Use of denaturing gradient gel electrophoresis for the identification of mixed oral yeasts in human saliva

Journal of Medical Microbiology

Volumn 62, Issue PART 2, 2013, Pages 319-330

  Weerasekera, Manjula M ^a,b   Sissons, Chris H ^a   Wong, Lisa ^a   Anderson, Sally ^a   Holmes, Ann R ^a   Cannon, Richard D ^a  

^a UNIVERSITY OF OTAGO   (New Zealand)

^b UNIVERSITY OF SRI JAYEWARDENEPURA   (Sri Lanka)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 18S; RNA 28S;

ARTICLE; CANDIDA; CANDIDA ALBICANS; CANDIDA DUBLINIENSIS; CANDIDA GLABRATA; CANDIDA KRUSEI; CANDIDA PARAPSILOSIS; CANDIDA RUGOSA; CANDIDA TROPICALIS; CONTROLLED STUDY; DENATURING GRADIENT GEL ELECTROPHORESIS; DIPODASCUS CAPITATUS; DNA SEQUENCE; FUNGAL STRAIN; FUNGUS CULTURE; FUNGUS IDENTIFICATION; HUMAN; KLUYVEROMYCES MARXIANUS; NONHUMAN; PICHIA GUILLIERMONDII; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SALIVA; SALIVA ANALYSIS; SPECIES IDENTIFICATION; TRICHOSPORON ASAHII; YEAST;

CANDIDA; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA PRIMERS; DNA, FUNGAL; GENES, RRNA; HUMANS; MOUTH; RNA, RIBOSOMAL, 18S; RNA, RIBOSOMAL, 28S; SALIVA; YEASTS;

EID: 84872717965     PISSN: 00222615     EISSN: None     Source Type: Journal    
DOI: 10.1099/jmm.0.050237-0     Document Type: Article

References (65)

1. Beighton, D., Ludford, R., Clark, D. T., Brailsford, S. R., Pankhurst, C. L., Tinsley, G. F., Fiske, J., Lewis, D., Daly, B. & other authors (1995). Use of CHROMagar Candida medium for isolation of yeasts from dental samples. J Clin Microbiol 33, 3025-3027.
2. Borman, A. M., Linton, C. J., Miles, S. J. & Johnson, E. M. (2008). Molecular identification of pathogenic fungi. J Antimicrob Chemother 61 (Suppl. 1), i7-i12.
3. Campanha, N. H., Neppelenbroek, K. H., Spolidorio, D. M., Spolidorio, L. C. & Pavarina, A. C. (2005). Phenotypic methods and commercial systems for the discrimination between C. albicans and C. dubliniensis. Oral Dis 11, 392-398.
4. Cannon, R. D., Holmes, A. R., Mason, A. B. & Monk, B. C. (1995). Oral Candida: clearance, colonization, or candidiasis? J Dent Res 74, 1152-1161.
5. Carvalho, A., Costa-De-Oliveira, S., Martins, M. L., Pina-Vaz, C., Rodrigues, A. G., Ludovico, P. & Rodrigues, F. (2007). Multiplex PCR identification of eight clinically relevant Candida species. Med Mycol 45, 619-627.
6. Cocolin, L., Bisson, L. F. & Mills, D. A. (2000). Direct profiling of the yeast dynamics in wine fermentations. FEMS Microbiol Lett 189, 81-87.
7. Cocolin, L., Aggio, D., Manzano, M., Cantoni, C. & Comi, G. (2002). An application of PCR-DGGE analysis to profile the yeast populations in raw milk. Int Dairy J 12, 407-411.
8. Coleman, D., Sullivan, D., Harrington, B., Haynes, K., Henman, M., Shanley, D., Bennett, D., Moran, G., McCreary, C. & O'Neill, L. (1997). Molecular and phenotypic analysis of Candida dubliniensis: a recently identified species linked with oral candidosis in HIV-infected and AIDS patients. Oral Dis 3 (Suppl. 1), S96-S101.
9. Dassanayake, R. S. & Samaranayake, L. P. (2003). Randomly amplified polymorphic DNA fingerprinting: the basics. Methods Mol Biol 226, 117-122.
10. Devillard, E., Burton, J. P. & Reid, G. (2005). Complexity of vaginal microflora as analyzed by PCR denaturing gradient gel electrophoresis in a patient with recurrent bacterial vaginosis. Infect Dis Obstet Gynecol 13, 25-30.
11. Ellepola, A. N. & Samaranayake, L. P. (2000). Oral candidal infections and antimycotics. Crit Rev Oral Biol Med 11, 172-198.
12. Ellepola, A. N., Hurst, S. F., Elie, C. M. & 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.
13. Ells, R., Kock, J. L. & Pohl, C. H. (2011). Candida albicans or Candida dubliniensis? Mycoses 54, 1-16.
14. Emmanouil-Nikoloussi, E., Kanellaki-Kyparissi, M., Papavassiliou, P., Koliakos, K., Dermentzopoulou, M. & Foroglou, C. (1994). "Hanseniaspora uvarum" the ultrastructural morphology of a rare ascomycete, isolated from oral thrush. Bull Group Int Rech Sci Stomatol Odontol 37, 13-17.
15. Fricke, S., Fricke, C., Schimmelpfennig, C., Oelkrug, C., Schönfelder, U., Blatz, R., Zilch, C., Faber, S., Hilger, N. & other authors (2010). A real-time PCR assay for the differentiation of Candida species. J Appl Microbiol 109, 1150-1158.
16. Giammanco, G. M., Melilli, D. & Pizzo, G. (2004). Candida pararugosa isolation from the oral cavity of an Italian denture wearer. Res Microbiol 155, 571-574.
17. Gonçalves, R. H., Miranda, E. T., Zaia, J. E. & Giannini, M. J. (2006). Species diversity of yeast in oral colonization of insulin-treated diabetes mellitus patients. Mycopathologia 162, 83-89.
18. Hierro, N., González, A., Mas, A. & Guillamón, J. M. (2006). Diversity and evolution of non-Saccharomyces yeast populations during wine fermentation: effect of grape ripeness and cold maceration. FEMS Yeast Res 6, 102-111.
19. Hospenthal, D. R., Beckius, M. L., Floyd, K. L., Horvath, L. L. & Murray, C. K. (2006). Presumptive identification of Candida species other than C. albicans, C. krusei, and C. tropicalis with the chromogenic medium CHROMagar Candida. Ann Clin Microbiol Antimicrob 5, 1.
20. Hsu, M.-C., Chen, K.-W., Lo, H.-J., Chen, Y.-C., Liao, M.-H., Lin, Y.-H. & Li, S.-Y. (2003). Species identification of medically important fungi by use of real-time LightCycler PCR. J Med Microbiol 52, 1071-1076.
21. Khan, Z., Mustafa, A. S. & Alam, F. F. (2009). Real-time LightCycler polymerase chain reaction and melting temperature analysis for identification of clinically important Candida spp. J Microbiol Immunol Infect 42, 290-295.
22. Klinke, T., Guggenheim, B., Klimm, W. & Thurnheer, T. (2011). Dental caries in rats associated with Candida albicans. Caries Res 45, 100-106.
23. Kowalchuk, G. A., Gerards, S. & Woldendorp, J. W. (1997). Detection and characterization of fungal infections of Ammophila arenaria (marram grass) roots by denaturing gradient gel electrophoresis of specifically amplified 18S rDNA. Appl Environ Microbiol 63, 3858-3865.
24. Kuba, K. (2008). [Molecular and immunological methods applied in diagnosis of mycoses]. Wiad Parazytol 54, 187-197 (in Polish).
25. Kurtzman, C. P. & Robnett, C. J. (1998). Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie van Leeuwenhoek 73, 331-371.
26. Ledder, R. G., Gilbert, P., Pluen, A., Sreenivasan, P. K., De Vizio, W. & McBain, A. J. (2006). Individual microflora beget unique oral microcosms. J Appl Microbiol 100, 1123-1131.
27. Li, Y., Saxena, D., Barnes, V. M., Trivedi, H. M., Ge, Y. & Xu, T. (2006). Polymerase chain reaction-based denaturing gradient gel electrophoresis in the evaluation of oral microbiota. Oral Microbiol Immunol 21, 333-339.
28. Li, S.-S., Cheng, C., Li, Z., Chen, J.-Y., Yan, B., Han, B.-Z. & Reeves, M. (2010). Yeast species associated with wine grapes in China. Int J Food Microbiol 138, 85-90.
29. Linton, C. J., Borman, A. M., Cheung, G., Holmes, A. D., Szekely, A., Palmer, M. D., Bridge, P. D., Campbell, C. K. & Johnson, E. M. (2007). Molecular identification of unusual pathogenic yeast isolates by large ribosomal subunit gene sequencing: 2 years of experience at the United Kingdom Mycology Reference Laboratory. J Clin Microbiol 45, 1152-1158.
30. López-Martínez, R. (2010). Candidosis, a new challenge. Clin Dermatol 28, 178-184.
31. Loreto, E. S., Scheid, L. A., Nogueira, C. W., Zeni, G., Santurio, J. M. & Alves, S. H. (2010). Candida dubliniensis: epidemiology and phenotypic methods for identification. Mycopathologia 169, 431-443.
32. Madhavan, P., Jamal, F., Chong, P. P. & Ng, K. P. (2011). Identification of local clinical Candida isolates using CHROMagar CandidaTM as a primary identification method for various Candida species. Trop Biomed 28, 269-274.
33. Marshall, M. N., Cocolin, L., Mills, D. A. & VanderGheynst, J. S. (2003). Evaluation of PCR primers for denaturing gradient gel electrophoresis analysis of fungal communities in compost. J Appl Microbiol 95, 934-948.
34. Martins, M., Henriques, M., Ribeiro, A. P., Fernandes, R., Gonçalves, V., Seabra, A., Azeredo, J. & Oliveira, R. (2010). Oral Candida carriage of patients attending a dental clinic in Braga, Portugal. Rev Iberoam Micol 27, 119-124.
35. Meroth, C. B., Hammes, W. P. & Hertel, C. (2003). Identification and population dynamics of yeasts in sourdough fermentation processes by PCR-denaturing gradient gel electrophoresis. Appl Environ Microbiol 69, 7453-7461.
36. Moran, G. P., Coleman, D. C. & Sullivan, D. J. (2012). Candida albicans versus Candida dubliniensis: why is C. albicans more pathogenic? Int J Microbiol 2012, 205921.
37. Moter, A. & Göbel, U. B. (2000). Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. J Microbiol Methods 41, 85-112.
38. Muccilli, S., Caggia, C., Randazzo, C. L. & Restuccia, C. (2011). Yeast dynamics during the fermentation of brined green olives treated in the field with kaolin and Bordeaux mixture to control the olive fruit fly. Int J Food Microbiol 148, 15-22.
39. Neppelenbroek, K. H., Campanha, N. H., Spolidorio, D. M., Spolidorio, L. C., Seó, R. S. & Pavarina, A. C. (2006). Molecular fingerprinting methods for the discrimination between C. albicans and C. dubliniensis. Oral Dis 12, 242-253.
40. Nielsen, D. S., Jacobsen, T., Jespersen, L., Koch, A. G. & Arneborg, N. (2008). Occurrence and growth of yeasts in processed meat products-implications for potential spoilage. Meat Sci 80, 919-926.
41. Oros-Sichler, M., Gomes, N. C., Neuber, G. & Smalla, K. (2006). A new semi-nested PCR protocol to amplify large 18S rRNA gene fragments for PCR-DGGE analysis of soil fungal communities. J Microbiol Methods 65, 63-75.
42. Polz, M. F. & Cavanaugh, C. M. (1998). Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64, 3724-3730.
43. Pryce, T. M., Kay, I. D., Palladino, S. & Heath, C. H. (2003). Real-time automated polymerase chain reaction (PCR) to detect Candida albicans and Aspergillus fumigatus DNA in whole blood from highrisk patients. Diagn Microbiol Infect Dis 47, 487-496.
44. Rasiah, I. A., Wong, L., Anderson, S. A. & Sissons, C. H. (2005). Variation in bacterial DGGE patterns from human saliva: over time, between individuals and in corresponding dental plaque microcosms. Arch Oral Biol 50, 779-787.
45. Romeo, O. & Criseo, G. (2011). Candida africana and its closest relatives. Mycoses 54, 475-486.
46. Samaranayake, L. (2009). Commensal oral Candida in Asian cohorts. Int J Oral Sci 1, 2-5.
47. San Millán, R. M., Wu, L. C., Salkin, I. F. & Lehmann, P. F. (1997). Clinical isolates of Candida guilliermondii include Candida fermentati. Int J Syst Bacteriol 47, 385-393.
48. Sandhu, G. S., Kline, B. C., Stockman, L. & Roberts, G. D. (1995). Molecular probes for diagnosis of fungal infections. J Clin Microbiol 33, 2913-2919.
49. Schmid, J., Voss, E. & Soll, D. R. (1990). Computer-assisted methods for assessing strain relatedness in Candida albicans by fingerprinting with the moderately repetitive sequence Ca3. J Clin Microbiol 28, 1236-1243.
50. Schmid, J., Hunter, P. R., White, G. C., Nand, A. K. & Cannon, R. D. (1995). Physiological traits associated with success of Candida albicans strains as commensal colonizers and pathogens. J Clin Microbiol 33, 2920-2926.
51. Seiler, H. & Busse, M. (1990). The yeasts of cheese brines. Int J Food Microbiol 11, 289-303.
52. Sidrim, J. J., Costa, A. K., Cordeiro, R. A., Brilhante, R. S., Moura, F. E., Castelo-Branco, D. S., Neto, M. P. & Rocha, M. F. (2010). Molecular methods for the diagnosis and characterization of Cryptococcus: a review. Can J Microbiol 56, 445-458.
53. Smit, E., Leeflang, P., Glandorf, B., Van Elsas, J. D. & Wernars, K. (1999). Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl Environ Microbiol 65, 2614-2621.
54. Soysa, N. S., Samaranayake, L. P. & Ellepola, A. N. (2006). Diabetes mellitus as a contributory factor in oral candidosis. Diabet Med 23, 455-459.
55. Trtkova, J. & Raclavsky, V. (2006). Molecular-genetic approaches to identification and typing of pathogenic Candida yeasts. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 150, 51-61.
56. Vainio, E. & Hantula, J. (2000). Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Mycol Res 104, 927-936.
57. Van Elsas, J. D., Duarte, G. F., Keijzer-Wolters, A. & Smit, E. (2000). Analysis of the dynamics of fungal communities in soil via fungalspecific PCR of soil DNA followed by denaturing gradient gel electrophoresis. J Microbiol Methods 43, 133-151.
58. Vilela, D. M., Pereira, G. V., Silva, C. F., Batista, L. R. & Schwan, R. F. (2010). Molecular ecology and polyphasic characterization of the microbiota associated with semi-dry processed coffee (Coffea arabica L.). Food Microbiol 27, 1128-1135.
59. Walter, J., Tannock, G. W., Tilsala-Timisjarvi, A., Rodtong, S., Loach, D. M., Munro, K. & Alatossava, T. (2000). Detection and identification of gastrointestinal Lactobacillus species by using denaturing gradient gel electrophoresis and species-specific PCR primers. Appl Environ Microbiol 66, 297-303.
60. White, T. J., Bruns, T., Lee, S. & Taylor, J. W. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols-a Guide to Methods and Applications, pp. 315-322. Edited by M. Innis, D. H. Gelfand, J. J. Sninsky & T. J. White. San Diego, CA: Academic Press.
61. White, P. L., Williams, D. W., Kuriyama, T., Samad, S. A., Lewis, M. A. & Barnes, R. A. (2004). Detection of Candida in concentrated oral rinse cultures by real-time PCR. J Clin Microbiol 42, 2101-2107.
62. Williams, D. & Lewis, M. (2011). Pathogenesis and treatment of oral candidosis. J Oral Microbiol 3, 1-11.
63. Willis, A. M., Coulter, W. A., Sullivan, D. J., Coleman, D. C., Hayes, J. R., Bell, P. M. & Lamey, P. J. (2000). Isolation of C. dubliniensis from insulin-using diabetes mellitus patients. J Oral Pathol Med 29, 86-90.
64. Yang, Y. L. (2003). Virulence factors of Candida species. J Microbiol Immunol Infect 36, 223-228.
65. Zijnge, V., Harmsen, H. J., Kleinfelder, J. W., Van der Rest, M. E., Degener, J. E. & Welling, G. W. (2003). Denaturing gradient gel electrophoresis analysis to study bacterial community structure in pockets of periodontitis patients. Oral Microbiol Immunol 18, 59-65.