Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-78c5997874-94fs2 Total loading time: 0 Render date: 2024-11-13T00:53:57.119Z Has data issue: false hasContentIssue false

16 - Multilocus sequence typing (MLST) and multilocus microsatellite typing (MLMT) in fungi

from V - Environmental population genetics of fungi

Published online by Cambridge University Press:  03 November 2009

By
Matthew C. Fisher
Edited by
Geoffrey Gadd ,
Sarah C. Watkinson  and
Paul S. Dyer
Matthew C. Fisher
Affiliation:
Imperial College Faculty of Medicine, London
Geoffrey Gadd
Affiliation:
University of Dundee
Sarah C. Watkinson
Affiliation:
University of Oxford
Paul S. Dyer
Affiliation:
University of Nottingham
Get access

Summary

What is multilocus typing?

Origins of the technique

The characterization of genetic variation has revolutionized our understanding of fungal populations and species. Traditionally, advances have been most rapid in the fields of medical mycology and phytopathology (Taylor et al., 1999b) owing to the need for effective molecular epidemiological tools. Epidemiological studies are typically concerned with disease outbreaks, the origin and spread of virulent strains, or the emergence of an interesting phenotype such as antibiotic resistance. Genetic variation in the genomes of pathogens provides a means by which isolates can be differentiated from one another (Taylor et al., 1999b). The characterization of this molecular variation has given rise to the field of molecular epidemiology, whereby genetic variation is used to address questions about the biology and transmission of infectious diseases. However, the techniques developed for molecular epidemiology are not limited to medical fields, and there is huge potential to apply these methodologies to non-disease-causing organisms.

The power of molecular epidemiology as an analytical tool has led to a period of rapid development, resulting in many methods for indexing genetic variation, such as VNTRs (variable number tandem repeats), MLEE (multilocus enzyme electrophoresis), RFLPs (restriction fragment length polymorphisms), RAPDs (randomly amplified polymorphic repeats) and PFGE (pulse field gel electrophoresis), to name but a few (Taylor et al., 1999b; McEwen et al., 2000). Typically, laboratories have tended to develop in-house techniques that are specifically focused on a particular problem, and are usually a variant on the above.

Type
Chapter
Information
Fungi in the Environment , pp. 340 - 354
Publisher: Cambridge University Press
Print publication year: 2007

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Bougnoux, M. E., Morand, S. & d'Enfert, C. (2002). Usefulness of multilocus sequence typing for characterization of clinical isolates of Candida albicans. Journal of Clinical Microbiology 40, 1290–7.CrossRefGoogle ScholarPubMed
Burt, A., Carter, D. A., Koenig, G. L., White, T. J. & Taylor, J. W. (1996). Molecular markers reveal cryptic sex in the human pathogen Coccidioides immitis. Proceedings of the National Academy of Sciences of the USA 93, 770–3.CrossRefGoogle ScholarPubMed
Chariyalertsak, S., Sirisanthana, T., Supparatpinyo, K., Praparattanapan, J. & Nelson, K. E. (1997). Case-control study of risk factors for Penicillium marneffei infection in human immunodeficiency virus-infected patients in northern Thailand. Clinical Infectious Diseases 24, 1080–6.CrossRefGoogle ScholarPubMed
Dodgson, A. R., Pujol, C., Denning, D. W., Soll, D. R. & Fox, A. J. (2003). Multilocus sequence typing of Candida glabrata reveals geographically enriched clades. Journal of Clinical Microbiology 41, 5709–17.CrossRefGoogle ScholarPubMed
Enright, M. C. & Spratt, B. G. (1999). Multilocus sequence typing. Trends in Microbiology 7, 482–7.CrossRefGoogle ScholarPubMed
Feil, E. J. & Spratt, B. G. (2001). Recombination and the population structures of bacterial pathogens. Annual Review of Microbiology 55, 561–90.CrossRefGoogle ScholarPubMed
Feil, E. J., Li, B. C., Aanensen, D. M., Hanage, W. P. & Spratt, B. G. (2004). eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. Journal of Bacteriology 186, 1518–30.CrossRefGoogle ScholarPubMed
Fisher, M. C., Koenig, G., White, T. J. & Taylor, J. W. (2000). A test for concordance between the multilocus genealogies of genes and microsatellites in the pathogenic fungus Coccidioides immitis. Molecular Biology and Evolution 17, 1164–74.CrossRefGoogle ScholarPubMed
Fisher, M. C., Koenig, G. L., White, T. J., San- Blas, G., Negroni, R., Alvarez, I. G., Wanke, B. & Taylor, J. W. (2001). Biogeographic range expansion into South America by Coccidioides immitis mirrors New World patterns of human migration. Proceedings of the National Academy of Sciences of the USA 98, 4558–62.CrossRefGoogle ScholarPubMed
Fisher, M., Koenig, G., White, T. & Taylor, J. (2002). Molecular and phenotypic description of Coccidioides posadasii sp. nov., previously recognized as the non-California population of Coccidioides immitis. Mycologia 94, 73–84.CrossRefGoogle ScholarPubMed
Fisher, M. C., Aanensen, D., Hoog, S. & Vanittanakom, N. (2004a). Multilocus microsatellite typing system for Penicillium marneffei reveals spatially structured populations. Journal of Clinical Microbiology 42, 5065–9.CrossRefGoogle Scholar
Fisher, M. C., Hoog, G. S. & Vannittanakom, N. (2004b). A highly discriminatory Multilocus Microsatellite Typing System (MLMT) for Penicillium marneffei. Molecular Ecology Notes 5, 231–4.Google Scholar
Fraser, C., Hanage, W. P. & Spratt, B. G. (2005). Neutral microepidemic evolution of bacterial pathogens. Proceedings of the National Academy of Sciences of the USA 102, 1968–73.CrossRefGoogle ScholarPubMed
Goldstein, D. B., Ruiz Linares, A., Cavalli-Sforza, L. L. & Feldman, M. W. (1995). An evaluation of genetic distances for use with microsatellite loci. Genetics 139, 463–71.Google ScholarPubMed
Hancock, J. M. (1999). Microsatellites and other simple sequences: genomic context and mutational mechanisms. In Microsatellites, ed. Goldstein, D. B. & Schlotterer, C., pp. 1–6. Oxford: Oxford University Press.Google Scholar
Henderson, S. T. & Petes, T. D. (1992). Instability of simple sequence DNA in Saccharomyces cerevisiae. Molecular and Cellular Biology 12, 2749–57.CrossRefGoogle ScholarPubMed
Johnson, L. J., Koufopanou, V., Goddard, M. R., Hetherington, R., Schafer, S. M. & Burt, A. (2004). Population genetics of the wild yeast Saccharomyces paradoxus. Genetics 166, 43–52.CrossRefGoogle ScholarPubMed
Kasuga, T., Taylor, J. W. & White, T. J. (1999). Phylogenetic relationships of varieties and geographical groups of the human pathogenic fungus, Histoplasma capsulatum Darling. Journal of Clinical Microbiology 37, 653–63.Google ScholarPubMed
Kasuga, T., White, T. J., Koenig, G., McEwen, J., Restrepo, A., Castaneda, E., Da Silva Lacaz, C., Heins-Vaccari, E. M., Freitas, R. S., Zancope-Oliveira, R. M., Qin, Z., Negroni, R., Carter, D. A., Mikami, Y., Tamura, M., Taylor, M. L., Miller, G. F., Poonwan, N. & Taylor, J. W. (2003). Phylogenetic relationships of varieties and geographical groups of the human pathogenic fungus Histoplasma capsulatum Darling. Molecular Ecology 12, 3383–401.CrossRefGoogle Scholar
Koufopanou, V., Burt, A. & Taylor, J. W. (1997). Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis. Proceedings of the National Academy of Sciences of the USA 94, 5478–82.CrossRefGoogle ScholarPubMed
Koufopanou, V., Burt, A. & Taylor, J. W. (1998). Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis. Proceedings of the National Academy of Sciences of the USA 95, 8414.Google Scholar
Kroken, S. & Taylor, J. W. (2001). Outcrossing and recombination in the lichenized fungus Letharia. Fungal Genetics and Biology 34, 83–92.CrossRefGoogle ScholarPubMed
Lockhart, S. R., Joly, S., Pujol, C., Sobel, J. D., Pfaller, M. A. & Soll, D. R. (1997). Development and verification of fingerprinting probes for Candida glabrata. Microbiology 143, 3733–46.CrossRefGoogle ScholarPubMed
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. Proceedings of the National Academy of Sciences of the USA 95, 3140–5.CrossRefGoogle ScholarPubMed
McEwen, J. G., Taylor, J. W., Carter, D., Xu, J., Felipe, M. S., Vilgalys, R., Mitchell, T. G., Kasuga, T., White, T., Bui, T. & Soares, C. M. (2000). Molecular typing of pathogenic fungi. Medical Mycology, 38 (suppl. 1), 189–97.CrossRefGoogle ScholarPubMed
Morehouse, E. A., James, T. Y., Ganley, A. R., Vilgalys, R., Berger, L., Murphy, P. J. & Longcore, J. E. (2003). Multilocus sequence typing suggests the chytrid pathogen of amphibians is a recently emerged clone. Molecular Ecology 12, 395–403.CrossRefGoogle ScholarPubMed
Nauta, M. J. & Weissing, F. J. (1996). Constraints on allele size at microsatellite loci: implications for genetic differentiation. Genetics 143, 1021–32.Google ScholarPubMed
O'Donnell, K., Ward, T. J., Geiser, D. M., Corby Kistler, H. & Aoki, T. (2004). Genealogical concordance between the mating type locus and seven other nuclear genes supports formal recognition of nine phylogenetically distinct species within the Fusarium graminearum clade. Fungal Genetics and Biology 41, 600–23.CrossRefGoogle ScholarPubMed
Tavanti, A., Gow, N. A., Senesi, S., Maiden, M. C. & Odds, F. C. (2003). Optimization and validation of multilocus sequence typing for Candida albicans. Journal of Clinical Microbiology 41, 3765–76.CrossRefGoogle ScholarPubMed
Taylor, J., Jacobson, D. & Fisher, M. (1999a). The evolution of asexual fungi: reproduction, speciation and classification. Annual Review of Phytopathology 37, 197–246.CrossRefGoogle Scholar
Taylor, J. W. & Fisher, M. C. (2003). Fungal multilocus sequence typing – it's not just for bacteria. Current Opinions in Microbiology 6, 351–6.CrossRefGoogle Scholar
Taylor, J. W., Geiser, D. M., Burt, A. & Koufopanou, V. (1999b). The evolutionary biology and population genetics underlying fungal strain typing. Clinical Microbiological Reviews 12, 126–46.Google Scholar
Weber, J. L. & Wong, C. (1993). Mutation of human short tandem repeats. Human Molecular Genetics 2, 1123–8.CrossRefGoogle ScholarPubMed
Xu, J., Vilgalys, R. & Mitchell, T. G. (2000). Multiple gene genealogies reveal recent dispersion and hybridization in the human pathogenic fungus Cryptococcus neoformans. Molecular Ecology 9, 1471–81.CrossRefGoogle ScholarPubMed

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×