1887

Abstract

The lipopolysaccharide (O) and flagellar (H) surface antigens of Escherichia coli are targets for serotyping that have traditionally been used to identify pathogenic lineages. These surface antigens are important for the survival of E. coli within mammalian hosts. However, traditional serotyping has several limitations, and public health reference laboratories are increasingly moving towards whole genome sequencing (WGS) to characterize bacterial isolates. Here we present a method to rapidly and accurately serotype E. coli isolates from raw, short read WGS data. Our approach bypasses the need for de novo genome assembly by directly screening WGS reads against a curated database of alleles linked to known and novel E. coli O-groups and H-types (the EcOH database) using the software package srst2. We validated the approach by comparing in silico results for 197 enteropathogenic E. coli isolates with those obtained by serological phenotyping in an independent laboratory. We then demonstrated the utility of our method to characterize isolates in public health and clinical settings, and to explore the genetic diversity of >1500 E. coli genomes from multiple sources. Importantly, we showed that transfer of O- and H-antigen loci between E. coli chromosomal backbones is common, with little evidence of constraints by host or pathotype, suggesting that E. coli ‘strain space’ may be virtually unlimited, even within specific pathotypes. Our findings show that serotyping is most useful when used in combination with strain genotyping to characterize microevolution events within an inferred population structure.

Keyword(s): diversity , E. coli , genotype , phenotype and serotype
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000064
2016-07-11
2019-10-23
Loading full text...

Full text loading...

/deliver/fulltext/mgen/2/7/mgen000064.html?itemId=/content/journal/mgen/10.1099/mgen.0.000064&mimeType=html&fmt=ahah

References

  1. Achtman M., Wain J., Weill F. X., Nair S., Zhou Z., Sangal V., Krauland M. G., Hale J. L., Harbottle H. et al. 2012; Multilocus sequence typing as a replacement for serotyping in Salmonella enterica. PLoS Pathog8:e100277619 [CrossRef][PubMed]
    [Google Scholar]
  2. Assefa S., Keane T. M., Otto T. D., Newbold C., Berriman M.. 2009; Abacas: algorithm-based automatic contiguation of assembled sequences. Bioinformatics25:1968–1969 [CrossRef][PubMed]
    [Google Scholar]
  3. Bankevich A., Nurk S., Antipov D., Gurevich A. A., Dvorkin M., Kulikov A. S., Lesin V. M., Nikolenko S. I., Pham S. et al. 2012; Spades: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol19:455–477 [CrossRef][PubMed]
    [Google Scholar]
  4. Bao E., Jiang T., Girke T.. 2014; Aligngraph: algorithm for secondary de novo genome assembly guided by closely related references. Bioinformatics30:i319–i328 [CrossRef][PubMed]
    [Google Scholar]
  5. Boetzer M., Henkel C. V., Jansen H. J., Butler D., Pirovano W.. 2011; Scaffolding pre-assembled contigs using SSPACE. Bioinformatics27:578–579 [CrossRef][PubMed]
    [Google Scholar]
  6. Boetzer M., Pirovano W.. 2012; Toward almost closed genomes with GapFiller. Genome Biol13:R56 [CrossRef][PubMed]
    [Google Scholar]
  7. Carver T., Berriman M., Tivey A., Patel C., Böhme U., Barrell B. G., Parkhill J., Rajandream M. A.. 2008; Artemis and Act: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics24:2672–2676 [CrossRef][PubMed]
    [Google Scholar]
  8. Chandler M. E., Bettelheim K. A.. 1974; A rapid method of identifying Escherichia coli H antigens. Zentralbl Bakteriol Orig A229:74–79
    [Google Scholar]
  9. Croxen M. A., Law R. J., Scholz R., Keeney K. M., Wlodarska M., Finlay B. B.. 2013; Recent advances in understanding enteric pathogenic Escherichia coli. Clin Microbiol Rev26:822–880 [CrossRef][PubMed]
    [Google Scholar]
  10. Dallman T. J., Ashton P. M., Byrne L., Perry N. T., Petrovska L., Ellis R., Allison L., Hanson M., Holmes A. et al. 2015; Applying phylogenomics to understand the emergence of Shiga-toxin-producing Escherichia coli O157:H7 strains causing severe human disease in the UK. Microb Genom1.:
    [Google Scholar]
  11. DebRoy C., Roberts E., Fratamico P. M.. 2011; Detection of O antigens in Escherichia coli. Anim Health Res Rev12:169–185 [CrossRef][PubMed]
    [Google Scholar]
  12. Donnenberg M. S., Finlay B. B.. 2013; Combating enteropathogenic Escherichia coli (EPEC) infections: the way forward. Trends Microbiol21:317–319 [CrossRef][PubMed]
    [Google Scholar]
  13. Feng L., Senchenkova S. N., Yang J., Shashkov A. S., Tao J., Guo H., Cheng J., Ren Y., Knirel Y. A. et al. 2004; Synthesis of the heteropolysaccharide O antigen of Escherichia coli O52 requires an Abc transporter: structural and genetic evidence. J Bacteriol186:4510–4519 [CrossRef][PubMed]
    [Google Scholar]
  14. Feng L., Liu B., Liu Y., Ratiner Y. A., Hu B., Li D., Zong X., Xiong W., Wang L.. 2008; A genomic islet mediates flagellar phase variation in Escherichia coli strains carrying the flagellin-specifying locus flk. J Bacteriol190:4470–4477 [CrossRef][PubMed]
    [Google Scholar]
  15. Francisco A. P., Vaz C., Monteiro P., Melo-Cristino J., Ramirez M., Carriço J. A.. 2012; Phyloviz: phylogenetic inference and data visualization for sequence based typing methods. BMC Bioinformatics13:1–10
    [Google Scholar]
  16. Frank C., Faber M. S., Askar M., Bernard H., Fruth A., Gilsdorf A., Hohle M., Karch H., Krause G. et al. 2011a; Large and ongoing outbreak of haemolytic uraemic syndrome, Germany, May 2011. Euro Surveill1–3
    [Google Scholar]
  17. Frank C., Werber D., Cramer J. P., Askar M., Faber M., an der Heiden M., Bernard H., Fruth A., Prager R. et al. 2011b; Epidemic profile of Shiga-toxin–producing Escherichia coli O104:H4 outbreak in Germany. New Engl J Med365:1771–1780
    [Google Scholar]
  18. Fratamico P. M., DebRoy C., Miyamoto T., Liu Y.. 2009; PCR detection of enterohemorrhagic Escherichia coli O145 in food by targeting genes in the Escherichia coli O145 O-antigen gene cluster and the shiga toxin 1 and shiga toxin 2 genes. Foodborne Pathog Dis6:605–611 [CrossRef][PubMed]
    [Google Scholar]
  19. Fu L., Niu B., Zhu Z., Wu S., Li W.. 2012; Cd-Hit: accelerated for clustering the next-generation sequencing data. Bioinformatics28:3150–3152 [CrossRef][PubMed]
    [Google Scholar]
  20. Gupta S. K., Padmanabhan B. R., Diene S. M., Lopez-Rojas R., Kempf M., Landraud L., Rolain J.-M.. 2013; Arg-Annot, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother (Bethesda)58:212–220
    [Google Scholar]
  21. Harmon L. J., Weir J. T., Brock C. D., Glor R. E., Challenger W.. 2007; Geiger: investigating evolutionary radiations. Bioinformatics24:129–131 [CrossRef][PubMed]
    [Google Scholar]
  22. Iguchi A., Iyoda S., Kikuchi T., Ogura Y., Katsura K., Ohnishi M., Hayashi T., Thomson N. R.. 2014; A complete view of the genetic diversity of the Escherichia coli O-antigen biosynthesis gene cluster. DNA Research22: [CrossRef][PubMed]
    [Google Scholar]
  23. Ingle D. J., Tauschek M., Edwards D. J., Hocking D. M., Pickard D. J., Azzopardi K. I., Amarasena T., Bennett-Wood V., Pearson J. S. et al. 2016; Evolution of atypical enteropathogenic E. coli by repeated acquisition of Lee pathogenicity island variants. Nat Micro1:1–9
    [Google Scholar]
  24. Inouye M., Dashnow H., Raven L., Schultz M. B., Pope B. J., Tomita T., Zobel J., Holt K. E.. 2014; Srst2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med6:1–16
    [Google Scholar]
  25. Irino K., Kato M. A., Vaz T. M., Ramos I. I., Souza M. A., Cruz A. S., Gomes T. A., Vieira M. A., Guth B. E.. 2005; Serotypes and virulence markers of Shiga toxin-producing Escherichia coli (STEC) isolated from dairy cattle in São Paulo State, Brazil. Vet Microbiol105:29–36 [CrossRef][PubMed]
    [Google Scholar]
  26. Jenkins C.. 2015; Whole-genome sequencing data for serotyping Escherichia coli – it's time for a change. J Clin Microbiol53:2402–2403 [CrossRef][PubMed]
    [Google Scholar]
  27. Joensen K. G., Tetzschner A. M., Iguchi A., Aarestrup F. M., Scheutz F.. 2015; Rapid and easy in silico serotyping of Escherichia coli isolates by use of whole-genome sequencing data. J Clin Microbiol53:2410–2426 [CrossRef][PubMed]
    [Google Scholar]
  28. Krogh A., Larsson B., Heijne von G., Sonnhammer E. L. L.. 2001; Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol305:567–580
    [Google Scholar]
  29. Kwong J. C., McCallum N., Sintchenko V., Howden B. P.. 2015; Whole genome sequencing in clinical and public health microbiology. Pathology47:199–210 [CrossRef][PubMed]
    [Google Scholar]
  30. Langmead B., Trapnell C., Pop M., Salzberg S. L.. 2009; Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol10:R25 [CrossRef][PubMed]
    [Google Scholar]
  31. Li D., Liu B., Chen M., Guo D., Guo X., Liu F., Feng L., Wang L.. 2010; A multiplex PCR method to detect 14 Escherichia coli serogroups associated with urinary tract infections. J Microbiol Methods82:71–77 [CrossRef][PubMed]
    [Google Scholar]
  32. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R.. 1000 Genome Project Data Processing Subgroup 2009; The Sequence Alignment/Map format and SAMtools. Bioinformatics25:2078–2079 [CrossRef][PubMed]
    [Google Scholar]
  33. Liu D., Cole R. A., Reeves P. R.. 1996; An O-antigen processing function for Wzx (RfbX): a promising candidate for O-unit flippase. J Bacteriol178:2102–2107[PubMed]
    [Google Scholar]
  34. Michino H., Araki K., Minami S., Takaya S., Sakai N., Miyazaki M., Ono A., Yanagawa H.. 1999; Massive outbreak of Escherichia coli O157:H7 infection in schoolchildren in Sakai City, Japan, associated with consumption of white radish sprouts. Am J Epidemiol150:787–796[PubMed]
    [Google Scholar]
  35. Nicolas-Chanoine M. H., Blanco J., Leflon-Guibout V., Demarty R., Alonso M. P., Caniça M. M., Park Y. J., Lavigne J. P., Pitout J., Johnson J. R.. 2008; Intercontinental emergence of Escherichia coli clone o25:H4-ST131 producing CTX-M-15. J Antimicrob Chemother61:273–281 [CrossRef][PubMed]
    [Google Scholar]
  36. Oksanen J., Blanchet F. G., Kindt R., Legendre P., Minchin P. R., OHara R. B., Simpson G. L., Solymos P., Stevens M. H. H., Wagner H.. 2015; vegan: Community Ecology Package.
  37. Oshima K., Toh H., Ogura Y., Sasamoto H., Morita H., Park S.-H., Ooka T., Iyoda S., Taylor T. D. et al. 2008; Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult. DNA Research15:375–386 [CrossRef]
    [Google Scholar]
  38. Paradis E., Claude J., Strimmer K.. 2004; Ape: Analyses of Phylogenetics and Evolution in R language. Bioinformatics20:289–290[PubMed]
    [Google Scholar]
  39. Petty N. K., Ben Zakour N. L., Stanton-Cook M., Skippington E., Totsika M., Forde B. M., Phan M. D., Gomes Moriel D., Peters K. M. et al. 2014; Global dissemination of a multidrug resistant Escherichia coli clone. Proc Natl Acad Sci U S A111:5694–5699 [CrossRef][PubMed]
    [Google Scholar]
  40. Plainvert C., Bidet P., Peigne C., Barbe V., Médigue C., Denamur E., Bingen E., Bonacorsi S.. 2007; A new O-antigen gene cluster has a key role in the virulence of the Escherichia coli meningitis clone O45:K1:H7. J Bacteriol189:8528–8536 [CrossRef][PubMed]
    [Google Scholar]
  41. Price L. B., Johnson J. R., Aziz M., Clabots C., Johnston B., Tchesnokova V., Nordstrom L., Billig M., Chattopadhyay S. et al. 2013; The epidemic of extended-spectrum-β-lactamase-producing Escherichia coli ST131 is driven by a single highly pathogenic subclone, H30-Rx. MBio4:1–10 [CrossRef][PubMed]
    [Google Scholar]
  42. Rasko D. A., Webster D. R., Sahl J. W., Bashir A., Boisen N., Scheutz F., Paxinos E. E., Sebra R., Chin C. S. et al. 2011; Origins of the Escherichia coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med365:709–717 [CrossRef][PubMed]
    [Google Scholar]
  43. Ratiner Y. A.. 1998; New flagellin-specifying genes in some Escherichia coli strains. J Bacteriol180:979–984[PubMed]
    [Google Scholar]
  44. Ratiner Y. A., Sihvonen L. M., Liu Y., Wang L., Siitonen A.. 2010; Alteration of flagellar phenotype of Escherichia coli strain P12b, the standard type strain for flagellar antigen H17, possessing a new non-fliC flagellin gene flnA, and possible loss of original flagellar phenotype and genotype in the course of subculturing through semisolid media. Arch Microbiol192:267–278 [CrossRef][PubMed]
    [Google Scholar]
  45. Rice P., Longden I., Bleasby A.. 2000; Emboss: the European Molecular Biology Open Software Suite. Trends Genet16:276–277[PubMed]
    [Google Scholar]
  46. Riley L. W., Remis R. S., Helgerson S. D., McGee H. B., Wells J. G., Davis B. R., Hebert R. J., Olcott E. S., Johnson L. M. et al. 1983; Hemorrhagic colitis associated with a rare Escherichia coli serotype. N Engl J Med308:681–685 [CrossRef][PubMed]
    [Google Scholar]
  47. Robins-Browne R. M.. 1987; Traditional enteropathogenic Escherichia coli of infantile diarrhea. Rev Infect Dis9:28–53
    [Google Scholar]
  48. Samuel G., Reeves P.. 2003; Biosynthesis of O-antigens: genes and pathways involved in nucleotide sugar precursor synthesis and O-antigen assembly. Carbohydr Res338:2503–2519[PubMed]
    [Google Scholar]
  49. Seemann T.. 2014; Prokka: rapid prokaryotic genome annotation. Bioinformatics30:2068–2069 [CrossRef][PubMed]
    [Google Scholar]
  50. Toh H., Oshima K., Toyoda A., Ogura Y., Ooka T., Sasamoto H., Park S. H., Iyoda S., Kurokawa K. et al. 2010; Complete genome sequence of the wild-type commensal Escherichia coli strain SE15, belonging to phylogenetic group B2. J Bacteriol192:1165–1166 [CrossRef][PubMed]
    [Google Scholar]
  51. Tominaga A.. 2004; Characterization of six flagellin genes in the H3, H53 and H54 standard strains of Escherichia coli. Genes Genet Syst79:1–8[PubMed]
    [Google Scholar]
  52. Tominaga A., Kutsukake K.. 2007; Expressed and cryptic flagellin genes in the H44 and H55 type strains of Escherichia coli. Genes Genet Syst82:1–8[PubMed]
    [Google Scholar]
  53. von Mentzer A., Connor T. R., Wieler L. H., Semmler T., Iguchi A., Thomson N. R., Rasko D. A., Joffre E., Corander J. et al. 2014; Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution. Nat Genet46:1321–1326 [CrossRef][PubMed]
    [Google Scholar]
  54. Wang L., Rothemund D., Curd H., Reeves P. R.. 2003; Species-wide variation in the Escherichia coli flagellin (H-antigen) gene. J Bacteriol185:2936–2943[PubMed]
    [Google Scholar]
  55. Wattam A. R., Abraham D., Dalay O., Disz T. L., Driscoll T., Gabbard J. L., Gillespie J. J., Gough R., Hix D. et al. 2013; Patric, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res42:D581–D591 [CrossRef][PubMed]
    [Google Scholar]
  56. Wirth T., Falush D., Lan R., Colles F., Mensa P., Wieler L. H., Karch H., Reeves P. R., Maiden M. C. et al. 2006; Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol60:1136–1151 [CrossRef][PubMed]
    [Google Scholar]
  57. Zerbino D. R., Birney E.. 2008; Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res18:821–829 [CrossRef][PubMed]
    [Google Scholar]
  58. Ingle, D. J. EcOH database: GitHubhttps://github.com/katholt/srst2 2016
  59. Ingle, D. J. UPEC ST131 datasethttp://microreact.org/project/Ny5Gg4Wg- 2016
  60. Ingle, D. J. GenomeTrakr datasethttp://microreact.org/project/VygdKU_0 2016
  61. Ingle, D. J. Supplementary information and data in Figsharehttps://dx.doi.org/10.4225/49/571996C105E03 2016
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000064
Loading
/content/journal/mgen/10.1099/mgen.0.000064
Loading

Data & Media loading...

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error