The Ins and Outs of DNA Fingerprinting the Infectious Fungi

doi:10.1128/CMR.13.2.332-370.2000

This Article

	Full Text
	Full Text (PDF)
	Alert me when this article is cited
	Alert me if a correction is posted

Services

	Similar articles in this journal
	Similar articles in PubMed
	Alert me to new issues of the journal
	Download to citation manager
	Copyright Information
	Books from ASM Press
	MicrobeWorld

Citing Articles

	Citing Articles via HighWire
	Citing Articles via Google Scholar

Google Scholar

	Articles by Soll, D. R.
	Search for Related Content

PubMed

	PubMed Citation
	Articles by Soll, D. R.

Clinical Microbiology Reviews, April 2000, p. 332-370, Vol. 13, No. 2
0893-8512/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

The Ins and Outs of DNA Fingerprinting the Infectious Fungi

David R. Soll^*

Department of Biological Sciences, University of Iowa, Iowa City, Iowa

DNA fingerprinting methods have evolved as major tools in fungal epidemiology. However, no single method has emerged as themethod of choice, and some methods perform better than othersat different levels of resolution. In this review, requirementsfor an effective DNA fingerprinting method are proposed and proceduresare described for testing the efficacy of a method. In light ofthe proposed requirements, the most common methods now being usedto DNA fingerprint the infectious fungi are described and assessed.These methods include restriction fragment length polymorphisms(RFLP), RFLP with hybridization probes, randomly amplified polymorphicDNA and other PCR-based methods, electrophoretic karyotyping,and sequencing-based methods. Procedures for computing similaritycoefficients, generating phylogenetic trees, and testing the stabilityof clusters are then described. To facilitate the analysis ofDNA fingerprinting data, computer-assisted methods are described.Finally, the problems inherent in the collection of test and controlisolates are considered, and DNA fingerprinting studies of strainmaintenance during persistent or recurrent infections, microevolutionin infecting strains, and the origin of nosocomial infectionsare assessed in light of the preceding discussion of the ins andouts of DNA fingerprinting. The intent of this review is to generatean awareness of the need to verify the efficacy of each DNA fingerprintingmethod for the level of genetic relatedness necessary to answerthe epidemiological question posed, to use quantitative methodsto analyze DNA fingerprint data, to use computer-assisted DNAfingerprint analysis systems to analyze data, and to file datain a form that can be used in the future for retrospective andcomparativestudies.

^* Mailing address: Department of Biological Sciences, University of Iowa, Iowa City, IA 52242. Phone: (319) 335-1117. Fax: (319)335-2772. E-mail: david-soll{at}uiowa.edu.

Clinical Microbiology Reviews, April 2000, p. 332-370, Vol. 13, No. 2
0893-8512/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

This article has been cited by other articles:

Fan, S R, Bai, F Y, Liao, Q P, Liu, Z H, Li, J, Liu, X P (2008). Genotype distribution of Candida albicans strains associated with different conditions of vulvovaginal candidiasis, as revealed by microsatellite typing. Sex. Transm. Infect. 84: 103-106 [Abstract] [Full Text]
Collery, M. M., Smyth, D. S., Twohig, J. M., Shore, A. C., Coleman, D. C., Smyth, C. J. (2008). Molecular typing of nasal carriage isolates of Staphylococcus aureus from an Irish university student population based on toxin gene PCR, agr locus types and multiple locus, variable number tandem repeat analysis. J Med Microbiol 57: 348-358 [Abstract] [Full Text]
McManus, B. A., Coleman, D. C., Moran, G., Pinjon, E., Diogo, D., Bougnoux, M.-E., Borecka-Melkusova, S., Bujdakova, H., Murphy, P., d'Enfert, C., Sullivan, D. J. (2008). Multilocus Sequence Typing Reveals that the Population Structure of Candida dubliniensis Is Significantly Less Divergent than That of Candida albicans. J. Clin. Microbiol. 46: 652-664 [Abstract] [Full Text]
Garcia-Hermoso, D., Cabaret, O., Lecellier, G., Desnos-Ollivier, M., Hoinard, D., Raoux, D., Costa, J.-M., 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 [Abstract] [Full Text]
Shin, J. H., Chae, M. J., Song, J. W., Jung, S.-I., Cho, D., Kee, S. J., Kim, S. H., Shin, M. G., Suh, S. P., Ryang, D. W. (2007). Changes in Karyotype and Azole Susceptibility of Sequential Bloodstream Isolates from Patients with Candida glabrata Candidemia. J. Clin. Microbiol. 45: 2385-2391 [Abstract] [Full Text]
Balajee, S. A., Tay, S. T., Lasker, B. A., Hurst, S. F., Rooney, A. P. (2007). Characterization of a Novel Gene for Strain Typing Reveals Substructuring of Aspergillus fumigatus across North America. Eukaryot Cell 6: 1392-1399 [Abstract] [Full Text]
Abdel-Rahman, S. M., Preuett, B., Gaedigk, A. (2007). Multilocus Genotyping Identifies Infections by Multiple Strains of Trichophyton tonsurans. J. Clin. Microbiol. 45: 1949-1953 [Abstract] [Full Text]
Zarnowski, R., Miyazaki, M., Dobrzyn, A., Ntambi, J. M., Woods, J. P. (2007). Typing of Histoplasma capsulatum strains by fatty acid profile analysis. J Med Microbiol 56: 788-797 [Abstract] [Full Text]
Bhardwaj, S., Sutar, R., Bachhawat, A. K., Singhi, S., Chakrabarti, A. (2007). PCR-based identification and strain typing of Pichia anomala using the ribosomal intergenic spacer region IGS1. J Med Microbiol 56: 185-189 [Abstract] [Full Text]
Odds, F. C., Davidson, A. D., Jacobsen, M. D., Tavanti, A., Whyte, J. A., Kibbler, C. C., Ellis, D. H., Maiden, M. C. J., Shaw, D. J., Gow, N. A. R. (2006). Candida albicans Strain Maintenance, Replacement, and Microvariation Demonstrated by Multilocus Sequence Typing.. J. Clin. Microbiol. 44: 3647-3658 [Abstract] [Full Text]
Jayshree, R. S., Shafiulla, M., George, J., David, J. K., Bapsy, P. P., Chakrabarti, A. (2006). Microscopic, cultural and molecular evidence of disseminated invasive aspergillosis involving the lungs and the gastrointestinal tract.. J Med Microbiol 55: 961-964 [Abstract] [Full Text]
Chen, K.-W., Chen, Y.-C., Lo, H.-J., Odds, F. C., Wang, T.-H., Lin, C.-Y., Li, S.-Y. (2006). Multilocus Sequence Typing for Analyses of Clonality of Candida albicans Strains in Taiwan.. J. Clin. Microbiol. 44: 2172-2178 [Abstract] [Full Text]
Tavanti, A., Davidson, A. D., Johnson, E. M., Maiden, M. C. J., Shaw, D. J., Gow, N. A. R., Odds, F. C. (2005). Multilocus Sequence Typing for Differentiation of Strains of Candida tropicalis. J. Clin. Microbiol. 43: 5593-5600 [Abstract] [Full Text]
Al Mosaid, A., Sullivan, D. J., Polacheck, I., Shaheen, F. A., Soliman, O., Al Hedaithy, S., Al Thawad, S., Kabadaya, M., Coleman, D. C. (2005). Novel 5-Flucytosine-Resistant Clade of Candida dubliniensis from Saudi Arabia and Egypt Identified by Cd25 Fingerprinting. J. Clin. Microbiol. 43: 4026-4036 [Abstract] [Full Text]
Sarvikivi, E., Lyytikainen, O., Soll, D. R., Pujol, C., Pfaller, M. A., Richardson, M., Koukila-Kahkola, P., Luukkainen, P., Saxen, H. (2005). Emergence of Fluconazole Resistance in a Candida parapsilosis Strain That Caused Infections in a Neonatal Intensive Care Unit. J. Clin. Microbiol. 43: 2729-2735 [Abstract] [Full Text]
Samaranayake, Y H, Dassanayake, R S, Jayatilake, J A., Cheung, B P., Yau, J Y., Yeung, K W., Samaranayake, L P (2005). Phospholipase B enzyme expression is not associated with other virulence attributes in Candida albicans isolates from patients with human immunodeficiency virus infection. J Med Microbiol 54: 583-593 [Abstract] [Full Text]
Pinjon, E., Jackson, C. J., Kelly, S. L., Sanglard, D., Moran, G., Coleman, D. C., Sullivan, D. J. (2005). Reduced Azole Susceptibility in Genotype 3 Candida dubliniensis Isolates Associated with Increased CdCDR1 and CdCDR2 Expression. Antimicrob. Agents Chemother. 49: 1312-1318 [Abstract] [Full Text]
Costa, J.-M., 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 [Abstract] [Full Text]
Oh, S.-H., Cheng, G., Nuessen, J. A., Jajko, R., Yeater, K. M., Zhao, X., Pujol, C., Soll, D. R., Hoyer, L. L. (2005). Functional specificity of Candida albicans Als3p proteins and clade specificity of ALS3 alleles discriminated by the number of copies of the tandem repeat sequence in the central domain. Microbiology 151: 673-681 [Abstract] [Full Text]
Chen, K.-W., Lo, H.-J., Lin, Y.-H., Li, S.-Y. (2005). Comparison of four molecular typing methods to assess genetic relatedness of Candida albicans clinical isolates in Taiwan. J Med Microbiol 54: 249-258 [Abstract] [Full Text]
Wu, W., Pujol, C., Lockhart, S. R., Soll, D. R. (2005). Chromosome Loss Followed by Duplication Is the Major Mechanism of Spontaneous Mating-Type Locus Homozygosis in Candida albicans. Genetics 169: 1311-1327 [Abstract] [Full Text]
Healy, M., Huong, J., Bittner, T., Lising, M., Frye, S., Raza, S., Schrock, R., Manry, J., Renwick, A., Nieto, R., Woods, C., Versalovic, J., Lupski, J. R. (2005). Microbial DNA Typing by Automated Repetitive-Sequence-Based PCR. J. Clin. Microbiol. 43: 199-207 [Abstract] [Full Text]
Tavanti, A., Pardini, G., Campa, D., Davini, P., Lupetti, A., Senesi, S. (2004). Differential Expression of Secretory Aspartyl Proteinase Genes (SAP1-10) in Oral Candida albicans Isolates with Distinct Karyotypes. J. Clin. Microbiol. 42: 4726-4734 [Abstract] [Full Text]
Moran, G., Stokes, C., Thewes, S., Hube, B., Coleman, D. C., Sullivan, D. (2004). Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis. Microbiology 150: 3363-3382 [Abstract] [Full Text]
Healy, M., Reece, K., Walton, D., Huong, J., Shah, K., Kontoyiannis, D. P. (2004). Identification to the Species Level and Differentiation between Strains of Aspergillus Clinical Isolates by Automated Repetitive-Sequence-Based PCR. J. Clin. Microbiol. 42: 4016-4024 [Abstract] [Full Text]
Pujol, C., Daniels, K. J., Lockhart, S. R., Srikantha, T., Radke, J. B., Geiger, J., Soll, D. R. (2004). The Closely Related Species Candida albicans and Candida dubliniensis Can Mate. Eukaryot Cell 3: 1015-1027 [Abstract] [Full Text]
Robles, J. C., Koreen, L., Park, S., Perlin, D. S. (2004). Multilocus Sequence Typing Is a Reliable Alternative Method to DNA Fingerprinting for Discriminating among Strains of Candida albicans. J. Clin. Microbiol. 42: 2480-2488 [Abstract] [Full Text]
Abdul Lattif, A., Banerjee, U., Prasad, R., Biswas, A., Wig, N., Sharma, N., Haque, A., Gupta, N., Baquer, N. Z., Mukhopadhyay, G. (2004). Susceptibility Pattern and Molecular Type of Species-Specific Candida in Oropharyngeal Lesions of Indian Human Immunodeficiency Virus-Positive Patients. J. Clin. Microbiol. 42: 1260-1262 [Abstract] [Full Text]
Pujol, C., Pfaller, M. A., Soll, D. R. (2004). Flucytosine Resistance Is Restricted to a Single Genetic Clade of Candida albicans. Antimicrob. Agents Chemother. 48: 262-266 [Abstract] [Full Text]
Brockert, P. J., Lachke, S. A., Srikantha, T., Pujol, C., Galask, R., Soll, D. R. (2003). Phenotypic Switching and Mating Type Switching of Candida glabrata at Sites of Colonization. Infect. Immun. 71: 7109-7118 [Abstract] [Full Text]
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. J. Clin. Microbiol. 41: 5709-5717 [Abstract] [Full Text]
Litvintseva, A. P., Marra, R. E., Nielsen, K., Heitman, J., Vilgalys, R., Mitchell, T. G. (2003). Evidence of Sexual Recombination among Cryptococcus neoformans Serotype A Isolates in Sub-Saharan Africa. Eukaryot Cell 2: 1162-1168 [Abstract] [Full Text]
Boldo, X. M., Villa-Tanaca, L., Zuniga, G., Hernandez-Rodriguez, C. (2003). Genetic Diversity among Clinical Isolates of Candida glabrata Analyzed by Randomly Amplified Polymorphic DNA and Multilocus Enzyme Electrophoresis Analyses. J. Clin. Microbiol. 41: 4799-4804 [Abstract] [Full Text]
Tavanti, A., Gow, N. A. R., Senesi, S., Maiden, M. C. J., Odds, F. C. (2003). Optimization and Validation of Multilocus Sequence Typing for Candida albicans. J. Clin. Microbiol. 41: 3765-3776 [Abstract] [Full Text]
Blignaut, E., Pujol, C., Joly, S., Soll, D. R. (2003). Racial Distribution of Candida dubliniensis Colonization among South Africans. J. Clin. Microbiol. 41: 1838-1842 [Abstract] [Full Text]
Pujol, C., Messer, S. A., Pfaller, M., Soll, D. R. (2003). Drug Resistance Is Not Directly Affected by Mating Type Locus Zygosity in Candida albicans. Antimicrob. Agents Chemother. 47: 1207-1212 [Abstract] [Full Text]
Samaranayake, Y.H., Samaranayake, L.P., Dassanayake, R.S., Yau, J.Y. Y., Tsang, W.K., Cheung, B.P. K., Yeung, K.W. S. (2003). `Genotypic shuffling' of sequential clones of Candida albicans in HIV-infected individuals with and without symptomatic oral candidiasis. J Med Microbiol 52: 349-359 [Abstract] [Full Text]
Reichart, P. A., Samaranayake, L. P., Samaranayake, Y. H., Grote, M., Pow, E., Cheung, B. (2002). High Oral Prevalence of Candida krusei in Leprosy Patients in Northern Thailand. J. Clin. Microbiol. 40: 4479-4485 [Abstract] [Full Text]
Lockhart, S. R., Pujol, C., Daniels, K. J., Miller, M. G., Johnson, A. D., Pfaller, M. A., Soll, D. R. (2002). In Candida albicans, White-Opaque Switchers Are Homozygous for Mating Type. Genetics 162: 737-745 [Abstract] [Full Text]
Pujol, C., Pfaller, M., Soll, D. R. (2002). Ca3 Fingerprinting of Candida albicans Bloodstream Isolates from the United States, Canada, South America, and Europe Reveals a European Clade. J. Clin. Microbiol. 40: 2729-2740 [Abstract] [Full Text]
Lasker, B. A. (2002). Evaluation of Performance of Four Genotypic Methods for Studying the Genetic Epidemiology of Aspergillus fumigatus Isolates. J. Clin. Microbiol. 40: 2886-2892 [Abstract] [Full Text]
Fisher, M. C., Rannala, B., Chaturvedi, V., Taylor, J. W. (2002). Disease surveillance in recombining pathogens: Multilocus genotypes identify sources of human Coccidioides infections. Proc. Natl. Acad. Sci. USA 99: 9067-9071 [Abstract] [Full Text]
Blignaut, E., Pujol, C., Lockhart, S., Joly, S., Soll, D. R. (2002). Ca3 Fingerprinting of Candida albicans Isolates from Human Immunodeficiency Virus-Positive and Healthy Individuals Reveals a New Clade in South Africa. J. Clin. Microbiol. 40: 826-836 [Abstract] [Full Text]
Vargas, K. G., Joly, S. (2002). Carriage Frequency, Intensity of Carriage, and Strains of Oral Yeast Species Vary in the Progression to Oral Candidiasis in Human Immunodeficiency Virus-Positive Individuals. J. Clin. Microbiol. 40: 341-350 [Abstract] [Full Text]
Gee, S. F., Joly, S., Soll, D. R., Meis, J. F. G. M., Verweij, P. E., Polacheck, I., Sullivan, D. J., Coleman, D. C. (2002). Identification of Four Distinct Genotypes of Candida dubliniensis and Detection of Microevolution In Vitro and In Vivo. J. Clin. Microbiol. 40: 556-574 [Abstract] [Full Text]
Muniz, M. d. M., Pizzini, C. V., Peralta, J. M., Reiss, E., Zancope-Oliveira, R. M. (2001). Genetic Diversity of Histoplasma capsulatum Strains Isolated from Soil, Animals, and Clinical Specimens in Rio de Janeiro State, Brazil, by a PCR-Based Random Amplified Polymorphic DNA Assay. J. Clin. Microbiol. 39: 4487-4494 [Abstract] [Full Text]
Trewatcharegon, S., Sirisinha, S., Romsai, A., Eampokalap, B., Teanpaisan, R., Chaiyaroj, S. C. (2001). Molecular Typing of Penicillium marneffei Isolates from Thailand by NotI Macrorestriction and Pulsed-Field Gel Electrophoresis. J. Clin. Microbiol. 39: 4544-4548 [Abstract] [Full Text]
Bartie, K. L., Williams, D. W., Wilson, M. J., Potts, A. J. C., Lewis, M. A. O. (2001). PCR Fingerprinting of Candida albicans Associated with Chronic Hyperplastic Candidosis and Other Oral Conditions. J. Clin. Microbiol. 39: 4066-4075 [Abstract] [Full Text]
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 [Abstract] [Full Text]
Helweg-Larsen, J., Lundgren, B., Lundgren, J. D. (2001). Heterogeneity and Compartmentalization of Pneumocystis carinii f. sp. hominis Genotypes in Autopsy Lungs. J. Clin. Microbiol. 39: 3789-3792 [Abstract] [Full Text]
Shemer, R., Weissman, Z., Hashman, N., Kornitzer, D. (2001). A highly polymorphic degenerate microsatellite for molecular strain typing of Candida krusei. Microbiology 147: 2021-2028 [Abstract] [Full Text]
Garcia-Hermoso, D., Dromer, F., Mathoulin-Pelissier, S., Janbon, G. (2001). Are Two Cryptococcus neoformans Strains Epidemiologically Linked?. J. Clin. Microbiol. 39: 1402-1406 [Abstract] [Full Text]
Dannaoui, E., Borel, E., Monier, M.-F., Piens, M.-A., Picot, S., Persat, F. (2001). Acquired itraconazole resistance in Aspergillus fumigatus. J Antimicrob Chemother 47: 333-340 [Abstract] [Full Text]
Enger, L., Joly, S., Pujol, C., Simonson, P., Pfaller, M., Soll, D. R. (2001). Cloning and Characterization of a Complex DNA Fingerprinting Probe for Candida parapsilosis. J. Clin. Microbiol. 39: 658-669 [Abstract] [Full Text]
Marr, K. A., Lyons, C. N., Ha, K., Rustad, T. R., White, T. C. (2001). Inducible Azole Resistance Associated with a Heterogeneous Phenotype in Candida albicans. Antimicrob. Agents Chemother. 45: 52-59 [Abstract] [Full Text]
Vargas, K., Messer, S. A., Pfaller, M., Lockhart, S. R., Stapleton, J. T., Hellstein, J., Soll, D. R. (2000). Elevated Phenotypic Switching and Drug Resistance of Candida albicans from Human Immunodeficiency Virus-Positive Individuals prior to First Thrush Episode. J. Clin. Microbiol. 38: 3595-3607 [Abstract] [Full Text]

Antimicrob. Agents Chemother.	Clin. Vaccine Immunol.
J. Clin. Microbiol.	ALL ASM JOURNALS