1887

Microbiology Society logo

Volume 161, Issue 5

Guide to the various phylogenetic classification schemes for and the correspondence among schemes Free

Abstract

Numerous tools allowing the rapid and universal identification of the clones/clonal complexes/phylogroups of have been developed, as it is a commensal of the vertebrate gut, a major pathogen in veterinary and human medicine, and a bacterial indicator of faecal contamination. The ability to identify clones/clonal complexes/phylogroups is crucial, as a strain’s ecological niche, lifestyle and propensity to cause disease vary with its phylogenetic origins. There are currently three multi-locus sequence typing (MLST) schemes for , as well as several PCR-based assays for determining a strain’s phylogroup or clonal complex. In this work, we present data that will enable investigators to determine the correspondence between the PCR-based assays and the three MLST schemes, and provide the means for assigning a sequence type (ST) to a phylogroup when no other data on the strain phylogroup membership are available. Such information will help the scientific community to accurately identify the clones reported in various publications. Although whole-genome sequencing will replace classical MLST and most alternative PCR-based methods, the ST nomenclature of the MLST scheme hosted at the University of Warwick will largely persist.

  • Received:
  • Accepted:
  • Published Online:
© Microbiology Society
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.000063
2015-05-01
2024-04-18
Loading full text...

Full text loading...

/deliver/fulltext/micro/161/5/980.html?itemId=/content/journal/micro/10.1099/mic.0.000063&mimeType=html&fmt=ahah

References

  1. Bidet P., Metais A., Mahjoub-Messai F., Durand L., Dehem M., Aujard Y., Bingen E., Nassif X., Bonacorsi S. 2007; Detection and identification by PCR of a highly virulent phylogenetic subgroup among extraintestinal pathogenic Escherichia coli B2 strains. Appl Environ Microbiol 73:2373–2377 [View Article][PubMed]
     [Google Scholar]
  2. Clermont O., Bonacorsi S., Bingen E. 2000; Rapid and simple determination of the Escherichia coli phylogenetic group. Appl Environ Microbiol 66:4555–4558 [View Article][PubMed]
     [Google Scholar]
  3. Clermont O., Lescat M., O’Brien C. L., Gordon D. M., Tenaillon O., Denamur E. 2008; Evidence for a human-specific Escherichia coli clone. Environ Microbiol 10:1000–1006 [View Article][PubMed]
     [Google Scholar]
  4. Clermont O., Dhanji H., Upton M., Gibreel T., Fox A., Boyd D., Mulvey M. R., Nordmann P., Ruppé E. et al. 2009; Rapid detection of the O25b-ST131 clone of Escherichia coli encompassing the CTX-M-15-producing strains. J Antimicrob Chemother 64:274–277 [View Article][PubMed]
     [Google Scholar]
  5. Clermont O., Gordon D. M., Brisse S., Walk S. T., Denamur E. 2011; Characterization of the cryptic Escherichia lineages: rapid identification and prevalence. Environ Microbiol 13:2468–2477 [View Article][PubMed]
     [Google Scholar]
  6. Clermont O., Christenson J. K., Denamur E., Gordon D. M. 2013; The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environ Microbiol Rep 5:58–65 [View Article][PubMed]
     [Google Scholar]
  7. Clermont O., Christenson J. K., Daubié A. S., Gordon D. M., Denamur E. 2014; Development of an allele-specific PCR for Escherichia coli B2 sub-typing, a rapid and easy to perform substitute of multilocus sequence typing. J Microbiol Methods 101:24–27 [View Article][PubMed]
     [Google Scholar]
  8. Croxen M. A., Finlay B. B. 2010; Molecular mechanisms of Escherichia coli pathogenicity. Nat Rev Microbiol 8:26–38[PubMed]
     [Google Scholar]
  9. Doumith M., Day M., Ciesielczuk H., Hope R., Underwood A., Reynolds R., Wain J., Livermore D. M., Woodford N. 2015; Rapid identification of major Escherichia coli sequence types causing urinary tract and bloodstream infections. J Clin Microbiol 53:160–166 [View Article][PubMed]
     [Google Scholar]
  10. Escobar-Páramo P., Sabbagh A., Darlu P., Pradillon O., Vaury C., Denamur E., Lecointre G. 2004; Decreasing the effects of horizontal gene transfer on bacterial phylogeny: the Escherichia coli case study. Mol Phylogenet Evol 30:243–250 [View Article][PubMed]
     [Google Scholar]
  11. Fernández-Romero N., Romero-Gómez M. P., Gómez-Gil M. R., Mingorance J. 2011; Epidemic population structure of extraintestinal pathogenic Escherichia coli determined by single nucleotide polymorphism pyrosequencing. Infect Genet Evol 11:1655–1663 [View Article][PubMed]
     [Google Scholar]
  12. Gordon D. M., Cowling A. 2003; The distribution and genetic structure of Escherichia coli in Australian vertebrates: host and geographic effects. Microbiology 149:3575–3586 [View Article][PubMed]
     [Google Scholar]
  13. Gordon D. M., Clermont O., Tolley H., Denamur E. 2008; Assigning Escherichia coli strains to phylogenetic groups: multi-locus sequence typing versus the PCR triplex method. Environ Microbiol 10:2484–2496 [View Article][PubMed]
     [Google Scholar]
  14. Hommais F., Pereira S., Acquaviva C., Escobar-Páramo P., Denamur E. 2005; Single-nucleotide polymorphism phylotyping of Escherichia coli. . Appl Environ Microbiol 71:4784–4792 [View Article][PubMed]
     [Google Scholar]
  15. Jaureguy F., Landraud L., Passet V., Diancourt L., Frapy E., Guigon G., Carbonnelle E., Lortholary O., Clermont O. et al. 2008; Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains. BMC Genomics 9:560 [View Article][PubMed]
     [Google Scholar]
  16. Johnson J. R., Owens K., Manges A. R., Riley L. W. 2004; Rapid and specific detection of Escherichia coli clonal group A by gene-specific PCR. J Clin Microbiol 42:2618–2622 [View Article][PubMed]
     [Google Scholar]
  17. Johnson J. R., Menard M., Johnston B., Kuskowski M. A., Nichol K., Zhanel G. G. 2009; Epidemic clonal groups of Escherichia coli as a cause of antimicrobial-resistant urinary tract infections in Canada, 2002 to 2004. Antimicrob Agents Chemother 53:2733–2739 [View Article][PubMed]
     [Google Scholar]
  18. Johnson J. R., Clermont O., Johnston B., Clabots C., Tchesnokova V., Sokurenko E., Junka A. F., Maczynska B., Denamur E. 2014; Rapid and specific detection, molecular epidemiology, and experimental virulence of the O16 subgroup within Escherichia coli sequence type 131. J Clin Microbiol 52:1358–1365 [View Article][PubMed]
     [Google Scholar]
  19. Kaas R. S., Friis C., Ussery D. W., Aarestrup F. M. 2012; Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes. BMC Genomics 13:577 [View Article][PubMed]
     [Google Scholar]
  20. Larsen M. V., Cosentino S., Rasmussen S., Friis C., Hasman H., Marvig R. L., Jelsbak L., Sicheritz-Pontén T., Ussery D. W. et al. 2012; Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50:1355–1361 [View Article][PubMed]
     [Google Scholar]
  21. Luo C., Walk S. T., Gordon D. M., Feldgarden M., Tiedje J. M., Konstantinidis K. T. 2011; Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species. Proc Natl Acad Sci U S A 108:7200–7205 [View Article][PubMed]
     [Google Scholar]
  22. Matsumura Y., Yamamoto M., Nagao M., Hotta G., Matsushima A., Ito Y., Takakura S., Ichiyama S.Kyoto-Shiga Clinical Microbiology Study Group 2012; Emergence and spread of B2-ST131-O25b, B2-ST131-O16 and D-ST405 clonal groups among extended-spectrum-β-lactamase-producing Escherichia coli in Japan. J Antimicrob Chemother 67:2612–2620 [View Article][PubMed]
     [Google Scholar]
  23. McArthur A. G., Waglechner N., Nizam F., Yan A., Azad M. A., Baylay A. J., Bhullar K., Canova M. J., De Pascale G. et al. 2013; The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57:3348–3357 [View Article][PubMed]
     [Google Scholar]
  24. Nicolas-Chanoine M. H., Bertrand X., Madec J. Y. 2014; Escherichia coli ST131, an intriguing clonal group. Clin Microbiol Rev 27:543–574 [View Article][PubMed]
     [Google Scholar]
  25. Ochman H., Selander R. K. 1984; Standard reference strains of Escherichia coli from natural populations. J Bacteriol 157:690–693[PubMed]
     [Google Scholar]
  26. 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 A 111:5694–5699 [View Article][PubMed]
     [Google Scholar]
  27. Picard B., Garcia J. S., Gouriou S., Duriez P., Brahimi N., Bingen E., Elion J., Denamur E. 1999; The link between phylogeny and virulence in Escherichia coli extraintestinal infection. Infect Immun 67:546–553[PubMed]
     [Google Scholar]
  28. 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. MBio 4:e00377-13 [View Article][PubMed]
     [Google Scholar]
  29. Ratajczak M., Laroche E., Berthe T., Clermont O., Pawlak B., Denamur E., Petit F. 2010; Influence of hydrological conditions on the Escherichia coli population structure in the water of a creek on a rural watershed. BMC Microbiol 10:222 [View Article][PubMed]
     [Google Scholar]
  30. Reid S. D., Herbelin C. J., Bumbaugh A. C., Selander R. K., Whittam T. S. 2000; Parallel evolution of virulence in pathogenic Escherichia coli . Nature 406:64–67 [View Article][PubMed]
     [Google Scholar]
  31. Sahl J. W., Matalka M. N., Rasko D. A. 2012; Phylomark, a tool to identify conserved phylogenetic markers from whole-genome alignments. Appl Environ Microbiol 78:4884–4892 [View Article][PubMed]
     [Google Scholar]
  32. Tchesnokova V., Billig M., Chattopadhyay S., Linardopoulou E., Aprikian P., Roberts P. L., Skrivankova V., Johnston B., Gileva A. et al. 2013; Predictive diagnostics for Escherichia coli infections based on the clonal association of antimicrobial resistance and clinical outcome. J Clin Microbiol 51:2991–2999 [View Article][PubMed]
     [Google Scholar]
  33. Tenaillon O., Skurnik D., Picard B., Denamur E. 2010; The population genetics of commensal Escherichia coli . Nat Rev Microbiol 8:207–217 [View Article][PubMed]
     [Google Scholar]
  34. Touchon M., Hoede C., Tenaillon O., Barbe V., Baeriswyl S., Bidet P., Bingen E., Bonacorsi S., Bouchier C. et al. 2009; Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 5:e1000344 [View Article][PubMed]
     [Google Scholar]
  35. Treangen T. J., Ondov B. D., Koren S., Phillippy A. M. 2014; The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol 15:524 [View Article][PubMed]
     [Google Scholar]
  36. van Elsas J. D., Semenov A. V., Costa R., Trevors J. T. 2011; Survival of Escherichia coli in the environment: fundamental and public health aspects. ISME J 5:173–183 [View Article][PubMed]
     [Google Scholar]
  37. Walk S. T., Alm E. W., Gordon D. M., Ram J. L., Toranzos G. A., Tiedje J. M., Whittam T. S. 2009; Cryptic lineages of the genus Escherichia . Appl Environ Microbiol 75:6534–6544 [View Article][PubMed]
     [Google Scholar]
  38. Weissman S. J., Johnson J. R., Tchesnokova V., Billig M., Dykhuizen D., Riddell K., Rogers P., Qin X., Butler-Wu S. et al. 2012; High-resolution two-locus clonal typing of extraintestinal pathogenic Escherichia coli . Appl Environ Microbiol 78:1353–1360 [View Article][PubMed]
     [Google Scholar]
  39. 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 Microbiol 60:1136–1151 [View Article][PubMed]
     [Google Scholar]
  40. Zhou Y., Liang Y., Lynch K. H., Dennis J. J., Wishart D. S. 2011; PHAST: a fast phage search tool. Nucleic Acids Res 39:Suppl. 2W347–W352 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.000063
Loading
Guide to the various phylogenetic classification schemes for Escherichia coli and the correspondence among schemes
Microbiology 161, 980 (2015); https://doi.org/10.1099/mic.0.000063
/content/journal/micro/10.1099/mic.0.000063
/content/journal/micro/10.1099/mic.0.000063
Loading

Data & Media loading...

Supplements

Supplementary Data

PDF

Most cited Most Cited RSS feed

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