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Chapter 35 : Molecular Detection and Identification of Fungal Pathogens

Authors: Katrien Lagrou1, Johan Maertens2, Marie Pierre Hayette3
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Affiliations: 1: University Hospitals Leuven, Leuven, Belgium.; 2: University Hospitals Leuven, Leuven, Belgium.; 3: University Hospitals Leuven, Leuven, Belgium.
Content Type: Reference
Publication Year: 2016

Category: Clinical Microbiology

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Molecular Detection and Identification of Fungal Pathogens, Page 1 of 2

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Abstract:

Fungi are a diverse group of eukaryotic organisms, most of which are found as saprophytes in soil and on decomposing organic material. Of the more than 100,000 fungal species, fewer than 500 have been implicated in human disease. Most fungi are opportunistic pathogens that only cause disease in (severely) immunocompromised patients. Many fungal diseases have a worldwide distribution, but some are restricted to specific geographical regions (e.g., endemic mycoses). Fungi cause a broad spectrum of diseases, ranging from superficial mycoses (infection of skin, hair, nails, and/or mucosal membranes), to allergic diseases, to life-threatening invasive diseases. Most dermatophytes are not able to survive as free-living saprophytes and are obligate pathogens of animals and humans that cause contagious infections. Millions of individuals worldwide are affected by superficial mycoses, mainly dermatophytoses and candidiasis (1, 2). An increase of invasive infections has been observed over the past decades due to the ever-increasing size of the population at risk for these infections (3) as well as the availability of better diagnostics.

Citation: Lagrou K, Maertens J, Hayette M. 2016. Molecular Detection and Identification of Fungal Pathogens, p 489-500. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch35
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Molecular Detection and Identification of Fungal Pathogens
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Citation: Lagrou K, Maertens J, Hayette M. 2016. Molecular Detection and Identification of Fungal Pathogens, p 489-500. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch35
/content/10.1128/9781555819071.ch35.ch35fig1
FIGURE 1

Schematic consensus representation of the rDNA gene complex for fungal genomes with the most frequently used internally transcribed spacer (ITS)–targeted primers (arrows). SSU, small subunit; LSU, large subunit.

10.1128/9781555819071/9071ch35f01_thmb.gif
10.1128/9781555819071/9071ch35f01.gif
Image of FIGURE 1
FIGURE 1

Schematic consensus representation of the rDNA gene complex for fungal genomes with the most frequently used internally transcribed spacer (ITS)–targeted primers (arrows). SSU, small subunit; LSU, large subunit.

Citation: Lagrou K, Maertens J, Hayette M. 2016. Molecular Detection and Identification of Fungal Pathogens, p 489-500. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch35
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References

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1. Burzykowski T, Molenberghs G, Abeck D, Haneke E, Hay R, Katsambas A, Roseeuw D, van de Kerkhof P, van Aelst R, Marynissen G . 2003. High prevalence of foot diseases in Europe: results of the Achilles Project. Mycoses 46 : 496– 505.[PubMed]
2. Ghannoum MA, Hajjeh RA, Scher R, Konnikov N, Gupta AK, Summerbell R, Sullivan S, Daniel R, Krusinski P, Fleckman P, Rich P, Odom R, Aly R, Pariser D, Zaiac M, Rebell G, Lesher J, Gerlach B, Ponce-De-Leon GF, Ghannoum A, Warner J, Isham N, Elewski B . 2000. A large-scale North American study of fungal isolates from nails: the frequency of onychomycosis, fungal distribution, and antifungal susceptibility patterns. J Am Acad Dermatol 43 : 641– 648.[PubMed]
3. Bitar D, Lortholary O, Le Strat Y, Nicolau J, Coignard B, Tattevin P, Che D, Dromer F . 2014. Population-based analysis of invasive fungal infections, France, 2001–2010. Emerg Infect Dis 20 : 1149– 1155.[PubMed]
4. Tchernev G, Penev PK, Nenoff P, Zisova LG, Cardoso JC, Taneva T, Ginter-Hanselmayer G, Ananiev J, Gulubova M, Hristova R, Nocheva D, Guarneri C, Martino G, Kanazawa N . 2013. Onychomycosis: modern diagnostic and treatment approaches. Wien Med Wochenschr 163 : 1– 12.[PubMed]
5. Cornely OA, Arikan-Akdagli S, Dannaoui E, Groll AH, Lagrou K, Chakrabarti A, Lanternier F, Pagano L, Skiada A, Akova M, Arendrup MC, Boekhout T, Chowdhary A, Cuenca-Estrella M, Freiberger T, Guinea J, Guarro J, de Hoog S, Hope W, Johnson E, Kathuria S, Lackner M, Lass-Flörl C, Lortholary O, Meis JF, Meletiadis J, Muñoz P, Richardson M, Roilides E, Tortorano AM, Ullmann AJ, van Diepeningen A, Verweij P, Petrikkos G , European Society of Clinical Microbiology and Infectious Diseases Fungal Infection Study Group, European Confederation of Medical Mycology . 2014. ESCMID and ECMM joint clinical guidelines for the diagnosis and management of mucormycosis 2013. Clin Microbiol Infect 20( Suppl 3) : 5– 26.[PubMed]
6. 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 : 611– 622.[PubMed]
7. Löffler J, Kurzai O . 2011. Diagnostic utility of DNA from Aspergillus in whole blood specimens. Curr Fungal Infect Rep 5 : 179– 185.
8. Mrazek C, Lass-Flörl C . 2011. Biopsy procedures for molecular tissue diagnosis of invasive fungal infections. Curr Infect Dis Rep 13 : 504– 509.
9. Imhof A, Schaer C, Schoedon G, Schaer DJ, Walter RB, Schaffner A, Schneemann M . 2003. Rapid detection of pathogenic fungi from clinical specimens using LightCycler real-time fluorescence PCR. Eur J Clin Microbiol Infect Dis 22 : 558– 560.[PubMed]
10. Sakai K, Trabasso P, Moretti ML, Mikami Y, Kamei K, Gonoi T . 2014. Identification of fungal pathogens by visible microarray system in combination with isothermal gene amplification. Mycopathologia 178 : 11– 26.[PubMed]
11. Park C, Kwon EY, Shin NY, Choi SM, Kim SH, Park SH, Lee DG, Choi JH, Yoo JH . 2011. Evaluation of nucleic acid sequence based amplification using fluorescence resonance energy transfer (FRET-NASBA) in quantitative detection of Aspergillus 18S rRNA. Med Mycol 49 : 73– 79.[PubMed]
12. Zhao Y, Park S, Kreiswirth BN, Ginocchio CC, Veyret R, Laayoun A, Troesch A, Perlin DS . 2009. Rapid real-time nucleic acid sequence-based amplification-molecular beacon platform to detect fungal and bacterial bloodstream infections. J Clin Microbiol 47 : 2067– 2078.[PubMed]
13. Alanio A, Bretagne S . 2014. Difficulties with molecular diagnostic tests for mould and yeast infections: where do we stand? Clin Microbiol Infect 20( Suppl 6) : 36– 41.[PubMed]
14. Willinger B, Haase G . 2013. State-of-the art procedures and quality management in diagnostic medical mycology. Curr Fungal Infect Rep 7 : 260– 272.
15. Xhaard A, Lanternier F, Porcher R, Dannaoui E, Bergeron A, Clement L, Lacroix C, Herbrecht R, Legrand F, Mohty M, Michallet M, Cordonnier C, Malak S, Guyotat D, Couderc LJ, Socié G, Milpied N, Lortholary O, Ribaud P . 2012. Mucormycosis after allogeneic haematopoietic stem cell transplantation: a French multicentre cohort study (2003–2008). Clin Microbiol Infect 18 : E396– E400.[PubMed]
16. Saegeman V, Maertens J, Meersseman W, Spriet I, Verbeken E, Lagrou K . 2010. Increasing incidence of mucormycosis in University Hospital, Belgium. Emerg Infect Dis 16 : 1456– 1458.[PubMed]
17. Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W Fungal Barcoding Consortium . 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA 109 : 6241– 6246.[PubMed]
18. Buitrago MJ, Bernal-Martinez L, Castelli MV, Rodriguez-Tudela JL, Cuenca-Estrella M . 2014. Performance of panfungal—and specific-PCR-based procedures for etiological diagnosis of invasive fungal diseases on tissue biopsy specimens with proven infection: a 7-year retrospective analysis from a reference laboratory. J Clin Microbiol 52 : 1737– 1740.[PubMed]
19. Babouee B, Goldenberger D, Elzi L, Lardinois D, Sadowski-Cron C, Bubendorf L, Savic Prince S, Battegay M, Frei R, Weisser M . 2013. Prospective study of a panfungal PCR assay followed by sequencing, for the detection of fungal DNA in normally sterile specimens in a clinical setting: a complementary tool in the diagnosis of invasive fungal disease? Clin Microbiol Infect 19 : e354– e357.[PubMed]
20. Sugawara Y, Nakase K, Nakamura A, Ohishi K, Sugimoto Y, Fujieda A, Monma F, Suzuki K, Masuya M, Matsushima Y, Wada H, Nobori T, Katayama N . 2013. Clinical utility of a panfungal polymerase chain reaction assay for invasive fungal diseases in patients with haematologic disorders. Eur J Haematol 90 : 331– 339.[PubMed]
21. Landlinger C, Preuner S, Bašková L, van Grotel M, Hartwig NG, Dworzak M, Mann G, Attarbaschi A, Kager L, Peters C, Matthes-Martin S, Lawitschka A, van den Heuvel-Eibrink MM, Lion T . 2010. Diagnosis of invasive fungal infections by a real-time panfungal PCR assay in immunocompromised pediatric patients. Leukemia 24 : 2032– 2038.[PubMed]
22. Marcos JY, Pincus DH . 2013. Fungal diagnostics: review of commercially available methods. Methods Mol Biol 968 : 25– 54.[PubMed]
23. 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—surface enhanced raman scattering assay for the diagnosis of invasive fungal disease. J Clin Microbiol 52 : 3536– 3543.
24. Arendrup MC, Sulim S, Holm A, Nielsen L, Nielsen SD, Knudsen JD, Drenck NE, Christensen JJ, Johansen HK . 2011. Diagnostic issues, clinical characteristics, and outcomes for patients with fungemia. J Clin Microbiol 49 : 3300– 3308.[PubMed]
25. Avni T, Leibovici L, Paul M . 2011. PCR diagnosis of invasive candidiasis: systematic review and meta-analysis. J Clin Microbiol 49 : 665– 670.[PubMed]
26. Berenguer J, Buck M, Witebsky F, Stock F, Pizzo PA, Walsh TJ . 1993. Lysis-centrifugation blood cultures in the detection of tissue-proven invasive candidiasis. Disseminated versus single-organ infection. Diagn Microbiol Infect Dis 17 : 103– 109.[PubMed]
27. Stone NR, Gorton RL, Barker K, Ramnarain P, Kibbler CC . 2013. Evaluation of PNA-FISH yeast traffic light for rapid identification of yeast directly from positive blood cultures and assessment of clinical impact. J Clin Microbiol 51 : 1301– 1302.[PubMed]
28. 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.[PubMed]
29. Cuenca-Estrella M, Verweij PE, Arendrup MC, Arikan-Akdagli S, Bille J, Donnelly JP, Jensen HE, Lass-Flörl C, Richardson MD, Akova M, Bassetti M, Calandra T, Castagnola E, Cornely OA, Garbino J, Groll AH, Herbrecht R, Hope WW, Kullberg BJ, Lortholary O, Meersseman W, Petrikkos G, Roilides E, Viscoli C, Ullmann AJ ESCMID Fungal Infection Study Group . 2012. ESCMID* guideline for the diagnosis and management of Candida diseases 2012: diagnostic procedures. Clin Microbiol Infect 18( Suppl 7) : 9– 18.[PubMed]
30. Khot PD, Fredricks DN . 2009. PCR-based diagnosis of human fungal infections. Expert Rev Anti Infect Ther 7 : 1201– 1221.[PubMed]
31. Vanhee LM, Meersseman W, Lagrou K, Maertens J, Nelis HJ, Coenye T . 2010. Rapid and direct quantification of viable Candida species in whole blood by use of immunomagnetic separation and solid-phase cytometry. J Clin Microbiol 48 : 1126– 1131.[PubMed]
32. Kasai M, Francesconi A, Petraitiene R, Petraitis V, Kelaher AM, Kim HS, Meletiadis J, Sein T, Bacher J, Walsh TJ . 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.[PubMed]
33. 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 : 1240– 1248.[PubMed]
34. De Pauw B, Walsh TJ, Donnelly JP, Stevens DA, Edwards JE, Calandra T, Pappas PG, Maertens J, Lortholary O, Kauffman CA, Denning DW, Patterson TF, Maschmeyer G, Bille J, Dismukes WE, Herbrecht R, Hope WW, Kibbler CC, Kullberg BJ, Marr KA, Muñoz P, Odds FC, Perfect JR, Restrepo A, Ruhnke M, Segal BH, Sobel JD, Sorrell TC, Viscoli C, Wingard JR, Zaoutis T, Bennett JE European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group, National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) Consensus Group . 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.[PubMed]
35. D'Haese J, Theunissen K, Vermeulen E, Schoemans H, De Vlieger G, Lammertijn L, Meersseman P, Meersseman W, Lagrou K, Maertens J . 2012. Detection of galactomannan in bronchoalveolar lavage fluid samples of patients at risk for invasive pulmonary aspergillosis: analytical and clinical validity. J Clin Microbiol 50 : 1258– 1263.[PubMed]
36. Zou M, Tang L, Zhao S, Zhao Z, Chen L, Chen P, Huang Z, Li J, Chen L, Fan X . 2012. Systematic review and meta-analysis of detecting galactomannan in bronchoalveolar lavage fluid for diagnosing invasive aspergillosis. PLoS One 7 : e43347.[PubMed]
37. White PL, Barton R, Guiver M, Linton CJ, Wilson S, Smith M, Gomez BL, Carr MJ, Kimmitt PT, Seaton S, Rajakumar K, Holyoake T, Kibbler CC, Johnson E, Hobson RP, Jones B, Barnes RA . 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.[PubMed]
38. White PL, Perry MD, Loeffler J, Melchers W, Klingspor L, Bretagne S, McCulloch E, Cuenca-Estrella M, Finnstrom N, Donnelly JP, Barnes RA European Aspergillus PCR Initiative . 2010. Critical stages of extracting DNA from Aspergillus fumigatus in whole-blood specimens. J Clin Microbiol 48 : 3753– 3755.[PubMed]
39. Springer J, Morton CO, Perry M, Heinz WJ, Paholcsek M, Alzheimer M, Rogers TR, Barnes RA, Einsele H, Loeffler J, White PL . 2013. Multicenter comparison of serum and whole-blood specimens for detection of Aspergillus DNA in high-risk hematological patients. J Clin Microbiol 51 : 1445– 1450.[PubMed]
40. Rickerts V, Mousset S, Lambrecht E, Tintelnot K, Schwerdtfeger R, Presterl E, Jacobi V, Just-Nübling G, Bialek R . 2007. Comparison of histopathological analysis, culture, and polymerase chain reaction assays to detect invasive mold infections from biopsy specimens. Clin Infect Dis 44 : 1078– 1083.[PubMed]
41. Torelli R, Sanguinetti M, Moody A, Pagano L, Caira M, De Carolis E, Fuso L, De Pascale G, Bello G, Antonelli M, Fadda G, Posteraro B . 2011. Diagnosis of invasive aspergillosis by a commercial real-time PCR assay for Aspergillus DNA in bronchoalveolar lavage fluid samples from high-risk patients compared to a galactomannan enzyme immunoassay. J Clin Microbiol 49 : 4273– 4278.[PubMed]
42. 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 : e61545.[PubMed]
43. Lu Y, Ling G, Qiang C, Ming Q, Wu C, Wang K, Ying Z . 2011. PCR diagnosis of Pneumocystis pneumonia: a bivariate meta-analysis. J Clin Microbiol 49 : 4361– 4363.[PubMed]
44. Fan LC, Lu HW, Cheng KB, Li HP, Xu JF . 2013. Evaluation of PCR in bronchoalveolar lavage fluid for diagnosis of Pneumocystis jirovecii pneumonia: a bivariate meta-analysis and systematic review. PLoS One 8 : e73099.[PubMed]
45. Hauser PM, Bille J, Lass-Flörl C, Geltner C, Feldmesser M, Levi M, Patel H, Muggia V, Alexander B, Hughes M, Follett SA, Cui X, Leung F, Morgan G, Moody A, Perlin DS, Denning DW . 2011. Multicenter, prospective clinical evaluation of respiratory samples from subjects at risk for Pneumocystis jirovecii infection by use of a commercial real-time PCR assay. J Clin Microbiol 49 : 1872– 1878.[PubMed]
46. Morris A, Norris KA . 2012. Colonization by Pneumocystis jirovecii and its role in disease. Clin Microbiol Rev 25 : 297– 317.[PubMed]
47. Botterel F, Cabaret O, Foulet F, Cordonnier C, Costa JM, Bretagne S . 2012. Clinical significance of quantifying Pneumocystis jirovecii DNA by using real-time PCR in bronchoalveolar lavage fluid from immunocompromised patients. J Clin Microbiol 50 : 227– 231.[PubMed]
48. Damiani C, Le Gal S, Da Costa C, Virmaux M, Nevez G, Totet A . 2013. Combined quantification of pulmonary Pneumocystis jirovecii DNA and serum (1->3)-β-D-glucan for differential diagnosis of pneumocystis pneumonia and Pneumocystis colonization. J Clin Microbiol 51 : 3380– 3388.[PubMed]
49. Costa JM, Botterel F, Cabaret O, Foulet F, Cordonnier C, Bretagne S . 2012. Association between circulating DNA, serum (1->3)-β-D-glucan, and pulmonary fungal burden in Pneumocystis pneumonia. Clin Infect Dis 55 : e5– e8.[PubMed]
50. Mahmud A, Lee R, Munfus-McCray D, Kwiatkowski N, Subramanian A, Neofytos D, Carroll K, Zhang SX . 2012. Actinomucor elegans as an emerging cause of mucormycosis. J Clin Microbiol 50 : 1092– 1095.[PubMed]
51. Layios N, Canivet J-L, Baron F, Moutschen M, Hayette M-P . 2014. Mortierella wolfii-associated invasive disease. Emerg Infect Dis 20 : 1591.
52. Gupta AK, Ryder JE, Chow M, Cooper EA . 2005. Dermatophytosis: the management of fungal infections. Skinmed 4 : 305– 310.[PubMed]
53. Wang W, Xi H, Huang M, Wang J, Fan M, Chen Y, Shao H, Li X . 2014. Performance of mass spectrometric identification of bacteria and yeasts routinely isolated in a clinical microbiology laboratory using MALDI-TOF MS. J Thorac Dis 6 : 524– 533.[PubMed]
54. Steensels D, Verhaegen J, Lagrou K . 2011. Matrix-assisted laser desorption ionization-time of flight mass spectrometry for the identification of bacteria and yeasts in a clinical microbiological laboratory: a review. Acta Clin Belg 66 : 267– 273.[PubMed]
55. Lacroix C, Gicquel A, Sendid B, Meyer J, Accoceberry I, François N, Morio F, Desoubeaux G, Chandenier J, Kauffmann-Lacroix C, Hennequin C, Guitard J, Nassif X, Bougnoux ME . 2014. Evaluation of two matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems for the identification of Candida species. Clin Microbiol Infect 20 : 153– 158.[PubMed]
56. Bille E, Dauphin B, Leto J, Bougnoux ME, Beretti JL, Lotz A, Suarez S, Meyer J, Join-Lambert O, Descamps P, Grall N, Mory F, Dubreuil L, Berche P, Nassif X, Ferroni A . 2012. MALDI-TOF MS Andromas strategy for the routine identification of bacteria, mycobacteria, yeasts, Aspergillus spp. and positive blood cultures. Clin Microbiol Infect 18 : 1117– 1125.[PubMed]
57. Hamprecht A, Christ S, Oestreicher T, Plum G, Kempf VA, Göttig S . 2014. Performance of two MALDI-TOF MS systems for the identification of yeasts isolated from bloodstream infections and cerebrospinal fluids using a time-saving direct transfer protocol. Med Microbiol Immunol (Berl) 203 : 93– 99.[PubMed]
58. Bader O . 2013. MALDI-TOF-MS-based species identification and typing approaches in medical mycology. Proteomics 13 : 788– 799.[PubMed]
59. Bader O, Weig M, Taverne-Ghadwal L, Lugert R, Gross U, Kuhns M . 2011. Improved clinical laboratory identification of human pathogenic yeasts by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Microbiol Infect 17 : 1359– 1365.[PubMed]
60. Marklein G, Josten M, Klanke U, Müller E, Horré R, Maier T, Wenzel T, Kostrzewa M, Bierbaum G, Hoerauf A, Sahl HG . 2009. Matrix-assisted laser desorption ionization-time of flight mass spectrometry for fast and reliable identification of clinical yeast isolates. J Clin Microbiol 47 : 2912– 2917.[PubMed]
61. Pence MA, McElvania TeKippe E, Wallace MA, Burnham CA . 2014. Comparison and optimization of two MALDI-TOF MS platforms for the identification of medically relevant yeast species. Eur J Clin Microbiol Infect Dis 33 : 1703– 1712.[PubMed]
62. Cassagne C, Ranque S, Normand AC, Fourquet P, Thiebault S, Planard C, Hendrickx M, Piarroux R . 2011. Mould routine identification in the clinical laboratory by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. PLoS One 6 : e28425.[PubMed]
63. Vlek A, Kolecka A, Khayhan K, Theelen B, Groenewald M, Boel E, Boekhout T Multicenter Study Group . 2014. Interlaboratory comparison of sample preparation methods, database expansions, and cutoff values for identification of yeasts by matrix-assisted laser desorption ionization-time of flight mass spectrometry using a yeast test panel. J Clin Microbiol 52 : 3023– 3029.[PubMed]
64. Idelevich EA, Grunewald CM, Wüllenweber J, Becker K . 2014. Rapid identification and susceptibility testing of Candida spp. from positive blood cultures by combination of direct MALDI-TOF mass spectrometry and direct inoculation of Vitek 2. PLoS One 9 : e114834.[PubMed]
65. Schulthess B, Bloemberg GV, Zbinden R, Böttger EC, Hombach M . 2014. Evaluation of the Bruker MALDI Biotyper for identification of Gram-positive rods: development of a diagnostic algorithm for the clinical laboratory. J Clin Microbiol 52 : 1089– 1097.[PubMed]
66. Ranque S, Normand AC, Cassagne C, Murat JB, Bourgeois N, Dalle F, Gari-Toussaint M, Fourquet P, Hendrickx M, Piarroux R . 2014. MALDI-TOF mass spectrometry identification of filamentous fungi in the clinical laboratory. Mycoses 57 : 135– 140.[PubMed]
67. Coulibaly O, Marinach-Patrice C, Cassagne C, Piarroux R, Mazier D, Ranque S . 2011. Pseudallescheria/Scedosporium complex species identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Med Mycol 49 : 621– 626.[PubMed]
68. L'Ollivier C, Cassagne C, Normand AC, Bouchara JP, Contet-Audonneau N, Hendrickx M, Fourquet P, Coulibaly O, Piarroux R, Ranque S . 2013. A MALDI-TOF MS procedure for clinical dermatophyte species identification in the routine laboratory. Med Mycol 51 : 713– 720.[PubMed]
69. Normand AC, Cassagne C, Ranque S, L'ollivier C, Fourquet P, Roesems S, Hendrickx M, Piarroux R . 2013. Assessment of various parameters to improve MALDI-TOF MS reference spectra libraries constructed for the routine identification of filamentous fungi. BMC Microbiol 13 : 76.[PubMed]
70. de Respinis S, Tonolla M, Pranghofer S, Petrini L, Petrini O, Bosshard PP . 2013. Identification of dermatophytes by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Med Mycol 51 : 514– 521.[PubMed]
71. Pounder JI, Williams S, Hansen D, Healy M, Reece K, Woods GL . 2005. Repetitive-sequence-PCR-based DNA fingerprinting using the Diversilab system for identification of commonly encountered dermatophytes. J Clin Microbiol 43 : 2141– 2147.[PubMed]
72. Müller FM, Werner KE, Kasai M, Francesconi A, Chanock SJ, Walsh TJ . 1998. Rapid extraction of genomic DNA from medically important yeasts and filamentous fungi by high-speed cell disruption. J Clin Microbiol 36 : 1625– 1629.[PubMed]
73. van Burik JA, Schreckhise RW, White TC, Bowden RA, Myerson D . 1998. Comparison of six extraction techniques for isolation of DNA from filamentous fungi. Med Mycol 36 : 299– 303.[PubMed]
74. Pryce TM, Palladino S, Kay ID, Coombs GW . 2003. Rapid identification of fungi by sequencing the ITS1 and ITS2 regions using an automated capillary electrophoresis system. Med Mycol 41 : 369– 381.[PubMed]
75. Castanheira M, Woosley LN, Diekema DJ, Jones RN, Pfaller MA . 2013. Candida guilliermondii and other species of Candida misidentified as Candida famata: assessment by vitek 2, DNA sequencing analysis, and matrix-assisted laser desorption ionization-time of flight mass spectrometry in two global antifungal surveillance programs. J Clin Microbiol 51 : 117– 124.[PubMed]
76. Nawrot U, Wlodarczyk K, Wrobel M, Wasik A, Dobosz T . 2010. Comparison of the utility of five commercial kits for extraction of DNA from Aspergillus fumigatus spores. Acta Biochim Pol 57 : 567– 571.[PubMed]
77. Liu D, Coloe S, Baird R, Pederson J . 2000. Rapid mini-preparation of fungal DNA for PCR. J Clin Microbiol 38 : 471.[PubMed]
78. Romanelli AM, Fu J, Herrera ML, Wickes BL . 2014. A universal DNA extraction and PCR amplification method for fungal rDNA sequence-based identification. Mycoses 57 : 612– 622.[PubMed]
79. Borman AM, Linton CJ, Miles SJ, Campbell CK, Johnson EM . 2006. Ultra-rapid preparation of total genomic DNA from isolates of yeast and mould using Whatman FTA filter paper technology: a reusable DNA archiving system. Med Mycol 44 : 389– 398.[PubMed]
80. Borman AM, Linton CJ, Miles SJ, Johnson EM . 2008. Molecular identification of pathogenic fungi. J Antimicrob Chemother 61( Suppl 1) : i7– i12.[PubMed]
81. Borman AM, Fraser M, Linton CJ, Palmer MD, Johnson EM . 2010. An improved protocol for the preparation of total genomic DNA from isolates of yeast and mould using Whatman FTA filter papers. Mycopathologia 169 : 445– 449.[PubMed]
82. Zhong KJ, Salas CJ, Shafer R, Gubanov A, Gasser RA Jr, Magill AJ, Forney JR, Kain KC . 2001. Comparison of IsoCode STIX and FTA Gene Guard collection matrices as whole-blood storage and processing devices for diagnosis of malaria by PCR. J Clin Microbiol 39 : 1195– 1196.[PubMed]
83. Li CC, Beck IA, Seidel KD, Frenkel LM . 2004. Persistence of human immunodeficiency virus type 1 subtype B DNA in dried-blood samples on FTA filter paper. J Clin Microbiol 42 : 3847– 3849.[PubMed]
84. Seifert KA . 2009. Progress towards DNA barcoding of fungi. Mol Ecol Resour 9( Suppl s1) : 83– 89.[PubMed]
85. Clinical and Laboratory Standards Institute . 2008. Interpretive Criteria for Identification of Bacteria and Fungi by DNA Target Sequencing: guideline. CLSI, Wayne, PA.
86. Balajee SA, Borman AM, Brandt ME, Cano J, Cuenca-Estrella M, Dannaoui E, Guarro J, Haase G, Kibbler CC, Meyer W, O'Donnell K, Petti CA, Rodriguez-Tudela JL, Sutton D, Velegraki A, Wickes BL . 2009. 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 47 : 877– 884.[PubMed]
87. Iwen PC, Hinrichs SH, Rupp ME . 2002. Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens. Med Mycol 40 : 87– 109.[PubMed]
88. Wang X, Fu YF, Wang RY, Li L, Cao YH, Chen YQ, Zhao HZ, Zhang QQ, Wu JQ, Weng XH, Cheng XJ, Zhu LP . 2014. Identification of clinically relevant fungi and prototheca species by rRNA gene sequencing and multilocus PCR coupled with electrospray ionization mass spectrometry. PLoS One 9 : e98110.[PubMed]
89. Op De Beeck M, Lievens B, Busschaert P, Declerck S, Vangronsveld J, Colpaert JV . 2014. Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies. PLoS One 9 : e97629.[PubMed]
90. Kwon-Chung KJ, Wickes BL, . 2006. The conversion from classical studies in fungal pathogenesis to the molecular era, p 49– 70. In Heitman J, Filler SG, Edwards JE Jr, Mitchell AP (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC.
91. White TJ, Bruns TD, Lee SB, Taylor JW, . 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, p 315– 322. In Innis MA, Gelfand DH, Sninsky JJ, White TJ (ed), PCR Protocols: A Guide to Methods and Applications. Academic Press, New York, NY.
92. Gardes M, Bruns TD . 1993. ITS primers with enhanced specificity for basidiomycetes: application to the identification of mycorrhizae and rusts. Mol Ecol 2 : 113– 118.[PubMed]
93. Dannaoui E, Paugam A, Develoux M, Chochillon C, Matheron J, Datry A, Bouges-Michel C, Bonnal C, Dromer F, Bretagne S . 2010. Comparison of antifungal MICs for yeasts obtained using the EUCAST method in a reference laboratory and the Etest in nine different hospital laboratories. Clin Microbiol Infect 16 : 863– 869.[PubMed]
94. Schwarz P, Bretagne S, Gantier JC, Garcia-Hermoso D, Lortholary O, Dromer F, Dannaoui E . 2006. Molecular identification of zygomycetes from culture and experimentally infected tissues. J Clin Microbiol 44 : 340– 349.[PubMed]
95. Vancov T, Keen B . 2009. Amplification of soil fungal community DNA using the ITS86F and ITS4 primers. FEMS Microbiol Lett 296 : 91– 96.[PubMed]
96. Turenne CY, Sanche SE, Hoban DJ, Karlowsky JA, Kabani AM . 1999. Rapid identification of fungi by using the ITS2 genetic region and an automated fluorescent capillary electrophoresis system. J Clin Microbiol 37 : 1846– 1851.[PubMed]
97. Kami M, Fukui T, Ogawa S, Kazuyama Y, Machida U, Tanaka Y, Kanda Y, Kashima T, Yamazaki Y, Hamaki T, Mori S, Akiyama H, Mutou Y, Sakamaki H, Osumi K, Kimura S, Hirai H . 2001. Use of real-time PCR on blood samples for diagnosis of invasive aspergillosis. Clin Infect Dis 33 : 1504– 1512.[PubMed]
98. Lott TJ, Burns BM, Zancope-Oliveira R, Elie CM, Reiss E . 1998. Sequence analysis of the internal transcribed spacer 2 (ITS2) from yeast species within the genus Candida. Curr Microbiol 36 : 63– 69.[PubMed]
99. Ferrer C, Colom F, Frasés S, Mulet E, Abad JL, Alió JL . 2001. Detection and identification of fungal pathogens by PCR and by ITS2 and 5.8S ribosomal DNA typing in ocular infections. J Clin Microbiol 39 : 2873– 2879.[PubMed]
100. Ge YP, Wang L, Lu GX, Shen YN, Liu WD . 2012. A simple and reliable PCR-restriction fragment length polymorphism assay to identify Candida albicans and its closely related Candida dubliniensis. Braz J Microbiol 43 : 873– 879.[PubMed]
101. Trama JP, Mordechai E, Adelson ME . 2005. Detection and identification of Candida species associated with Candida vaginitis by real-time PCR and pyrosequencing. Mol Cell Probes 19 : 145– 152.[PubMed]
102. Pannanusorn S, Elings MA, Römling U, Fernandez V . 2012. Pyrosequencing of a hypervariable region in the internal transcribed spacer 2 to identify clinical yeast isolates. Mycoses 55 : 172– 180.[PubMed]
103. Trama JP, Mordechai E, Adelson ME . 2005. Detection of Aspergillus fumigatus and a mutation that confers reduced susceptibility to itraconazole and posaconazole by real-time PCR and pyrosequencing. J Clin Microbiol 43 : 906– 908.[PubMed]
104. Souza AC, Ferreira RC, Gonçalves SS, Quindós G, Eraso E, Bizerra FC, Briones MR, Colombo AL . 2012. Accurate identification of Candida parapsilosis ( sensu lato) by use of mitochondrial DNA and real-time PCR. J Clin Microbiol 50 : 2310– 2314.[PubMed]
105. McTaggart L, Richardson SE, Seah C, Hoang L, Fothergill A, Zhang SX . 2011. Rapid identification of Cryptococcus neoformans var. grubii, C. neoformans var. neoformans, and C. gattii by use of rapid biochemical tests, differential media, and DNA sequencing. J Clin Microbiol 49 : 2522– 2527.[PubMed]
106. Balajee SA, Sigler L, Brandt ME . 2007. DNA and the classical way: identification of medically important molds in the 21st century. Med Mycol 45 : 475– 490.[PubMed]
107. Oechsler RA, Feilmeier MR, Ledee DR, Miller D, Diaz MR, Fini ME, Fell JW, Alfonso EC . 2009. Utility of molecular sequence analysis of the ITS rRNA region for identification of Fusarium spp. from ocular sources. Invest Ophthalmol Vis Sci 50 : 2230– 2236.[PubMed]
108. Dubey SC, Priyanka K, Singh V . 2014. Phylogenetic relationship between different race representative populations of Fusarium oxysporum f. sp. ciceris in respect of translation elongation factor-1α, β-tubulin, and internal transcribed spacer region genes. Arch Microbiol 196 : 445– 452.[PubMed]
109. Tortorano AM, Prigitano A, Esposto MC, Arsic Arsenijevic V, Kolarovic J, Ivanovic D, Paripovic L, Klingspor L, Nordøy I, Hamal P, Arikan Akdagli S, Ossi C, Grancini A, Cavanna C, Lo Cascio G, Scarparo C, Candoni A, Caira M, Drogari Apiranthitou M ECMM Working Group . 2014. European Confederation of Medical Mycology (ECMM) epidemiological survey on invasive infections due to Fusarium species in Europe. Eur J Clin Microbiol Infect Dis 33 : 1623– 1630.[PubMed]
110. Geiser DM, Jiménez-Gasco Md M, Kang S, Makalowska I, Veeraraghavan N, Ward TJ, Zhang N, Kuldau GA, O'Donnell K . 2004. FUSARIUM-ID v. 1.0: a DNA sequence database for identifying Fusarium. Eur J Plant Pathol 110 : 473– 479.
111. Cafarchia C, Iatta R, Latrofa MS, Gräser Y, Otranto D . 2013. Molecular epidemiology, phylogeny and evolution of dermatophytes. Infect Genet Evol 20 : 336– 351.[PubMed]
112. Verrier J, Krähenbühl L, Bontems O, Fratti M, Salamin K, Monod M . 2013. Dermatophyte identification in skin and hair samples using a simple and reliable nested polymerase chain reaction assay. Br J Dermatol 168 : 295– 301.[PubMed]
113. Ninet B, Jan I, Bontems O, Léchenne B, Jousson O, Panizzon R, Lew D, Monod M . 2003. Identification of dermatophyte species by 28S ribosomal DNA sequencing with a commercial kit. J Clin Microbiol 41 : 826– 830.[PubMed]
114. Gräser Y, El Fari M, Vilgalys R, Kuijpers AF, De Hoog GS, Presber W, Tietz H . 1999. Phylogeny and taxonomy of the family Arthrodermataceae (dermatophytes) using sequence analysis of the ribosomal ITS region. Med Mycol 37 : 105– 114.[PubMed]
115. Gräser Y, Scott J, Summerbell R . 2008. The new species concept in dermatophytes: a polyphasic approach. Mycopathologia 166 : 239– 256.[PubMed]
116. Gräser Y, Czaika V, Ohst T . 2012. Diagnostic PCR of dermatophytes: an overview. J Dtsch Dermatol Ges 10 : 721– 725.[PubMed]
117. Symoens F, Jousson O, Packeu A, Fratti M, Staib P, Mignon B, Monod M . 2013. The dermatophyte species Arthroderma benhamiae: intraspecies variability and mating behaviour. J Med Microbiol 62 : 377– 385.[PubMed]

Tables

Molecular Detection and Identification of Fungal Pathogens
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Citation: Lagrou K, Maertens J, Hayette M. 2016. Molecular Detection and Identification of Fungal Pathogens, p 489-500. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch35
/content/10.1128/9781555819071.ch35.ch35tab1
TABLE 1

The most currently used primers targeting the ITS region of the fungal rDNA genes complex

Generic image for table
TABLE 1

The most currently used primers targeting the ITS region of the fungal rDNA genes complex

Citation: Lagrou K, Maertens J, Hayette M. 2016. Molecular Detection and Identification of Fungal Pathogens, p 489-500. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch35

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