Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Origins of pandemic Vibrio cholerae from environmental gene pools

Nature Microbiology volume 2, Article number: 16240 (2017) Cite this article

Subjects

This article has been updated

Abstract

Some microorganisms can transition from an environmental lifestyle to a pathogenic one1–3. This ecological switch typically occurs through the acquisition of horizontally acquired virulence genes4,5. However, the genomic features that must be present in a population before the acquisition of virulence genes and emergence of pathogenic clones remain unknown. We hypothesized that virulence adaptive polymorphisms (VAPs) circulate in environmental populations and are required for this transition. We developed a comparative genomic framework for identifying VAPs, using Vibrio cholerae as a model. We then characterized several environmental VAP alleles to show that while some of them reduced the ability of clinical strains to colonize a mammalian host, other alleles conferred efficient host colonization. These results show that VAPs are present in environmental bacterial populations before the emergence of virulent clones. We propose a scenario in which VAPs circulate in the environment and become selected and enriched under certain ecological conditions, and finally a genomic background containing several VAPs acquires virulence factors that allow for its emergence as a pathogenic clone.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Comparative genomics reveals candidate VAPs.
Figure 2: Phenotypic characterization of ompU alleles.
Figure 3: Model of pandemic clone emergence from an environmental gene pool.

Similar content being viewed by others

Change history

  • 14 July 2017

    In the PDF version of this article previously published, the year of publication provided in the footer of each page and in the 'How to cite' section was erroneously given as 2017, it should have been 2016. This error has now been corrected. The HTML version of the article was not affected.

References

  1. McNally, A., Thomson, N. R., Reuter, S. & Wren, B. W. ‘Add, stir and reduce’: Yersinia spp. as model bacteria for pathogen evolution. Nat. Rev. Microbiol. 14, 177–190 (2016).

    Article  CAS  Google Scholar 

  2. Luo, C. et al. Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species. Proc. Natl Acad. Sci. USA 108, 7200–7205 (2011).

    Article  CAS  Google Scholar 

  3. Reen, F. J., Almagro-Moreno, S., Ussery, D. & Boyd, E. F. The genomic code: inferring Vibrionaceae niche specialization. Nat. Rev. Microbiol. 4, 697–704 (2006).

    Article  CAS  Google Scholar 

  4. Ochman, H. Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292, 1096–1099 (2001).

    Article  CAS  Google Scholar 

  5. Shapiro, B. J. How clonal are bacteria over time? Curr. Opin. Microbiol. 31, 116–123 (2016).

    Article  Google Scholar 

  6. Cui, Y. et al. Epidemic clones, oceanic gene pools, and eco-LD in the free living marine pathogen Vibrio parahaemolyticus. Mol. Biol. Evol. 32, 1396–1410 (2015).

    Article  CAS  Google Scholar 

  7. Chun, J. et al. Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae. Proc. Natl Acad. Sci. USA 106, 15442–15447 (2009).

    Article  CAS  Google Scholar 

  8. Boucher, Y. Sustained local diversity of Vibrio cholerae O1 biotypes in a previously cholera-free country. mBio 7, e00570–16 (2016).

    Article  CAS  Google Scholar 

  9. Mutreja, A. et al. Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 477, 462–465 (2011).

    Article  CAS  Google Scholar 

  10. Taylor, R. K., Miller, V. L., Furlong, D. B. & Mekalanos, J. J. Use of phoA gene fusions to identify a pilus colonization factor coordinately regulated with cholera toxin. Proc. Natl Acad. Sci. USA 84, 2833–2837 (1987).

    Article  CAS  Google Scholar 

  11. Waldor, M. K. & Mekalanos, J. J. Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272, 1910–1914 (1996).

    Article  CAS  Google Scholar 

  12. Karaolis, D. K. et al. A Vibrio cholerae pathogenicity island associated with epidemic and pandemic strains. Proc. Natl Acad. Sci. USA 95, 3134–3139 (1998).

    Article  CAS  Google Scholar 

  13. Faruque, S. M. et al. Genetic diversity and virulence potential of environmental Vibrio cholerae population in a cholera-endemic area. Proc. Natl Acad. Sci. USA 101, 2123–2128 (2004).

    Article  CAS  Google Scholar 

  14. Rivera, I. N., Chun, J., Huq, A., Sack, R. B. & Colwell, R. R. Genotypes associated with virulence in environmental isolates of Vibrio cholerae. Appl. Environ. Microbiol. 67, 2421–2429 (2001).

    Article  CAS  Google Scholar 

  15. Gennari, M., Ghidini, V. & Lleo, M. M. Virulence genes and pathogenicity islands in environmental Vibrio strains non-pathogenic to humans. FEMS Microbiol. Ecol. 82, 563–573 (2012).

    Article  CAS  Google Scholar 

  16. Dziejman, M. et al. Genomic characterization of non-O1, non-O139 Vibrio cholerae reveals genes for a type III secretion system. Proc. Natl Acad. Sci. USA 102, 3465–3470 (2005).

    Article  CAS  Google Scholar 

  17. Schuster, B. M. et al. Ecology and genetic structure of a northern temperate Vibrio cholerae population related to toxigenic isolates. Appl. Environ. Microbiol. 77, 7568–7575 (2011).

    Article  CAS  Google Scholar 

  18. Orata, F. D. et al. The dynamics of genetic interactions between Vibrio metoecus and Vibrio cholerae, two close relatives co-occurring in the environment. Genome Biol. Evol. 7, 2941–2954 (2015).

    Article  CAS  Google Scholar 

  19. Keymer, D. P. & Boehm, A. B. Recombination shapes the structure of an environmental Vibrio cholerae population. Appl. Environ. Microbiol. 77, 537–544 (2011).

    Article  CAS  Google Scholar 

  20. Provenzano, D., Schuhmacher, D. A., Barker, J. L. & Klose, K. E. The virulence regulatory protein ToxR mediates enhanced bile resistance in Vibrio cholerae and other pathogenic Vibrio species. Infect. Immun. 68, 1491–1497 (2000).

    Article  CAS  Google Scholar 

  21. Mathur, J. & Waldor, M. K. The Vibrio cholerae ToxR-regulated porin OmpU confers resistance to antimicrobial peptides. Infect. Immun. 72, 3577–3583 (2004).

    Article  CAS  Google Scholar 

  22. Almagro-Moreno, S., Pruss, K. & Taylor, R. K. Intestinal colonization dynamics of Vibrio cholerae. PLoS Pathogens 11, e1004787 (2015).

    Article  Google Scholar 

  23. Merrell, D. S., Bailey, C., Kaper, J. B. & Camilli, A. The ToxR-mediated organic acid tolerance response of Vibrio cholerae requires OmpU. J. Bacteriol. 183, 2746–2754 (2001).

    Article  CAS  Google Scholar 

  24. Watnick, P. I. & Kolter, R. Steps in the development of a Vibrio cholerae El Tor biofilm. Mol. Microbiol. 34, 586–595 (1999).

    Article  CAS  Google Scholar 

  25. Valeru, S. P., Wai, S. N., Saeed, A., Sandström, G. & Abd, H. Toxr of Vibrio cholerae affects biofilm, rugosity and survival with Acanthamoeba castellanii. BMC Res. Notes 5, 33 (2012).

    Article  CAS  Google Scholar 

  26. Yildiz, F. H. & Schoolnik, G. K. Vibrio cholerae O1 El Tor: identification of a gene cluster required for the rugose colony type, exopolysaccharide production, chlorine resistance, and biofilm formation. Proc. Natl Acad. Sci. USA 96, 4028–4033 (1999).

    Article  CAS  Google Scholar 

  27. Hsiao, A., Liu, Z., Joelsson, A. & Zhu, J. Vibrio cholerae virulence regulator-coordinated evasion of host immunity. Proc. Natl Acad. Sci. USA 103, 14542–14547 (2006).

    Article  CAS  Google Scholar 

  28. Boucher, Y., Orata, F. D. & Alam, M. The out-of-the-delta hypothesis: dense human populations in low-lying river deltas served as agents for the evolution of a deadly pathogen. Front. Microbiol. 6, 1120 (2015).

    Article  Google Scholar 

  29. Friedman, J., Alm, E. J. & Shapiro, B. J. Sympatric speciation: when is it possible in bacteria? PLoS ONE 8, e53539 (2013).

    Article  CAS  Google Scholar 

  30. Chen, P. E. & Shapiro, B. J. The advent of genome-wide association studies for bacteria. Curr. Opin. Microbiol. 25, 17–24 (2015).

    Article  CAS  Google Scholar 

  31. Nair, G. B. et al. New variants of Vibrio cholerae O1 biotype El Tor with attributes of the classical biotype from hospitalized patients with acute diarrhea in Bangladesh. J. Clin. Microbiol. 40, 3296–3299 (2002).

    Article  Google Scholar 

  32. Son, M. S., Megli, C. J., Kovacikova, G., Qadri, F. & Taylor, R. K. Characterization of Vibrio cholerae O1 El Tor biotype variant clinical isolates from Bangladesh and Haiti, including a molecular genetic analysis of virulence genes. J. Clin. Microbiol. 49, 3739–3749 (2011).

    Article  CAS  Google Scholar 

  33. Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

    Article  CAS  Google Scholar 

  34. Boisvert, S., Raymond, F., Godzaridis, É., Laviolette, F. & Corbeil, J. Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol. 13, R122 (2012).

    Article  Google Scholar 

  35. Samuel, V & Angiuoli, S. L. S. Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics 27, 334–342 (2011).

    Article  Google Scholar 

  36. Aziz, R. K. et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9, 75 (2008).

    Article  Google Scholar 

  37. Li, L., Stoeckert, C. J. & Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178–2189 (2003).

    Article  CAS  Google Scholar 

  38. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).

    Article  CAS  Google Scholar 

  39. Price, M. N., Dehal, P. S. & Arkin, A. P. Fasttree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).

    Article  Google Scholar 

  40. Bryant, D. & Moulton, V. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol. 21, 255–265 (2004).

    Article  CAS  Google Scholar 

  41. McDonald, J. H. & Kreitman, M. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351, 652–654 (1991).

    Article  CAS  Google Scholar 

  42. Shapiro, J. A. et al. Adaptive genic evolution in the Drosophila genomes. Proc. Natl Acad. Sci. USA 104, 2271–2276 (2007).

    Article  Google Scholar 

  43. Skorupski, K. & Taylor, R. K. Positive selection vectors for allelic exchange. Gene 169, 47–52 (1996).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank the anonymous reviewers for their comments and suggestions, and O. Cordero, Y. Terrat, N. Tromas and B. Privett for comments on the manuscript. The authors thank L. Shelven for his technical assistance. B.J.S. was supported by a Canada Research Chair and the Canadian Institutes for Health Research. R.K.T. was supported by National Institutes of Health grants AI039654 and AI025096. S.A.-M. was supported by startup funds from the Burnett School of Biomedical Sciences at the University of Central Florida and Dartmouth College's E. E. Just Postdoctoral Fellowship. This Letter is dedicated to the memory of R.K. Taylor.

Author information

Author notes

  1. Inès Levade and Gabriela Kovacikova: These authors contributed equally to this work

  2. Ronald K. Taylor: Deceased.

Authors and Affiliations

  1. Department of Biological Sciences, University of Montreal, Montreal, H2V 2S9, Quebec, Canada

    B. Jesse Shapiro & Inès Levade

  2. Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, 03755, New Hampshire, USA

    Gabriela Kovacikova, Ronald K. Taylor & Salvador Almagro-Moreno

  3. Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, 32827, Florida, USA

    Salvador Almagro-Moreno

Authors
  1. B. Jesse Shapiro
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Inès Levade
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gabriela Kovacikova
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ronald K. Taylor
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Salvador Almagro-Moreno
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

S.A.-M. conceived the study. B.J.S., R.K.T. and S.A.-M. designed the study. I.L. sequenced genomes. B.J.S. performed computational analysis. G.K. and S.A.-M. performed phenotypic characterization. B.J.S. and S.A.-M. analysed and interpreted data and wrote the article. All authors have read a version of the manuscript.

Corresponding author

Correspondence to Salvador Almagro-Moreno.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Notes 1 and 2, Supplementary Figures 1–10, Supplementary Tables 1–8. (PDF 3641 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Shapiro, B., Levade, I., Kovacikova, G. et al. Origins of pandemic Vibrio cholerae from environmental gene pools. Nat Microbiol 2, 16240 (2017). https://doi.org/10.1038/nmicrobiol.2016.240

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1038/nmicrobiol.2016.240

This article is cited by

Search

Advanced search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: Microbiology