Improving molecular detection of Candida DNA in whole blood: Comparison of seven fungal DNA extraction protocols using real-time PCR

Journal of Medical Microbiology

Volumn 57, Issue 3, 2008, Pages 296-303

  Metwally, L ^a   Fairley, D J ^a   Coyle, P V ^a   Hay, R J ^b   Hedderwick, S ^a   McCloskey, B ^a   O'Neill, H J ^a   Webb, C H ^a   Elbaz, W ^a   McMullan, R ^a  

^a ROYAL VICTORIA HOSPITAL   (United Kingdom)

^b QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL DNA; GENOMIC DNA; REAGENT;

ARTICLE; BLOOD; CANDIDA ALBICANS; DNA DETERMINATION; DNA EXTRACTION; INOCULATION; NONHUMAN; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; ULTRAVIOLET SPECTROSCOPY;

CANDIDA; CANDIDA ALBICANS; CANDIDIASIS; DNA, FUNGAL; FUNGEMIA; HUMANS; MYCOLOGICAL TYPING TECHNIQUES; POLYMERASE CHAIN REACTION; REAGENT KITS, DIAGNOSTIC; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; TIME FACTORS;

EID: 40549115614     PISSN: 00222615     EISSN: None     Source Type: Journal    
DOI: 10.1099/jmm.0.47617-0     Document Type: Article

References (38)

1. Ahmad, S., Khan, Z., Mustafa, A. S. & Khan, Z. U. (2002). Seminested PCR for diagnosis of candidemia: comparison with culture, antigen detection, and biochemical methods for species identification. J Clin Microbiol 40, 2483-2489.
2. Arishima, T. & Takezawa, J. (2006). Use of PCR based diagnosis for common invasive fungal infections in the intensive care unit. Nippon Ishinkin Gakkai Zasshi 47, 283-288.
3. Ascioglu, S., Rex, J. H., de Pauw, B., Bennett, J. E., Bille, J., Crokaert, F., Denning, D. W., Donnelly, J. P., Edwards, J. E. & other authors (2002). Defining opportunistic invasive fungal infections in immunocompromised patients with cancer and hematopoietic stem cell transplants: an international consensus. Clin Infect Dis 34, 7-14.
4. Bougnoux, M., Dupont, C., Mateo, J., Saulnier, P., Faivre, V., Payen, D. & Nicolas-Chanoine, M. (1999). Serum is more suitable than whole blood for diagnosis of systemic candidiasis by nested PCR. J Clin Miaobiol 37, 925-930.
5. Bretagne, S. & Costa, J. M. (2005). Towards a molecular diagnosis of invasive aspergillosis and disseminated candidosis. FEMS Immunol Med Microbiol 45, 361-368.
6. Buchheidt, D., Hummel, M., Schleiermacher, D., Spiess, B., Schwerdtfeger, R., Cornely, O. A., Wilhelm, S., Reuter, S., Kern, W. & other authors (2004). Prospective clinical evaluation of a LightCycler-mediated polymerase chain reaction assay, a nested-PCR assay and a galactomannan enzyme-linked immunosorbent assay for detection of invasive aspergillosis in neutropenic cancer patients and haematological stem cell transplant recipients. Br J Haematol 125, 196-202.
7. Challier, S., Boyer, S., Abachin, E. & Berche, P. (2004). Development of a serum-based TaqMan real-time PCR assay for diagnosis of invasive aspergillosis. J Clin Microbiol 42, 844-846.
8. Einsele, H., Hebart, H., Roller, G., Löffler, J., Rothenhofer, I., Muller, C. A., Bowden, R. A., van Burik, J., Engelhard, D. & other authors (1997). Detection and identification of fungal pathogens in blood by using molecular probes. J Clin Microbiol 35, 1353-1360.
9. Ellis, M. (2002). Invasive fungal infections: evolving challenges for diagnosis and therapeutics. Mol Immunol 38, 947-957.
10. Flahaut, M., Sanglard, D., Monod, M., Bille, J. & Rossier, M. (1998). Rapid detection of Candida albicans in clinical samples by DNA amplification of common regions from C. albicans-secreted aspartic proteinase genes. J Clin Microbiol 36, 395-401.
11. Fredricks, D. N. & Relman, D. A. (1998). Improved amplification of microbial DNA from blood cultures by removal of the PCR inhibitor sodium polyanetholesulfonate. J Clin Microbiol 36, 2810-2816.
12. Fredricks, D. N., Smith, C. & Meier, A. (2005). Comparison of six DNA extraction methods for recovery of fungal DNA as assessed by quantitative PCR. J Clin Microbiol 43, 5122-5128.
13. Gallagher, M. L., Burke, W. F. & Orzech, K. (1987). Carrier RNA enhancement of recovery of DNA from dilute solutions. Biochem Biophys Res Commun 144, 271-276.
14. Innings, A., Ullberg, M., Johansson, A., Rubin, C. J., Noreus, N., Isaksson, M. & Herrmann, B. (2007). Multiplex real-time PCR targeting the RNase P RNA gene for detection and identification of Candida species in blood. J Clin Microbiol 45, 874-880.
15. Jaeger, E. E., Carroll, N. M., Choudhury, S., Dunlop, A. A., Towler, H. M., Matheson, M. M., Adamson, P., Okhravi, N. & Lightman, S. (2000). Rapid detection and identification of Candida, Aspergillus, and Fusarium species in ocular samples using nested PCR. J Clin Microbiol 38, 2902-2908.
16. Karakousis, A., Tan, L., Ellis, D., Alexiou, H. & Wormald, P. J. (2006). An assessment of the efficiency of fungal DNA extraction methods for maximizing the detection of medically important fungi using PCR. J Microbiol Methods 65, 38-48.
17. Kasai, M., Francesconi, A., Petraitiene, R., Petraitis, V., Kelaher, A. M., Kim, H. S., Meletiadis, J., Sein, T., Bacher, J. & Walsh, T. J. (2006). Use of quantitative real-time PCR to study the kinetics of extracellular DNA released from Candida albicans, with implications for diagnosis of invasive candidiasis. J Clin Microbiol 44, 143-150.
18. Kishore, R., Reef Hardy, W., Anderson, V. J., Sanchez, N. A. & Buoncristiani, M. R. (2006). Optimization of DNA extraction from low-yield and degraded samples using the BioRobot EZ1 and BioRobot M48. J Forensic Sci 51, 1055-1061.
19. Klingspor, L. & Jalal, S. (2006). Molecular detection and identification of Candida and Aspergillus spp. from clinical samples using real-time PCR. Clin Microbiol Infect 12, 745-753.
20. Löffler, J., Hebart, H., Schumacher, U., Reitze, H. & Einsele, H. (1997). Comparison of different methods for extraction of DNA of fungal pathogens from cultures and blood. J Clin Microbiol 35, 3311-3312.
21. Löffler, J., Henke, N., Hebart, H., Schmidt, D., Hagmeyer, L., Schumacher, U. & Einsele, H. (2000). Quantification of fungal DNA by using fluorescence resonance energy transfer and the light cycler system. J Clin Microbiol 38, 586-590.
22. Lugert, R., Schettler, C. & Gross, U. (2006). Comparison of different protocols for DNA preparation and PCR for the detection of fungal pathogens in vitro. Mycoses 49, 298-304.
23. Maaroufi, Y., Heymans, C., De Bruyne, J. M., Duchateau, V., Rodriguez-Villalobos, H., Aoun, M. & Crokaert, F. (2003). Rapid detection of Candida albicans in clinical blood samples by using a TaqMan-based PCR assay. J Clin Microbiol 41, 3293-3298.
24. Maaroufi, Y., Ahariz, N., Husson, M. & Crokaert, F. (2004). Comparison of different methods of isolation of DNA of commonly encountered Candida species and its quantitation by using a real-time PCR-based assay. J Clin Microbiol 42, 3159-3163.
25. Metwally, L., Hogg, G., Coyle, P. V., Hay, R. J., Hedderwick, S., McCloskey, B., O'Neill, H. J., Ong, G. M., Thompson, G. & other authors (2007). Rapid differentiation between fluconazole-sensitive and -resistant species of Candida directly from positive blood-culture bottles by real-time PCR. J Med Microbiol 56, 964-970.
26. Millar, B. C., Jiru, X., Moore, J. E. & Earle, J. A. (2000). A simple and sensitive method to extract bacterial, yeast and fungal DNA from blood culture material. J Microbiol Methods 42, 139-147.
27. Moreira-Oliveira, M. S., Mikami, Y., Miyaji, M., Imai, T., Schreiber, A. Z. & Moretti, M. L. (2005). Diagnosis of candidemia by polymerase chain reaction and blood culture: prospective study in a high-risk population and identification of variables associated with development of candidemia. Eur J Clin Microbiol Infect Dis 24, 721-726.
28. Müller, F. M., Werner, K. E., Kasai, M., Francesconi, A., Chanock, S. J. & Walsh, T. J. (1998). Rapid extraction of genomic DNA from medically important yeasts and filamentous fungi by high-speed cell disruption. J Clin Microbiol 36, 1625-1629.
29. 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 high-risk patients. Diagn Microbiol Infect Dis 47, 487-496.
30. Rustchenko, E. P., Curran, T. M. & Sherman, F. (1993). Variations in the number of ribosomal DNA units in morphological mutants and normal strains of Candida albicans and in normal strains of Saccharomyces cerevisiae. J Bacteriol 175, 7189-7199.
31. Schabereiter-Gurtner, C., Selitsch, B., Rotter, M. L., Hirschl, A. M. & Willinger, B. (2007). Development of novel real-time PCR assays for detection and differentiation of eleven medically important Aspergillus and Candida species in clinical specimens. J Clin Microbiol 45, 906-914.
32. Scherer, S. & Magee, P. T. (1990). Genetics of Candida albicans. Microbiol Mol Biol Rev 54, 226-241.
33. Stahlberg, A., Hakansson, J., Xian, X., Semb, H. & Kubista, M. (2004). Properties of the reverse transcription reaction in mRNA quantification. Clin Chem 50, 509-515.
34. Wahyuningsih, R., Freisleben, H. J., Sonntag, H. G. & Schnitzler, P. (2000). Simple and rapid detection of Candida albicans DNA in serum by PCR for diagnosis of invasive candidiasis. J Clin Microbiol 38, 3016-3021.
35. White, P. L., Shetty, A. & Barnes, R. A. (2003). Detection of seven Candida species using the Light-Cycler system. J Med Microbiol 52, 229-238.
36. White, P. L., Barton, R., Guiver, M., Linton, C. J., Wilson, S., Smith, M., Gomez, B. L., Carr, M. J., Kimmitt, P. T. & other authors (2006). A consensus on fungal polymerase chain reaction diagnosis?: a United Kingdom-Ireland evaluation of polymerase chain reaction methods for detection of systemic fungal infections. J Mol Diagn 8, 376-384.
37. Wickes, B., Staudinger, J., Magee, B. B., Kwon-Chung, K. J., Magee, P. T. & Scherer, S. (1991). Physical and genetic mapping of Candida albicans: several genes previously assigned to chromosome 1 map to chromosome R, the rDNA-containing linkage group. Infect Immun 59, 2480-2484.
38. Widjojoatmodjo, M. N., Borst, A., Schukkink, R. A., Box, A. T., Tacken, N. M., Van Gemen, B., Verhoef, J., Top, B. & Fluit, A. C. (1999). Nucleic acid sequence-based amplification (NASBA) detection of medically important Candida species. J Microbiol Methods 38, 81-90.