Molecular techniques for the evaluation of fungi have shown rapid advances since the
mid-1990s. Nucleic acid assays have been used in studies involving phylogenetics,
epidemiologic typing, gene expression regulation, culture identification, and direct
detection and identification from clinical material. In the clinical mycology laboratory,
a critical need exists for the development of rapid detection and identification methods
that can be applied directly to clinical specimens. This need comes from the inability
of current laboratory tests to provide a timely result and from the fact that fungal
infections in immunocompromised patients usually appear suddenly, progress rapidly,
and often are fatal unless treatment is started earlier in the course of infection.
This article provides information on some of the basic molecular mycology assays used
in clinical mycology research for diagnostic and epidemiologic typing purposes. For
generalized reviews on the subject of molecular mycology, please refer to the articles
by Mitchell et al [
[1]
], Hopfer [
[2]
], Reiss et al [
3
,
4
], and Walsh and Chanock [
[5]
].To read this article in full you will need to make a payment
Purchase one-time access:
Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online accessOne-time access price info
- For academic or personal research use, select 'Academic and Personal'
- For corporate R&D use, select 'Corporate R&D Professionals'
Subscribers receive full online access to your subscription and archive of back issues up to and including 2002.
Content published before 2002 is available via pay-per-view purchase only.
Subscribe:
Subscribe to Clinics in Laboratory MedicineAlready a print subscriber? Claim online access
Already an online subscriber? Sign in
Register: Create an account
Institutional Access: Sign in to ScienceDirect
References
- Molecular mycology: DNA probes and applications of PCR technology.J Med Vet Mycol. 1994; 32: 351-366
- Contemporary techniques for molecular diagnoses of mycoses.Clin Microbiol News. 1997; 19: 169-176
- Non-culture based diagnostic tests for mycotic infections.Med Mycol. 2000; 38: 147-159
- Molecular diagnosis and epidemiology of fungal infections.Med Mycol. 1998; 36: 249-257
- Diagnosis of invasive fungal infections: advances in nonculture systems.Curr Clin Top Infect Dis. 1998; 18: 101-153
- Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens.Med Mycol. 2002; 40: 87-109
- Evaluation of a chemiluminescent probe assay for identification of Histoplasma capsulatum isolates.J Clin Microbiol. 1992; 30: 3003-3004
- Comparative evaluation of chemiluminescent DNA probe assays and exoantigen tests for rapid identification of Blastomyces dermatitidis and Coccidioides immitis.J Clin Microbiol. 1994; 32: 867-870
- Evaluation of commercially available acridinium esther-labeled chemiluminescent DNA probes for culture identification of Blastomyces dermatitidis, Coccidioides immitis, Cryptococcus neoformans, and Histoplasma capsulatum.J Clin Microbiol. 1993; 31: 845-850
- Rapid diagnosis of Histoplasma capsulatum endocarditis using the AccuProbe on an excised valve.J Clin Microbiol. 2001; 39: 2640-2641
- Complete nucleotide sequence of Candida albicans 5.8S rRNA coding gene and flanking internal transcribed spacers.Nucleic Acids Res. 1993; 21: 4640
- Nucleotide sequence analysis of the 5.8S rDNA and adjacent ITS2 region of Candida albicans and related species.Yeast. 1993; 9: 1199-1206
- Identification of medically important yeasts using PCR-based detection of DNA sequence polymorphisms in the internal transcribed spacer 2 region of the rRNA gens.J Clin Microbiol. 2000; 38: 2302-2310
- Specific identification of Candida albicans by hybridization with digonucleotides derived from ribosomal DNA internal spacers.Yeast. 1994; 10: 709-717
- Geographic grouping of Cryptococcus neoformans var gcottii by random amplified polymorphic DNA fingerprint patterns and ITS sequence divergence.Clin Lab. 2000; 46: 345-354
- Analysis of the internal transcribed spacer regions of ribosomal DNA in common airborne allergenic fungi.Electrophoresis. 1997; 18: 1567-1569
- Rapid identification of up to three Candida species in a single reaction tube by a 5′ endonuclease assay using fluorescent DNA probes.J Clin Microbiol. 1999; 37: 165-170
- Rapid identification of Candida species with species-specific DNA probes.J Clin Microbiol. 1998; 36: 3260-3265
Hinrikson HP, Hurst SF, Lott TJ, Warnock DW, Morrison CJ. Molecular identification of medically important Aspergillus species. General Meeting of the American Society for Microbiology. May 21–25, 2000. Salt Lake City, Utah.
- Genetic diversity and biochemical characteristics of Trichosporon asahii isolated from clinical specimens, houses of patients with summer-type-hypersensitivity pneumonitis, and environmental materials.J Clin Microbiol. 2001; 39: 2405-2411
- Molecular identification of Paracoccidioides brasiliensis by PCR amplification of ribosomal DNA.J Clin Microbiol. 2000; 38: 3106-3109
- Design of a primer for ribosomal DNA internal transcribed spacer with enhanced specificity for ascomycetes.J Biotechnol. 1999; 75: 187-194
- PCR-ribotyping of type isolates of currently accepted Exophiala and Phaeococcomyces species.Antonie van Leeuwenhock. 1995; 68: 35-42
- rDNA-RFLP and ITS 1 sequencing of species of the genus Fonsecaea, agents of chromoblastomycosis.Med Mycol. 1998; 36: 219-225
- Molecular differentiation of seven Malassezia species.J Clin Microbiol. 2000; 38: 1869-1875
- Intergenic transcribed spacer PCR ribotyping for differentiation of Saccharomyces species and interspecific hybrids.J Clin Microbiol. 1998; 36: 1035-1038
- Identification of Candida species by PCR and restriction fragment length polymorphism analysis of intergenic spacer regions of ribosomal DNA.J Clin Microbiol. 1995; 33: 2476-2479
- Species identification and strain differentiation of dermatophyte fungi by analysis of ribosomal-DNA intergenic spacer regions.J Clin Microbiol. 1999; 37: 931-936
- Simple and rapid detection of Candida albicans DNA in serum by PCR for diagnosis of invasive candidiasis.J Clin Microbiol. 2000; 38: 3016-3021
- Detection and identification of fungal pathogens in blood by using molecular probes.J Clin Microbiol. 1997; 35: 1353-1360
- General primer-mediated PCR for the detection of Aspergillus species.J Clin Microbiol. 1994; 32: 1710-1717
- Prediction of invasive pulmonary aspergillosis from colonisation of lower respiratory tract before marrow transplantation.Lancet. 1998; 352: 1443-1446
- Development of an oligonucleotide probe specific for Trichophyton rubrum.Br J Dermatol. 1999; 141: 240-245
- Fast, simple and highly sensitive double-rounded polymerase chain reaction assay to detect medically relevant fungi in dermatological specimens.Eur J Clin Invest. 2000; 30: 511-518
- Aspergillus endocarditis in a leukemia patient diagnosed by a PCR assay.Kansenshogaku Zasshi. 1997; 32: 269-272
- Pre-AIDS era isolates of Pneumocystis carinii f. sp. hominis: high genotypic similarity with contemporary isolates.J Clin Microbiol. 1998; 36: 90-93
- Panfungal PCR and multiplex liquid hybridization for detection of fungi in tissue specimens.J Clin Microbiol. 2000; 38: 4186-4192
- Rapid identification of yeasts in positive blood cultures by a multiplex PCR method.J Clin Microbiol. 2001; 10: 3466-3471
- Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics.in: Innis M.A. Gelfland D.H. Sninsky J.J. White T.J. PCR protocols. A guide to methods and applications. Academic Press, Inc, San Diego1990: 315-322
- Multiplex PCR using internal transcribed spacer 1 and 2 regions for rapid detection and identification of yeast strains.J Clin Microbiol. 2001; 39: 3617-3622
- Specific detection of Aspergillus species in blood and bronchoalveolar lavage samples of immunocompromised patients by two-step PCR.J Clin Microbiol. 1999; 37: 3865-3871
- Detection and identification of fungal pathogens by PCR and by ITS2 and 5.8S ribosomal DNA typing in ocular infections.J Clin Microbiol. 2001; 39: 2873-2879
- A single-tube nested PCR for Pneumocystis carinii f. sp. hominis.J Clin Microbiol. 1997; 35: 1597-1599
- Serum is more suitable than whole blood for diagnosis of systemic candidiasis by nested PCR.J Clin Microbiol. 1999; 37: 925-930
- Evaluation of two nested PCR assays for detection of Histoplasma capsulatum DNA in human tissue.J Clin Microbiol. 2002; 40: 1644-1647
- Rapid cycle real-time PCR: a revolution of clinical microbiology.ASM News. 2002; 68: 77-83
- Rapid identification of Candida species by TaqMan PCR.J Clin Pathol. 2001; 54: 362-366
- Quantification of fungal DNA by using fluorescence resonance energy transfer and the light cycler system.J Clin Microbiol. 2000; 38: 586-590
- Development and evaluation of a quantitative, touch-down, real-time PCR assay for diagnosing Pneumocystis carinii pneumonia.J Clin Microbiol. 2002; 40: 490-494
- Development of two real-time quantitative TaqMan PCR assays to detect circulating Aspergillus fumigatus DNA in serum.J Microbiol Methods. 2001; 44: 263-269
- The evolutionary biology and population genetics underlying fungal strain typing.Clin Microbiol Rev. 1999; 12: 126-146
- Electrophoretic karyotype analysis of sequential Candida parapsilosis isolates from patients with persistent or recurrent fungemia.J Clin Microbiol. 2001; 39: 1258-1263
- Comparison of four methods for DNA typing of clinical isolates of Candida glabrata.J Med Microbiol. 1999; 48: 955-963
- Chromosome length polymorphisms in fungi.Microbiol Rev. 1995; 59: 686-698
- Study of the authenticity of commercial wine yeast strains by molecular techniques.Int J Food Microbiol. 2001; 70: 1-10
- Rapid identification and fingerprinting of Candida krusei by PCR-based amplification of the species-specific repetitive polymorphic sequence CKRS-1.J Clin Microbiol. 1997; 35: 1337-1343
- Rapid discrimination among dermatophytes, Scytalidium spp, and other fungi with a PCR-restriction fragment length polymorphism ribotyping method.J Clin Microbiol. 2001; 39: 685-690
- Strain identification of Trichophyton rubrum by specific amplification of subrepeat elements in the ribosomal DNA nontranscribed spacer.J Clin Microbiol. 2000; 38: 4527-4534
- DNA polymorphism amplified by arbitrary primers are useful as genetic markers.Nucleic Acids Res. 1990; 18: 6531-6535
- Comparison of four DNA-based methods for strain delineation of Candida lusitaniae.J Clin Microbiol. 1995; 33: 1467-1470
- Comparison of three typing methods for clinical and environmental isolates of Aspergillus fumigatus.J Clin Microbiol. 1995; 33: 1596-1601
- Genetic diversity of Histoplasma capsulatum strains isolated from soil, animal, and clinical specimens in Rio de Janeiro state, Brazil, by a PCR-based random amplified polymorphic DNA assay.J Clin Microbiol. 2001; 39: 4487-4494
- Differentiation of Aspergillus ustus strains by random amplification of polymorphic DNA.J Clin Microbiol. 2002; 40: 2231-2233
- Typing of Pneumocystis carinii strains that infect humans based on nucleotide sequence variations of internal transcribed spacers of rRNA gene.J Clin Microbiol. 1994; 32: 2904-2912
- Biodiversity of Pneumocystis carinii hominis: typing with different DNA regions.J Clin Microbiol. 1997; 35: 383-387
- Typing with internal transcribed spacer regions of Pneumocystis carinii from AIDS patients with recurrent pneumonia.Res Microbiol. 1998; 149: 595-599
- Typing of Histoplasma capsulatum isolates based on nucleotide sequence variation in the internal transcribed spacer regions of rRNA genes.J Clin Microbiol. 2000; 38: 241-245
Iwen PC, Henry T, Lodes AR, Hinrichs SH. Culture identification of Histoplasma capsulatum using the rDNA internal transcribed spacer regions 1 and 2 as a molecular target. In: Microbiology ASF, ed. 100th General Meeting of the American Society for Microbiology. May 21–25, 2002: Los Angeles.
- Three distinct genotypes within Candida parapsilosis from clinical sources.J Clin Microbiol. 1995; 33: 1815-1821
- Identification of four distint genotypes of Candida dubliniensis and detection of microevolution in vitro and in vivo.J Clin Microbiol. 2002; 40: 556-574
- Genetic diversity of Pneumocystis carinii f. sp. hominis based on variations in nucleotide sequences of internal transcribed spacers of rRNA genes.J Clin Microbiol. 2002; 40: 1146-1151
- Polymerase chain reaction for the diagnosis of candidemia.J Infect Dis. 1993; 168: 779-783
- Quantification of Candida albicans actin mRNA by the LightCycler system as a means of assessing viability in a model of cutaneous candidiasis.J Clin Microbiol. 2001; 39: 3491-3494
- The alkaline protease of Aspergillus fumigatus is not a virulence determinate in two murine models of invasive pulmonary aspergillosis.Infect Immun. 1993; 61: 1650-1656
- Phylogenetic relation of Epidermophyton floccosum to the species of Microsporum and Trichophyton in chitin synthase 1 (CHS1) gene sequences.Mycopathologia. 1999; 146: 111-113
- Typing of Candida albicans isolates by sequence analysis of the cytochrome b gene and differentiation from Candida stellatoidea.J Clin Microbiol. 2001; 39: 1600-1603
- Application of DNA amplification to pneumocystosis: presence of serum Pneumocystis carinii DNA during human and experimentally induced Pneumocystis carinii pneumonia.J Exp Med. 1992; 176: 1327-1333
- Application of the polymerase chain reaction to the diagnosis of candidiosis by amplification of an HSP 90 gene fragment.J Med Microbiol. 1993; 39: 233-238
- Specific amplification of Aspergillus fumigatus DNA by polymerase chain reaction.Mol Cell Probes. 1993; 7: 121-126
- Detection of Aspergillus species DNA in bronchoalveolar lavage samples by competitive PCR.J Clin Microbiol. 1995; 33: 1164-1168
- DNA amplification on induced sputum samples for diagnosis of Pneumocystis carinii pneumonia.Lancet. 1991; 337: 1378-1379
- Detection of Candida albicans DNA in cerebrospinal fluid.J Med Vet Mycol. 1993; 31: 353-358
- Detection of Pneumocystis carinii DNA in sputum and bronchoalveolar lavage samples by polymerase chain reaction.J Clin Microbiol. 1993; 31: 221-226
- Detection of Candida albicans and other yeasts in blood by PCR.J Clin Microbiol. 1994; 32: 228-231
- Diagnosis of Pneumocystis carinii pneumonia by 5S ribosomal DNA amplification.J Protozool. 1991; 38: 90S-91S
- Polymerase chain reaction as a diagnostic tool for invasive aspergillosis: evaluation in bronchoalveolar lavage fluid from low risk patients.Serodiagn Immunother Infect Dis. 1994; 6: 203-208
- PCR for detection and differentiation of various fungal pathogens in blood samples.J Clin Microbiol. 1997; 35: 1353-1360
- Universal fungus-specific primer systems and group-specific hybridization oligonucleotides for 18S rDNA.Mycoses. 1996; 39: 25-30
- Detection of Aspergillus fumigatus by polymerase chain reaction.J Clin Microbiol. 1993; 31 ([published erratum appears in J Clin Microbiol 1994;32(8):2039]): 615-621
- Rapid identification of Candida albicans and other human pathogenic yeasts by using short oligonucleotides in a PCR.J Clin Microbiol. 1998; 36: 1634-1641
- Molecular epidemiological study of Aspergillus fumigatus in a bone marrow transplantation unit by PCR amplification of ribosomal intergenic spacer sequences.J Clin Microbiol. 1998; 36: 1294-1299
- Sequence analysis of the ribosomal DNA intergenic spacer 1 regions of Trichosporon species.J Clin Microbiol. 2002; 40: 1826-1830
- Evaluation of PCR for detection of DNA specific for Aspergillus species in sera of patients with various forms of pulmonary aspergillosis.J Clin Microbiol. 1998; 36: 3619-3623
- Rapid detection and identification of Candida, Aspergillus, and Fusarium species in ocular samples using nested PCR.J Clin Microbiol. 2000; 38: 2902-2908
- Diagnosis and monitoring of murine histoplasmosis by a nested PCR assay.J Clin Microbiol. 2001; 39: 1506-1509
- Direct detection of Histoplasma capsulatum in soil suspensions by two-stage PCR.Mol Cell Probes. 1999; 13: 269-273
- Molecular analysis of Malassezia microflora on the skin of atopic dermatitis patients and healthy subjects.J Clin Microbiol. 2001; 39: 3486-3490
- Detection of Paracoccidioides brasiliensis in tissue samples by a nested PCR assay.J Clin Microbiol. 2000; 38: 2940-2942
- Ribosomal genes of Histoplasma capsulatum var. duboisii and var. farciminosum.Mycoses. 1998; 41: 355-362
- Species identification and strain typing of Malassezia species stock strains and clinical isolates based on the DNA sequences of nuclear ribosomal internal transcribed spacer 1 regions.J Med Microbiol. 2000; 49: 29-35
- Update on Pneumocystis carinii f. sp. hominis typing based on nucleotide sequence variations in internal transcribed spacer regions of rRNA genes.J Clin Microbiol. 1998; 36: 734-741
- Heterogeneity and compartmentalization of Pneumocystis carinii f. sp. hominis genotypes in autopsy lungs.J Clin Microbiol. 2001; 39: 3789-3792
Article info
Identification
Copyright
© 2003 Elsevier Inc. Published by Elsevier Inc. All rights reserved.
