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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References
World Health Organization. Diarrhoeal Diseases (Updated February 2009) (World Health Organization, Geneva, 2009).
Gaastra, W. & Svennerholm, A.M. Colonization factors of human enterotoxigenic Escherichia coli (ETEC). Trends Microbiol. 4, 444–452 (1996).
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).
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).
Svennerholm, A.M. & Lundgren, A. Recent progress toward an enterotoxigenic Escherichia coli vaccine. Expert. Rev. Vaccines 11, 495–507 (2012).
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).
Smith, H.W. The exploitation of transmissible plasmids to study the pathogenesis of E. coli diarrhoea. Proc. R. Soc. Med. 66, 272–273 (1973).
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).
Steinsland, H., Lacher, D.W., Sommerfelt, H. & Whittam, T.S. Ancestral lineages of human enterotoxigenic Escherichia coli. J. Clin. Microbiol. 48, 2916–2924 (2010).
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).
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).
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).
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).
Sahl, J.W. & Rasko, D.A. Analysis of global transcriptional profiles of enterotoxigenic Escherichia coli isolate E24377A. Infect. Immun. 80, 1232–1242 (2012).
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).
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).
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).
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).
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).
Johnson, T.J. & Nolan, L.K. Pathogenomics of the virulence plasmids of Escherichia coli. Microbiol. Mol. Biol. Rev. 73, 750–774 (2009).
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).
Croucher, N.J. et al. Rapid pneumococcal evolution in response to clinical interventions. Science 331, 430–434 (2011).
Didelot, X. et al. Microevolutionary analysis of Clostridium difficile genomes to investigate transmission. Genome Biol. 13, R118 (2012).
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).
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).
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).
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).
Mutreja, A. et al. Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 477, 462–465 (2011).
Harris, S.R. et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science 327, 469–474 (2010).
Holt, K.E. et al. Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat. Genet. 44, 1056–1059 (2012).
Okoro, C.K. et al. Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat. Genet. 44, 1215–1221 (2012).
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).
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).
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).
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).
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).
Marttinen, P. et al. Detection of recombination events in bacterial genomes from large population samples. Nucleic Acids Res. 40, e6 (2012).
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).
Castillo-Ramírez, S. et al. Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus. Genome Biol. 13, R126 (2012).
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).
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).
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).
Willems, R.J.L. et al. Restricted gene flow among hospital subpopulations of Enterococcus faecium. MBio 3, e00151–12 (2012).
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).
Croucher, N.J. et al. Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat. Genet. 45, 656–663 (2013).
Drummond, A.J. & Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214 (2007).
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).
Drummond, A.J., Ho, S.Y., Phillips, M.J. & Rambaut, A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88 (2006).
Carattoli, A. et al. Identification of plasmids by PCR-based replicon typing. J. Microbiol. Methods 63, 219–228 (2005).
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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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.
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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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DOI: https://doi.org/10.1038/ng.3145
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