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Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution

Nature Genetics volume 46, pages 1321–1326 (2014)Cite this article

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Abstract

Enterotoxigenic Escherichia coli (ETEC), a major cause of infectious diarrhea, produce heat-stable and/or heat-labile enterotoxins and at least 25 different colonization factors that target the intestinal mucosa. The genes encoding the enterotoxins and most of the colonization factors are located on plasmids found across diverse E. coli serogroups. Whole-genome sequencing of a representative collection of ETEC isolated between 1980 and 2011 identified globally distributed lineages characterized by distinct colonization factor and enterotoxin profiles. Contrary to current notions, these relatively recently emerged lineages might harbor chromosome and plasmid combinations that optimize fitness and transmissibility. These data have implications for understanding, tracking and possibly preventing ETEC disease.

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Figure 1: Population structure of ETEC isolates.
Figure 2: Most common recent ancestors of the five major lineages L1–L5.

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References

  1. World Health Organization. Diarrhoeal Diseases (Updated February 2009) (World Health Organization, Geneva, 2009).

  2. Gaastra, W. & Svennerholm, A.M. Colonization factors of human enterotoxigenic Escherichia coli (ETEC). Trends Microbiol. 4, 444–452 (1996).

    Article  CAS  Google Scholar 

  3. Qadri, F., Svennerholm, A.M., Faruque, A.S. & Sack, R.B. Enterotoxigenic Escherichia coli in developing countries: epidemiology, microbiology, clinical features, treatment, and prevention. Clin. Microbiol. Rev. 18, 465–483 (2005).

    Article  Google Scholar 

  4. Isidean, S.D., Riddle, M.S., Savarino, S.J. & Porter, C.K. A systematic review of ETEC epidemiology focusing on colonization factor and toxin expression. Vaccine 29, 6167–6178 (2011).

    Article  CAS  Google Scholar 

  5. Svennerholm, A.M. & Lundgren, A. Recent progress toward an enterotoxigenic Escherichia coli vaccine. Expert. Rev. Vaccines 11, 495–507 (2012).

    Article  CAS  Google Scholar 

  6. Wolf, M.K. Occurrence, distribution, and associations of O and H serogroups, colonization factor antigens, and toxins of enterotoxigenic Escherichia coli. Clin. Microbiol. Rev. 10, 569–584 (1997).

    Article  CAS  Google Scholar 

  7. Smith, H.W. The exploitation of transmissible plasmids to study the pathogenesis of E. coli diarrhoea. Proc. R. Soc. Med. 66, 272–273 (1973).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Turner, S.M. et al. Phylogenetic comparisons reveal multiple acquisitions of the toxin genes by enterotoxigenic Escherichia coli strains of different evolutionary lineages. J. Clin. Microbiol. 44, 4528–4536 (2006).

    Article  CAS  Google Scholar 

  9. Steinsland, H., Lacher, D.W., Sommerfelt, H. & Whittam, T.S. Ancestral lineages of human enterotoxigenic Escherichia coli. J. Clin. Microbiol. 48, 2916–2924 (2010).

    Article  CAS  Google Scholar 

  10. Escobar-Páramo, P. et al. A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli. Mol. Biol. Evol. 21, 1085–1094 (2004).

    Article  Google Scholar 

  11. Regua-Mangia, A.H. et al. Genotypic and phenotypic characterization of enterotoxigenic Escherichia coli (ETEC) strains isolated in Rio de Janeiro city, Brazil. FEMS Immunol. Med. Microbiol. 40, 155–162 (2004).

    Article  CAS  Google Scholar 

  12. Steinsland, H., Valentiner-Branth, P., Aaby, P., Mølbak, K. & Sommerfelt, H. Clonal relatedness of enterotoxigenic Escherichia coli strains isolated from a cohort of young children in Guinea-Bissau. J. Clin. Microbiol. 42, 3100–3107 (2004).

    Article  Google Scholar 

  13. Valvatne, H., Steinsland, H. & Sommerfelt, H. Clonal clustering and colonization factors among thermolabile and porcine thermostable enterotoxin-producing Escherichia coli. APMIS 110, 665–672 (2002).

    Article  Google Scholar 

  14. Sahl, J.W. & Rasko, D.A. Analysis of global transcriptional profiles of enterotoxigenic Escherichia coli isolate E24377A. Infect. Immun. 80, 1232–1242 (2012).

    Article  CAS  Google Scholar 

  15. Herzer, P.J., Inouye, S., Inouye, M. & Whittam, T.S. Phylogenetic distribution of branched RNA–linked multicopy single-stranded DNA among natural isolates of Escherichia coli. J. Bacteriol. 172, 6175–6181 (1990).

    Article  CAS  Google Scholar 

  16. Corander, J., Marttinen, P., Sirén, J. & Tang, J. Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinformatics 9, 539 (2008).

    Article  Google Scholar 

  17. Lasaro, M.A., Mathias-Santos, C., Rodrigues, J.F. & Ferreira, L.C.S. Functional and immunological characterization of a natural polymorphic variant of a heat-labile toxin (LT-I) produced by enterotoxigenic Escherichia coli (ETEC). FEMS Immunol. Med. Microbiol. 55, 93–99 (2009).

    Article  CAS  Google Scholar 

  18. Rodrigues, J. et al. Clonal structure and virulence factors in strains of Escherichia coli of the classic serogroup O55. Infect. Immun. 64, 2680–2686 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Froehlich, B., Parkhill, J., Sanders, M., Quail, M.A. & Scott, J.R. The pCoo plasmid of enterotoxigenic Escherichia coli is a mosaic cointegrate. J. Bacteriol. 187, 6509–6516 (2005).

    Article  CAS  Google Scholar 

  20. Johnson, T.J. & Nolan, L.K. Pathogenomics of the virulence plasmids of Escherichia coli. Microbiol. Mol. Biol. Rev. 73, 750–774 (2009).

    Article  CAS  Google Scholar 

  21. Crossman, L.C. et al. A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407. J. Bacteriol. 192, 5822–5831 (2010).

    Article  CAS  Google Scholar 

  22. Croucher, N.J. et al. Rapid pneumococcal evolution in response to clinical interventions. Science 331, 430–434 (2011).

    Article  CAS  Google Scholar 

  23. Didelot, X. et al. Microevolutionary analysis of Clostridium difficile genomes to investigate transmission. Genome Biol. 13, R118 (2012).

    Article  Google Scholar 

  24. Fischer Walker, C.L., Perin, J., Aryee, M.J., Boschi-Pinto, C. & Black, R.E. Diarrhea incidence in low- and middle-income countries in 1990 and 2010: a systematic review. BMC Public Health 12, 220 (2012).

    Article  Google Scholar 

  25. Sahl, J.W. et al. A comparative genomic analysis of diverse clonal types of enterotoxigenic Escherichia coli reveals pathovar-specific conservation. Infect. Immun. 79, 950–960 (2011).

    Article  CAS  Google Scholar 

  26. Sabui, S. et al. Allelic variation in colonization factor CS6 of enterotoxigenic Escherichia coli isolated from patients with acute diarrhoea and controls. J. Med. Microbiol. 59, 770–779 (2010).

    Article  CAS  Google Scholar 

  27. Pupo, G.M., Karaolis, D.K., Lan, R. & Reeves, P.R. Evolutionary relationships among pathogenic and nonpathogenic Escherichia coli strains inferred from multilocus enzyme electrophoresis and mdh sequence studies. Infect. Immun. 65, 2685–2692 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. 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 

  29. Harris, S.R. et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science 327, 469–474 (2010).

    Article  CAS  Google Scholar 

  30. Holt, K.E. et al. Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat. Genet. 44, 1056–1059 (2012).

    Article  CAS  Google Scholar 

  31. Okoro, C.K. et al. Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat. Genet. 44, 1215–1221 (2012).

    Article  CAS  Google Scholar 

  32. Darsley, M.J. et al. The oral, live attenuated enterotoxigenic Escherichia coli vaccine ACE527 reduces the incidence and severity of diarrhea in a human challenge model of diarrheal disease. Clin. Vaccine Immunol. 19, 1921–1931 (2012).

    Article  CAS  Google Scholar 

  33. Sjöling, A., Wiklund, G., Savarino, S.J., Cohen, D.I. & Svennerholm, A.M. Comparative analyses of phenotypic and genotypic methods for detection of enterotoxigenic Escherichia coli toxins and colonization factors. J. Clin. Microbiol. 45, 3295–3301 (2007).

    Article  Google Scholar 

  34. Rodas, C. et al. Development of multiplex PCR assays for detection of enterotoxigenic Escherichia coli colonization factors and toxins. J. Clin. Microbiol. 47, 1218–1220 (2009).

    Article  CAS  Google Scholar 

  35. Quail, M.A., Swerdlow, H. & Turner, D.J. Improved protocols for the Illumina Genome Analyzer sequencing system. Curr. Protoc. Hum. Genet. Unit 18.2 1–27 (2009).

  36. Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).

    Article  CAS  Google Scholar 

  37. Marttinen, P. et al. Detection of recombination events in bacterial genomes from large population samples. Nucleic Acids Res. 40, e6 (2012).

    Article  CAS  Google Scholar 

  38. McNally, A., Cheng, L., Harris, S.R. & Corander, J. The evolutionary path to extraintestinal pathogenic, drug-resistant Escherichia coli is marked by drastic reduction in detectable recombination within the core genome. Genome Biol. Evol. 5, 699–710 (2013).

    Article  Google Scholar 

  39. Castillo-Ramírez, S. et al. Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus. Genome Biol. 13, R126 (2012).

    Article  Google Scholar 

  40. Tang, J., Hanage, W.P., Fraser, C. & Corander, J. Identifying currents in the gene pool for bacterial populations using an integrative approach. PLOS Comput. Biol. 5, e1000455 (2009).

    Article  Google Scholar 

  41. Cheng, L., Connor, T.R., Sirén, J., Aanensen, D.M. & Corander, J. Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. Mol. Biol. Evol. 30, 1224–1228 (2013).

    Article  CAS  Google Scholar 

  42. Corander, J., Connor, T.R., O'Dwyer, C.A., Kroll, J.S. & Hanage, W.P. Population structure in the Neisseria, and the biological significance of fuzzy species. J. R. Soc. Interface 9, 1208–1215 (2012).

    Article  Google Scholar 

  43. Willems, R.J.L. et al. Restricted gene flow among hospital subpopulations of Enterococcus faecium. MBio 3, e00151–12 (2012).

    Article  CAS  Google Scholar 

  44. Hanage, W.P., Fraser, C., Tang, J., Connor, T.R. & Corander, J. Hyper-recombination, diversity, and antibiotic resistance in pneumococcus. Science 324, 1454–1457 (2009).

    Article  CAS  Google Scholar 

  45. Croucher, N.J. et al. Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat. Genet. 45, 656–663 (2013).

    Article  CAS  Google Scholar 

  46. Drummond, A.J. & Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214 (2007).

    Article  Google Scholar 

  47. Drummond, A.J., Rambaut, A., Shapiro, B. & Pybus, O.G. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 22, 1185–1192 (2005).

    Article  CAS  Google Scholar 

  48. Drummond, A.J., Ho, S.Y., Phillips, M.J. & Rambaut, A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88 (2006).

    Article  Google Scholar 

  49. Carattoli, A. et al. Identification of plasmids by PCR-based replicon typing. J. Microbiol. Methods 63, 219–228 (2005).

    Article  CAS  Google Scholar 

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Acknowledgements

This work was supported by the Wellcome Trust (grant 098051), the Swedish Research Council (grants 2012-3464 and 2011-3435), the Swedish Strategic Foundation (grant SB12-0072) and the European Research Council (grant 239784).

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Authors and Affiliations

  1. Department of Microbiology and Immunology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden

    Astrid von Mentzer, Enrique Joffre, Gudrun Wiklund, Ann-Mari Svennerholm & Åsa Sjöling

  2. Wellcome Trust Sanger Institute, Hinxton, UK

    Astrid von Mentzer, Thomas R Connor, Nicholas R Thomson, Derek Pickard & Gordon Dougan

  3. Organisms and Environment Division, Cardiff University School of Biosciences, Cardiff University, Cardiff, UK

    Thomas R Connor

  4. Centre of Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany

    Lothar H Wieler & Torsten Semmler

  5. Interdisciplinary Research Organization, University of Miyazaki, Miyazaki, Japan

    Atsushi Iguchi

  6. Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA

    David A Rasko

  7. Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland

    Jukka Corander

  8. Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden

    Åsa Sjöling

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  1. Astrid von Mentzer
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Contributions

A.v.M., G.D., A.-M.S., Å.S., T.R.C. and D.A.R. contributed to the design of the study and data interpretation. A.v.M. and G.W. extracted DNA. A.v.M. screened the sequence data and performed the majority of the bioinformatics analyses with input from T.R.C. and N.R.T. A.v.M. interpreted and analyzed the results from the recombination detection and BAPS analyses, executed by J.C. T.S. and L.H.W. identified the MCG and determined sequence types from whole-genome data. A.I. performed the BLASTN analysis to identify O antigen genotypes in all ETEC isolates included. E.J. analyzed the genes encoding toxins. D.P. was responsible for forwarding extracted DNA samples to the sequencing pipeline at the Wellcome Trust Sanger Institute. G.D., Å.S. and A.-M.S. supervised the work. All authors contributed to the writing of the manuscript.

Corresponding authors

Correspondence to Astrid von Mentzer, Ann-Mari Svennerholm, Åsa Sjöling or Gordon Dougan.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Heat map depicting the virulence profiles, O antigens and incompatibility groups of isolates in L1–L5.

Presence of colonization factors, toxins, O antigens and plasmid incompatibility groups (FII, FIIS, FIB, FII-s, FrepB, HI1, I1, K and X1) within lineages L1–L5. UG designation is used for isolates. An asterisk indicates isolates ± CS21; n.i., not identified.

Supplementary Figure 2 Heat map depicting the virulence profiles, O antigens and incompatibility groups of isolates in L6–L10.

Presence of colonization factors, toxins, O antigens and plasmid incompatibility groups (FII, FIIS, FIB, FII-s, FrepB, HI1, I1, K and X1) within lineages L6–L10. UG designation is used for isolates. An asterisk indicates isolates ± CS21; n.i., not identified.

Supplementary Figure 3 Midpoint-rooted phylogenetic tree displaying the colonization factor profile or each lineage.

The phylogenetic tree is SNP based with probable recombination events removed, colored according to lineage and displaying the colonization factor profile for each lineage. Lineages L1–L21 and reference strains are indicated.

Supplementary Figure 4 Midpoint-rooted phylogenetic tree showing the country of isolation for each isolate.

The phylogenetic tree is SNP based with probable recombination events removed, depicting the country of isolation for each isolate as colored symbols on branch tips. Reference strains are indicated.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–4 and Supplementary Tables 1–3. (PDF 1987 kb)

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von Mentzer, A., Connor, T., Wieler, L. et al. Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution. Nat Genet 46, 1321–1326 (2014). https://doi.org/10.1038/ng.3145

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