Abstract
Multilocus sequence typing (MLST) was first proposed in 1998 as a typing approach that enables the unambiguous characterization of bacterial isolates in a standardized, reproducible, and portable manner using the human pathogen Neisseria meningitidis as the exemplar organism. Since then, the approach has been applied to a large and growing number of organisms by public health laboratories and research institutions. MLST data, shared by investigators over the world via the Internet, have been successfully exploited in applications ranging from molecular epidemiological investigations to population biology and evolutionary analyses. This chapter describes the practical steps in the development and application of an MLST scheme and some of the common tools and techniques used to obtain the maximum benefit from the data. Considerations pertinent to the implementation of high-capacity MLST projects (i.e., those involving thousands of isolates) are discussed.
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References
Maiden, M. C. J., Bygraves, J. A., Feil, E., Morelli, G., Russell, J. E., Urwin, R., (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.
Maiden, M. C. (2006). Multilocus sequence typing of bacteria. Annu. Rev. Microbiol. 60, 561–588.
Urwin, R., and Maiden, M. C. (2003). Multi-locus sequence typing: a tool for global epidemiology. Trends Microbiol. 11, 479–487.
Selander, R. K., Caugant, D. A., Ochman, H., Musser, J. M., Gilmour, M. N., and Whittam, T. S. (1986). Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl. Environ. Microbiol. 51, 837–884.
Maynard Smith, J., Smith, N. H., O’Rourke, M., and Spratt, B. G. (1993). How clonal are bacteria?. Proc. Natl. Acad. Sci. U S A 90, 4384–4388.
Maynard Smith, J., Dowson, C. G., and Spratt, B. G. (1991). Localized sex in bacteria. Nature 349, 29–31.
Maynard Smith, J., Feil, E. J., and Smith, N. H. (2000). Population structure and evolutionary dynamics of pathogenic bacteria. BioEssay 22, 1115–1122.
Maiden, M. C. J. (2000). High-throughput sequencing in the population analysis of bacterial pathogens. Int. J. Med. Microbiol 290, 183–190.
Jolley, K. A., Chan, M. S., and Maiden, M. C. (2004). mlstdbNet—distributed multi-locus sequence typing (MLST) databases. BMC Bioinformatics 5, 86.
Chan, M. S., Maiden, M. C., and Spratt, B. G. (2001). Database-driven multi locus sequence typing (MLST) of bacterial pathogens. Bioinformatics. 17, 1077–1083.
Caugant, D. A., Frøholm, L. O., Bovre, K., Holten, E., Frasch, C. E., Mocca, L. F., (1986). Intercontinental spread of a genetically distinctive complex of clones of Neisseria meningitidis causing epidemic disease. Proc. Natl. Acad. Sci U S A 83, 4927–4931.
Olyhoek, T., Crowe, B. A., and Achtman, M. (1987). Clonal population structure of Neisseria meningitidis serogroup A isolated from epidemics and pandemics between 1915 and 1983. Rev. Infect. Dis. 9, 665–682.
Zhang, Q. Y., Jones, D. M., Saez Nieto, J. A., Perez Trallero, E., and Spratt, B. G. (1990). Genetic diversity of penicillin-binding protein 2 genes of penicillin-resistant strains of Neisseria meningitidis revealed by fingerprinting of amplified DNA. Antimicrob. Agents Chemother. 34, 1523–1528.
Feavers, I. M., Heath, A. B., Bygraves, J. A., and Maiden, M. C. (1992). Role of horizontal genetic exchange in the antigenic variation of the class 1 outer membrane protein of Neisseria meningitidis. Mol. Microbiol. 6, 489–495.
Maniatis, T., Fritsch, E. F., and Sambrook, J. (1982). Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
Staden, R. (1996). The Staden sequence analysis package. Mol. Biotechnol. 5, 233–241.
Womble, D. D. (2000). GCG: The Wisconsin package of sequence analysis programs. Methods Mol. Biol. 132, 3–22.
Jolley, K. A., Feil, E. J., Chan, M. S., and Maiden, M. C. (2001). Sequence type analysis and recombinational tests (START). Bioinformatics. 17, 1230–1231.
Field, D., Tiwari, B., and Snape, J. (2005). Bioinformatics and data management support for environmental genomics. PLoS Biol. 3, e297.
Gupta, S., and Maiden, M. C. J. (2001). Exploring the evolution of diversity in pathogen populations. Trends Microbiol. 9, 181–192.
Holmes, E. C., Urwin, R., and Maiden, M. C. J. (1999). The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis. Mol. Biol. Evol. 16, 741–749.
Dykhuizen, D. E., Polin, D. S., Dunn, J. J., Wilske, B., Preac Mursic, V., Dattwyler, R. J., (1993). Borrelia burgdorferi is clonal: implications for taxonomy and vaccine development. Proc. Natl. Acad. Sci U S A 90, 10163–10167.
Feil, E. J., Li, B. C., Aanensen, D. M., Hanage, W. P., and Spratt, B. G. (2004). eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J. Bacteriol. 186, 1518–1530.
Kumar, S., Tamura, K., and Nei, M. (2004). MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5, 150–163.
Huson, D. H. (1998). SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics. 14, 68–73.
Jefferies, J., Clarke, S., Diggle, M., Smith, A., Dowson, C., and Mitchell, T. (2003). Automated pneumococcal MLST using liquid-handling robotics and a capillary DNA sequencer. Mol. Biotechnol. 24, 303–308.
Clarke, S. C. (2002). Nucleotide sequence-based typing of bacteria and the impact of automation. Bioessays 24, 858–862.
Diggle, M. A., and Clarke, S. C. (2002). What a load of old sequence!!!. J. Clin. Microbiol. 40, 2707.
Kriz, P., Kalmusova, J., and Felsberg, J. (2002). Multilocus sequence typing of Neisseria meningitidis directly from cerebrospinal fluid. Epidemiol. Infect. 12 8, 157–160.
Diggle, M. A., Bell, C. M., and Clarke, S. C. (2003). Nucleotide sequence-based typing of meningococci directly from clinical samples. J. Med. Microbiol. 52, 505–508.
Bygraves, J. A., Urwin, R., Fox, A. J., Gray, S. J., Russell, J. E., Feavers, I. M., (1999). Population genetic and evolutionary approaches to the analysis of Neisseria meningitidis isolates belonging to the ET-5 complex. J. Bacteriol. 181, 5551–5556.
Feavers, I. M., Gray, S. J., Urwin, R., Russell, J. E., Bygraves, J. A., Kaczmarski, E. B., (1999). Multilocus sequence typing and antigen gene sequencing in the investigation of a meningococcal disease outbreak. J. Clin. Microbiol. 37, 3883–3887.
Brehony, C., Jolley, K. A., and Maiden, M. C. (2007). Multilocus sequence typing for global surveillance of meningococcal disease. FEMS Microbiol. Rev. 31, 15–26.
Zhang, X. B., Shao, Z. J., Yang, E., Xu, L., Xu, X. Y., Li, M. C., (2007). Molecular characterization of serogroup C Neisseria meningitidis isolated in China. J. Med. Microbiol. 56, 1224–1229.
Cartwright, K., Reilly, S., White, D., Stuart, J., Begg, N., and Constantine, C. (1993). Management of early meningococcal disease. Lancet 342, 985–986.
Cartwright, K., Reilly, S., White, D., and Stuart, J. (1992). Early treatment with parenteral penicillin in meningococcal disease. BMJ. 305, 143–147.
Ni, H., Knight, A. I., Cartwright, K., Palmer, W. H., and McFadden, J. (1992). Polymerase chain reaction for diagnosis of meningococcal meningitis. Lancet 340, 1432–1434.
Mantel, N. (1967). The detection of disease clustering and a generalized regression approach. Cancer Res. 27, 209–220.
Schneider, S., Roessli, D., and Excoffier, L. (2000). Arlequin Version 2.000: A Software for Population Genetic Data Analysis. University of Geneva, Geneva, Switzerland.
Wright, S. (1951). The genetical structure of populations. Ann. Eugen. 15, 323–354.
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Ibarz Pavón, A., Maiden, M.C. (2009). Multilocus Sequence Typing. In: Caugant, D. (eds) Molecular Epidemiology of Microorganisms. Methods in Molecular Biology™, vol 551. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60327-999-4_11
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DOI: https://doi.org/10.1007/978-1-60327-999-4_11
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