Abstract
To gain more insight into the epidemiological relationships between isolates of Candida spp. obtained from various origins, several molecular typing techniques have been developed. Two methods have emerged in the 2000s as soon as enough knowledge of the Candida spp. genomes was available to choose adequate loci and primers, namely microsatellite length polymorphism (MLP) and multilocus sequence typing (MLST). To contrast with previous PCR-based methods, specific amplifications with stringent conditions easily reproducible are the basis of MLP and MLST. MLST relies on Sanger sequencing to detect single-nucleotide polymorphisms within housekeeping genes. MLP needs a first in silico step to select tandemly repeated stretches of two to five nucleotides. One of the two primers used to amplify a microsatellite locus is labeled and fragment sizing is automatically performed using high-resolution electrophoresis platforms. MLST provides results easily comparable between laboratories and active MLST schemes are publicly available for the main Candida species. For comparative studies, MLP needs standards to compensate for the electrophoretic variations depending on the platforms used. Both methods can help us gain insight into the genetic relatedness of fungal isolates, both with advantages and drawbacks, and the choice of one method rather than the other depends on the task in question.
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References
Hunter PR (1991) A critical review of typing methods for Candida albicans and their applications. Crit Rev Microbiol 17:417–434
Soll DR (2000) The ins and outs of DNA fingerprinting the infectious fungi. Clin Microbiol Rev 13:332–370
Graser Y, Volovsek M, Arrington J, Schonian G, Presber W, Mitchell TG, Vilgalys R (1996) Molecular markers reveal that population structure of the human pathogen Candida albicans exhibits both clonality and recombination. Proc Natl Acad Sci U S A 93:12473–12477
Tavanti A, Hensgens LA, Ghelardi E, Campa M, Senesi S (2007) Genotyping of Candida orthopsilosis clinical isolates by amplification fragment length polymorphism reveals genetic diversity among independent isolates and strain maintenance within patients. J Clin Microbiol 45:1455–1462
Gil-Lamaignere C, Roilides E, Hacker J, Muller FM (2003) Molecular typing for fungi—a critical review of the possibilities and limitations of currently and future methods. Clin Microbiol Infect 9:172–185
Bretagne S, Costa JM, Besmond C, Carsique R, Calderone R (1997) Microsatellite polymorphism in the promoter sequence of the elongation factor 3 gene of Candida albicans as the basis for a typing system. J Clin Microbiol 35:1777–1780
Botterel F, Desterke C, Costa C, Bretagne S (2001) Analysis of microsatellite markers of Candida albicans used for rapid typing. J Clin Microbiol 39:4076–4081
Bougnoux ME, Tavanti A, Bouchier C, Gow NA, Magnier A, Davidson AD, Maiden MC, D’Enfert C, Odds FC (2003) Collaborative consensus for optimized multilocus sequence typing of Candida albicans. J Clin Microbiol 41:5265–5266
Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580
Bougnoux ME, Morand S, d’Enfert C (2002) Usefulness of multilocus sequence typing for characterization of clinical isolates of Candida albicans. J Clin Microbiol 40:1290–1297
Dodgson AR, Pujol C, Denning DW, Soll DR, Fox AJ (2003) Multilocus sequence typing of Candida glabrata reveals geographically enriched clades. J Clin Microbiol 41:5709–5717
Bently DR, Dunham I (1995) Mapping human chromosomes. Curr Opin Genet Dev 5:328–334
Eloy O, Marque S, Botterel F, Stephan F, Costa JM, Lasserre V, Bretagne S (2006) Uniform distribution of three Candida albicans microsatellite markers in two French ICU populations supports a lack of nosocomial cross-contamination. BMC Infect Dis 6:162
Stephan F, Bah MS, Desterke C, Rezaiguia-Delclaux S, Foulet F, Duvaldestin P, Bretagne S (2002) Molecular diversity and routes of colonization of Candida albicans in a surgical intensive care unit, as studied using microsatellite markers. Clin Infect Dis 35:1477–1483
Albano L, Bretagne S, Mamzer-Bruneel MF, Kacso I, Desnos-Ollivier M, Guerrini P, Le Luong T, Cassuto E, Dromer F, Lortholary O (2009) Evidence that graft-site candidiasis after kidney transplantation is acquired during organ recovery: a multicenter study in France. Clin Infect Dis 48:194–202
Sampaio P, Gusmao L, Correia A, Alves C, Rodrigues AG, Pina-Vaz C, Amorim A, Pais C (2005) New microsatellite multiplex PCR for Candida albicans strain typing reveals microevolutionary changes. J Clin Microbiol 43:3869–3876
Foulet F, Nicolas N, Eloy O, Botterel F, Gantier JC, Costa JM, Bretagne S (2005) Microsatellite marker analysis as a typing system for Candida glabrata. J Clin Microbiol 43:4574–4579
Grenouillet F, Millon L, Bart JM, Roussel S, Biot I, Didier E, Ong AS, Piarroux R (2007) Multiple-locus variable-number tandem-repeat analysis for rapid typing of Candida glabrata. J Clin Microbiol 45:3781–3784
Desnos-Ollivier M, Bretagne S, Bernede C, Robert V, Raoux D, Chachaty E, Forget E, Lacroix C, Dromer F (2008) Clonal population of flucytosine-resistant Candida tropicalis from blood cultures, Paris, France. Emerg Infect Dis 14:557–565
Lasker BA, Butler G, Lott TJ (2006) Molecular genotyping of Candida parapsilosis group I clinical isolates by analysis of polymorphic microsatellite markers. J Clin Microbiol 44:750–759
Sabino R, Sampaio P, Rosado L, Stevens DA, Clemons KV, Pais C (2010) New polymorphic microsatellite markers able to distinguish among Candida parapsilosis sensu stricto isolates. J Clin Microbiol 48:1677–1682
Garcia-Hermoso D, Cabaret O, Lecellier G, Desnos-Ollivier M, Hoinard D, Raoux D, Costa JM, Dromer F, Bretagne S (2007) Comparison of microsatellite length polymorphism and multilocus sequence typing for DNA-based typing of Candida albicans. J Clin Microbiol 45:3958–3963
de Valk HA, Meis JF, Klaassen CH (2007) Microsatellite based typing of Aspergillus fumigatus: strengths, pitfalls and solutions. J Microbiol Methods 69:268–272
Pasqualotto AC, Denning DW, Anderson MJ (2007) A cautionary tale: lack of consistency in allele sizes between two laboratories for a published multilocus microsatellite typing system. J Clin Microbiol 45:522–528
Garcia-Hermoso D, MacCallum DM, Lott TJ, Sampaio P, Serna MJ, Grenouillet F, Klaassen CH, Bretagne S (2010) Multicenter collaborative study for standardization of Candida albicans genotyping using a polymorphic microsatellite marker. J Clin Microbiol 48:2578–2581
Costa JM, Garcia-Hermoso D, Olivi M, Cabaret O, Farrugia C, Lecellier G, Dromer F, Bretagne S (2010) Genotyping of Candida albicans using length fragment and high-resolution melting analyses together with minisequencing of a polymorphic microsatellite locus. J Microbiol Methods 80:306–309
Enright MC, Spratt BG (1999) Multilocus sequence typing. Trends Microbiol 7:482–487
Tavanti A, Davidson AD, Johnson EM, Maiden MC, Shaw DJ, Gow NA, Odds FC (2005) Multilocus sequence typing for differentiation of strains of Candida tropicalis. J Clin Microbiol 43:5593–5600
Jacobsen MD, Gow NA, Maiden MC, Shaw DJ, Odds FC (2007) Strain typing and determination of population structure of Candida krusei by multilocus sequence typing. J Clin Microbiol 45:317–323
Daniel HM, Lachance MA, Kurtzman CP (2014) On the reclassification of species assigned to Candida and other anamorphic ascomycetous yeast genera based on phylogenetic circumscription. Antonie Van Leeuwenhoek 106:67–84
Lachance MA, Boekhout T, Scorzetti G, Fell JW, Kurtzman CP (2011) Candida Berkhout (1923). In: Kurtzman CP, Fell JW, Boekhout T (eds) The Yeasts, a taxonomic study. Elsevier, Amsterdam, pp 987–1278
Donnelly SM, Sullivan DJ, Shanley DB, Coleman DC (1999) Phylogenetic analysis and rapid identification of Candida dubliniensis based on analysis of ACT1 intron and exon sequences. Microbiology 145(Pt 8):1871–1882
Costa JM, Eloy O, Botterel F, Janbon G, Bretagne S (2005) Use of microsatellite markers and gene dosage to quantify gene copy numbers in Candida albicans. J Clin Microbiol 43:1387–1389
Jolley KA, Chan MS, Maiden MC (2004) Mlstdbnet—distributed multi-locus sequence typing (MLST) databases. BMC Bioinformatics 5:86
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Garcia-Hermoso, D., Desnos-Ollivier, M., Bretagne, S. (2016). Typing Candida Species Using Microsatellite Length Polymorphism and Multilocus Sequence Typing. In: Calderone, R., Cihlar, R. (eds) Candida Species. Methods in Molecular Biology, vol 1356. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3052-4_15
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DOI: https://doi.org/10.1007/978-1-4939-3052-4_15
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