High-throughput detection of pathogenic yeasts of the genus Trichosporon

Journal of Clinical Microbiology

Volumn 42, Issue 8, 2004, Pages 3696-3706

  Diaz, Mara R ^a   Fell, Jack W ^a  

^a UNIVERSITY OF MIAMI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA;

AMPLICON; ARTICLE; DIAGNOSTIC ACCURACY; DNA HYBRIDIZATION; DNA TRANSCRIPTION; FLOW CYTOMETRY; FLUORESCENCE; FUNGAL DETECTION; FUNGAL VIRULENCE; GENE AMPLIFICATION; HIGH THROUGHPUT SCREENING; LASER; MYCOSIS; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; TRICHOSPORON; VALIDATION PROCESS; YEAST;

ANIMALS; BASE SEQUENCE; CELLS, CULTURED; DNA PRIMERS; DNA, FUNGAL; HUMANS; MYCOSES; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; POLYMERASE CHAIN REACTION; TRICHOSPORON;

EID: 3843096144     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.42.8.3696-3706.2004     Document Type: Article

References (38)

1. Abd-Elsalam, K. A., N. Ibrahim, M. A. Abdel-Satar, M. S. Khalil, and J. A. Verreett. 2003. PCR identification of Fusarium genus based on nuclear ribosomal-DNA sequence data. Afr. J. Biotechnol. 2:82-85.
2. Abou-ela, F., D. Koh, I. Tinoco, Jr., and F. J. Martin. 1985. Base-base mistmatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,T). Nucleic Acids Res. 13:3944-3948.
3. Armstrong, B., M. Stewart, and A. Mazumder. 2000. Suspension arrays for high throughput multiplexed single nucleotide polymorphism genotyping. Cytometry 40:102-108.
4. Diaz, M. R., J. W. Fell, T. Boekhout, and B. Theelen. 2000. Molecular sequence analyses of the intergenic spacer (IGS) associated with rDNA of the two varieties of the pathogenic yeast, Cryptococcus neoformans. Syst. Appl. Microbiol. 23:535-545.
5. Dunbar, S. A., C. A. Vander Zee, K. G. Oliver, K. L. Karem, and J. W. Jacobson. 2003. Quantitative, multiplexed detection of bacterial pathogens: DNA and protein applications of the Luminex LabMap system. J. Microbiol. Methods 53:245-252.
6. Fell, J. W. 1995. rDNA targeted oligonucleotide primers for the identification of pathogenic yeasts in a polymerase chain reaction. J. Ind. Microbiol. 14:475-477.
7. Fell, J. W., T. Boekhout, A. Fonseca, G. Scorzetti, and A. Statzell-Tallman. 2000. Biodiversity and systematics of basidiomycetous yeasts as determined by large subunit rDNA D1/D2 domain sequence analysis. Int. J. Syst. Bacteriol. 50:1351-1371.
8. Fleming, R. V., T. J. Walsh, and E. J. Anaissie. 2002. Emerging and less common fungal pathogens. Infect. Dis. Clin. North Am. 16:915-933.
9. Fujita, S. I., Y. Senda, S. Nakaguchi, and T. Hashimoto. 2001. Multiplex PCR using internal transcribed spacer 1 and 2 regions for rapid detection and identification of yeast strains. J. Clin. Microbiol. 39:3617-3622.
10. Fulton, R., R. McDade, P. Smith, L. Kienker, and J. Kettman. 1997. Advanced multiplexed analysis with the FlowMetrix system. Clin. Chem. 43: 1749-1756.
11. Gardes, M., T. J. White, J. A. Fortin, T. D. Bruns, and J. W. Taylor. 1991. Identification of indigenous and introduced symbiotic fungi in ectomycorrhizae by amplification of nuclear and mitochondrial ribosomal DNA. Can. J. Bot. 69:180-190.
12. Gotoh, M., Y. Hasegawa, Y. Shinohara, M. Schimizu, and M. Tosu. 1995. A new approach to determine the effect of mismatches on kinetic parameters in DNA hybridization using an optical biosensor. DNA Res. 2:285-293.
13. Haynes, K. A., T. J. Westerneng, J. W. Fell, and W. Moens. 1995. Rapid detection of pathogenic fungi by polymerase chain reaction amplification of large subunit ribosomal DNA. J. Med. Vet. Mycol. 33:319-325.
14. Itoh, T., U. Hosokawa, N. Kondera, N. Toyazaki, and Y. Asada. 1996. Disseminated infection with Trichosporon asahii. Mycoses 39:195-199.
15. Kanj, S. S., K. Welty-Wolf, J. Madden, V. Tapson, M. A. Baz, and D. Davis. 1996. Fungal infections in lung and heart-lung transplant recipients, report of 9 cases and review of the literature. Medicine 75:142-156.
16. Kiesling, T., M. R. Diaz, A. Statzell-Tallman, and J. W. Fell. 2002. Field identification of marine yeasts using DNA hybridization macroarrays, p. 69-80. In K. D. Hyde, S. T. Moss, and L. L. P. Vrijmoed (ed.), Fungi in marine environments. Fungal Diversity Press, Hong Kong.
17. Kwon-Chung, K. J., and J. E. Bennett. 1992. Medical mycology, p. 866. Lea & Febiger, Philadelphia, Pa.
18. Livshits, M. A., and A. D. Mirzabekov. 1996. Theoretical analysis of the kinetics of DNA hybridization with gel immobilized oligonucleotides. Biophys. J. 71:2795-2801.
19. Makimura, K., S. Murayama, and H. Yamaguchi. 1994. Detection of a wide range of medically important fungi by polymerase chain reaction. J. Med. Microbiol. 40:358-364.
20. Maskos, U., and E. M. Southern. 1993. A study of oligonucleotide reassociation using large arrays of oligonucleotides synthesized on a large support. Nucleic Acids Res. 21:4663-4669.
21. Maskos, U., and E. M. Southern. 1992. Parallel analysis of oligodeoxyribonucleotide (oligonucleotide) interactions. I. Analysis of factors influencing duplex formation. Nucleic Acids Res. 20:1675-1678.
22. Middelhoven, W. J., G. Scorzetti, and J. W. Fell. 2004. Systematics of the anamorphic basidiomycetous yeast genus Trichosporon Behrend with the description of five novel species: Trichosporon vadense, T. smithiae, T. dehoogii, T. scarabeorum, and T. gamsii. Int. J. Sys. Evol. Microbiol. 54:975-986.
23. Nagai, H., Y. Yamakami, A. Hashimoto, I. Tokimatsu, and M. Nasu. 1999. PCR detection of DNA specific for Trichosporon species in serum patients with disseminated trichosporonosis. J. Clin. Microbiol. 37:694-699.
24. Padhye, A. A., S. Verghese, P. Ravichandran, G. Balamurugan, L. Hall, P. Padma, and M. C. Fernandez. 2003. Trichosporon loubieri infection in a patient with adult polycystic kidney disease. J. Clin. Microbiol. 41:479-482.
25. Santa Lucia, J., Jr. 1998. A unified view of polymer, dumbbell and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA 95:1460-1465.
26. Scorzetti, G., J. W. Fell, A. Fonseca, and A. Statzell-Tallman. 2002. Systematics of basidiomycetous yeasts: a comparison of large subunit D1D2 and internal transcribed spacer rDNA regions. FEMS Yeast Res. 2:495-517.
27. Spiro, A., M. Lowe, and D. Brown. 2000. A bead-based method for the multiplexed quantitation of DNA sequences using flow cytometry. Appl. Environ. Microbiol. 66:4258-4265.
28. Staib, F. 1987. Cryptococcosis in AIDS-mycological, diagnostic and epidemiological observations. AIDS Forsch. 2:363-382.
29. Steel, A. B., T. M. Herne, and M. J. Tarlov. 1998. Electrochemical quantitation of DNA immobilized on gold. Anal. Chem. 70:4670-4677.
30. Sugita, T. A., M. Nikishikawa, and T. Shinoda. 1998. Rapid detection of species opportunistic yeast Trichosporon by PCR. J. Clin. Microbiol. 36: 1458-1460.
31. Sugita, T. A., M. Nikishikawa, R. Ikeda, and T. Shinoda. 1999. Identification of medically relevant Trichoporon species based on sequences of internal transcribed spacer regions and construction of a database for Trichosporon identification. J. Clin. Microbiol. 37:1985-1993.
32. Sugita, T. A., M. Nakajima, R. Ikeda, T. Matsuhima, and T. Shinoda. 2002. Sequence analysis of ribosomal DNA intergenic spacer 1 regions of Trichoporon species. J. Clin. Microbiol. 40:1826-1830.
33. Sutton, D. A. 2002. Laboratory evaluation of new antifungal agents against rare and refractory mycoses. Curr, Opin. Infect. Dis. 15:576-582.
34. Tsourkas, A., M. A. Behlke, S. D. Rose, and G. Bao. 2003. Hybridization kinetics and thermodynamics of molecular beacons. Nucleic Acids Res. 31: 1319-1330.
35. Walling, D. M., D. J. McGraw, W. G. Merz, J. E. Karp, and G. M. Hutchins. 1987. Disseminated infection with Trichosporon beigelii. Rev. Infect. Dis. 9:1013-1019.
36. Walsh, T. J. 1989. Trichosporonosis. Infect. Dis. Clin. North Am. 3:43-52.
37. Williams, J. C., S. C. Case-Green, S. C. Mir., and E. M. Southern. 1994. Studies of oligonucleotide interactions by hybridization to arrays: the influence of dangling ends on duplex yield. Nucleic Acids Res. 22:1365-1367.
38. Ye, F., M. S. Li, J. D. Taylor, Q. Nguyen, H. M. Colton, W. M. Casey, M. Wagner, M. P. Weiner, and J. Chen. 2001. Fluorescent microsphere-based readout technology for multiplexed human single nucleotide polymorphism analysis and bacterial identification. Hum. Mutat. 17:305-316.