The development and validation of a rapid genetic method for species identification and genotyping of medically important fungal pathogens using high-resolution melting curve analysis

Molecular Oral Microbiology

Volumn 29, Issue 3, 2014, Pages 117-130

  Alnuaimi, A D ^a   Wiesenfeld, D ^a,b   O'Brien Simpson, N M ^a   Reynolds, E C ^a   Peng, B ^a   Mccullough, M J ^a  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b ROYAL MELBOURNE HOSPITAL   (Australia)

Author keywords

Candida albicans; Candida genotyping; High resolution melting curve analysis; Rapid identification

Indexed keywords

GENOMIC DNA; INTERNAL TRANSCRIBED SPACER 1; INTERNAL TRANSCRIBED SPACER 2; RIBOSOME DNA; FUNGAL DNA;

AGAR GEL ELECTROPHORESIS; AMPLICON; ARTICLE; CANDIDA; CANDIDA ALBICANS; CANDIDA DUBLINIENSIS; CANDIDA GLABRATA; CANDIDA KRUSEI; CANDIDA PARAPSILOSIS; CANDIDA TROPICALIS; CLAVISPORA LUSITANIAE; CONTROLLED STUDY; DNA SEQUENCE; FEASIBILITY STUDY; FUNGAL STRAIN; FUNGUS IDENTIFICATION; GENETIC ANALYSIS; GENOTYPE; HIGH RESOLUTION MELTING ANALYSIS; INTERMETHOD COMPARISON; INTRON; NONHUMAN; PICHIA GUILLIERMONDII; REAL TIME POLYMERASE CHAIN REACTION; SPECIES DIFFERENTIATION; SPECIES IDENTIFICATION; VALIDATION STUDY; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; DNA DENATURATION; GENETICS; HUMAN; SPECIES DIFFERENCE;

CANDIDA; DNA, FUNGAL; DNA, RIBOSOMAL; FEASIBILITY STUDIES; GENOTYPE; HUMANS; NUCLEIC ACID DENATURATION; REAL-TIME POLYMERASE CHAIN REACTION; SPECIES SPECIFICITY;

EID: 84899481615     PISSN: 20411006     EISSN: 20411014     Source Type: Journal    
DOI: 10.1111/omi.12050     Document Type: Article

References (47)

1. Alnuaimi, A.D., O'Brien-Simpson, N.M., Reynolds, E.C. and McCullough, M.J. (2013) Clinical isolates and laboratory reference Candida species and strains have varying abilities to form biofilms. FEMS Yeast Res 13: 689-699.
2. Arancia, S., Sandini, S., De Bernardis, F. and Fortini, D. (2011) Rapid, simple, and low-cost identification of Candida species using high-resolution melting analysis. Digno Microbiol Infect Dis 69: 283-285.
3. Belazi, M., Velegraki, A., Koussidou-Eremondi, T. et al. (2004) Oral Candida isolates in patients undergoing radiotherapy for head and neck cancer: prevalence, azole susceptibility profiles and response to antifungal treatment. Oral Microbiol Immunol 19: 347-351.
4. Borman, A.M., Petch, R., Linton, C.J., Palmer, M.D., Bridge, P.D. and Johnson, E.M. (2008) Candida nivariensis, an emerging pathogenic fungus with multidrug resistance to antifungal agents. J Clin Microbiol 46: 933-938.
5. Bougnoux, M.E., Aanensen, D.M., Morand, S., Theraud, M., Spratt, B.G. and d'Enfert, C. (2004) Multilocus sequence typing of Candida albicans: strategies, data exchange and applications. Infect Genet Evol 4: 243-252.
6. Cannon, R.D. and Chaffin, W.L. (1999) Oral colonization by Candida albicans. Crit Rev Oral Biol Med 10: 359-383.
7. Carvalho, A., Costa-De-Oliveira, S., Martins, M.L. et al. (2007) Multiplex PCR identification of eight clinically relevant Candida species. Med Mycol 45: 619-627.
8. Cheng, J.C., Huang, C.L., Lin, C.C. et al. (2006) Rapid detection and identification of clinically important bacteria by high-resolution melting analysis after broad-range ribosomal RNA real-time PCR. Clin Chem 52: 1997-2004.
9. Ciardo, D.E., Schar, G., Bottger, E.C., Altwegg, M. and Bosshard, P.P. (2006) Internal transcribed spacer sequencing versus biochemical profiling for identification of medically important yeasts. J Clin Microbiol 44: 77-84.
10. Clark, A.E., Kaleta, E.J., Arora, A. and Wolk, D.M. (2013) Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev 26: 547-603.
11. Decat, E., Van Mechelen, E., Saerens, B. et al. (2013) Rapid and accurate identification of isolates of Candida species by melting peak and melting curve analysis of the internally transcribed spacer region 2 fragment (ITS2-MCA). Res Microbiol 164: 110-117.
12. Dhiman, N., Hall, L., Wohlfiel, S.L., Buckwalter, S.P. and Wengenack, N.L. (2011) Performance and cost analysis of matrix-assisted laser desorption ionization-time of flight mass spectrometry for routine identification of yeast. J Clin Microbiol 49: 1614-1616.
13. Do, H., Krypuy, M., Mitchell, P.L., Fox, S.B. and Dobrovic, A. (2008) High resolution melting analysis for rapid and sensitive EGFR and KRAS mutation detection in formalin fixed paraffin embedded biopsies. BMC Cancer 8: 142.
14. Ellepola, A.N., Hurst, S.F., Elie, C.M. and Morrison, C.J. (2003) Rapid and unequivocal differentiation of Candida dubliniensis from other Candida species using species-specific DNA probes: comparison with phenotypic identification methods. Oral Microbiol Immunol 18: 379-388.
15. Fenn, J.P., Segal, H., Barland, B. et al. (1994) Comparison of updated Vitek yeast biochemical card and API 20C yeast identification systems. J Clin Microbiol 32: 1184-1187.
16. Gammelsrud, K.W., Lindstad, B.L., Gaustad, P. et al. (2012) Multilocus sequence typing of serial Candida albicans isolates from children with cancer, children with cystic fibrosis and healthy controls. Med Mycol 50: 619-626.
17. Hamprecht, A., Christ, S., Oestreicher, T., Plum, G., Kempf, V.A. and Göttig, S.. 2013. Performance of two MALDI-TOF MS systems for the identification of yeasts isolated from bloodstream infections and cerebrospinal fluids using a time-saving direct transfer protocol. Med Microbiol Immunol 203: 93-99.
18. Jeffery, N., Gasser, R.B., Steer, P.A. and Noormohammadi, A.H. (2007) Classification of Mycoplasma synoviae strains using single-strand conformation polymorphism and high-resolution melting-curve analysis of the vlhA gene single-copy region. Microbiology 153: 2679-2688.
19. Kao, A.S., Brandt, M.E., Pruitt, W.R. et al. (1999) The epidemiology of candidemia in two United States cities: results of a population-based active surveillance. Clin Infect Dis 29: 1164-1170.
20. Krypuy, M., Newnham, G.M., Thomas, D.M., Conron, M. and Dobrovic, A. (2006) High resolution melting analysis for the rapid and sensitive detection of mutations in clinical samples: KRAS codon 12 and 13 mutations in non-small cell lung cancer. BMC Cancer 6: 295.
21. Leaw, S.N., Chang, H.C., Sun, H.F., Barton, R., Bouchara, J.P. and Chang, T.C. (2006) Identification of medically important yeast species by sequence analysis of the internal transcribed spacer regions. J Clin Microbiol 44: 693-699.
22. Li, L., Redding, S. and Dongari-Bagtzoglou, A. (2007) Candida glabrata: an emerging oral opportunistic pathogen. J Dent Res 86: 204-215.
23. Liew, M., Pryor, R., Palais, R. et al. (2004) Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons. Clin Chem 50: 1156-1164.
24. Lin, J.H., Tseng, C.P., Chen, Y.J. et al. (2008) Rapid differentiation of influenza A virus subtypes and genetic screening for virus variants by high-resolution melting analysis. J Clin Microbiol 46: 1090-1097.
25. Lockhart, S.R., Messer, S.A., Gherna, M. et al. (2009) Identification of Candida nivariensis and Candida bracarensis in a large global collection of Candida glabrata isolates: comparison to the literature. J Clin Microbiol 47: 1216-1217.
26. Mandviwala, T., Shinde, R., Kalra, A., Sobel, J.D. and Akins, R.A. (2010) High-throughput identification and quantification of Candida species using high resolution derivative melt analysis of panfungal amplicons. J Mol Diagn 12: 91-101.
27. McCullough, M.J. and Savage, N.W. (2005) Oral candidosis and the therapeutic use of antifungal agents in dentistry. Aust Dent J 50 (4 Suppl. 2): S36-S39.
28. McCullough, M.J., Clemons, K.V. and Stevens, D.A. (1999) Molecular and phenotypic characterization of genotypic Candida albicans subgroups and comparison with Candida dubliniensis and Candida stellatoidea. J Clin Microbiol 37: 417-421.
29. Neppelenbroek, K., Seo, R., Urban, V. et al. 2013. Identification of Candida species in the clinical laboratory: a review of conventional, commercial, and molecular techniques. Oral Dis 20: 329-344.
30. Odds, F.C. (1988) In Candida and Candidosis-A Review and Bibliography, 2nd edn. London: Bailliere Tindall.
31. Odds, F.C. and Bernaerts, R. (1994) CHROMagar Candida, a new differential isolation medium for presumptive identification of clinically important Candida species. J Clin Microbiol 32: 1923-1929.
32. Pfaller, M.A. (1995) Epidemiology of fungal infections: the promise of molecular typing. Clin Infect Dis 20: 1535-1539.
33. Pfaller, M.A. (1996) Nosocomial candidiasis: emerging species, reservoirs, and modes of transmission. Clin Infect Dis 22(Suppl. 2): S89-S94.
34. Price, E.P., Smith, H., Huygens, F. and Giffard, P.M. (2007) High-resolution DNA melt curve analysis of the clustered, regularly interspaced short-palindromic-repeat locus of Campylobacter jejuni. Appl Environ Microbiol 73: 3431-3436.
35. Rasmussen, J.P., Saint, C.P. and Monis, P.T. (2007) Use of DNA melting simulation software for in silico diagnostic assay design: targeting regions with complex melting curves and confirmation by real-time PCR using intercalating dyes. BMC Bioinformatics 8: 107.
36. Rautemaa, R., Rusanen, P., Richardson, M. and Meurman, J.H. (2006) Optimal sampling site for mucosal candidosis in oral cancer patients is the labial sulcus. J Med Microbiol 55: 1447-1451.
37. Reed, G.H., Kent, J.O. and Wittwer, C.T. (2007) High-resolution DNA melting analysis for simple and efficient molecular diagnostics. Pharmacogenomics 8: 597-608.
38. Richardson, M.D. and Warnock, D.W. (2003) In Fungal Infections: Diagnosis and Management, 3rd edn. Oxford: Blackwell Publishing.
39. Steer, P.A., Kirkpatrick, N.C., O'Rourke, D. and Noormohammadi, A.H. (2009) Classification of fowl adenovirus serotypes by use of high-resolution melting-curve analysis of the hexon gene region. J Clin Microbiol 47: 311-321.
40. Stevens, D.A., Odds, F.C. and Scherer, S. 1990. Application of DNA typing methods to Candida albicans epidemiology and correlations with phenotype. Rev Infect Dis 12, 258-266.
41. Sullivan, D.J. and Coleman, D.C. 2002. Molecular approaches to identification and typing of Candida species. In: Calderone R.A. ed. Candida and Candidiasis. Washington, DC: American Society for Microbiology (ASM) Press, pp. 427-441.
42. Sullivan, D.J., Westerneng, T.J., Haynes, K.A., Bennett, D.E. and Coleman, D.C. (1995) Candida dubliniensis sp. nov.: phenotypic and molecular characterization of a novel species associated with oral candidosis in HIV-infected individuals. Microbiology 141: 1507-1521.
43. Trost, A., Graf, B., Eucker, J. et al. (2004) Identification of clinically relevant yeasts by PCR/RFLP. J Microbiol Methods 56: 201-211.
44. Williams, D.W., Wilson, M.J., Lewis, M.A. and Potts, A.J. (1995) Identification of Candida species by PCR and restriction fragment length polymorphism analysis of intergenic spacer regions of ribosomal DNA. J Clin Microbiol 33: 2476-2479.
45. Wilson, M.J., Williams, D.W., Forbes, M.D., Finlay, I.G. and Lewis, M.A. (2001) A molecular epidemiological study of sequential oral isolates of Candida albicans from terminally ill patients. J Oral Pathol Med 30: 206-212.
46. Wittwer, C.T. (2009) High-resolution DNA melting analysis: advancements and limitations. Hum Mutat 30: 857-859.
47. Wittwer, C.T., Reed, G.H., Gundry, C.N., Vandersteen, J.G. and Pryor, R.J.. (2003) High-resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem 49: 853-860.