1887

Abstract

The DiversiLab system, which uses repetitive sequence-based PCR (rep-PCR) to genotype micro-organisms, was evaluated as a molecular typing tool for members of the genus . Initially, 41 clinical spp. (7 , 10 , 7 , 10 and 7 ), previously identified at the species level by morphological and biochemical analysis, were analysed with the DiversiLab system. Species identification was confirmed by DNA sequence analysis of the contiguous internal transcribed spacer (ITS) region (ITS1–5.8S–ITS2). On the basis of an 80 % similarity threshold, rep-PCR consistently clustered like species and this set of isolates, along with five ATCC reference strains, was used to create a DNA fingerprint library with the DiversiLab software. Subsequently, an additional set of 115 clinical isolates, identified biochemically as (=94), (=8), (=5), (=3), (=3) and (=2), isolated at a regional reference laboratory, were typed using DiversiLab. One hundred and six of these isolates clustered with members of the library at >80 % similarity and thus could be assigned species identification, and initial calculations showed that identification via rep-PCR fingerprinting was 95 % concordant (101/106) with the biochemical/morphological identification. However, ITS region sequencing of the five discrepant samples, as well as the nine isolates that were <80 % similar to the database samples, showed that nine were misidentified with traditional biochemical/morphological methods. For the misidentified isolates, the sequence-based identification was in agreement with the DiversiLab clustering, yielding an actual correlation of >99 %. As traditional techniques can take several days to provide information about at the genus/species level, genotyping with the DiversiLab system holds promise for more-rapid speciation of members of this genus. This system may also be useful for epidemiological studies such as source tracking that require subspecies discrimination.

Loading

Article metrics loading...

/content/journal/jmm/10.1099/jmm.0.47106-0
2007-06-01
2019-11-20
Loading full text...

Full text loading...

/deliver/fulltext/jmm/56/6/778.html?itemId=/content/journal/jmm/10.1099/jmm.0.47106-0&mimeType=html&fmt=ahah

References

  1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. ( 1990; ). Basic local alignment search tool. J Mol Biol 215, 403–410.[CrossRef]
    [Google Scholar]
  2. Bart-Delabesse, E., Sarfati, J., Debeaupuis, J. P., van Leeuwen, W., van Belkum, A., Bretagne, S. & Latge, J. P. ( 2001; ). Comparison of restriction fragment length polymorphism, microsatellite length polymorphism, and random amplification of polymorphic DNA analyses for fingerprinting Aspergillus fumigatus isolates. J Clin Microbiol 39, 2683–2686.[CrossRef]
    [Google Scholar]
  3. Botterel, F., Desterke, C., Costa, C. & Bretagne, S. ( 2001; ). Analysis of microsatellite markers of Candida albicans used for rapid typing. J Clin Microbiol 39, 4076–4081.[CrossRef]
    [Google Scholar]
  4. Bougnoux, M. E., Morand, S. & d'Enfert, C. ( 2002; ). Usefulness of multilocus sequence typing for characterization of clinical isolates of Candida albicans. J Clin Microbiol 40, 1290–1297.[CrossRef]
    [Google Scholar]
  5. Chau, A. S., Mendrick, C. A., Sabatelli, F. J., Loebenberg, D. & McNicholas, P. M. ( 2004; ). Application of real-time quantitative PCR to molecular analysis of Candida albicans strains exhibiting reduced susceptibility to azoles. Antimicrob Agents Chemother 48, 2124–2131.[CrossRef]
    [Google Scholar]
  6. Clark, T. A. & Hajjeh, R. A. ( 2002; ). Recent trends in the epidemiology of invasive mycoses. Curr Opin Infect Dis 15, 569–574.[CrossRef]
    [Google Scholar]
  7. Dalle, F., Dumont, L., Franco, N., Mesmacque, D., Caillot, D., Bonnin, P., Moiroux, C., Vagner, O., Cuisenier, B. & other authors ( 2003; ). Genotyping of Candida albicans oral strains from healthy individuals by polymorphic microsatellite locus analysis. J Clin Microbiol 41, 2203–2205.[CrossRef]
    [Google Scholar]
  8. Dodgson, A. R., Pujol, C., Denning, D. W., Soll, D. R. & Fox, A. J. ( 2003; ). Multilocus sequence typing of Candida glabrata reveals geographically enriched clades. J Clin Microbiol 41, 5709–5717.[CrossRef]
    [Google Scholar]
  9. Dooley, D. P., Beckius, M. L. & Jeffrey, B. S. ( 1994; ). Misidentification of clinical yeast isolates by using the updated Vitek yeast biochemical card. J Clin Microbiol 32, 2889–2892.
    [Google Scholar]
  10. Eggimann, P., Garbino, J. & Pittet, D. ( 2003; ). Epidemiology of Candida species infections in critically ill non-immunosuppressed patients. Lancet Infect Dis 3, 685–702.[CrossRef]
    [Google Scholar]
  11. Foongladda, S., Sakulmaiwatana, P., Petlum, P. & Vanprapar, N. ( 2004; ). Candida species, genotypes and antifungal susceptibility of Candida isolates from blood samples of patients at the largest tertiary care hospital in Thailand during 1999–2002. J Med Assoc Thai 87, 92–99.
    [Google Scholar]
  12. Foulet, F., Nicolas, N., Eloy, O., Botterel, F., Gantier, J. C., Costa, J. M. & Bretagne, S. ( 2005; ). Microsatellite marker analysis as a typing system for Candida glabrata. J Clin Microbiol 43, 4574–4579.[CrossRef]
    [Google Scholar]
  13. Fujita, S. & Hashimoto, T. ( 2000; ). DNA fingerprinting patterns of Candida species using HinfI endonuclease. Int J Syst Evol Microbiol 50, 1381–1389.[CrossRef]
    [Google Scholar]
  14. Goulding, J. N., Hookey, J. V., Stanley, J., Olver, W., Neal, K. R., Ala'Aldeen, D. A. & Arnold, C. ( 2000; ). Fluorescent amplified-fragment length polymorphism genotyping of Neisseria meningitidis identifies clones associated with invasive disease. J Clin Microbiol 38, 4580–4585.
    [Google Scholar]
  15. Guarro, J., Gene, J. & Stchigel, A. M. ( 1999; ). Developments in fungal taxonomy. Clin Microbiol Rev 12, 454–500.
    [Google Scholar]
  16. Healy, M., Reece, K., Walton, D., Huong, J., Shah, K. & Kontoyiannis, D. P. ( 2004; ). Identification to the species level and differentiation between strains of Aspergillus clinical isolates by automated repetitive-sequence-based PCR. J Clin Microbiol 42, 4016–4024.[CrossRef]
    [Google Scholar]
  17. Healy, M., Huong, J., Bittner, T., Lising, M., Frye, S., Raza, S., Schrock, R., Manry, J., Renwick, A. & other authors ( 2005a; ). Microbial DNA typing by automated repetitive-sequence-based PCR. J Clin Microbiol 43, 199–207.[CrossRef]
    [Google Scholar]
  18. Healy, M., Reece, K., Walton, D., Huong, J., Frye, S., Raad, I. I. & Kontoyiannis, D. P. ( 2005b; ). Use of the DiversiLab system for species and strain differentiation of Fusarium species isolates. J Clin Microbiol 43, 5278–5280.[CrossRef]
    [Google Scholar]
  19. 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.[CrossRef]
    [Google Scholar]
  20. Imhof, A., Balajee, S. A., Fredricks, D. N., Englund, J. A. & Marr, K. A. ( 2004; ). Breakthrough fungal infections in stem cell transplant recipients receiving voriconazole. Clin Infect Dis 39, 743–746.[CrossRef]
    [Google Scholar]
  21. Kauffman, C. A. ( 2006; ). Fungal infections. Proc Am Thorac Soc 3, 35–40.[CrossRef]
    [Google Scholar]
  22. Koeuth, T., Versalovic, J. & Lupski, J. R. ( 1995; ). Differential subsequence conservation of interspersed repetitive Streptococcus pneumoniae BOX elements in diverse bacteria. Genome Res 5, 408–418.[CrossRef]
    [Google Scholar]
  23. Kontoyiannis, D. P., Lionakis, M. S., Lewis, R. E., Chamilos, G., Healy, M., Perego, C., Safdar, A., Kantarjian, H., Champlin, R. & other authors ( 2005; ). Zygomycosis in a tertiary-care cancer center in the era of Aspergillus-active antifungal therapy: a case–control observational study of 27 recent cases. J Infect Dis 191, 1350–1360.[CrossRef]
    [Google Scholar]
  24. Li, Y. L., Leaw, S. N., Chen, J. H., Chang, H. C. & Chang, T. C. ( 2003; ). Rapid identification of yeasts commonly found in positive blood cultures by amplification of the internal transcribed spacer regions 1 and 2. Eur J Clin Microbiol Infect Dis 22, 693–696.[CrossRef]
    [Google Scholar]
  25. Li, X., Brown, N., Chau, A. S., Lopez-Ribot, J. L., Ruesga, M. T., Quindos, G., Mendrick, C. A., Hare, R. S., Loebenberg, D. & other authors ( 2004; ). Changes in susceptibility to posaconazole in clinical isolates of Candida albicans. J Antimicrob Chemother 53, 74–80.
    [Google Scholar]
  26. Lockhart, S. R., Pujol, C., Dodgson, A. R. & Soll, D. R. ( 2005; ). Deoxyribonucleic acid fingerprinting methods for Candida species. Methods Mol Med 118, 15–25.
    [Google Scholar]
  27. Lott, T. J., Fundyga, R. E., Brandt, M. E., Harrison, L. H., Sofair, A. N., Hajjeh, R. A. & Warnock, D. W. ( 2003; ). Stability of allelic frequencies and distributions of Candida albicans microsatellite loci from US population-based surveillance isolates. J Clin Microbiol 41, 1316–1321.[CrossRef]
    [Google Scholar]
  28. Luo, G. & Mitchell, T. G. ( 2002; ). Rapid identification of pathogenic fungi directly from cultures by using multiplex PCR. J Clin Microbiol 40, 2860–2865.[CrossRef]
    [Google Scholar]
  29. Marchetti, O., Bille, J., Fluckiger, U., Eggimann, P., Ruef, C., Garbino, J., Calandra, T., Glauser, M. P., Tauber, M. G. & other authors ( 2004; ). Epidemiology of candidemia in Swiss tertiary care hospitals: secular trends, 1991–2000. Clin Infect Dis 38, 311–320.[CrossRef]
    [Google Scholar]
  30. Olive, D. M. & Bean, P. ( 1999; ). Principles and applications of methods for DNA-based typing of microbial organisms. J Clin Microbiol 37, 1661–1669.
    [Google Scholar]
  31. Page, B. T. & Kurtzman, C. P. ( 2005; ). Rapid identification of Candida species and other clinically important yeast species by flow cytometry. J Clin Microbiol 43, 4507–4514.[CrossRef]
    [Google Scholar]
  32. Pfaller, M. A., Diekema, D. J., Jones, R. N., Messer, S. A. & Hollis, R. J. ( 2002; ). Trends in antifungal susceptibility of Candida spp. isolated from pediatric and adult patients with bloodstream infections: SENTRY Antimicrobial Surveillance Program, 1997 to 2000. J Clin Microbiol 40, 852–856.[CrossRef]
    [Google Scholar]
  33. Pounder, J. I., Williams, S., Hansen, D., Healy, M., Reece, K. & Woods, G. L. ( 2005; ). Repetitive-sequence-PCR-based DNA fingerprinting using the DiversiLab system for identification of commonly encountered dermatophytes. J Clin Microbiol 43, 2141–2147.[CrossRef]
    [Google Scholar]
  34. Pounder, J. I., Hansen, D. & Woods, G. L. ( 2006; ). Identification of Histoplasma capsulatum, Blastomyces dermatitidis, and Coccidioides species by repetitive-sequence-based PCR. J Clin Microbiol 44, 2977–2982.[CrossRef]
    [Google Scholar]
  35. Redkar, R. J., Dube, M. P., McCleskey, F. K., Rinaldi, M. G. & Del Vecchio, V. G. ( 1996; ). DNA fingerprinting of Candida rugosa via repetitive sequence-based PCR. J Clin Microbiol 34, 1677–1681.
    [Google Scholar]
  36. Reiss, E., Tanaka, K., Bruker, G., Chazalet, V., Coleman, D., Debeaupuis, J. P., Hanazawa, R., Latge, J. P., Lortholary, J. & other authors ( 1998; ). Molecular diagnosis and epidemiology of fungal infections. Med Mycol 36, (Suppl. 1), 249–257.[CrossRef]
    [Google Scholar]
  37. Richards, M. J., Edwards, J. R., Culver, D. H. & Gaynes, R. P. ( 1999; ). Nosocomial infections in medical intensive care units in the United States. Crit Care Med 27, 887–892.[CrossRef]
    [Google Scholar]
  38. Rigby, S., Procop, G. W., Haase, G., Wilson, D., Hall, G., Kurtzman, C., Oliveira, K., Von Oy, S., Hyldig-Nielsen, J. J. & other authors ( 2002; ). Fluorescence in situ hybridization with peptide nucleic acid probes for rapid identification of Candida albicans directly from blood culture bottles. J Clin Microbiol 40, 2182–2186.[CrossRef]
    [Google Scholar]
  39. Robles, J. C., Koreen, L., Park, S. & Perlin, D. S. ( 2004; ). Multilocus sequence typing is a reliable alternative method to DNA fingerprinting for discriminating among strains of Candida albicans. J Clin Microbiol 42, 2480–2488.[CrossRef]
    [Google Scholar]
  40. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  41. Sampaio, P., Gusmao, L., Alves, C., Pina-Vaz, C., Amorim, A. & Pais, C. ( 2003; ). Highly polymorphic microsatellite for identification of Candida albicans strains. J Clin Microbiol 41, 552–557.[CrossRef]
    [Google Scholar]
  42. Selvarangan, R., Bui, U., Limaye, A. P. & Cookson, B. T. ( 2003; ). Rapid identification of commonly encountered Candida species directly from blood culture bottles. J Clin Microbiol 41, 5660–5664.[CrossRef]
    [Google Scholar]
  43. Stephan, F., Bah, M. S., Desterke, C., Rezaiguia-Delclaux, S., Foulet, F., Duvaldestin, P. & Bretagne, S. ( 2002; ). Molecular diversity and routes of colonization of Candida albicans in a surgical intensive care unit, as studied using microsatellite markers. Clin Infect Dis 35, 1477–1483.[CrossRef]
    [Google Scholar]
  44. Stern, M. J., Ames, G. F., Smith, N. H., Robinson, E. C. & Higgins, C. F. ( 1984; ). Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell 37, 1015–1026.[CrossRef]
    [Google Scholar]
  45. Tavanti, A., Gow, N. A., Senesi, S., Maiden, M. C. & Odds, F. C. ( 2003; ). Optimization and validation of multilocus sequence typing for Candida albicans. J Clin Microbiol 41, 3765–3776.[CrossRef]
    [Google Scholar]
  46. Tortorano, A. M., Peman, J., Bernhardt, H., Klingspor, L., Kibbler, C. C., Faure, O., Biraghi, E., Canton, E., Zimmermann, K. & other authors ( 2004; ). Epidemiology of candidaemia in Europe: results of 28-month European Confederation of Medical Mycology (ECMM) hospital-based surveillance study. Eur J Clin Microbiol Infect Dis 23, 317–322.[CrossRef]
    [Google Scholar]
  47. Turenne, C. Y., Sanche, S. E., Hoban, D. J., Karlowsky, J. A. & Kabani, A. M. ( 1999; ). Rapid identification of fungi by using the ITS2 genetic region and an automated fluorescent capillary electrophoresis system. J Clin Microbiol 37, 1846–1851.
    [Google Scholar]
  48. Vermitsky, J. P. & Edlind, T. D. ( 2004; ). Azole resistance in Candida glabrata: coordinate upregulation of multidrug transporters and evidence for a Pdr1-like transcription factor. Antimicrob Agents Chemother 48, 3773–3781.[CrossRef]
    [Google Scholar]
  49. Versalovic, J. & Lupski, J. R. ( 2002; ). Molecular detection and genotyping of pathogens: more accurate and rapid answers. Trends Microbiol 10, S15–S21.[CrossRef]
    [Google Scholar]
  50. Versalovic, J., Koeuth, T. & Lupski, J. R. ( 1991; ). Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19, 6823–6831.[CrossRef]
    [Google Scholar]
  51. Versalovic, J., Kapur, V., Mason, E. O., Jr, Shah, U., Koeuth, T., Lupski, J. R. & Musser, J. M. ( 1993; ). Penicillin-resistant Streptococcus pneumoniae strains recovered in Houston: identification and molecular characterization of multiple clones. J Infect Dis 167, 850–856.[CrossRef]
    [Google Scholar]
  52. Viscoli, C., Girmenia, C., Marinus, A., Collette, L., Martino, P., Vandercam, B., Doyen, C., Lebeau, B., Spence, D. & other authors ( 1999; ). Candidemia in cancer patients: a prospective, multicenter surveillance study by the Invasive Fungal Infection Group (IFIG) of the European Organization for Research and Treatment of Cancer (EORTC). Clin Infect Dis 28, 1071–1079.[CrossRef]
    [Google Scholar]
  53. Warren, N. G. & Hazen, K. C. ( 1999; ). Candida, Cryptococcus, and other yeasts of medical importance. In Manual of Clinical Microbiology, pp. 1184–1199. Edited by P. R. Murray, E. J. Baron, M. A. Pfaller, F. C. Tenover & R. H. Yolken. Washington DC: American Society for Microbiology.
  54. White, T., Burns, T., Lee, S. & Taylor, J. ( 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. A. Innis, D. H. Gelfand, J. J. Sninsky & T. J. White. San Diego: Academic Press.
http://instance.metastore.ingenta.com/content/journal/jmm/10.1099/jmm.0.47106-0
Loading
/content/journal/jmm/10.1099/jmm.0.47106-0
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