrays

Part of the Methods in Molecular Biology™ book series (MIMB, volume 646)

Abstract

Clostridium difficile is a pathogen on the move, as evidenced by the rapid transcontinental spread of the so-called hypervirulent 027 strains, followed by the emergence of further PCR ribotypes such as 017, 078 and 106. This provides a rare opportunity to study the evolution of virulence in action. However, to fully exploit this opportunity, robust phylogenetic methods on a diverse set of characterised strains are required to provide a reference evolutionary framework to study C. difficile epidemiology, ecology and virulence. Traditional phylogenetic classification of bacteria to study evolutionary relatedness is based on the characterisation of a limited number of genes, rRNA or signature sequences. However, due to the acquisition of DNA through lateral gene transfer, the differences between closely related bacterial strains can be vast. By contrast, whole genome sequencing comparisons allow all genes to be compared. Nevertheless, whole-scale genome sequencing remains an expensive endeavour and such comparisons are limited to only a handful of strains. DNA microarrays represent an alternative technology for whole genome comparisons enabling a “birds eye view” of all the genes absent or present in a given genome as compared to the reference genome on the microarray.

Key words

Clostridium difficile microarray comparative phylogenomics Bayesian data analysis 

Notes

Acknowledgments

The work described in this chapter was funded by the Biotechnology and Biological Sciences Research Council and the Wellcome Trust.

References

  1. 1.
    Champion OL, Gaunt MW, Gundogdu O, Elmi A, Witney AA, Hinds J, Dorrell N and Wren BW. (2005) Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source. Proc Natl Acad Sci USA 102(44), 16043–16048.PubMedCrossRefGoogle Scholar
  2. 2.
    Hinchliffe SJ, Isherwood KE, Stabler RA, Prentice MB, Rakin A, Nichols RA, Oyston PC, Hinds J, Titball RW and Wren BW. (2003) Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis. Genome Res 13(9), 2018–2029.PubMedCrossRefGoogle Scholar
  3. 3.
    Howard SL, Gaunt MW, Hinds J, Witney AA, Stabler R and Wren BW. (2006) Application of comparative phylogenomics to study the evolution of Yersinia enterocolitica and to identify genetic differences relating to pathogenicity. J Bacteriol 188(10), 3645–3653.PubMedCrossRefGoogle Scholar
  4. 4.
    Stabler RA, Gerding DN, Songer JG, Drudy D, Brazier JS, Trinh HT, Witney AA, Hinds J and Wren BW. (2006) Comparative phylogenomics of Clostridium difficile reveals clade specificity and microevolution of hypervirulent strains. J Bacteriol 188(20), 7297–7305.PubMedCrossRefGoogle Scholar
  5. 5.
    Dorrell N, Mangan JA, Laing KG, Hinds J, Linton D, Al-Ghusein H, Barrell BG, Parkhill J, Stoker NG, Karlyshev AV, Butcher PD and Wren BW. (2001 Oct) Whole genome comparison of Campylobacter jejuni human isolates using a low-cost microarray reveals extensive genetic diversity. Genome Res 11(10), 1706–1715.PubMedCrossRefGoogle Scholar
  6. 6.
    Kim CC, Joyce EA, Chan K and Falkow S. (2002) Improved analytical methods for microarray-based genome-composition analysis. Genome Biol 3, 11.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Department of Infectious and Tropical DiseasesLondon School of Hygiene and Tropical MedicineLondonUK

Personalised recommendations