Abstract
PCR can aid in the diagnosis of invasive fungal disease (IFD). While the large number of “in-house” methodologies drives technological diversity, providing robustness, they make it difficult to identify optimal strategies, limiting standardization, and widespread acceptance. No matter how efficient, PCR utility will be limited by the quality of extracted nucleic acid. This chapter highlights benefits and limitations affecting the nucleic acid extraction process, before focusing on recent recommendations that through multicenter evaluation have provided optimal and standardized methodology.
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References
Barnes RA, Stocking K, Bowden S, Poynton MH, White PL (2013) Prevention and diagnosis of invasive fungal disease in high-risk patients within an integrative care pathway. J Infect 67(3):206–214
Morrissey CO, Chen SC, Sorrell TC et al (2013) Galactomannan and PCR versus culture and histology for directing use of antifungal treatment for invasive aspergillosis in high-risk haematology patients: a randomised controlled trial. Lancet Infect Dis 13(6):519–528
Aguado JM, Vázquez L, Fernández-Ruiz M, Villaescusa T et al (2014) Serum galactomannan versus a combination of galactomannan and PCR-based Aspergillus DNA detection for early therapy of invasive aspergillosis in high-risk hematological patients: a randomized controlled trial. Clin Infect Dis 60(3):405–414
Leeflang MM, Debets-Ossenkopp YJ, Visser CE, Scholten RJ, Hooft L, Bijlmer HA, Reitsma JB, Bossuyt PM, Vandenbroucke-Grauls CM (2009) Galactomannan detection for invasive aspergillosis in immunocompromized patients. Cochrane Database Syst Rev 8, CD007394
Pfeiffer CD, Fine JP, Safdar N (2006) Diagnosis of invasive aspergillosis using a galactomannan assay: a meta-analysis. Clin Infect Dis 42:1417–1427
Mikulska M, Calandra T, Sanguinetti M, Poulain D, Viscoli C (2010) Third European Conference on Infections in Leukemia Group. The use of mannan antigen and anti-mannan antibodies in the diagnosis of invasive candidiasis: recommendations from the Third European Conference on Infections in Leukemia. Crit Care 14(6):R222
Huang HR, Fan LC, Rajbanshi B, Xu JF (2015) Evaluation of a new cryptococcal antigen lateral flow immunoassay in serum, cerebrospinal fluid and urine for the diagnosis of cryptococcosis: a meta-analysis and systematic review. PLoS One 10(5):e0127117
Carmona EM, Limper AH (2011) Update on the diagnosis and treatment of Pneumocystis pneumonia. Ther Adv Respir Dis 5:41–59
Karageorgopoulos DE, Vouloumanou EK, Ntziora F, Michalopoulos A, Rafailidis PI, Falagas ME (2011) B-D-Glucan assay for the diagnosis of invasive fungal infections: a meta-analysis. Clin Infect Dis 52:750–770
Arvanitis M, Anagnostou T, Mylonakis E (2015) Galactomannan and polymerase chain reaction-based screening for invasive aspergillosis among high-risk hematology patients: a diagnostic meta-analysis. Clin Infect Dis 61(8):1263–1272
White PL, Barnes RA. Molecular diagnosis of fungal disease. (In Press) In: Barton R and Christopher Kibbler (eds) The Oxford textbook of medical mycology, section 5—diagnosis. Oxford University Press, Oxford, UK
White PL, Donnelly JP, Barnes RA (2014) Developments in the molecular diagnosis of invasive fungal disease in: fungal infections in cancer patients online book. Bilimsel Tıp Publishing, Ankara, http://www.ifikitap.org
Donnelly JP (2006) Polymerase chain reaction for diagnosing invasive aspergillosis: getting closer but still a ways to go. Clin Infect Dis 42:487–489
Blennow O, Mattsson J (2011) Standardization of Aspergillus PCR is needed. Bone Marrow Transplant 46(7):1018
Ascioglu S, Rex JH, de Pauw B et al (2002) Defining opportunistic invasive fungal infections in immunocompromised patients with cancer and hematopoietic stem cell transplants: an international consensus. Clin Infect Dis 34(1):7–14
De Pauw B, Walsh TJ, Donnelly JP 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(12):1813–1821
Jordanides NE, Allan EK, McLintock LA, Copland M, Devaney M, Stewart K, Parker AN, Johnson PRE, Holyoake TL, Jones BL (2005) A prospective study of real-time panfungal PCR for the early diagnosis of invasive fungal infection in haemato-oncology patients. BMT 35(4):389–395
Landlinger C, Preuner S, Willinger B, Haberpursch B, Racil Z, Mayer J, Lion T (2009) Species-specific identification of a wide range of clinically relevant fungal pathogens by use of Luminex xMAP technology. J Clin Microbiol 47(4):1063–1073
White PL, Wingard JR, Bretagne S, Löffler J, Patterson TF, Slavin MA, Barnes RA, Pappas PG, Donnelly JP (2015) Aspergillus PCR: a systematic review of evidence for clinical use in comparison with antigen testing. Clin Infect Dis. 61:1293–1303
Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55(4):611–622
Yamakami Y, Hashimoto A, Yamagata E, Kamberi P, Karashima R, Nagai H, Nasu M (1998) Evaluation of PCR for detection of DNA specific for Aspergillus species in sera of patients with various forms of pulmonary aspergillosis. J Clin Microbiol 36:3619–3623
Halliday C, Hoile R, Sorrell T et al (2005) Role of prospective screening of blood for invasive aspergillosis by polymerase chain reaction in febrile neutropenic recipients of haematopoietic stem cell transplants and patients with acute leukaemia. Br J Haematol 132:478–486
Buchheidt D, Hummel M, Schleiermacher D et al (2004) Prospective clinical evaluation of a light cycler-mediated polymerase chain reaction assay, a nested-PCR assay and a galactomannan enzyme-linked immunosorbent assay for the detection of invasive aspergillosis in neutropenic cancer patients and haematological stem cell transplant recipients. Br J Haematol 125:196–202
Verweij PE (2005) Advances in diagnostic testing. Med Mycol 43(Suppl 1):121–124
Lass-Flörl C, Gunsilius E, Gastl G et al (2004) Diagnosing invasive aspergillosis during antifungal therapy by PCR analysis of blood samples. J Clin Microbiol 42(9):4154–4157
Lass-Flörl C, Aigner J, Gunsilius E, Petzer A, Nachbaur D, Gastl G, Einsele H, Löffler J, Dierich MP, Würzner R (2001) Screening for Aspergillus spp. using polymerase chain reaction of whole blood samples from patients with haematological malignancies. Br J Haematol 113(1):180–184
Bart-Delabesse E, Marmarot-Khuong A, Costa JM, Dubreuil-Lemaire ML, Bretagne S (1996) Detection of Aspergillus DNA in bronchoalveolar lavage fluid of AIDS patients by polymerase chain reaction. Euro J Clin Microbiol Infect Dis 15:24–25
Latge JP (1999) Aspergillus fumigatus and Aspergillosis. Clin Microbiol Rev 12:310–350
Bretagne S, Costa JM, Marmarot-Khuong A, Poron F, Cordonnier C, Vidaud M, Fleury-Feith J (1995) Detection of Aspergillus species DNA in bronchoalveolar lavage samples by competitive PCR. J Clin Microbiol 33:1164–1168
Williamson ECM (2001) Molecular approaches to fungal infections in immunocompromised patients. MD Thesis. University of Bristol
Harrison E, Stalhberger T, Whelan R, Sugrue M, Wingard JR, Alexander BD, Follett SA, Bowyer P, Denning DW, Aspergillus Technology Consortium (AsTeC) (2010) Aspergillus DNA contamination in blood collection tubes. Diagn Microbiol Infect Dis 67(4):392–394
Loeffler J, Hebart H, Bialek R, Hagmeyer L, Schmidt D, Serey FP, Hartmann M, Eucker J, Einsele H (1999) Contaminations occurring in fungal PCR assays. J Clin Microbiol 7(4):1200–1202
Rimek D, Garg AP, Haas WH, Kappe R (1999) Identification of contaminating fungal DNA sequences in Zymolyase. J Clin Microbiol 37(3):830–831
Perry MD, White PL, Barnes RA (2014) Comparison of four automated nucleic acid extraction platforms for the recovery of DNA from Aspergillus fumigatus. J Med Microbiol 63:1160–1166
Jaeger EE, Carroll NM, Choudhury S et al (2000) Rapid detection and identification of Candida, Aspergillus, and Fusarium species in ocular samples using nested PCR. J Clin Microbiol 38(8):2902–2908
Garcia ME, Blanco JL, Caballero J, Gargallo-Viola D (2002) Anticoagulants interfere with PCR used to diagnose Invasive Aspergillosis. J Clin Microbiol 40:1567–1568
White PL, Bretagne S, Klingspor L et al (2010) Aspergillus PCR: one step closer to standardization. J Clin Microbiol 48(4):1231–1240
White PL, Mengoli C, Bretagne S et al (2011) Evaluation of Aspergillus PCR protocols for testing serum specimens. J Clin Microbiol 49(11):3842–3848
Clancy CJ, Nguyen MH (2013) Finding the “missing 50 %”of invasive candidiasis: how nonculture diagnostics will improve understanding of disease spectrum and transform patient care. Clin Infect Dis 56:1284–1292
Nguyen MH, Wissel MC, Shields RK, Salomoni MA, Hao B, Press EG, Shields RM, Cheng S, Mitsani D, Vadnerkar A, Silveira FP, Kleiboeker SB, Clancy CJ (2012) Performance of Candida real-time polymerase chain reaction, β-D-glucan assay, and blood cultures in the diagnosis of invasive candidiasis. Clin Infect Dis 54(9):1240–1248
Lau A, Halliday C, Chen SCA, Playford EG, Stanley K, Sorrell TC (2010) Comparison of whole blood, serum and plasma for early detection of candidemia by multiplex-tandem PCR. J Clin Microbiol 48:811–816
Metwally L, Fairley DJ, Coyle PV, Hay RJ, Hedderwick S, McCloskey B, O'Neill HJ, Webb CH, McMullan R (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
Fuller DD, Davis TE Jr, Denys GA, York MK (2001) Evaluation of BACTEC MYCO/Flytic medium for recovery of mycobacteria, fungi and bacteria from blood. J Clin Microbiol 39:2933–2936
Vetter E, Torgerson C, Feuker A et al (2001) Comparison of the BACTEC/MYCO/flytic bottle to the isolator tube, BACTEC plus aerobic F/bottle and BACTEC anaerobic lytic/10 bottle and comparison of the BACTEC plus aerobic F/bottle to the isolator tube for recovery of bacteria, mycobacteria and fungi from blood. J Clin Microbiol 39:4830–4836
Simonneau E, Kelly M, Labbe AC, Roy J, Laverdierem M (2005) What is the clinical significance of positive blood cultures with Aspergillus spp. in hematopoietic stem cell transplant recipients? A 23 year experience. Bone Marrow Transplant 35:303–306
Furuyama A, Kanno S, Kobayashi T, Hirano S (2009) Extrapulmonary translocation of intratracheally instilled fine and ultrafine particles via direct and alveolar macrophage-associated routes. Arch Toxicol 83(5):429–437
White PL, Wiederhold N, Loeffler J, Najvar L, Melchers M, Herrera M, Bretagne S, Wickes B, Kirkpatrick W, Barnes RA, Donnelly JP, Patterson TF (2016) A comparison of the non-culture blood-based tests available to aid in the diagnosis of invasive aspergillosis in an animal model. J Clin Microbiol 64: 960–966.
Morton CO, Loeffler J, De Luca A, Frost S, Kenny C, Duval S, Romani L, Rogers TR (2010) Dynamics of extracellular release of Aspergillus fumigatus DNA and galactomannan during growth in blood and serum. J Med Microbiol 59:408–413
White PL, Barnes RA (2009) Aspergillus PCR. In: Latge J-P, Steinbach WJ (eds) Aspergillus fumigatus and aspergillosis, 1st edn. ASM Press, Washington DC, USA, pp 373–388
Loeffler J, Henke N, Herbart H et al (2000) Quantification of fungal DNA by using fluorescence resonance energy transfer and the light cycler system. J Clin Microbiol 38:586–590
Loeffler J, Herbart H, Sepe S et al (1998) Detection of PCR-amplified fungal DNA by using a PCR-ELISA system. Med Mycol 36:275–279
Van Burik JAH, Schreckhise RW, White TC, Bowden RA, Myerson D (1998) Comparison of six extraction techniques for isolation of DNA from filamentous fungi. Med Mycol 1998(36):299–303
Rogers TR, Morton CO, Springer J, Conneally E, Heinz W, Kenny C, Frost S, Einsele H, Loeffler J (2013) Combined real-time PCR and galactomannan surveillance improves diagnosis of invasive aspergillosis in high risk patients with haematological malignancies. Br J Haematol 161(4):517–524
White PL, Parr C, Thornton C, Barnes RA (2013) Evaluation of real-time PCR, galactomannan enzyme-linked immunosorbent assay (ELISA), and a novel lateral-flow device for diagnosis of invasive aspergillosis. J Clin Microbiol 51(5):1510–1516
Springer J, Morton CO, Perry M et al (2013) Multicenter comparison of serum and whole-blood specimens for detection of Aspergillus DNA in high-risk hematological patients. J Clin Microbiol 51(5):1445–1450
Ramírez M, Castro C, Palomares JC, Torres MJ, Aller AI, Ruiz M, Aznar J, Martín-Mazuelos E (2009) Molecular detection and identification of Aspergillus spp. from clinical samples using real-time PCR. Mycoses 52(2):129–134
Barnes RA, White PL, Bygrave C, Evans N, Healy B, Kell J (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
White PL, Linton CJ, Perry MD, Johnson EM, Barnes RA (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(4):479–486
Chong GL, van de Sande WW, Dingemans GJ et al (2015) Validation of a new Aspergillus real-time PCR assay for direct detection of Aspergillus and azole resistance of Aspergillus fumigatus on bronchoalveolar lavage fluid. J Clin Microbiol 53:868–874
Guinea J, Padilla C, Escribano P, Muñoz P, Padilla B, Gijón P, Bouza E (2013) Evaluation of MycAssay™ Aspergillus for diagnosis of invasive pulmonary aspergillosis in patients without hematological cancer. PLoS One 8(4), e61545
Luong ML, Clancy CJ, Vadnerkar A, Kwak EJ, Silveira FP, Wissel MC, Grantham KJ, Shields RK, Crespo M, Pilewski J, Toyoda Y, Kleiboeker SB, Pakstis D, Reddy SK, Walsh TJ, Nguyen MH (2011) Comparison of an Aspergillus real-time polymerase chain reaction assay with galactomannan testing of bronchoalvelolar lavage fluid for the diagnosis of invasive pulmonary aspergillosis in lung transplant recipients. Clin Infect Dis 52(10):1218–1226
Khot PD, Ko DL, Hackman RC, Fredricks DN (2008) Development and optimization of quantitative PCR for the diagnosis of invasive aspergillosis with bronchoalveolar lavage fluid. BMC Infect Dis 8:73
Melchers WJ, Verweij PE, van den Hurk P, van Belkum A, De Pauw BE, Hoogkamp-Korstanje JA, Meis JF (1994) General primer-mediated PCR for detection of Aspergillus species. J Clin Microbiol 32(7):1710–1717
Bretagne S, Costa JM (2006) Towards a nucleic acid-based diagnosis in clinical parasitology and mycology. Clin Chim Acta 363:221–228
Löffler J, Schimdt K, Herbart H, Schumacher U, Einsele H (2002) Automated extraction of genomic DNA from medically important yeast species and filamentous fungi by using the MagNA Pure LC system. J Clin Microbiol 40:2240–2243
White PL, Hibbitts SJ, Perry MD, Green J, Stirling E, Woodford L, McNay G, Stevenson R, Barnes RA (2014) Evaluation of a commercially developed semi-automated PCR-SERS assay for the diagnosis of invasive fungal disease. J Clin Microbiol 52(10):3536–3543
Costa C, Costa JM, Desterke C 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
White PL, Posso RB, Barnes RA (2015) Analytical and clinical evaluation of the PathoNostics AsperGenius assay for detection of invasive aspergillosis and resistance to azole antifungal drugs during testing of serum samples. J Clin Microbiol 53(7):2115–2121
Loeffler J, Mengoli C, Springer J, Bretagne S, Cuenca Estrella M, Klingspor L, Lagrou K, Melchers WJG, Morton CO, Barnes RA, Donnelly JP, White PL (2015) Analytical comparison of in vitro spiked human serum and plasma for the PCR-based detection of Aspergillus fumigatus DNA—a study by the European Aspergillus PCR Initiative J Clin Microbiol 53:2838–2845
White PL, Barnes RA (2006) Aspergillus PCR: platforms, strengths and weaknesses. Med Mycol 44(Suppl 1):191–198
Beyda ND, Alam MJ, Garey KW (2013) Comparison of the T2Dx instrument with T2Candida assay and automated blood culture in the detection of Candida species using seeded blood samples. Diagn Microbiol Infect Dis 77(4):324–326
White PL, Perry MD, Loeffler J, Melchers W, Klingspor L et al (2010) Critical stages of extracting DNA from Aspergillus fumigatus in whole-blood specimens. J Clin Microbiol 48(10):3753–3755
Springer J, Schloßnagel H, Heinz W, Doedt T, Soeller R, Einsele H, Loeffler J (2012) A novel extraction method combining plasma with a whole-blood fraction shows excellent sensitivity and reproducibility for patients at high risk for invasive aspergillosis. J Clin Microbiol 50(8):2585–2591
McCulloch E, Ramage G, Jones B, Warn P, Kirkpatrick WR, Patterson TF, Williams C (2009) Don't throw your blood clots away: use of blood clot may improve sensitivity of PCR diagnosis in invasive aspergillosis. J Clin Pathol 62:539–541
Munoz-Cadavid, Rudd S, Zaki SR, Patel M, Moser SA, Brandt ME, Gomez BL (2010) Improving molecular detection of fungal DNA in formalin fixed paraffin embedded tissues: Comparison of five tissue DNA extraction methods using panfungal PCR. J Clin Microbiol 48(6):2147–2153
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White, P.L., Barnes, R.A. (2017). Isolation of Nucleic Acids for Fungal Diagnosis. In: Lion, T. (eds) Human Fungal Pathogen Identification. Methods in Molecular Biology, vol 1508. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6515-1_12
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