Use of a suspension array for rapid identification of the varieties and genotypes of the Cryptococcus neoformans species complex

Journal of Clinical Microbiology

Volumn 43, Issue 8, 2005, Pages 3662-3672

  Diaz, Mara R ^a   Fell, Jack W ^a  

^a UNIVERSITY OF MIAMI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICROSPHERE; PHYCOERYTHRIN; RIBOSOME RNA; SPACER DNA; STREPTAVIDIN;

AMPLICON; ARTICLE; BIOTINYLATION; CHRONIC DISEASE; CONJUGATE; COVALENT BOND; CROSS REACTION; CRYPTOCOCCOSIS; CRYPTOCOCCUS NEOFORMANS; DIAGNOSTIC VALUE; FATALITY; FLOW CYTOMETRY; FLUORESCENCE; FUNGUS IDENTIFICATION; GENE AMPLIFICATION; GENE SEQUENCE; GENOME ANALYSIS; GENOTYPE; HIGH THROUGHPUT SCREENING; HUMAN; HYBRIDIZATION; IMMUNE DEFICIENCY; INHALATION; LASER; MENINGOENCEPHALITIS; MISMATCH REPAIR; NONHUMAN; OLIGONUCLEOTIDE PROBE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; TECHNOLOGY; VALIDATION PROCESS; VARIETAS;

CRYPTOCOCCUS NEOFORMANS; FLOW CYTOMETRY; GENOTYPE; HUMANS; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SUSPENSIONS;

FILOBASIDIELLA NEOFORMANS;

EID: 23744446231     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.43.8.3662-3672.2005     Document Type: Article

References (74)

1. Aguirre, L., S. F. Hurst, J. S. Choi, J. H. Shin, H. P. Hinrikson, and C. J. Morrison. 2004. Rapid differentiation of Aspergillus species from other medically important opportunistic molds and yeasts by PCR-enzyme immunoassay. J. Clin. Microbiol. 42:3495-3504.
2. Atkins, S. D., and I. A. M. Clark. 2004. Fungal molecular diagnostics: a mini-review. J. Appl. Genet. 45:3-15.
3. Bava, A. J., R. Negroni, and M. Bianchi. 1993. Cryptococcosis by a urease negative strain of Cryptococcus neoformans. J. Med. Vet. Mycol. 31:87-89.
4. Bennett, J. E., K. J. Kwon-Chung, and D. Howard. 1977. Epidemiologic differences among serotypes of Cryptococcus neoformans. Am. J. Epidemiol. 105:582-586.
5. Bialek, R., M. Weiss, K. Bekure-Nemariam, L. K. Najvar, M. B. Alberdi, J. R. Graybill, and U. Reischl. 2002. Cryptococcus neoformans DNA in tissue samples by nested and real-time PCR assay. Clin. Diagn. Lab. Immunol. 9:461-469.
6. Boekhout, T., B. Theelen, M. Diaz, J. W. Fell, C. J. Hop, E. C. A. Abeln, F. Drommer, and W. Meyer. 2001. Hybrid genotypes in the pathogenic yeast Cryptococcus neoformans. Microbiology 147:891-907.
7. Calvo, B. M., A. L. Combo, O. Fischman, A. S. Santiago, L. Thompson, M. Lazera, F. Telles, K. Fukushima, K. Nishimura, R. Tanaka, M. Mvajy, and L. Morettii-Branchini. 2001. Antifungal susceptibilities, varieties, and electrophoretic karyotipes of clinical isolates of Cryptococcus neoformans from Brazil, Chile, and Venezuela. J. Clin. Microbiol. 30:2348-2350.
8. Casadevall, A., and J. R. Perfect. 1998. Cryptococcus neoformans, p. 1-541. ASM Press, Washington, D.C.
9. Chang, H. C., S. N. Leaw, A. H. Huang, T. L. Wu, and T. C. Chang. 2001. Rapid identification of yeasts in positive blood cultures by a multiplex PCR method. J. Clin. Microbiol. 39:3466-3471.
10. Chang, H. C., J. J. Chang, A. H. Huang, and T. C. Chang. 2000. Evaluation of a capacitance method for direct antifungal susceptibility testing of yeasts in positive cultures. J. Clin. Microbiol. 38:971-976.
11. Chen, J., M. A. Iannone, M. S. Li, J. D. Taylor, P. Rivers, A. J. Nelsen, K. A. Slentz-Kesler, A. Roses, and M. P. Weiner. 2000. A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension. Genome Res. 10:549-556.
12. Cogliati, M., M. Allaria, A. M. Tortorano, and M. A. Viviani. 2000. Genotyping Cryptococcus neoformans var. neoformans with specific primers designed from PCR-fingerprinting bands sequenced using a modified PCR-based strategy. Med. Mycol. 38:97-103.
13. Corrêa, M. P. S. C., E. C. Oliveira, R. R. B. S. Duarte, P. P. O. Pardal, F. M. Oliveira, and L. C. Severo. 1999. Criptococose em crianças no Estado do Pará, Brasil. Rev. Soc. Bras. Med. Trop. 32:505-550.
14. Darzé, C., R. Lucena, I. Gomes, and A. Melo. 2000. Características clínicas laboratoriais de 104 casos de meningoencefalite criptocócica. Rev. Soc. Bras. Med. Trop. 33:21-26.
15. 14a. Diaz, M. R., T. Boekhout, T. Riesling, and J. W. Fell. Comparative analysis of the intergenic spacer regions and population structure of the species complex of the pathogenic fungus Cryptococcus neoformans. FEMS Yeast Res., in press.
16. Diaz, M. R., and J. W. Fell. 2004. High-throughput detection of pathogenic yeasts in the genus Trichosporon. J. Clin. Microbiol. 42:3696-3706.
17. Diaz, M. R., T. Boekhout, B. Theelen, and J. W. Fell. 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.
18. Diaz, M. R., and J. W. Fell. 2000. Molecular analyses of the IGS and ITS regions rDNA of the psychrophilic yeasts in the genus Mrakia. Antonie Leeuwenhoek 77:7-12.
19. Dromer, F., S. Mathoulin-Pelissier, A. Fontanet, O. Ronin, B. Dupont, O. Lortholary, and the French Cryptococcosis Study Group. 2004. Epidemiology of HIV-associated cryptococcosis in France (1985-2001): comparison of the pre and post-HAART eras. AIDS 18:555-562.
20. Dromer, F., A. Varma, O. Ronin, S. Mathhoulin, and B. Dupont. 1994. Molecular typing of Cryptococcus neoformans var. neoformans serotype D clinical isolates. J. Clin. Microbiol. 32:2364-2371.
21. 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.
22. Dupont, B., H. H. Crewe Brown, K. Westermann, M. D. Martins, J. H. Rex, O. Lortholary, and C. A. Kauffmann. 2000. Mycoses in AIDS. Med. Mycol. 38:259-267.
23. Elie, C. M., T. J. Lott, E. Reiss, and C. J. Morrison. 1998. Rapid identification of Candida species with species-specific probes. J. Clin. Microbiol. 36:3260-3265.
24. Ellis, D., D. Marriott, R. A. Haijjeh, D. Warnock, W. Meyer, and R. Barton. 2000. Epidemiology: surveillance of fungal infections. Med. Mycol. 38:173-182.
25. Ellis, D. H., and T. J. Pfeiffer. 1990. Natural habitat of Cryptococcus neoformans var. gatti. J. Clin. Microbiol. 28:1642-1644.
26. Fell, J., and G. Blatt. 1999. Separation of strains of the yeasts Xanthophyllomyces dendrorhous and Phaffia rhodozyma based on rDNA IGS and ITS sequence analysis. J. Ind. Microbiol. Biotechnol. 23:677-681.
27. 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.
28. Fuchs, B. E., K. Syutsubo, L. Wolfgang, and R. Amann. 2001. In situ accessibility of Escherichia coli to 23S rRNA to fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 67:961-968.
29. Fulton, R., R. McDade, P. Smith, L. Kienker, and J. Kettman. 1997. Advanced multiplexed analysis with the FlowMetrix system. Clin. Chem. 43:1749-1756.
30. Goldman, D. L., H. Khine, J. Abadi, D. J. Lindenberg, L. Pirofski, R. Niang, and A. Casadevall. 2001. Serologic evidence for Ctyptococcus neoformans Infection in early childhood. Pediatrics 107:66.
31. 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.
32. Graves, J. D. 1999. Powerful tools for genetic analysis come to age. Trends Biochem. Technol. 17:127-134.
33. Hendolin, P. H., L. Paulin, P. Koukila-Kahkola, V. J. Anttila, H. Malmberg, M. Richardson, and J. Ylikoski. 2000. Panfungal PCR and multiplex liquid hybridization for detection of fungi in tissue specimens. J. Clin. Microbiol. 38:4186-4192.
34. Hsu, M. C., K. W. Chen, H. J. Lo, Y. C. Chen, M. H. Liao, Y. H. Lin, and S. Y. Li. 2003. Species identification of medically important fungi by use of real time light cycler PCR. J. Med. Microbiol. 52:1071-1076.
35. Husain, S., M. Wagener, and A. Singh. 2001. Cryptococcus infection in organ transplant recipients: variables influencing clinical characteristics and outcome. Emerg. Infect. Dis. 7:375-381.
36. Ikuta, S., K. Takagi, R. B. Wallace, and K. Ikura. 1987. Dissociation kinetics of 19 base paired oligonucleotide-DNA duplexes containing single mismatched base pairs. Nucleic Acids Res. 15:797-811.
37. Inacio, J., S. Behrens, B. M. Fuchs, A. Fonseca, I. Spencer-Martins, and R. Amann. 2003. In situ accessibility of Saccharomyces cerevisiae 26S rRNA to Cy3-labeled oligonucleotide probes comprising the D1 and D2 domains. Appl. Environ. Microbiol. 69:2899-2905.
38. Jaeger, E. E. M., N. M. Carrol, S. Choudhury, A. A. S. Dunlop, H. M. A. Towler, M. M. Matheson, P. Adamson, N. Okhravi, and S. Lightman. 2000. Rapid detection and identification of Candida, Aspergillus, and Fusarium species in ocular samples using nested PCR. J. Clin. Microbiol. 38:2902-2908.
39. Katsu, M., S. Kidd, A. Ando, M. L. Morettii-Branchini, Y. Mikami, K. Nishimura, and W. Meyer. 2004. The internal transcribed spacers and 5.8S rRNA gene show extensive diversity among isolates of Cryptococcus neoformans species complex. FEMS Yeast Res. 4:377-388.
40. Kidd, S. E., F. Hagen, R. L. Tscharke, M. Huynh, K. H. Barlett, M. Fyfe, L. Macdougall, T. Boekhout, K. J. Kwong-Chung, and W. Meyer. 2004. A rare genotype of Cryptococcus gattii caused the cryptococcosis outbreak on Vancouver Island (British Columbia, Canada). Proc. Natl. Acad. Sci. USA 101:17258-17263.
41. Kovacs, J. A., A. A. Kovacs, M. Polis, W. C. Wright, V. J. Gill, C. U. Tuazon, E. P. Gelmann, H. C. Lane, R. Longfield, G. Overturf, A. M. Macher, A. S. Fauci, J. E. Parrillo, J. E. Bennett, and H. Masur. 1985. Cryptococcosis in the acquired immunodeficiency syndrome. Ann. Intern. Med. 103:533-538.
42. Kovayashi, T., D. J. Heck, M. Nomura, and T. Horiuchi. 1998. Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I. Genes Dev. 12:3821-3830.
43. Kwon-Chung, K. J., and J. E. Bennett. 1984. Epidemiologic differences between the two varieties of Cryptococcus neoformans. Am. J. Epidemiol. 120:123-130.
44. Latouche, G. N., M. Huynh, T. C. Sorrell, and W. Meyer. 2003. PCR-restriction fragment polymorphism analysis of the phospholipase B (PLB1) gene for subtyping of Cryptococcus neoformans isolates. Appl. Environ. Microbiol. 69:2080-2085.
45. Lazera, M. S., M. A. Salmito Cavalcanti, A. T. Londero, L. Trilles, M. M. Nishikawa, and B. Wanke. 2000. Possible primary ecological niche of Cryptococcus neoformans. Med. Mycol. 38:379-383.
46. Lee, I., A. A. Dombkowski, and B. D. Athey. 2004. Guidelines for incorporating non perfectly matched oligonucleotides into target-specific hybridization probes for DNA microarray. Nucleic Acids Res. 32:681-690.
47. Lindsley, M. D., S. F. Hurst, N. J. Iqbal, and C. J. Morrison. 2001. Rapid identification of dimorphic and yeast like fungal pathogens using specific probes. J. Clin. Microbiol. 39:3505-3511.
48. Liu, W. T., A. D. Mirzabekov, and D. A. Stahl. 2001. Optimization of an oligonucleotide microchip for microbial identification studies: a non equilibrium dissociation approach. Environ. Microbiol. 3:619-629.
49. Lott, T. J., R. J. Kuykendall, and E. Reiss. 1993. Nucleotide sequence analysis of the 5.8S rDNA and adjacent ITS2 region of Candida albicans and related species. Yeast 9:1199-1206.
50. Loy, A., A. Lehner, N. Lee, J. Adamczyk, H. Meier, J. Ernst, K. H. Schleifer, and M. Wagner. 2002. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol. 68:5064-5081.
51. Luo, G., and T. G. Mitchell. 2002. Rapid identification of pathogenic fungi directly from cultures by using multiplex PCR. J. Clin. Microbiol. 40:2860-2865.
52. Meinkoth, J., and G. Wahl. 1984. Hybridization of nucleic acids immobilized on solid supports. Anal. Chem. 138:267-284.
53. Meyer, W., A. Castan̄eda, S. Jackson, M. Huynh, and E. Castan̄eda. 2003. Molecular typing of IberoAmerican Cryptococcus neoformans isolates. Emerg. Infect. Dis. 2:189-195.
54. Meyer, W., K. Marszewska, M. Amirmostofian, R. P. Igreja, C. Hardtke, K. Methling, M. A. Viviani, A. Chindamporn, S. Sukroongreung, M. A. John, D. H. Ellis, and T. C. Sorrell. 1999. Molecular typing of global isolates of Cryptococcus neoformans by a polymerase chain reaction fingerprinting and randomly amplified polymorphic DNA: a pilot study to standardize techniques on which to base a detailed epidemiological survey. Electrophoresis 20:1790-1799.
55. Mirza, S. A., M. Phelan, D. Rimland, E. Graviss, R. Hamill, M. E. Brandt, T. Gardner, M. Sattah, G. P. de Leon, W. Baughman, and R. A. Hajjeh. 2003. The changing epidemiology of cryptococcosis: an update from population-based active surveillance in 2 large metropolitan areas, 1992-2000. Clin. Infect. Dis. 36:789-794.
56. O'Donnell, E. Cigelnik, N. S. Weber, and J. M. Trappe. 1997. Phylogenetic relationships among ascomycetous truffles and the true and false morels inferred from 18S and 28S ribosomal DNA sequence analysis. Mycologia 89:48-65.
57. Pappalardo, M. C., and M. S. Melhem. 2003. Cryptococcosis: a review of the Brazilian experience for the disease. Rev. Inst. Med. Trop. Sao Paulo 45:299-305.
58. Park, S., M. Wong, A. Salvatore, E. Marras, E. W. Cross, T. E. Kiehn, V. Chaturvedi, S. Tyagi, and D. S. Perlin. 2000. Rapid identification of Candida dubliniensis using a species-specific molecular beacon. J. Clin. Microbiol. 38:2829-2836.
59. Peplies, J., F. O. Glockner, and R. Amann. 2003. Optimization strategies for DNA microarray-based detection of bacteria with 16s RNA-targeting oligonucleotide probes. Appl. Environ. Microbiol. 69:1397-1407.
60. Perfect, J. R., N. Ketabchi, G. M. Cox, C. W. Ingram, and C. L. Beiser. 1993. Karyotyping of Cryptococcus neoformans as an epidemiological tool. J. Clin. Microbiol. 31:3305-3309.
61. Perfect, J. R., D. T. Durack, and H. A. Gallis. 1983. Cryptococcemia. Medicine 62:98-109.
62. Picken, M. M., R. N. Picken, D. Han, Y. Cheng, and F. Strle. 1996. Single-tube nested polymerase chain reaction assay based on flagellin gene sequences for detection of Boirelia burgdorferi sensu lato. Eur. J. Clin. Microbiol. Infect. Dis. 15:489-498.
63. Polanco, C., and M. Pérez de la Vega. 1994. The structure of the rDNA intergenic spacer of Avena sativa L.: a comparative study. Plant Mol. Biol. 25:751-756.
64. Posteraro, B., M. Sanguinetti, L. Masucci, L. Romano, G. Morace, and G. Fadda. 2000. Reverse cross blot hybridization assay for rapid detection of PCR amplified from Candida species, Cryptococcus neoformans, and Saccharomyces cerevisiae in clinical samples. J. Clin. Microbiol. 38:1609-1614.
65. Prokopowich, C. D., T. R. Gregory, and T. J. Crease. 2003. The correlation between rDNA copy numbers and genome size in eukaryoKes. Genome 46:48-50.
66. Rappelli, P., R. Are, G. Casu, P. L. Fiori, P. Cappuccinelli, and A. Aceti. 1998. Development of a nested PCR for detection of Cryptococcus neoformans in cerebrospinal fluid. J. Clin. Microbiol. 36:3438-3440.
67. Saag, M. S., G. A. Cloud, J. R. Graybill, J. D. Sobel, C. U. Tuazon, P. C. Johnson, W. J. Fessel, B. L. Moskovitz, B. Wiesinger, D. Cosmatos, L. Riser, C. Thomas, R. Hafner, W. E. Dismukes, et al. 1999. A comparison of itraconazole versus fluconazole as maintenance therapy for AIDS-associated cryptococcal meningitis. Clin. Infect. Dis. 30:291-296.
68. Sar, B., D. Monchy, M. Vann, C. Keo, J. L. Sarthou, and Y. Buisson. 2004. Increasing in vitro resistance to fluconazole in Cryptococcus neoformans Cambodian. J. Antimicrob. Chemother. 54:563-565.
69. Singh, N., S. Husain, M. De Vera, T. Gayowski, and T. V. Cacdarelli. 2004. Cryptococcus neoformans infection in patients with cirrhosis, including liver transplant. Medicine 83:188-192.
70. Southern, E., K. Mir, and M. Shchepinov. 1999. Molecular interactions on microarrays. Nat. Genet. 21(Suppl.):5-9.
71. Steenbergen, J. N., and A. Casadevall. 2000. Prevalence of Cryptococcus neoformans var. neoformans (serotype D) and Cryptococcus neoformans var. grubii (serotype A) isolates in New York City. J. Clin. Microbiol. 38:1974-1976.
72. Stephen, C., S. Lester, W. Black, M. Fyfe, and S. Raverty. 2002. Multispecies outbreak of cryptococcosis on southern Vancouver Island, British Columbia. Can. Vet. J. 43:792-794.
73. Tanaka, K. I., T. Miyazaki, S. Maesaki, K. Mitsutake, H. Kakeya, Y. Yamamoto, K. Yanagihara, M. A. Hossain, T. Tashiro, and S. Kohno. 1996. Detection of Cryptococcus neoformans in patients with pulmonary cryptococcosis. J. Clin. Microbiol. 34:3438-3440.
74. Wood, W., J. Gitschier, L. A. Lasky, and R. M. Lawn. 1985. Base pair composition-independent hybridization in tetramethylammonium chloride: a method for oligonucleotide screening of highly complex gene libraries. Proc. Natl. Acad. Sci. USA 82:1585-1588.