Article | Published:

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

Nature Genetics volume 40, pages 987993 (2008) | Download Citation

Abstract

Isolates of Salmonella enterica serovar Typhi (Typhi), a human-restricted bacterial pathogen that causes typhoid, show limited genetic variation. We generated whole-genome sequences for 19 Typhi isolates using 454 (Roche) and Solexa (Illumina) technologies. Isolates, including the previously sequenced CT18 and Ty2 isolates, were selected to represent major nodes in the phylogenetic tree. Comparative analysis showed little evidence of purifying selection, antigenic variation or recombination between isolates. Rather, evolution in the Typhi population seems to be characterized by ongoing loss of gene function, consistent with a small effective population size. The lack of evidence for antigenic variation driven by immune selection is in contrast to strong adaptive selection for mutations conferring antibiotic resistance in Typhi. The observed patterns of genetic isolation and drift are consistent with the proposed key role of asymptomatic carriers of Typhi as the main reservoir of this pathogen, highlighting the need for identification and treatment of carriers.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1.

    , , , & Typhoid fever. N. Engl. J. Med. 347, 1770–1782 (2002).

  2. 2.

    , & Salmonella, the host and disease: a brief review. Immunol. Cell Biol. 85, 112–118 (2007).

  3. 3.

    et al. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413, 848–852 (2001).

  4. 4.

    et al. Composition, acquisition, and distribution of the Vi exopolysaccharide-encoding Salmonella enterica pathogenicity island SPI-7. J. Bacteriol. 185, 5055–5065 (2003).

  5. 5.

    et al. Evolutionary history of Salmonella Typhi. Science 314, 1301–1304 (2006).

  6. 6.

    et al. Antimicrobial drug resistance of Salmonella enterica serovar Typhi in Asia and molecular mechanism of reduced susceptibility to the fluoroquinolones. Antimicrob. Agents Chemother. 51, 4315–4323 (2007).

  7. 7.

    et al. Clonal expansion and microevolution of quinolone-resistant Salmonella enterica serotype Typhi in Vietnam from 1996 to 2004. J. Clin. Microbiol. 45, 3485–3492 (2007).

  8. 8.

    et al. Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J. Bacteriol. 185, 2330–2337 (2003).

  9. 9.

    Advanced sequencing technologies and their wider impact in microbiology. J. Exp. Biol. 210, 1518–1525 (2007).

  10. 10.

    et al. Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing. Proc. Natl. Acad. Sci. USA 101, 13536–13541 (2004).

  11. 11.

    et al. High-throughput genotyping of Salmonella Typhi allows geographical assignment of haplotypes and pathotypes within an urban district of Jakarta, Indonesia. J. Clin. Microbiol. 46, 1741–1746 (2008).

  12. 12.

    et al. Comparisons of dN/dS are time dependent for closely related bacterial genomes. J. Theor. Biol. 239, 226–235 (2006).

  13. 13.

    , & The acquisition of full fluoroquinolone resistance in Salmonella Typhi by accumulation of point mutations in the topoisomerase targets. J. Antimicrob. Chemother. 58, 733–740 (2006).

  14. 14.

    , & Salmonellae interplay with host cells. Nat. Rev. Microbiol. 6, 53–66 (2008).

  15. 15.

    & Genome-wide association mapping in bacteria? Trends Microbiol. 14, 353–355 (2006).

  16. 16.

    , , , & A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: convergence or divergence by homologous recombination? Genome Res. 17, 61–68 (2007).

  17. 17.

    et al. The role of prophage-like elements in the diversity of Salmonella enterica serovars. J. Mol. Biol. 339, 279–300 (2004).

  18. 18.

    & Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 22, 2196–2203 (2006).

  19. 19.

    , , & Differences in gene content among Salmonella enterica serovar Typhi isolates. J. Clin. Microbiol. 41, 3823–3828 (2003).

  20. 20.

    et al. Salmonella enterica serovar Typhi strains from which SPI7, a 134-kilobase island with genes for Vi exopolysaccharide and other functions, has been deleted. J. Bacteriol. 186, 3214–3223 (2004).

  21. 21.

    et al. Precise excision of the large pathogenicity island, SPI7, in Salmonella enterica serovar Typhi. J. Bacteriol. 186, 3202–3213 (2004).

  22. 22.

    , , , & Endless possibilities: translation termination and stop codon recognition. Microbiology 147, 255–269 (2001).

  23. 23.

    et al. The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081. PLoS Genet. 2, e206 (2006).

  24. 24.

    et al. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat. Genet. 35, 32–40 (2003).

  25. 25.

    et al. Massive gene decay in the leprosy bacillus. Nature 409, 1007–1011 (2001).

  26. 26.

    & Genome degradation is an ongoing process in Rickettsia. Mol. Biol. Evol. 16, 1178–1191 (1999).

  27. 27.

    L. et al. Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome. J. Bacteriol. 189, 8186–8195 (2007).

  28. 28.

    et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc. Natl. Acad. Sci. USA 102, 13950–13955 (2005).

  29. 29.

    & Single nucleotide polymorphism typing and genetic relationships of Salmonella enterica serovar Typhi isolates. J. Clin. Microbiol. 45, 3795–3801 (2007).

  30. 30.

    , & Getting in or out: early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters. J. Mol. Evol. 48, 22–41 (1999).

  31. 31.

    & The importance of efflux pumps in bacterial antibiotic resistance. J. Antimicrob. Chemother. 51, 9–11 (2003).

  32. 32.

    et al. Free recombination within Helicobacter pylori. Proc. Natl. Acad. Sci. USA 95, 12619–12624 (1998).

  33. 33.

    et al. Evolution of Chlamydia trachomatis diversity occurs by widespread interstrain recombination involving hotspots. Genome Res. 17, 50–60 (2007).

  34. 34.

    et al. Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. BMC Evol. Biol. 6, 95 (2006).

  35. 35.

    et al. Epidemiology of typhoid carriers among blood donors and patients with biliary, gastrointestinal and other related diseases. Microbiol. Immunol. 49, 107–112 (2005).

  36. 36.

    , & Precise estimation of the number of chronic carriers of Salmonella typhi in Santiago, Chile, an endemic area. J. Infect. Dis. 146, 724–726 (1982).

  37. 37.

    et al. Typhoid fever: a massive, single-point source, multidrug-resistant outbreak in Nepal. Clin. Infect. Dis. 40, 554–561 (2005).

  38. 38.

    , & The use of Moore swabs for isolation of Salmonella typhi from irrigation water in Santiago, Chile. J. Infect. Dis. 149, 640–642 (1984).

  39. 39.

    & Viable, but non-culturable, state of a green fluorescence protein-tagged environmental isolate of Salmonella typhi in groundwater and pond water. FEMS Microbiol. Lett. 170, 257–264 (1999).

  40. 40.

    , & Source-sink dynamics of virulence evolution. Nat. Rev. Microbiol. 4, 548–555 (2006).

  41. 41.

    et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004).

Download references

Acknowledgements

This work was supported by the Wellcome Trust. M.A. and C.J.M. are supported in Ireland by grant 05/FE1/B882 from the Scientific Foundation Ireland and C.J.M. was supported in Berlin by a Wellcome Trust grant to J. Farrar. We gratefully acknowledge the support of the Sanger Institute core sequencing and informatics groups. Isolates were provided by the Oxford University Clinical Research Unit (CT18, J185SM, AG3); B. Holmes at the National Collection of Type Cultures (M223); the Wellcome Trust Sanger Institute (404ty, Ty2); and F.-X.W. (all other isolates).

Author information

Author notes

    • Ian Goodhead

    Present address: School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK.

Affiliations

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

    • Kathryn E Holt
    • , Julian Parkhill
    • , Ian Goodhead
    • , Richard Rance
    • , Stephen Baker
    • , John Wain
    •  & Gordon Dougan
  2. Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland.

    • Camila J Mazzoni
    •  & Mark Achtman
  3. Max-Planck-Institut für Infektionsbiologie, Department of Molecular Biology, Charitéplatz 1, 10117, Berlin, Germany.

    • Camila J Mazzoni
    • , Philippe Roumagnac
    •  & Mark Achtman
  4. Université Mixte de Recherche 6191 Centre National de la Recherche Scientifique - Commissariat à l'Énergie Atomique-Aix-Marseille Université, Commissariat à l'Énergie Atomique Cadarache, 13108 Saint Paul lez Durance, France.

    • Philippe Roumagnac
  5. Institut Pasteur, Laboratoire des Bactéries Pathogènes Entériques, 28 rue du docteur Roux, 75724 Paris cedex 15, France.

    • François-Xavier Weill
  6. Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 190 Ben Ham Tu, District 5, Ho Chi Minh City, Vietnam.

    • Stephen Baker
    •  & Christiane Dolecek
  7. Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK.

    • Duncan J Maskell

Authors

  1. Search for Kathryn E Holt in:

  2. Search for Julian Parkhill in:

  3. Search for Camila J Mazzoni in:

  4. Search for Philippe Roumagnac in:

  5. Search for François-Xavier Weill in:

  6. Search for Ian Goodhead in:

  7. Search for Richard Rance in:

  8. Search for Stephen Baker in:

  9. Search for Duncan J Maskell in:

  10. Search for John Wain in:

  11. Search for Christiane Dolecek in:

  12. Search for Mark Achtman in:

  13. Search for Gordon Dougan in:

Contributions

G.D., J.P., M.A., P.R. and J.W. designed the study; F.-X.W. and C.D. contributed isolates for analysis; I.G. and R.R. performed 454 and Solexa sequencing; K.E.H. and S.B. performed validation experiments; D.J.M. co-supervises the PhD studies of K.E.H. and contributed to experimental design; K.E.H. and C.J.M. analysed data and K.E.H., J.P., P.R. and G.D. wrote the manuscript.

Corresponding author

Correspondence to Kathryn E Holt.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–3, Supplementary Tables 1 and 3, Supplementary Methods, Supplementary Note

Excel files

  1. 1.

    Supplementary Table 2

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/ng.195

Further reading