337
Views
124
CrossRef citations to date
0
Altmetric
Review

PCR-based diagnosis of human fungal infections

&
Pages 1201-1221 | Published online: 10 Jan 2014

References

  • Bustin SA, Benes V, Garson JA et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem.55, 611–622 (2009).
  • Loeffler J, Hebart H, Bialek R et al. Contaminations occurring in fungal PCR assays. J. Clin. Microbiol.37, 1200–1202 (1999).
  • Van Burik JA, Myerson D, Schreckhise RW, Bowden RA. Panfungal PCR assay for detection of fungal infection in human blood specimens. J. Clin. Microbiol.36, 1169–1175 (1998).
  • Ou CY, Moore JL, Schochetman G. Use of UV irradiation to reduce false positivity in polymerase chain reaction. Biotechniques10, 442, 444, 446 (1991).
  • Khot PD, Ko DL, Hackman RC, Fredricks DN. Development and optimization of quantitative PCR for the diagnosis of invasive aspergillosis with bronchoalveolar lavage fluid. BMC Infect. Dis.8, 73 (2008).
  • Wages JM Jr, Cai D, Fowler AK. Removal of contaminating DNA from PCR reagents by ultrafiltration. Biotechniques16, 1014–1017 (1994).
  • Jordan JA, Durso MB. Comparison of 16S rRNA gene PCR and BACTEC 9240 for detection of neonatal bacteremia. J. Clin. Microbiol.38, 2574–2578 (2000).
  • Silkie SS, Tolcher MP, Nelson KL. Reagent decontamination to eliminate false-positives in Escherichia coli qPCR. J. Microbiol. Methods72, 275–282 (2008).
  • Kwok S, Higuchi R. Avoiding false positives with PCR. Nature339, 237–238 (1989).
  • Longo MC, Berninger MS, Hartley JL. Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions. Gene93, 125–128 (1990).
  • Einsele H, Hebart H, Roller G et al. Detection and identification of fungal pathogens in blood by using molecular probes. J. Clin. Microbiol.35, 1353–1360 (1997).
  • Herrera ML, Vallor AC, Gelfond JA, Patterson TF, Wickes BL. Strain-dependent variation in 18S ribosomal DNA copy numbers in Aspergillus fumigatus. J. Clin. Microbiol.47, 1325–1332 (2009).
  • Landlinger C, Preuner S, Willinger B et al. Species-specific identification of a wide range of clinically relevant fungal pathogens by use of Luminex xMAP technology. J. Clin. Microbiol.47, 1063–1073 (2009).
  • De Pauw B, Walsh TJ, Donnelly JP et al. 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 (2008).
  • Segal BH. Aspergillosis. N. Engl. J. Med.360, 1870–1884 (2009).
  • Balajee SA, Gribskov JL, Hanley E, Nickle D, Marr KA. Aspergillus lentulus sp. nov., a new sibling species of A. fumigatus. Eukaryot. Cell4, 625–632 (2005).
  • Reichenberger F, Habicht J, Matt P et al. Diagnostic yield of bronchoscopy in histologically proven invasive pulmonary aspergillosis. Bone Marrow Transplant24, 1195–1199 (1999).
  • Levy H, Horak DA, Tegtmeier BR, Yokota SB, Forman SJ. The value of bronchoalveolar lavage and bronchial washings in the diagnosis of invasive pulmonary aspergillosis. Respir. Med.86, 243–248 (1992).
  • Wheat LJ, Hackett E, Durkin M et al. Histoplasmosis-associated cross-reactivity in the BioRad Platelia Aspergillus enzyme immunoassay. Clin. Vaccine Immunol.14, 638–640 (2007).
  • Aquino VR, Goldani LZ, Pasqualotto AC. Update on the contribution of galactomannan for the diagnosis of invasive aspergillosis. Mycopathologia163, 191–202 (2007).
  • Fortun J, Martin-Davila P, Alvarez ME et al. False-positive results of Aspergillus galactomannan antigenemia in liver transplant recipients. Transplantation87, 256–260 (2009).
  • Alhambra A, Cuetara MS, Ortiz MC et al. False positive galactomannan results in adult hematological patients treated with piperacillin–tazobactam. Rev. Iberoam. Micol.24, 106–112 (2007).
  • Asano-Mori Y, Kanda Y, Oshima K et al. False-positive Aspergillus galactomannan antigenaemia after haematopoietic stem cell transplantation. J. Antimicrob. Chemother.61, 411–416 (2008).
  • Lim ZY, Ho AY, Devereux S et al. False positive results of galactomannan ELISA assay in haemato-oncology patients: a single centre experience. J. Infect.55, 201–202 (2007).
  • Kawazu M, Kanda Y, Nannya Y et al. Prospective comparison of the diagnostic potential of real-time PCR, double-sandwich enzyme-linked immunosorbent assay for galactomannan, and a (1≥3)-β-D-glucan test in weekly screening for invasive aspergillosis in patients with hematological disorders. J. Clin. Microbiol.42, 2733–2741 (2004).
  • Musher B, Fredricks D, Leisenring W et al.Aspergillus galactomannan enzyme immunoassay and quantitative PCR for diagnosis of invasive aspergillosis with bronchoalveolar lavage fluid. J. Clin. Microbiol.42, 5517–5522 (2004).
  • Suarez F, Lortholary O, Buland S et al. 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 (2008).
  • Sanguinetti M, Posteraro B, Pagano L et al. Comparison of real-time PCR, conventional PCR, and galactomannan antigen detection by enzyme-linked immunosorbent assay using bronchoalveolar lavage fluid samples from hematology patients for diagnosis of invasive pulmonary aspergillosis. J. Clin. Microbiol.41, 3922–3925 (2003).
  • Florent M, Katsahian S, Vekhoff A et al. Prospective evaluation of a polymerase chain reaction-ELISA targeted to Aspergillus fumigatus and Aspergillus flavus for the early diagnosis of invasive aspergillosis in patients with hematological malignancies. J. Infect. Dis.193, 741–747 (2006).
  • Kami M, Fukui T, Ogawa S et al. Use of real-time PCR on blood samples for diagnosis of invasive aspergillosis. Clin. Infect. Dis.33, 1504–1512 (2001).
  • Scotter JM, Campbell P, Anderson TP et al. Comparison of PCR-ELISA and galactomannan detection for the diagnosis of invasive aspergillosis. Pathology37, 246–253 (2005).
  • Buchheidt D, Hummel M, Schleiermacher D et al. 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 (2004).
  • Hebart H, Loffler J, Meisner C et al. Early detection of aspergillus infection after allogeneic stem cell transplantation by polymerase chain reaction screening. J. Infect. Dis.181, 1713–1719 (2000).
  • Halliday C, Hoile R, Sorrell T et al. 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 (2006).
  • Raad I, Hanna H, Huaringa A et al. Diagnosis of invasive pulmonary aspergillosis using polymerase chain reaction-based detection of Aspergillus in BAL. Chest121, 1171–1176 (2002).
  • 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.42, 479–486 (2006).
  • Cuenca-Estrella M, Meije Y, Diaz-Pedroche C et al. 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 (2009).
  • Frealle E, Decrucq K, Botterel F et al. 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 (2009).
  • Jones ME, Fox AJ, Barnes AJ et al. PCR-ELISA for the early diagnosis of invasive pulmonary aspergillus infection in neutropenic patients. J. Clin. Pathol.51, 652–656 (1998).
  • Hardak E, Yigla M, Avivi I et al. Impact of PCR-based diagnosis of invasive pulmonary aspergillosis on clinical outcome. Bone Marrow Transplant (2009) (Epub ahead of print).
  • Skladny H, Buchheidt D, Baust C et al. Specific detection of Aspergillus species in blood and bronchoalveolar lavage samples of immunocompromised patients by two-step PCR. J. Clin. Microbiol.37, 3865–3871 (1999).
  • Tuon FF. 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 (2007).
  • Mengoli C, Cruciani M, Barnes RA, Loeffler J, Donnelly JP. Use of PCR for diagnosis of invasive aspergillosis: systematic review and meta-analysis. Lancet Infect. Dis.9, 89–96 (2009).
  • Orenstein A, Masur H. A diagnostic approach to Pneumocystis jiroveci pneumonia. In: Diagnosis of Fungal Infections. Maertens JA, Marr KA (Eds). Informa Healthcare, Essex, UK, 267–289 (2007).
  • Thomas CF Jr, Limper AH. Pneumocystis pneumonia. N. Engl. J. Med.350, 2487–2498 (2004).
  • Wyder MA, Rasch EM, Kaneshiro ES. Quantitation of absolute Pneumocystis carinii nuclear DNA content. Trophic and cystic forms isolated from infected rat lungs are haploid organisms. J. Eukaryot. Microbiol.45, 233–239 (1998).
  • Tang X, Bartlett MS, Smith JW, Lu JJ, Lee CH. Determination of copy number of rRNA genes in Pneumocystis carinii f. sp. hominis. J. Clin. Microbiol.36, 2491–2494 (1998).
  • Kaneshiro ES, Amit Z, Chandra J et al. Sterols of Pneumocystis carinii hominis organisms isolated from human lungs. Clin. Diagn. Lab. Immunol.6, 970–976 (1999).
  • Sing A, Trebesius K, Roggenkamp A et al. Evaluation of diagnostic value and epidemiological implications of PCR for Pneumocystis carinii in different immunosuppressed and immunocompetent patient groups. J. Clin. Microbiol.38, 1461–1467 (2000).
  • Torres J, Goldman M, Wheat LJ et al. Diagnosis of Pneumocystis carinii pneumonia in human immunodeficiency virus-infected patients with polymerase chain reaction: a blinded comparison to standard methods. Clin. Infect. Dis.30, 141–145 (2000).
  • Olsson M, Stralin K, Holmberg H. Clinical significance of nested polymerase chain reaction and immunofluorescence for detection of Pneumocystis carinii pneumonia. Clin Microbiol Infect.7, 492–497 (2001).
  • Flori P, Bellete B, Durand F et al. Comparison between real-time PCR, conventional PCR and different staining techniques for diagnosing Pneumocystis jiroveci pneumonia from bronchoalveolar lavage specimens. J. Med. Microbiol.53, 603–607 (2004).
  • Pinlaor S, Mootsikapun P, Pinlaor P et al. PCR diagnosis of Pneumocystis carinii on sputum and bronchoalveolar lavage samples in immuno-compromised patients. Parasitol. Res.94, 213–218 (2004).
  • Fillaux J, Malvy S, Alvarez M et al. Accuracy of a routine real-time PCR assay for the diagnosis of Pneumocystis jirovecii pneumonia. J. Microbiol. Methods75, 258–261 (2008).
  • Huggett JF, Taylor MS, Kocjan G et al. Development and evaluation of a real-time PCR assay for detection of Pneumocystis jirovecii DNA in bronchoalveolar lavage fluid of HIV-infected patients. Thorax63, 154–159 (2008).
  • Bandt D, Monecke S. Development and evaluation of a real-time PCR assay for detection of Pneumocystis jiroveci. Transpl. Infect. Dis.9, 196–202 (2007).
  • Nuchprayoon S, Saksirisampant W, Jaijakul S, Nuchprayoon I. FlindersTechnology Associates (FTA) filter paper-based DNA extraction with polymerase chain reaction (PCR) for detection of Pneumocystis jirovecii from respiratory specimens of immunocompromised patients. J. Clin. Lab. Anal.21, 382–386 (2007).
  • Fischer S, Gill VJ, Kovacs J et al. The use of oral washes to diagnose Pneumocystis carinii pneumonia: a blinded prospective study using a polymerase chain reaction-based detection system. J. Infect. Dis.184, 1485–1488 (2001).
  • Larsen HH, Huang L, Kovacs JA et al. A prospective, blinded study of quantitative touch-down polymerase chain reaction using oral-wash samples for diagnosis of Pneumocystis pneumonia in HIV-infected patients. J. Infect. Dis.189, 1679–1683 (2004).
  • Nyamande K, Lalloo UG, York D et al. Low sensitivity of a nested polymerase chain reaction in oropharyngeal washings for the diagnosis of pneumocystis pneumonia in HIV-infected patients. Chest128, 167–171 (2005).
  • Anttila VJ, Ruutu P, Bondestam S et al. Hepatosplenic yeast infection in patients with acute leukemia: a diagnostic problem. Clin. Infect. Dis.18, 979–981 (1994).
  • Bretagne S, Costa JM. Towards a molecular diagnosis of invasive aspergillosis and disseminated candidosis. FEMS Immunol. Med. Microbiol.45, 361–368 (2005).
  • Metwally L, Fairley DJ, Coyle PV et al. 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 (2008).
  • McMullan R, Metwally L, Coyle PV et al. A prospective clinical trial of a real-time polymerase chain reaction assay for the diagnosis of candidemia in nonneutropenic, critically ill adults. Clin. Infect. Dis.46, 890–896 (2008).
  • Morace G, Pagano L, Sanguinetti M et al. PCR-restriction enzyme analysis for detection of Candida DNA in blood from febrile patients with hematological malignancies. J. Clin. Microbiol.37, 1871–1875 (1999).
  • Ahmad S, Khan Z, Mustafa AS, Khan ZU. Seminested PCR for diagnosis of candidemia: comparison with culture, antigen detection, and biochemical methods for species identification. J. Clin. Microbiol.40, 2483–2489 (2002).
  • Dunyach C, Bertout S, Phelipeau C et al. Detection and identification of Candida spp. in human serum by LightCycler real-time polymerase chain reaction. Diagn. Microbiol. Infect. Dis.60, 263–271 (2008).
  • Maaroufi Y, Heymans C, De Bruyne JM et al. Rapid detection of Candida albicans in clinical blood samples by using a TaqMan-based PCR assay. J. Clin. Microbiol.41, 3293–3298 (2003).
  • Bergman A, Fernandez V, Holmstrom KO, Claesson BE, Enroth H. Rapid identification of pathogenic yeast isolates by real-time PCR and two-dimensional melting-point analysis. Eur. J. Clin. Microbiol. Infect. Dis.26, 813–818 (2007).
  • Evertsson U, Monstein HJ, Johansson AG. Detection and identification of fungi in blood using broad-range 28S rDNA PCR amplification and species-specific hybridisation. Apmis108, 385–392 (2000).
  • Kurtzman CP, Robnett CJ. Identification of clinically important ascomycetous yeasts based on nucleotide divergence in the 5´ end of the large-subunit (26S) ribosomal DNA gene J. Clin. Microbiol.35, 1216–1223 (1997).
  • Rakeman JL, Bui U, Lafe K et al. Multilocus DNA sequence comparisons rapidly identify pathogenic molds. J. Clin. Microbiol.43, 3324–3333 (2005).
  • Sandhu GS, Kline BC, Stockman L, Roberts GD. Molecular probes for diagnosis of fungal infections. J. Clin. Microbiol.33, 2913–2919 (1995).
  • Vollmer T, Stormer M, Kleesiek K, Dreier J. Evaluation of novel broad-range real-time PCR assay for rapid detection of human pathogenic fungi in various clinical specimens. J. Clin. Microbiol.46, 1919–1926 (2008).
  • Khot PD, Ko DL, Fredricks DN. Sequencing and analysis of fungal rRNA operons for development of broad-range fungal PCR assays. Appl. Environ. Microbiol.75, 1559–1565 (2009).
  • Lau A, Chen S, Sorrell T et al. Development and clinical application of a panfungal PCR assay to detect and identify fungal DNA in tissue specimens. J. Clin. Microbiol.45, 380–385 (2007).
  • Jordanides NE, Allan EK, McLintock LA et al. A prospective study of real-time panfungal PCR for the early diagnosis of invasive fungal infection in haemato-oncology patients. Bone Marrow Transplant35, 389–395 (2005).
  • Hebart H, Loffler J, Reitze H et al. Prospective screening by a panfungal polymerase chain reaction assay in patients at risk for fungal infections: implications for the management of febrile neutropenia. Br. J. Haematol.111, 635–640 (2000).
  • Williamson EC, Leeming JP, Palmer HM et al. Diagnosis of invasive aspergillosis in bone marrow transplant recipients by polymerase chain reaction. Br. J. Haematol.108, 132–139 (2000).
  • Buchheidt D, Baust C, Skladny H et al. Detection of Aspergillus species in blood and bronchoalveolar lavage samples from immunocompromised patients by means of 2-step polymerase chain reaction: clinical results. Clin. Infect. Dis.33, 428–435 (2001).
  • Raad I, Hanna H, Sumoza D, Albitar M. Polymerase chain reaction on blood for the diagnosis of invasive pulmonary aspergillosis in cancer patients. Cancer94, 1032–1036 (2002).
  • Rantakokko-Jalava K, Laaksonen S, Issakainen J et al. Semiquantitative detection by real-time PCR of Aspergillus fumigatus in bronchoalveolar lavage fluids and tissue biopsy specimens from patients with invasive aspergillosis. J. Clin. Microbiol.41, 4304–4311 (2003).
  • Challier S, Boyer S, Abachin E, Berche P. Development of a serum-based Taqman real-time PCR assay for diagnosis of invasive aspergillosis. J. Clin. Microbiol.42, 844–846 (2004).
  • Cesaro S, Stenghele C, Calore E et al. Assessment of the lightcycler PCR assay for diagnosis of invasive aspergillosis in paediatric patients with onco-haematological diseases. Mycoses51, 497–504 (2008).
  • Botterel F, Farrugia C, Ichai P et al. Real-time PCR on the first galactomannan-positive serum sample for diagnosing invasive aspergillosis in liver transplant recipients. Transpl. Infect. Dis.10, 333–338 (2008).
  • White PL, Archer AE, Barnes RA. Comparison of non-culture-based methods for detection of systemic fungal infections, with an emphasis on invasive Candida infections. J. Clin. Microbiol.43, 2181–2187 (2005).
  • Loeffler J, Henke N, Hebart H et al. Quantification of fungal DNA by using fluorescence resonance energy transfer and the light cycler system. J. Clin. Microbiol.38, 586–590 (2000).
  • El-Mahallawy HA, Shaker HH, Ali Helmy H, Mostafa T, Razak Abo-Sedah A. Evaluation of pan-fungal PCR assay and Aspergillus antigen detection in the diagnosis of invasive fungal infections in high risk paediatric cancer patients. Med. Mycol.44, 733–739 (2006).
  • Ribeiro P, Costa F, Monteiro A et al. Polymerase chain reaction screening for fungemia and/or invasive fungal infections in patients with hematologic malignancies. Support Care Cancer14, 469–474 (2006).
  • Badiee P, Kordbacheh P, Alborzi A et al. Study on invasive fungal infections in immunocompromised patients to present a suitable early diagnostic procedure. Int. J. Infect. Dis.13, 97–102 (2009).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.