1887

Abstract

Yeasts of the genus have been associated with a variety of dermatological disorders in humans and domestic animals. With the recent recognition of new members of the genus, new questions are emerging with regard to the pathogenesis and epidemiology of the new species. As new species are recognized, a precise and comprehensive identification system is needed. Herein is described a bead suspension culture-based array that combines the specificity and reliability of nucleic acid hybridization analysis with the speed and sensitivity of the Luminex analyser. The developed 16-plex array consisted of species- and group-specific capture probes that acted as ‘microcodes' for species identification. The probes, which were designed from sequence analysis in the D1/D2 region of rRNA and internal transcribed spacer (ITS) regions, were covalently bound to unique sets of fluorescent beads. Upon hybridization, the biotinylated amplicon was detected by the addition of a fluorochrome coupled to a reporter molecule. The hybridized beads were subsequently analysed by flow cytometric techniques. The developed array, which allowed the detection of species in a multiplex and high-throughput format, was accurate and fast, since it allowed precise identification of species and required less than 1 h following PCR amplification. The described protocol, which can integrate uniplex or multiplex PCR reactions, permitted the simultaneous detection of target sequences in a single reaction, and allowed single mismatch discrimination between probe and non-target sequences. The assay has the capability to be expanded to include other medically important pathogenic species in a single or multiplex array format.

Loading

Article metrics loading...

/content/journal/jmm/10.1099/jmm.0.46630-0
2006-09-01
2019-10-18
Loading full text...

Full text loading...

/deliver/fulltext/jmm/55/9/1197.html?itemId=/content/journal/jmm/10.1099/jmm.0.46630-0&mimeType=html&fmt=ahah

References

  1. Anthony, R. M., Howell, S. A., Lloyd, D. H. & Pinter, L. ( 1994; ). Application of DNA typing methods to the study of the epidemiology of Malassezia pachydermatis. Microb Ecol Health Dis 7, 161–168.[CrossRef]
    [Google Scholar]
  2. Ashbee, H. R. & Evans, E. G. ( 2002; ). Immunology of diseases associated with Malassezia species. Clin Microbiol Rev 15, 21–57.[CrossRef]
    [Google Scholar]
  3. Batra, R., Boekhout, T., Gueho, E., Cabañes, F. J., Dawson, T. L., Jr & Gupta, A. K. ( 2005; ). Malassezia Baillon, emerging clinical yeasts. FEMS Yeast Res 5, 1101–1113.[CrossRef]
    [Google Scholar]
  4. Boekhout, T. & Bosboom, R. W. ( 1994; ). Karyotyping of Malassezia yeasts: taxonomic and epidemiological implications. Syst Appl Microbiol 17, 146–153.[CrossRef]
    [Google Scholar]
  5. Boekhout, T., Kamp, M. & Gueho, E. ( 1998; ). Molecular typing of Malassezia species with PFGE and RAPD. Med Mycol 36, 356–372.
    [Google Scholar]
  6. Cabañes, F. J., Hernández, J. J. & Castellá, G. ( 2005; ). Molecular analysis of Malassezia sympodialis-related strains from domestic animals. J Clin Microbiol 43, 277–283.[CrossRef]
    [Google Scholar]
  7. Castellá, G., Hernández, J. J. & Cabañes, F. J. ( 2005; ). Genetic typing of Malassezia pachydermatis from different domestic animals. Vet Microbiol 108, 291–296.[CrossRef]
    [Google Scholar]
  8. Chang, H. J., Miller, H. L., Watkins, N. & 10 other authors ( 1998; ). An epidemic of Malassezia pachydermatis in an intensive care nursery associated with colonization of health care workers' pet dogs. N Engl J Med 338, 706–711.[CrossRef]
    [Google Scholar]
  9. Chryssanthou, E., Broberger, U. & Petrini, B. ( 2001; ). Malassezia pachydermatis fungemia in a neonatal intensive care unit. Acta Paediatr 90, 323–327.[CrossRef]
    [Google Scholar]
  10. Crespo, M. J., Abarca, M. L. & Cabañes, F. J. ( 2000; ). Otitis externa associated with Malassezia sympodialis in two cats. J Clin Microbiol 38, 1263–1266.
    [Google Scholar]
  11. Crespo-Erchiga, V. & Florencio, V. D. ( 2006; ). Malassezia yeasts and pityriasis versicolor. Curr Opin Infect Dis 19, 139–147.[CrossRef]
    [Google Scholar]
  12. Diaz, M. R. & Fell, J. W. ( 2004; ). High-throughput detection of pathogenic yeasts in the genus Trichosporon. J Clin Microbiol 42, 3696–3706.[CrossRef]
    [Google Scholar]
  13. Diaz, M. R. & Fell, J. W. ( 2005; ). Use of a suspension array for rapid identification of the varieties and genotypes of the Cryptococcus neoformans species complex. J Clin Microbiol 43, 3662–3672.[CrossRef]
    [Google Scholar]
  14. Dunbar, S. A., Vander Zee, C. A., Oliver, K. G., Karem, K. L. & Jacobson, J. W. ( 2003; ). Quantitative, multiplexed detection of bacterial pathogens: DNA and protein applications of the Luminex LabMap system. J Microbiol Methods 53, 245–252.[CrossRef]
    [Google Scholar]
  15. Fode-Vaughan, K. A., Maki, J. S., Benson, J. A. & Collins, M. L. P. ( 2003; ). Direct PCR detection of Escherichia coli O157 : H7. Lett Appl Microbiol 37, 239–243.[CrossRef]
    [Google Scholar]
  16. Friedland, L. R., Menon, A. G., Reising, S. F., Ruddy, R. M. & Hassett, D. J. ( 1994; ). Development of a polymerase chain reaction assay to detect the presence of Streptococcus pneumoniae DNA. Diagn Microbiol Infect Dis 20, 187–193.[CrossRef]
    [Google Scholar]
  17. Fulton, R., McDade, R., Smith, P., Kienker, L. & Kettman, J. ( 1997; ). Advanced multiplexed analysis with the FlowMetrix system. Clin Chem 43, 1749–1756.
    [Google Scholar]
  18. Gemmer, C. M., DeAngelis, Y. D., Theelen, B., Boekhout, T. & Dawson, T. L. ( 2002; ). Fast, non invasive method for molecular detection and differentiation of Malassezia yeast species on human skin and application of the method to dandruff microbiology. J Clin Microbiol 40, 3350–3357.[CrossRef]
    [Google Scholar]
  19. Gotoh, M., Hasegawa, Y., Shinohara, Y., Schimizu, M. & Tosu, M. ( 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.[CrossRef]
    [Google Scholar]
  20. Guého, E., Midgley, G. & Guillot, J. ( 1996; ). The genus Malassezia with description of four new species. Antonie van Leeuwenhoek 69, 337–355.[CrossRef]
    [Google Scholar]
  21. Guého, E., Boekhout, T., Ashbee, H. R., Guillot, J., van Belkum, A. & Faergemann, J. ( 1998; ). The role of Malassezia species in the ecology of human skin and as pathogens. Med Mycol 36, 220–229.
    [Google Scholar]
  22. Guillot, J. & Guého, E. ( 1995; ). The diversity of Malassezia yeasts confirmed by rRNA sequence and nuclear DNA comparisons. Antonie van Leeuwenhoek 67, 297–314.[CrossRef]
    [Google Scholar]
  23. Guillot, J., Guého, E., Lesourd, M., Midgley, G., Chévrier, G. & Dupont, B. ( 1996; ). Identification of Malassezia species: a practical approach. J Mycol Med 6, 103–110.
    [Google Scholar]
  24. Guillot, J. & Bond, R. ( 1999; ). Malassezia pachydermatis: a review. Med Mycol 37, 295–306.[CrossRef]
    [Google Scholar]
  25. Gupta, A. K., Kohli, Y. & Summerbell, R. C. ( 2000; ). Molecular differentiation of seven Malassezia species. J Clin Microbiol 38, 1869–1875.
    [Google Scholar]
  26. Gupta, A. K., Kohli, Y., Faergemann, J. & Summerbell, R. C. ( 2001; ). Epidemiology of Malassezia yeasts associated with pityriasis versiolor in Ontario Canada. Med Mycol 39, 199–206.[CrossRef]
    [Google Scholar]
  27. Gupta, A. K., Batra, R., Bluhm, R., Boekhout, T. & Dawson, T. L., Jr ( 2004a; ). Skin disease associated with Malassezia species. J Am Acad Dermatol 51, 785–798.[CrossRef]
    [Google Scholar]
  28. Gupta, A. K., Boekhout, T., Theelen, B., Summerbell, R. & Batra, R. ( 2004b; ). Identification and typing of Malassezia species by amplified fragment length polymorphism and sequence analyses of the internal transcribed spacer and large-subunit regions of ribosomal DNA. J Clin Microbiol 42, 4253–4260.[CrossRef]
    [Google Scholar]
  29. Hacia, J. G. ( 1999; ). Resequencing and mutational analysis using oligonucleotide microarrays. Nat Genet 21, 42–47.[CrossRef]
    [Google Scholar]
  30. Hazen, K. C. ( 1995; ). New and emerging yeast pathogens. Clin Microbiol Rev 8, 462–478.
    [Google Scholar]
  31. Hirai, A., Kano, R., Makimura, K., Duarte, E. R., Hamdan, J. S., Lachance, M. A., Yamaguchi, H. & Hasegawa, A. ( 2004; ). Malassezia nana sp. nov., a novel lipid-dependent yeast species isolated from animals. Int J Syst Evol Microbiol 54, 623–627.[CrossRef]
    [Google Scholar]
  32. Iannone, M. A., Taylor, J. D., Chen, J., Li, M. S., Rivers, P., Slentz-Kesler, K. A. & Weiner, M. P. ( 2000; ). Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry. Cytometry 39, 131–140.[CrossRef]
    [Google Scholar]
  33. Ikuta, S., Takagi, K., Wallace, R. B. & Itakura, K. ( 1987; ). Dissociation kinetics of 19 base paired oligonucleotide-DNA duplexes containing single mismatched base pairs. Nucleic Acid Res 15, 797–811.[CrossRef]
    [Google Scholar]
  34. Karaman, M. W., Groshen, S., Lee, C. C., Pike, B. L. & Hacia, J. G. ( 2005; ). Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays. Nucleic Acids Res 33, e33.[CrossRef]
    [Google Scholar]
  35. Lockhart, D. J., Dong, H., Byrne, M. C. & 8 other authors ( 1996; ). Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14, 1675–1680.[CrossRef]
    [Google Scholar]
  36. Mayser, P., Haze, P., Papavassilis, C., Pickel, M., Gründer, K. & Guého, E. ( 1997; ). Differentiation of Malassezia species: selectivity of Cremophor EL, castor oil and ricinoleic acid for M. furfur. Br J Dermatol 137, 208–213.[CrossRef]
    [Google Scholar]
  37. McEwan, N. R. & Wheeler, T. ( 1995; ). PCR on the Gram-positive organism Frankia without prior DNA extraction. Trends Genet 11, 168.[CrossRef]
    [Google Scholar]
  38. Morris, D. O., O'Shea, K., Shofer, F. S. & Rankin, S. ( 2005; ). Malassezia pachydermatis carriage in dog owners. Emerg Infect Dis 11, 83–88.[CrossRef]
    [Google Scholar]
  39. Morrison, V. A. & Weisdorf, D. J. ( 2000; ). The spectrum of Malassezia infections in the bone marrow transplant population. Bone Marrow Transplant 26, 645–648.[CrossRef]
    [Google Scholar]
  40. Nell, A., James, S. A., Bond, C. J., Hunt, B. & Herrtage, M. E. ( 2002; ). Identification and distribution of a novel Malassezia yeast species on normal equine skin. Vet Rec 150, 395–398.[CrossRef]
    [Google Scholar]
  41. O'Donnell, K., Cigelnik, E., Weber, N. S. & Trappe, J. M. ( 1997; ). Phylogenetic relationships among ascomycetous truffles and the true and false morels inferred from 18S and 28S rDNA sequence analysis. Mycologia 89, 48–65.[CrossRef]
    [Google Scholar]
  42. Page, B. & Kurtzman, C. P. ( 2005; ). Rapid detection of Candida species and other clinically important yeasts species by flow cytometry. J Clin Microbiol 43, 4507–4514.[CrossRef]
    [Google Scholar]
  43. Polz, M. F. & Cavanaugh, C. M. ( 1998; ). Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64, 3724–3730.
    [Google Scholar]
  44. Prokopowich, C. D., Gregory, T. R. & Crease, T. J. ( 2003; ). The correlation between rDNA copy numbers and genome size in eukaryotes. Genome 46, 48–50.[CrossRef]
    [Google Scholar]
  45. Richet, H. M., McNeil, M. M., Edwards, M. C. & Jarvis, W. R. ( 1989; ). Cluster of Malassezia furfur pulmonary infections in infants in a neonatal intensive-care unit. J Clin Microbiol 27, 1197–1200.
    [Google Scholar]
  46. Rippon, J. W. ( 1982; ). Medical mycology: In The Pathogenic Fungi and the Pathogenic Actinomycetes, 2nd edn. Philadelphia, PA: W. B. Saunders.
  47. Simmons, R. B. & Guého, E. ( 1990; ). A new species of Malassezia. Mycol Res 94, 1146–1149.[CrossRef]
    [Google Scholar]
  48. Southern, E., Mir, K. & Shchepinov, M. ( 1999; ). Molecular interactions on microarrays. Nat Genet 21, 5–9.[CrossRef]
    [Google Scholar]
  49. Summerbell, R. C., Levesque, C. A, Seifert, K. A. & 7 other authors ( 2005; ). Microcoding: the second step in DNA barcoding. Philos Trans R Soc Lond B Biol Sci 360, 1897–1903.[CrossRef]
    [Google Scholar]
  50. Spiro, A., Lowe, M. & Brown, D. ( 2000; ). A bead-based method for multiplexed identification and quantitation of DNA sequences using flow cytometry. Appl Environ Microbiol 66, 4258–4265.[CrossRef]
    [Google Scholar]
  51. Stuart, S. M. & Lane, A. T. ( 1992; ). Candida and Malassezia as nursery pathogens. Semin Dermatol 11, 19–23.
    [Google Scholar]
  52. Sugita, T., Takashima, M., Shinoda, T., Suto, H., Unno, T., Tsuboi, R., Ogawa, H. & Nishikawa, A. ( 2002; ). New yeast species Malassezia dermatis isolated from patients with atopic dermatitis. J Clin Microbiol 40, 1363–1367.[CrossRef]
    [Google Scholar]
  53. Sugita, T., Kodama, M., Saito, M., Ito, T., Kato, Y., Tsuboi, R. & Nishikawa, A. ( 2003a; ). Sequence diversity of the intergenic spacer region of the rRNA gene of Malassezia globosa colonizing the skin of patients with atopic dermatitis and healthy individuals. J Clin Microbiol 41, 3022–3027.[CrossRef]
    [Google Scholar]
  54. Sugita, T., Takashima, M., Kodama, M., Tsuboi, R. & Nishikawa, A. ( 2003b; ). Description of a new yeast species, Malassezia japonica, and its detection in patients with atopic dermatitis and healthy subjects. J Clin Microbiol 41, 4695–4699.[CrossRef]
    [Google Scholar]
  55. Sugita, T., Tajima, M., Takashima, M., Amaya, M., Saito, M., Tsuboi, R. & Nishikawa, A. ( 2004; ). A new yeast, Malassezia yamatoensis, isolated from a patient with seborrheic dermatitis, and its distribution in patients and healthy subjects. Microbiol Immunol 48, 579–583.[CrossRef]
    [Google Scholar]
  56. Sugita, T., Takeo, K., Hama, K. & 10 other authors ( 2005; ). DNA sequence diversity of intergenic spacer region 1 in the non-lipid-dependent species Malassezia pachydermatis isolated from animals. Med Mycol 43, 21–26.[CrossRef]
    [Google Scholar]
  57. Theelen, B., Silvestri, M., Guého, E., van Belkum, A. & Boekhout, T. ( 2001; ). Identification and typing using amplified fragment length polymorphism (AFLPTM), random amplified polymorphism DNA (RAPD) and denaturing gradient gel electrophoresis (DGGE). FEMS Yeast Res 1, 79–86.[CrossRef]
    [Google Scholar]
  58. Tirasophon, W., Ponglikitmongkol, M., Wilairat, P., Boonsaeng, V. & Panyim, S. ( 1991; ). A novel detection of a single Plasmodium falciparum in infected blood. Biochem Biophys Res Commun 175, 179–184.[CrossRef]
    [Google Scholar]
  59. van Belkum, A., Boekhout, T. & Bosboom, R. ( 1994; ). Monitoring spread of Malassezia infections in neonatal intensive care unit by PCR-mediated genetic typing. J Clin Microbiol 32, 2528–2532.
    [Google Scholar]
  60. von Ahsen, N., Oellerich, M. & Schütz, E. ( 2000; ). DNA base bulge vs unmatched end formation in probe based diagnostic insertion/deletion genotyping: genotyping the UGTIAI (TA)n polymorphism by real time fluorescence PCR. Clin Chem 46, 1939–1945.
    [Google Scholar]
  61. Wilson, W. J., Erler, A. M., Nasarabadi, S. L., Skowronski, E. W. & Imbro, P. M. ( 2005; ). A multiplexed PCR coupled-liquid bead array for the simultaneous detection of four biothreat agents. Mol Cell Probes 19, 137–144.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jmm/10.1099/jmm.0.46630-0
Loading
/content/journal/jmm/10.1099/jmm.0.46630-0
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error