Sequenced-Based Typing of Prokaryotes

  • Henrik ChristensenEmail author
  • John Elmerdahl Olsen
Part of the Learning Materials in Biosciences book series (LMB)


The reason to investigate prokaryotic populations is introduced with focus on the population-genetic mechanisms responsible for the formation and conservation of populations. Multilocus sequence typing revolutionized molecular typing by proving information that could be compared between different laboratories and that could be analyzed in well-curated databases on servers via the Internet. The success of MLST has continued based on the analysis of the whole genomic sequence whereby the genetic information analyzed has been extended with hundreds of genes for wgMLST. The other use of whole genomic sequences for typing has been single-nucleotide polymorphism (SNP) analysis where the reads from high-throughput sequencing are compared to a reference sequence allowing very detailed comparison at the single-nucleotide level in order to trace single strains. For certain, mainly human pathogenic bacteria like Escherichia coli and Salmonella enterica, organism-specific prediction in databases on dedicated servers is available where serotype, antimicrobial resistance profile, and wgMLST can be predicted based on the whole genomic sequence uploaded via the Internet.


  1. Alikhan, N.-F., Zhou, Z., Sergeant, M.J. & Achtman, M. (2018) A genomic overview of the population structure of Salmonella. PLoS Genet 14: e1007261.CrossRefPubMedPubMedCentralGoogle Scholar
  2. Bell, G. 2008. Selection. The mechanism of evolution. 2nd ed. Oxford Univ. Press.Google Scholar
  3. Davies, R.L., MacCorquodale, R., Baillie, S., Caffrey, B., 2003. Characterization and comparison of Pasteurella multocida strains associated with porcine pneumonia and atrophic rhinitis. J. Med. Microbiol. 52, 59–67.CrossRefPubMedGoogle Scholar
  4. Didelot X, Falush D. 2007. Inference of bacterial microevolution using multilocus sequence dta. Genetics 175:1251–66.CrossRefPubMedPubMedCentralGoogle Scholar
  5. Didelot X, Lawson D, Darling A, Falush D. 2010. Inference of homologous recombination in bacteria using whole-genome sequences. Genetics. 186:1435–1449.CrossRefPubMedPubMedCentralGoogle Scholar
  6. Francisco AP, Vaz C, Monteiro PT, Melo-Cristino J, Ramirez M, Carriço JA. 2012. PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. BMC Bioinformatics 13:87.CrossRefPubMedPubMedCentralGoogle Scholar
  7. Joensen, K.G., Scheutz, F., Lund, O., Hasman, H., Kaas, R.S., Nielsen, E.M., Aarestrup, F.M., 2014. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J. Clin. Microbiol. 52, 1501–1510.CrossRefPubMedPubMedCentralGoogle Scholar
  8. Joensen, K. G., Tetzschner, A. M., Iguchi, A., Aarestrup, F. M., Scheutz, F., 2015. Rapid and easy in silico serotyping of Escherichia coli using whole genome sequencing (WGS) data. J. Clin. Microbiol. 5, 2410–2426.CrossRefGoogle Scholar
  9. Jolley, K. A. & Maiden, M. C. J. 2010. BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11:595CrossRefPubMedPubMedCentralGoogle Scholar
  10. Jolley, K.A., Bliss, C.M., Bennett, J.S., Bratcher, H.B., Brehony, C., Colles, F.M., Wimalarathna, H., Harrison, O.B., Sheppard, S.K., Cody, AJ. & Maiden, M.C. 2012. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 158, 1005–1015.CrossRefPubMedPubMedCentralGoogle Scholar
  11. Jones, D. and Sneath, P. H. 1970. Genetic transfer and bacterial taxonomy. Bacteriol Rev. 34, 40–81.PubMedPubMedCentralGoogle Scholar
  12. Kumar, S., Stecher, G., Tamura, K., 2016. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874.CrossRefPubMedGoogle Scholar
  13. Koeppel A, Perry EB, Sikorski J, Krizanc D, Warner A, Ward DM, Rooney AP, Brambilla E, Connor N, Ratcliff RM, Nevo E, Cohan FM. 2008. Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. Proc Natl Acad Sci U S A. 105: 2504–9.CrossRefPubMedPubMedCentralGoogle Scholar
  14. Kwong, J.C., Mercoulia, K., Tomita, T., Easton, M., Li, H.Y., Bulach, D.M., Stinear, T.P., Seemann, T., Howden, B.P., 2016. Prospective whole-genome sequencing enhances national surveillance of Listeria monocytogenes. J Clin Microbiol. 54, 333–342.CrossRefPubMedPubMedCentralGoogle Scholar
  15. Larsen, M.V., Cosentino, S., Rasmussen, S., Friis, C., Hasman, H., Marvig, R.L., Jelsbak, L., Sicheritz-Pontén, T., Ussery, D.W., Aarestrup, F.M., Lund, O., 2012. Multilocus sequence typing of total genome sequenced bacteria. J. Clin. Microbiol. 50, 1355–1361.CrossRefPubMedPubMedCentralGoogle Scholar
  16. Leekitcharoenphon, P., Kaas, R.S., Thomsen, M.C.F., Friis, C., Rasmussen, S., Aarestrup, F.M., 2012. snpTree-a web-server to identify and construct SNP trees from whole genome sequence data. BMC Genomics 13 Suppl 7:S6CrossRefPubMedPubMedCentralGoogle Scholar
  17. Levin, B. R. 1981. Periodic selection, infectious gene exchange and the genetic structure of E. coli populations. Genetics 99, 1–12.PubMedPubMedCentralGoogle Scholar
  18. Librado P & Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25:1451–1452.CrossRefPubMedGoogle Scholar
  19. Luria, S.E. & Delbrück M. 1943. Mutations of Bacteria from Virus Sensitivity to Virus Resistance. Genetics 28, 491–511.PubMedPubMedCentralGoogle Scholar
  20. Madigan, M. T., Bender, K. S., Buckley, D. H., Sattley, W. M. & Stahl, D. A. 2018. Brock biology of microorganisms. 15th ed. Global Edition. Pearson, New York.Google Scholar
  21. Milkman R. 1973. Electrophoretic variation in Escherichia coli from natural sources. Science182, 1024–6.CrossRefPubMedGoogle Scholar
  22. Maiden, M.C., Bygraves, J.A., Feil, E., Morelli, G., Russell, J.E., Urwin, R., Zhang, Q., Zhou, J., Zurth, K., Caugant, D.A., Feavers, I.M., Achtman, M. & Spratt, B.G. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A. 95, 3140–3145.CrossRefPubMedPubMedCentralGoogle Scholar
  23. Maughan, H., Sinha, S., Wilson L. and Redfield, R. 2008. Competence, DNA Uptake and Transformation in the Pasteurellaceae. In Kuhnert, P and Christensen, H. Pasteurellaceae, Biology, genomics and molecular aspects. Caister Acad. Press. In press.Google Scholar
  24. Nei, M. (2005). Selectionism and neutralism in molecular evolution. Mol. Biol. Evol. 22, 2318–42.CrossRefPubMedPubMedCentralGoogle Scholar
  25. Pope et al. 2008. A practical guide to measuring mutation rates in antibiotic resistance. Antimicrob. Agents Chemotherapy 52, 1209–14.CrossRefGoogle Scholar
  26. Schürch, A.C., Arredondo-Alonso, S., Willems, R.J.L., Goering, R.V. 2018. Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches. Clin. Microbiol. Infect. 24, 350–354.CrossRefPubMedGoogle Scholar
  27. Selander RK, Levin BR. Genetic diversity and structure in Escherichia coli populations. 1980. Science 210, 545–7.CrossRefPubMedGoogle Scholar
  28. Spratt, B. G., M. C. J. Maiden (1999): Bacterial population genetics, evolution and epidemiology. Phil. Trans. R. Soc. Lond. B, 354, 701–10.CrossRefGoogle Scholar
  29. Subaaharan, S., Blackall, L.L., Blackall, P.J., 2010. Development of a multi locus sequence typing scheme for avian isolates of Pasteurella multocida. Vet. Microbiol. 141, 354–361.CrossRefPubMedGoogle Scholar
  30. Whiteside MD, Laing CR, Manji A, Kruczkiewicz P, Taboada EN, Gannon VP. 2016. SuperPhy: predictive genomics for the bacterial pathogen Escherichia coli. BMC Microbiol. 16:65.CrossRefPubMedPubMedCentralGoogle Scholar
  31. Whittam, T. S. 1995. Genetic population structure and pathogenicity in enteric bacteria. In Population genetics of bacteria. Eds. Baumberg, S., Young, J. P. W., Wellington, E. M. H. and Saunders, J. R. 1995. 52nd Symposium of the Society for General Microbiology. pp. 217–245. Cambridge Univ. Press.Google Scholar
  32. Ørskov, F., I. Ørskov (1983): Summary of a workshop on the clone concept in the epidemiology, taxonomy, and evolution of the Enterobacteriaceae and other bacteria. J. Infect. Dis. 148, 346–357.CrossRefPubMedGoogle Scholar

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© Springer Nature Switzerland AG 2018

Authors and Affiliations

  1. 1.Department of Veterinary Animal SciencesUniversity of CopenhagenCopenhagenDenmark

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