A quick and low-cost PCR-based assay for Candida spp. identification in positive blood culture bottles

BMC Infectious Diseases

Volumn 13, Issue 1, 2013, Pages

  Xafranski, Hemílio ^a   Melo, Analy S A ^a   Machado, Antonia M ^a   Briones, Marcelo R S ^a   Colombo, Arnaldo L ^a  

^a FEDERAL UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Candidemia; Fungal DNA extraction; ITS region sequencing; Molecular diagnosis

Indexed keywords

DNA FRAGMENT; FUNGAL DNA; INTERNAL TRANSCRIBED SPACER; LIQUID NITROGEN; ORGANIC SOLVENT; RIBOSOME DNA;

ARTICLE; BLOOD CULTURE; CANDIDA; CANDIDA ALBICANS; CANDIDA GLABRATA; CANDIDA KRUSEI; CANDIDA PARAPSILOSIS; CANDIDA TROPICALIS; CANDIDEMIA; CLAVISPORA LUSITANIAE; CONTROLLED STUDY; COST CONTROL; CYTOLYSIS; DIAGNOSTIC TEST ACCURACY STUDY; DNA CONTENT; DNA DETERMINATION; DNA EXTRACTION; DNA SEQUENCE; FUNGUS IDENTIFICATION; GENBANK; GENE AMPLIFICATION; INTERMETHOD COMPARISON; LABORATORY AUTOMATION; MOLECULAR DIAGNOSIS; NONHUMAN; PICHIA ANOMALA; PICHIA GUILLIERMONDII; POLYMERASE CHAIN REACTION; RDNA GENE; REPRODUCIBILITY; SENSITIVITY ANALYSIS; SOLVENT EXTRACTION; VALIDATION PROCESS;

BLOOD; BLOOD SPECIMEN COLLECTION; CANDIDA; CANDIDIASIS; HUMANS; POLYMERASE CHAIN REACTION;

EID: 84885004002     PISSN: None     EISSN: 14712334     Source Type: Journal    
DOI: 10.1186/1471-2334-13-467     Document Type: Article

References (41)

1. Wenzel RP, Gennings C. Bloodstream infections due to Candida species in the intensive care unit: identifying especially high-risk patients to determine prevention strategies. Clin Infect Dis 2005, 41(Suppl 6):S389-S393.
2. Colombo AL, Thompson L, Graybill JR. The north and south of candidemia: issues for Latin America. Drugs Today 2008, 44:1-34. Suppl A.
3. Antonelli M, Azoulay E, Bonten M, Chastre J, Citerio G, Conti G, Backer D, Lemaire F, Gerlach H, Hedenstierna G, et al. Year in review in Intensive Care Medicine 2009: I. Pneumonia and infections, sepsis, outcome, acute renal failure and acid base, nutrition and glycaemic control. Intensive Care Med 2010, 36(2):196-209. 10.1007/s00134-009-1742-7, 2816797, 20057995.
4. Gudlaugsson O, Gillespie S, Lee K, Vande Berg J, Hu J, Messer S, Herwaldt L, Pfaller M, Diekema D. Attributable mortality of nosocomial candidemia, revisited. Clin Infect Dis 2003, 37(9):1172-1177. 10.1086/378745, 14557960.
5. Ellepola AN, Morrison CJ. Laboratory diagnosis of invasive candidiasis. J Microbiol 2005, 43:65-84. Spec No.
6. Morrell M, Fraser VJ, Kollef MH. Delaying the empiric treatment of Candida bloodstream infection until positive blood culture results are obtained: a potential risk factor for hospital mortality. Antimicrob Agents Chemother 2005, 49(9):3640-3645. 10.1128/AAC.49.9.3640-3645.2005, 1195428, 16127033.
7. Lehmann LE, Hunfeld K-P, Emrich T, Haberhausen G, Wissing H, Hoeft A, Stüber F. A multiplex real-time PCR assay for rapid detection and differentiation of 25 bacterial and fungal pathogens from whole blood samples. Med Microbiol Immunol 2007, 197(3):313-324.
8. Charles PE, Dalle F, Aho S, Quenot J-P, Doise J-M, Aube H, Olsson N-O, Blettery B. Serum procalcitonin measurement contribution to the early diagnosis of candidemia in critically ill patients. Intensive Care Med 2006, 32(10):1577-1583. 10.1007/s00134-006-0306-3, 16896850.
9. Garey KW, Rege M, Pai MP, Mingo DE, Suda KJ, Turpin RS, Bearden DT. Time to initiation of fluconazole therapy impacts mortality in patients with candidemia: a multi-institutional study. Clin Infect Dis 2006, 43(1):25-31. 10.1086/504810, 16758414.
10. Fujita SI, Senda Y, Nakaguchi S, Hashimoto T. Multiplex PCR using internal transcribed spacer 1 and 2 regions for rapid detection and identification of yeast strains. J Clin Microbiol 2001, 39(10):3617-3622. 10.1128/JCM.39.10.3617-3622.2001, 88398, 11574582.
11. White PL, Linton CJ, Perry MD, Johnson EM, Barnes RA. The evolution and evaluation of a whole blood polymerase chain reaction assay for the detection of invasive aspergillosis in hematology patients in a routine clinical setting. Clin Infect Dis 2006, 42(4):479-486. 10.1086/499949, 16421791.
12. Maertens J, Deeren D, Dierickx D, Theunissen K. Preemptive antifungal therapy: still a way to go. Curr Opin Infect Dis 2006, 19(6):551-556. 10.1097/QCO.0b013e3280106854, 17075330.
13. Metwally L, Fairley DJ, Coyle PV, Hay RJ, Hedderwick S, McCloskey B, O'Neill HJ, Webb CH, McMullan R. Comparison of serum and whole-blood specimens for the detection of Candida DNA in critically ill, non-neutropenic patients. J Med Microbiol 2008, 57(Pt 10):1269-1272.
14. Khlif M, Mary C, Sellami H, Sellami A, Dumon H, Ayadi A, Ranque S. Evaluation of nested and real-time PCR assays in the diagnosis of Candidaemia. Clin Microbiol Infect 2009, 15(7):656-661. 10.1111/j.1469-0691.2009.02762.x, 19438623.
15. Lau A, Halliday C, Chen SC, Playford EG, Stanley K, Sorrell TC. Comparison of whole blood, serum, and plasma for early detection of candidemia by multiplex-tandem PCR. J Clin Microbiol 2010, 48(3):811-816. 10.1128/JCM.01650-09, 2832453, 20042634.
16. Avni T, Leibovici L, Paul M. PCR diagnosis of invasive candidiasis: systematic review and meta-analysis. J Clin Microbiol 2011, 49(2):665-670. 10.1128/JCM.01602-10, 3043518, 21106797.
17. Maaroufi Y, Ahariz N, Husson M, Crokaert F. 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 2004, 42(7):3159-3163. 10.1128/JCM.42.7.3159-3163.2004, 446303, 15243076.
18. Fredricks DN, Smith C, Meier A. Comparison of six DNA extraction methods for recovery of fungal DNA as assessed by quantitative PCR. J Clin Microbiol 2005, 43(10):5122-5128. 10.1128/JCM.43.10.5122-5128.2005, 1248488, 16207973.
19. Van Burik JA, Myerson D, Schreckhise RW, Bowden RA. Panfungal PCR assay for detection of fungal infection in human blood specimens. J Clin Microbiol 1998, 36(5):1169-1175. 104793, 9574670.
20. Haugland RA, Heckman JL, Wymer LJ. Evaluation of different methods for the extraction of DNA from fungal conidia by quantitative competitive PCR analysis. J Microbiol Methods 1999, 37(2):165-176. 10.1016/S0167-7012(99)00061-5, 10445315.
21. Sandhu GS, Kline BC, Stockman L, Roberts GD. Molecular probes for diagnosis of fungal infections. J Clin Microbiol 1995, 33(11):2913-2919. 228606, 8576345.
22. Pfeiffer CD, Samsa GP, Schell WA, Reller LB, Perfect JR, Alexander BD. Quantitation of Candida CFU in initial positive blood cultures. J Clin Microbiol 2011, 49(8):2879-2883. 10.1128/JCM.00609-11, 3147732, 21677065.
23. Leaw SN, Chang HC, Sun HF, Barton R, Bouchara JP, Chang TC. Identification of medically important yeast species by sequence analysis of the internal transcribed spacer regions. J Clin Microbiol 2006, 44(3):693-699. 10.1128/JCM.44.3.693-699.2006, 1393093, 16517841.
24. Al-Soud WA, Radstrom P. Purification and characterization of PCR-inhibitory components in blood cells. J Clin Microbiol 2001, 39(2):485-493. 10.1128/JCM.39.2.485-493.2001, 87763, 11158094.
25. Kreader CA. Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl Environ Microbiol 1996, 62(3):1102-1106. 167874, 8975603.
26. Maaroufi Y, De Bruyne JM, Duchateau V, Georgala A, Crokaert F. Early detection and identification of commonly encountered Candida species from simulated blood cultures by using a real-time PCR-based assay. J Mol Diagnostics: JMD 2004, 6(2):108-114.
27. White PL. Detection of seven Candida species using the Light-Cycler system. J Med Microbiol 2003, 52(3):229-238. 10.1099/jmm.0.05049-0, 12621088.
28. Bennett J. Is real-time polymerase chain reaction ready for real use in detecting candidemia?. Clin Infect Dis 2008, 46(6):897-898. 10.1086/528692, 18260754.
29. Shin JH, Nolte FS, Morrison CJ. Rapid identification of Candida species in blood cultures by a clinically useful PCR method. J Clin Microbiol 1997, 35(6):1454-1459. 229766, 9163461.
30. Chang HC, Leaw SN, Huang AH, Wu TL, Chang TC. Rapid identification of yeasts in positive blood cultures by a multiplex PCR method. J Clin Microbiol 2001, 39(10):3466-3471. 10.1128/JCM.39.10.3466-3471.2001, 88373, 11574557.
31. Lau A, Sorrell TC, Chen S, Stanley K, Iredell J, Halliday C. Multiplex tandem PCR: a novel platform for rapid detection and identification of fungal pathogens from blood culture specimens. J Clin Microbiol 2008, 46(9):3021-3027. 10.1128/JCM.00689-08, 2546768, 18632914.
32. Cerikcioglu N, Aksu B, Dal TD, Deniz U, Bilgen HS, Ozek E, Soyletir G. Seminested PCR for detection and identification of Candida species directly from blood culture bottles. New Microbiol 2010, 33(1):57-62.
33. Pryce TM, Palladino S, Price DM, Gardam DJ, Campbell PB, Christiansen KJ, Murray RJ. Rapid identification of fungal pathogens in BacT/ALERT, BACTEC, and BBL MGIT media using polymerase chain reaction and DNA sequencing of the internal transcribed spacer regions. Diagn Microbiol Infect Dis 2006, 54(4):289-297. 10.1016/j.diagmicrobio.2005.11.002, 16466900.
34. Quiles-Melero I, Garcia-Rodriguez J, Romero-Gomez MP, Gomez-Sanchez P, Mingorance J. Rapid identification of yeasts from positive blood culture bottles by pyrosequencing. Eur J Clin Microbiol Infect Dis 2011, 30(1):21-24. 10.1007/s10096-010-1045-5, 20803046.
35. Landlinger C, Baskova L, Preuner S, Willinger B, Buchta V, Lion T. Identification of fungal species by fragment length analysis of the internally transcribed spacer 2 region. Eur J Clin Microbiol Infect Dis 2009, 28(6):613-622. 10.1007/s10096-008-0683-3, 19104852.
36. Nguyen MH, Wissel MC, Shields RK, Salomoni MA, Hao B, Press EG, Shields RM, Cheng S, Mitsani D, Vadnerkar A, et al. Performance of Candida real-time polymerase chain reaction, beta-D-glucan assay, and blood cultures in the diagnosis of invasive candidiasis. Clin Infect Dis 2012, 54(9):1240-1248. 10.1093/cid/cis200, 22431804.
37. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998, 8(3):175-185. 10.1101/gr.8.3.175, 9521921.
38. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8(3):186-194.
39. Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Res 1998, 8(3):195-202. 10.1101/gr.8.3.195, 9521923.
40. Hall L, Wohlfiel S, Roberts GD. Experience with the MicroSeq D2 large-subunit ribosomal DNA sequencing kit for identification of commonly encountered, clinically important yeast species. J Clin Microbiol 2003, 41(11):5099-5102. 10.1128/JCM.41.11.5099-5102.2003, 262493, 14605145.
41. Balajee SA, Borman AM, Brandt ME, Cano J, Cuenca-Estrella M, Dannaoui E, Guarro J, Haase G, Kibbler CC, Meyer W, et al. Sequence-based identification of Aspergillus, fusarium, and mucorales species in the clinical mycology laboratory: where are we and where should we go from here?. J Clin Microbiol 2009, 47(4):877-884. 10.1128/JCM.01685-08, 2668331, 19073865.