Advances and prospects for molecular diagnostics of fungal infections

Current Infectious Disease Reports

Volumn 12, Issue 6, 2010, Pages 430-436

  Bretagne, Stéphane ^a,b,c  

^a HENRI MONDOR HOSPITAL   (France)

^b INSTITUT PASTEUR   (France)

^c UNIVERSITÉ PARIS EST CRÉTEIL   (France)

Author keywords

Diagnosis; Invasive aspergillosis; Invasive candidiasis; Real time quantitative PCR

Indexed keywords

FUNGAL DNA;

ASPERGILLOSIS; CANDIDIASIS; CHECKLIST; DIAGNOSTIC PROCEDURE; DNA EXTRACTION; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; HUMAN; LUNG LAVAGE; MYCOSIS; NONHUMAN; POLYMERASE CHAIN REACTION; RELIABILITY; REVIEW; SENSITIVITY AND SPECIFICITY; SYSTEMIC MYCOSIS;

EID: 77958184866     PISSN: 15233847     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11908-010-0139-7     Document Type: Review

References (49)

1. B De Pauw TJ Walsh JP Donnelly, et al. 2008 Revised definitions of invasive fungal disease from the European organization for research and treatment of cancer/invasive fungal infections cooperative group and the national institute of allergy and infectious diseases mycoses study group (EORTC/MSG) consensus group Clin Infect Dis 46 1813 1821 10.1086/588660 18462102
2. CD Pfeiffer JP Fine N Safdar 2006 Diagnosis of invasive aspergillosis using a galactomannan assay: a meta-analysis Clin Infect Dis 42 1417 1427 1:CAS:528:DC%2BD28Xlt1Cqu74%3D 10.1086/503427 16619154
3. MA Mennink-Kersten JP Donnelly PE Verweij 2004 Detection of circulating galactomannan for the diagnosis and management of invasive aspergillosis Lancet Infect Dis 4 349 357 1:CAS:528:DC%2BD2cXltlCktLg%3D 10.1016/S1473-3099(04)01045- X 15172343 (Pubitemid 38692699)
4. PD Khot DN Fredricks 2009 PCR-based diagnosis of human fungal infections Expert Rev Anti Infect Ther 7 1201 1221 1:CAS:528:DC%2BD1MXhsFaqsbbP 10.1586/eri.09.104 19968513
5. SA Bustin V Benes JA Garson, et al. 2009 The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments Clin Chem 55 611 622 1:CAS:528:DC%2BD1MXktVWqs7g%3D 10.1373/clinchem.2008.112797 19246619
6. S Bretagne JM Costa 2005 Towards a molecular diagnosis of invasive aspergillosis and disseminated candidosis FEMS Immunol Med Microbiol 45 361 368 1:CAS:528:DC%2BD2MXpvFemsb4%3D 10.1016/j.femsim.2005.05.012 16054349 (Pubitemid 41247773)
7. S Kwok R Higuchi 1989 Avoiding false positives with PCR. Nature 339 237 238 1:STN:280:DyaL1M3jvVGqsw%3D%3D
8. S Bretagne JM Costa A Marmorat-Khuong, et al. 1995 Detection of Aspergillus species DNA in bronchoalveolar lavage samples by competitive PCR J Clin Microbiol 33 1164 1168 1:CAS:528:DyaK2MXmtVajtLo%3D 7615723
9. HJ Burkardt 2000 Standardization and quality control of PCR analyses Clin Chem Lab Med 38 87 91 1:CAS:528:DC%2BD3cXktl2lur8%3D 10.1515/CCLM.2000.014 10834394
10. J Loeffler H Hebart R Bialek, et al. 1999 Contaminations occurring in fungal PCR assays J Clin Microbiol 37 1200 1202 1:CAS:528:DyaK1MXitFGktLg%3D 10074553
11. D Rimek AP Garg WH Haas R Kappe 1999 Identification of contaminating fungal DNA sequences in zymolyase J Clin Microbiol 37 830 831 1:CAS:528:DyaK1MXhsleitL4%3D 9986868
12. PL White S Bretagne L Klingspor, et al. 2010 Aspergillus PCR: one step closer towards standardisation J Clin Microbiol 48 1231 1240 1:CAS:528:DC%2BC3cXmt1Kgtbc%3D 10.1128/JCM.01767-09 20147637
13. ME Garcia JL Blanco J Caballero D Gargallo-Viola 2002 Anticoagulants interfere with PCR used to diagnose invasive aspergillosis J Clin Microbiol 40 1567 1568 1:CAS:528:DC%2BD38XjtlCmsbw%3D 10.1128/JCM.40.4.1567-1568.2002 11923400 (Pubitemid 34279944)
14. Harrison E, Bowyer P, Sugrue MW, et al.: Fungal DNA contamination of blood collection tubes. Presented at the 48th Interscience Conference on Antimicrobial Agents and Chemotherapy. American Society for Microbiology. Washington, DC; October 25-28, 2008.
15. C Costa JM Costa C Desterke, et al. 2002 Real-time PCR coupled with automated DNA extraction and detection of galactomannan antigen in serum by enzyme-linked immunosorbent assay for diagnosis of invasive aspergillosis J Clin Microbiol 40 2224 2227 1:CAS:528:DC%2BD38XltFOntbo%3D 10.1128/JCM.40.6.2224- 2227.2002 12037092 (Pubitemid 34596412)
16. L Millon F Grenouillet J Crouzet, et al. 2010 False-positive Aspergillus real-time PCR assay due to a nutritional supplement in a bone marrow transplant recipient with gvh disease Med Mycol 48 661 664 1:CAS:528:DC%2BC3cXlvFOiu7w%3D 10.3109/13693780903451836 20392146
17. RR Paterson 2007 Internal amplification controls have not been employed in fungal PCR hence potential false negative results J Appl Microbiol 102 1 10 1:CAS:528:DC%2BD2sXitlOms7Y%3D 10.1111/j.1365-2672.2006.03220.x 17184314 (Pubitemid 44952782)
18. PL White CJ Linton MD Perry, et al. 2006 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 42 479 486 1:CAS:528:DC%2BD28XhvFynu7c%3D 10.1086/499949 16421791 (Pubitemid 43202519)
19. GJ van Doornum J Guldemeester AD Osterhaus HG Niesters 2003 Diagnosing herpes virus infections by real-time amplification and rapid culture J Clin Microbiol 41 576 580 10.1128/JCM.41.2.576-580.2003 12574249 (Pubitemid 36184164)
20. JM Costa P Ernault E Gautier S Bretagne 2001 Prenatal diagnosis of congenital toxoplasmosis by duplex real-time PCR using fluorescence resonance energy transfer hybridization probes Prenat Diagn 21 85 88 1:CAS:528: DC%2BD3MXis1equrs%3D 10.1002/1097-0223(200102)21:2<85::AID-PD18>3.0.CO;2-1 11241531 (Pubitemid 32220707)
21. JM Costa C Pautas P Ernault, et al. 2000 Real-time PCR for diagnosis and follow-up of Toxoplasma reactivation after allogeneic stem cell transplantation using fluorescence resonance energy transfer hybridization probes J Clin Microbiol 38 2929 2932 1:CAS:528:DC%2BD3cXlvFKgsrc%3D 10921953
22. N Raddadi A Belaouis I Tamagnini, et al. 2009 Characterization of polyvalent and safe bacillus thuringiensis strains with potential use for biocontrol J Basic Microbiol 49 293 303 1:CAS:528:DC%2BD1MXovFShtrc%3D 10.1002/jobm.200800182 19025870
23. V Swarup MR Rajeswari 2007 Circulating (cell-free) nucleic acids-a promising, noninvasive tool for early detection of several human diseases FEBS Lett 581 795 799 1:CAS:528:DC%2BD2sXit12iu7w%3D 10.1016/j.febslet.2007.01.051 17289032 (Pubitemid 46282711)
24. C Mengoli M Cruciani RA Barnes, et al. 2009 Use of PCR for diagnosis of invasive aspergillosis: systematic review and meta-analysis Lancet Infect Dis 9 89 96 1:CAS:528:DC%2BD1MXjt1Snt7s%3D 10.1016/S1473-3099(09)70019-2 19179225
25. F Suarez O Lortholary S Buland, et al. 2008 Detection of circulating Aspergillus fumigatus DNA by real-time PCR assay of large serum volumes improves early diagnosis of invasive aspergillosis in high-risk adult patients under hematologic surveillance J Clin Microbiol 46 3772 3777 1:CAS:528: DC%2BD1cXhsVyqsL%2FF 10.1128/JCM.01086-08 18845828
26. CO Morton J Loeffler A De Luca, et al. 2010 Dynamics of extracellular release of Aspergillus fumigatus DNA and galactomannan during growth in blood and serum J Med Microbiol 59 408 413 1:CAS:528:DC%2BC3cXlsleksbc%3D 10.1099/jmm.0.017418-0 20035025
27. HP Horz S Scheer ME Vianna G Conrads 2010 New methods for selective isolation of bacterial DNA from human clinical specimens Anaerobe 16 47 53 1:CAS:528:DC%2BC3cXhvFGjtrY%3D 10.1016/j.anaerobe.2009.04.009 19463963
28. E Bellemain T Carlsen C Brochmann, et al. 2010 ITS as DNA barcode for fungi: an in silico approach reveals potential PCR biases BMC Microbiology 10 189 10.1186/1471-2180-10-189 20618939
29. A Gomez-Lopez MT Martin-Gomez P Martin-Davila, et al. 2006 Detection of fungal DNA by real-time polymerase chain reaction: evaluation of 2 methodologies in experimental pulmonary aspergillosis Diagn Microbiol Infect Dis 56 387 393 1:CAS:528:DC%2BD28Xht12rtb3K 10.1016/j.diagmicrobio.2006.06.010 16876374 (Pubitemid 44854352)
30. ML Herrera AC Vallor JA Gelfond, et al. 2009 Strain-dependent variation in 18 s ribosomal DNA copy numbers in Aspergillus fumigatus J Clin Microbiol 47 1325 1332 1:CAS:528:DC%2BD1MXmt1Cqsr8%3D 10.1128/JCM.02073-08 19261786
31. FF Tuon 2007 A systematic literature review on the diagnosis of invasive aspergillosis using polymerase chain reaction (PCR) from bronchoalveolar lavage clinical samples Rev Iberoam Micol 24 89 94 10.1016/S1130-1406(07)70020-7 17604424
32. PD Khot DL Ko RC Hackman DN Fredricks 2008 Development and optimization of quantitative PCR for the diagnosis of invasive aspergillosis with bronchoalveolar lavage fluid BMC Infect Dis 8 73 10.1186/1471-2334-8-73 18510764 (Pubitemid 351943432)
33. E Frealle K Decrucq F Botterel, et al. 2009 Diagnosis of invasive aspergillosis using bronchoalveolar lavage in haematology patients: influence of bronchoalveolar lavage human DNA content on real-time PCR performance Eur J Clin Microbiol Infect Dis 28 223 232 1:CAS:528:DC%2BD1MXitlGnsr8%3D 10.1007/s10096-008-0616-1 18763000
34. Lass-Flörl C, Cui X, Hughes M, et al.: Clinical performance of FXG: resp (asp +) assay for Aspergillus on lung and other tissue samples. Presented at the 48th Interscience Conference on Antimicrobial Agents and Chemotherapy. American Society for Microbiology. Washington, DC; October 25-28, 2008.
35. M Cuenca-Estrella Y Meije C Diaz-Pedroche, et al. 2009 Value of serial quantification of fungal DNA by a real-time PCR-based technique for early diagnosis of invasive aspergillosis in patients with febrile neutropenia J Clin Microbiol 47 379 384 1:CAS:528:DC%2BD1MXjtVyltLY%3D 10.1128/JCM.01716-08 19109479
36. RA Barnes PL White C Bygrave, et al. 2009 Clinical impact of enhanced diagnosis of invasive fungal disease in high-risk haematology and stem cell transplant patients J Clin Pathol 62 64 69 1:STN:280:DC%2BD1M%2Fgslykug%3D%3D 10.1136/jcp.2008.058354 19103864
37. H Hebart L Klingspor T Klingebiel, et al. 2009 A prospective randomized controlled trial comparing PCR-based and empirical treatment with liposomal amphotericin B in patients after allo-SCT Bone Marrow Transplant 43 553 561 1:CAS:528:DC%2BD1MXktFCjtLg%3D 10.1038/bmt.2008.355 19079316
38. F Botterel C Farrugia P Ichai, et al. 2008 Real-time PCR on the first galactomannan-positive serum sample for diagnosing invasive aspergillosis in liver transplant recipients Transpl Infect Dis 10 333 338 1:STN:280: DC%2BD1cnltFahsA%3D%3D 10.1111/j.1399-3062.2008.00323.x 18627580
39. L Millon R Piarroux E Deconinck, et al. 2005 Use of real-time PCR to process the first galactomannan-positive serum sample in diagnosing invasive aspergillosis J Clin Microbiol 43 5097 5101 1:CAS:528:DC%2BD2MXhtFGqtrfN 10.1128/JCM.43.10.5097-5101.2005 16207969 (Pubitemid 41484011)
40. M Hummel B Spiess OA Cornely, et al. 2010 Aspergillus PCR testing: results from a prospective PCR study within the Ambiload trial Eur J Haematol 85 164 169 1:CAS:528:DC%2BC3cXhtVOntbzF 20374275
41. A Lau C Halliday SC Chen, et al. 2009 Comparison of whole blood, serum, and plasma for early detection of candidemia by multiplex-tandem PCR J Clin Microbiol 48 811 816 10.1128/JCM.01650-09 20042634
42. L Metwally DJ Fairley PV Coyle, et al. 2008 Comparison of serum and whole-blood specimens for the detection of Candida DNA in critically ill, non-neutropenic patients J Med Microbiol 57 1269 1272 1:STN:280: DC%2BD1cnitVCksA%3D%3D 10.1099/jmm.0.2008/002444-0 18809556
43. MJ Struelens 2010 Detection of microbial DNAemia: does it matter for sepsis management? Intensive Care Med 36 193 195 10.1007/s00134-009-1710-2 19924397
44. A Lau S Chen S Sleiman T Sorrell 2009 Current status and future perspectives on molecular and serological methods in diagnostic mycology Future Microbiol 4 1185 1222 1:CAS:528:DC%2BD1MXhtl2kt7vF 10.2217/fmb.09.70 19895220
45. M von Lilienfeld-Toal LE Lehmann AD Raadts, et al. 2009 Utility of a commercially available multiplex real-time PCR assay to detect bacterial and fungal pathogens in febrile neutropenia J Clin Microbiol 47 2405 2410 10.1128/JCM.00491-09
46. RM Madej J Davis MJ Holden, et al. 2010 International standards and reference materials for quantitative molecular infectious disease testing J Mol Diagn 12 133 143 1:CAS:528:DC%2BC3cXkvVCmt70%3D 10.2353/jmoldx.2010.090067 20075208
47. BE de Pauw JP Donnelly 2009 Timely intervention for invasive fungal disease: should the road now lead to the laboratory instead of the pharmacy? Clin Infect Dis 48 1052 1054 10.1086/597396 19281329
48. R Whitley 2008 The new age of molecular diagnostics for microbial agents N Engl J Med 358 988 989 1:CAS:528:DC%2BD1cXjtVSmu78%3D 10.1056/NEJMp0708085 18256386 (Pubitemid 351347097)
49. G Palacios J Druce L Du, et al. 2008 A new arenavirus in a cluster of fatal transplant-associated diseases N Engl J Med 358 991 998 1:CAS:528:DC%2BD1cXjtVSltLo%3D 10.1056/NEJMoa073785 18256387 (Pubitemid 351347098)