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The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome

Nature Genetics volume 38, pages 779–786 (2006)Cite this article

Abstract

We determined the complete genome sequence of Clostridium difficile strain 630, a virulent and multidrug-resistant strain. Our analysis indicates that a large proportion (11%) of the genome consists of mobile genetic elements, mainly in the form of conjugative transposons. These mobile elements are putatively responsible for the acquisition by C. difficile of an extensive array of genes involved in antimicrobial resistance, virulence, host interaction and the production of surface structures. The metabolic capabilities encoded in the genome show multiple adaptations for survival and growth within the gut environment. The extreme genome variability was confirmed by whole-genome microarray analysis; it may reflect the organism's niche in the gut and should provide information on the evolution of virulence in this organism.

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Figure 1: Circular representations of the genome of C. difficile.
Figure 2: Representation of the distribution, by functional categories, of the shared and unique C. difficile CDSs relative to the sequenced clostridial genomes.
Figure 3: Comparison (displayed using ACT) between the conjugative transposons (CTns) of C. difficile with Tn916 and Tn1549 from E. faecalis.
Figure 4: Sequences of the chromosomal ends and joints of circular forms of CTn4 and CTn5.
Figure 5: Comparative genome analysis using microarrays.

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References

  1. McDonald, L.C. et al. An epidemic, toxin gene-variant strain of Clostridium difficile . N. Engl. J. Med. 353, 2433–2441 (2005).

    Article  CAS  PubMed  Google Scholar 

  2. Loo, V.G. et al. A predominantly clonal multi-institutional outbreak of Clostridium difficile-associated diarrhea with high morbidity and mortality. N. Engl. J. Med. 353, 2442–2449 (2005).

    Article  CAS  PubMed  Google Scholar 

  3. Voth, D.E. & Ballard, J.D. Clostridium difficile toxins: mechanism of action and role in disease. Clin. Microbiol. Rev. 18, 247–263 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Wust, J., Sullivan, N.M., Hardegger, U. & Wilkins, T.D. Investigation of an outbreak of antibiotic-associated colitis by various typing methods. J. Clin. Microbiol. 16, 1096–1101 (1982).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Nolling, J. et al. Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum . J. Bacteriol. 183, 4823–4838 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Shimizu, T. et al. Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc. Natl. Acad. Sci. USA 99, 996–1001 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Bruggemann, H. et al. The genome sequence of Clostridium tetani, the causative agent of tetanus disease. Proc. Natl. Acad. Sci. USA 100, 1316–1321 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Farrow, K.A., Lyras, D. & Rood, J.I. Genomic analysis of the erythromycin resistance element Tn5398 from Clostridium difficile . Microbiology 147, 2717–2728 (2001).

    Article  CAS  PubMed  Google Scholar 

  9. Haraldsen, J.D. & Sonenshein, A.L. Efficient sporulation in Clostridium difficile requires disruption of the sigmaK gene. Mol. Microbiol. 48, 811–821 (2003).

    Article  CAS  PubMed  Google Scholar 

  10. Braun, V. et al. A chimeric ribozyme in Clostridium difficile combines features of group I introns and insertion elements. Mol. Microbiol. 36, 1447–1459 (2000).

    Article  CAS  PubMed  Google Scholar 

  11. Burrus, V., Pavlovic, G., Decaris, B. & Guedon, G. Conjugative transposons: the tip of the iceberg. Mol. Microbiol. 46, 601–610 (2002).

    Article  CAS  PubMed  Google Scholar 

  12. Mullany, P. et al. Genetic analysis of a tetracycline resistance element from Clostridium difficile and its conjugal transfer to and from Bacillus subtilis . J. Gen. Microbiol. 136, 1343–1349 (1990).

    Article  CAS  PubMed  Google Scholar 

  13. Wang, H. et al. Characterization of the ends and target sites of the novel conjugative transposon Tn5397 from Clostridium difficile: excision and circularization is mediated by the large resolvase, TndX. J. Bacteriol. 182, 3775–3783 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Franke, A.E. & Clewell, D.B. Evidence for a chromosome-borne resistance transposon (Tn916) in Streptococcus faecalis that is capable of “conjugal” transfer in the absence of a conjugative plasmid. J. Bacteriol. 145, 494–502 (1981).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Roberts, A.P., Johanesen, P.A., Lyras, D., Mullany, P. & Rood, J.I. Comparison of Tn5397 from Clostridium difficile, Tn916 from Enterococcus faecalis and the CW459tet(M) element from Clostridium perfringens shows that they have similar conjugation regions but different insertion and excision modules. Microbiology 147, 1243–1251 (2001).

    Article  CAS  PubMed  Google Scholar 

  16. Garnier, F., Taourit, S., Glaser, P., Courvalin, P. & Galimand, M. Characterization of transposon Tn1549, conferring VanB-type resistance in Enterococcus spp. Microbiology 146, 1481–1489 (2000).

    Article  CAS  PubMed  Google Scholar 

  17. Jansen, R., Embden, J.D., Gaastra, W. & Schouls, L.M. Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol. 43, 1565–1575 (2002).

    Article  CAS  PubMed  Google Scholar 

  18. Mojica, F.J., Diez-Villasenor, C., Garcia-Martinez, J. & Soria, E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 60, 174–182 (2005).

    Article  CAS  PubMed  Google Scholar 

  19. Makarova, K.S., Grishin, N.V., Shabalina, S.A., Wolf, Y.I. & Koonin, E.V. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol. Direct 1, 7 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  20. Calabi, E. et al. Molecular characterization of the surface layer proteins from Clostridium difficile . Mol. Microbiol. 40, 1187–1199 (2001).

    Article  CAS  PubMed  Google Scholar 

  21. Wright, A. et al. Proteomic analysis of cell surface proteins from Clostridium difficile . Proteomics 5, 2443–2452 (2005).

    Article  CAS  PubMed  Google Scholar 

  22. Waligora, A.J. et al. Characterization of a cell surface protein of Clostridium difficile with adhesive properties. Infect. Immun. 69, 2144–2153 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Savariau-Lacomme, M.P., Lebarbier, C., Karjalainen, T., Collignon, A. & Janoir, C. Transcription and analysis of polymorphism in a cluster of genes encoding surface-associated proteins of Clostridium difficile . J. Bacteriol. 185, 4461–4470 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Hennequin, C., Janoir, C., Barc, M.C., Collignon, A. & Karjalainen, T. Identification and characterization of a fibronectin-binding protein from Clostridium difficile . Microbiology 149, 2779–2787 (2003).

    Article  CAS  PubMed  Google Scholar 

  25. Poilane, I., Karjalainen, T., Barc, M.C., Bourlioux, P. & Collignon, A. Protease activity of Clostridium difficile strains. Can. J. Microbiol. 44, 157–161 (1998).

    Article  CAS  PubMed  Google Scholar 

  26. Dramsi, S., Trieu-Cuot, P. & Bierne, H. Sorting sortases: a nomenclature proposal for the various sortases of Gram-positive bacteria. Res. Microbiol. 156, 289–297 (2005).

    Article  CAS  PubMed  Google Scholar 

  27. Mazmanian, S.K., Ton-That, H., Su, K. & Schneewind, O. An iron-regulated sortase anchors a class of surface protein during Staphylococcus aureus pathogenesis. Proc. Natl. Acad. Sci. USA 99, 2293–2298 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Borriello, S.P., Welch, A.R., Barclay, F.E. & Davies, H.A. Mucosal association by Clostridium difficile in the hamster gastrointestinal tract. J. Med. Microbiol. 25, 191–196 (1988).

    Article  CAS  PubMed  Google Scholar 

  29. Davies, H.A. & Borriello, S.P. Detection of capsule in strains of Clostridium difficile of varying virulence and toxigenicity. Microb. Pathog. 9, 141–146 (1990).

    Article  CAS  PubMed  Google Scholar 

  30. Depardieu, F., Bonora, M.G., Reynolds, P.E. & Courvalin, P. The vanG glycopeptide resistance operon from Enterococcus faecalis revisited. Mol. Microbiol. 50, 931–948 (2003).

    Article  CAS  PubMed  Google Scholar 

  31. Arthur, M., Depardieu, F., Molinas, C., Reynolds, P. & Courvalin, P. The vanZ gene of Tn1546 from Enterococcus faecium BM4147 confers resistance to teicoplanin. Gene 154, 87–92 (1995).

    Article  CAS  PubMed  Google Scholar 

  32. Champion, O.L. et al. Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source. Proc. Natl. Acad. Sci. USA 102, 16043–16048 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Selmer, T. & Andrei, P.I. p-Hydroxyphenylacetate decarboxylase from Clostridium difficile. A novel glycyl radical enzyme catalysing the formation of p-cresol. Eur. J. Biochem. 268, 1363–1372 (2001).

    Article  CAS  PubMed  Google Scholar 

  34. Elsden, S.R., Hilton, M.G. & Waller, J.M. The end products of the metabolism of aromatic amino acids by clostridia. Arch. Microbiol. 107, 283–288 (1976).

    Article  CAS  PubMed  Google Scholar 

  35. Begley, M., Gahan, C.G. & Hill, C. The interaction between bacteria and bile. FEMS Microbiol. Rev. 29, 625–651 (2005).

    Article  CAS  PubMed  Google Scholar 

  36. Sleator, R.D., Wemekamp-Kamphuis, H.H., Gahan, C.G., Abee, T. & Hill, C.A. PrfA-regulated bile exclusion system (BilE) is a novel virulence factor in Listeria monocytogenes . Mol. Microbiol. 55, 1183–1195 (2005).

    Article  CAS  PubMed  Google Scholar 

  37. Paredes, C.J., Alsaker, K.V. & Papoutsakis, E.T. A comparative genomic view of clostridial sporulation and physiology. Nat. Rev. Microbiol. 3, 969–978 (2005).

    Article  CAS  PubMed  Google Scholar 

  38. Moir, A., Corfe, B.M. & Behravan, J. Spore germination. Cell. Mol. Life Sci. 59, 403–409 (2002).

    Article  CAS  PubMed  Google Scholar 

  39. Broussolle, V. et al. Molecular and physiological characterisation of spore germination in Clostridium botulinum and C. sporogenes . Anaerobe 8, 89–100 (2002).

    Article  CAS  Google Scholar 

  40. Carter, G.P., Purdy, D., Williams, P. & Minton, N.P. Quorum sensing in Clostridium difficile: analysis of a luxS-type signalling system. J. Med. Microbiol. 54, 119–127 (2005).

    Article  CAS  PubMed  Google Scholar 

  41. Whitehead, N.A., Barnard, A.M., Slater, H., Simpson, N.J. & Salmond, G.P. Quorum-sensing in Gram-negative bacteria. FEMS Microbiol. Rev. 25, 365–404 (2001).

    Article  CAS  PubMed  Google Scholar 

  42. Lee, A.S. & Song, K.P. LuxS/autoinducer-2 quorum sensing molecule regulates transcriptional virulence gene expression in Clostridium difficile . Biochem. Biophys. Res. Commun. 335, 659–666 (2005).

    Article  CAS  PubMed  Google Scholar 

  43. Ohtani, K., Hayashi, H. & Shimizu, T. The luxS gene is involved in cell-cell signalling for toxin production in Clostridium perfringens . Mol. Microbiol. 44, 171–179 (2002).

    Article  CAS  PubMed  Google Scholar 

  44. Lyon, G.J. & Novick, R.P. Peptide signaling in Staphylococcus aureus and other Gram-positive bacteria. Peptides 25, 1389–1403 (2004).

    Article  CAS  PubMed  Google Scholar 

  45. van Schaik, W. & Abee, T. The role of sigmaB in the stress response of Gram-positive bacteria–targets for food preservation and safety. Curr. Opin. Biotechnol. 16, 218–224 (2005).

    Article  CAS  PubMed  Google Scholar 

  46. de Vries, Y.P. et al. Deletion of sigB in Bacillus cereus affects spore properties. FEMS Microbiol. Lett. 252, 169–173 (2005).

    Article  CAS  PubMed  Google Scholar 

  47. Wilson, K.H. Efficiency of various bile salt preparations for stimulation of Clostridium difficile spore germination. J. Clin. Microbiol. 18, 1017–1019 (1983).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Bell, K.S. et al. Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors. Proc. Natl. Acad. Sci. USA 101, 11105–11110 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Rutherford, K. et al. Artemis: sequence visualization and annotation. Bioinformatics 16, 944–945 (2000).

    Article  CAS  PubMed  Google Scholar 

  50. Carver, T.J. et al. ACT: the Artemis comparison tool. Bioinformatics 21, 3422–3423 (2005).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We would like to acknowledge the support of the Wellcome Trust Sanger Institute core sequencing and informatics groups. We thank D. Gerding and G. Songer for provision of C. difficile strains, F. Barbut and J. Emerson for help with the antibiotic susceptibility tests, and the BUGs microarray facility at St. George's Hospital for provision of the C. difficile 630 microarray. This work was supported by the Wellcome Trust.

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Authors and Affiliations

  1. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, Cambridge, UK

    Mohammed Sebaihia, Nicholas R Thomson, Ana M Cerdeño-Tárraga, Matthew TG Holden, Carol Churcher, Michael A Quail, Stephen Baker, Nathalie Bason, Karen Brooks, Tracey Chillingworth, Ann Cronin, Paul Davis, Linda Dowd, Audrey Fraser, Theresa Feltwell, Zahra Hance, Simon Holroyd, Kay Jagels, Sharon Moule, Karen Mungall, Claire Price, Ester Rabbinowitsch, Sarah Sharp, Mark Simmonds, Kim Stevens, Louise Unwin, Sally Whithead, Gordon Dougan, Bart Barrell & Julian Parkhill

  2. Department of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

    Brendan W Wren & Richard Stabler

  3. Eastman Dental Institute for Oral Health Care Sciences, University College London, 256 Gary's Inn Road, London, WC1X 8LD, UK

    Peter Mullany, Adam P Roberts & Hongmei Wang

  4. Centre for Molecular Microbiology and Infection, Imperial College London, London, SW7 2AZ, UK

    Neil F Fairweather & Anne Wright

  5. Centre for Biomolecular Sciences, Institute of Infection, Immunity and Inflammation, University of Nottingham, University Park, Nottingham, NG7 2RD, UK

    Nigel Minton

  6. Unité de Génétique Moléculaire Bactérienne, Institut Pasteur, 28 Rue du Dr Roux, Paris, 75724, Cedex 15, France

    Bruno Dupuy

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Correspondence to Julian Parkhill.

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Supplementary information

Supplementary Table 1

Features of the C. difficile CRISPRs. (PDF 60 kb)

Supplementary Table 2

Antibiotic susceptibility of C. difficile strain 630. (PDF 50 kb)

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Sebaihia, M., Wren, B., Mullany, P. et al. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet 38, 779–786 (2006). https://doi.org/10.1038/ng1830

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