Identification of moulds in the diagnostic laboratory-an algorithm implementing molecular and phenotypic methods

Diagnostic Microbiology and Infectious Disease

Volumn 59, Issue 1, 2007, Pages 49-60

  Ciardo, Diana E ^a   Schär, Gertrud ^a   Altwegg, Martin ^a   Böttger, Erik C ^a   Bosshard, Philipp P ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Algorithm; Diagnostics; Fungi; Identification; ITS; Moulds; PCR; Sequencing

Indexed keywords

DNA; RIBOSOME RNA;

ALGORITHM; ARTICLE; CONTROLLED STUDY; FUNGUS ISOLATION; GENETIC PROCEDURES; ISOLATION PROCEDURE; LABORATORY DIAGNOSIS; MOLECULAR MODEL; MOULD; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PRIORITY JOURNAL; PROSPECTIVE STUDY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ALGORITHMS; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; FUNGI; HUMANS; MICROBIOLOGICAL TECHNIQUES; MYCOSES; PHENOTYPE;

EID: 34548599650     PISSN: 07328893     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.diagmicrobio.2007.04.020     Document Type: Article

References (25)

1. Bosshard P.P., Abels S., Zbinden R., Böttger E.C., and Altwegg M. Ribosomal DNA sequencing for identification of aerobic Gram-positive rods in the clinical laboratory. J. Clin. Microbiol. 41 (2003) 4134-4140
2. Bosshard P.P., Abels S., Altwegg M., Böttger E.C., and Zbinden R. Comparison of conventional and molecular methods for identification of aerobic catalase-negative Gram-positive cocci in the clinical laboratory. J. Clin. Microbiol. 42 (2004) 2065-2073
3. Chen S.C., Halliday C.L., and Meyer W. A review of nucleic acid-based diagnostic tests for systemic mycoses with an emphasis on polymerase chain reaction-based assays. Med. Mycol. 40 (2002) 333-357
4. Christensen J.J., Andresen K., Justesen T., and Kemp M. Ribosomal DNA sequencing: experiences from use in the Danish National Reference Laboratory for Identification of Bacteria. APMIS 113 (2005) 621-628
5. Ciardo D.E., Schär G., Böttger E.C., Altwegg M., and Bosshard P.P. Internal transcribed spacer sequencing versus biochemical profiling for identification of medically important yeasts. J. Clin. Microbiol. 44 (2006) 77-84
6. de Hoog G.S., Guarro J., Gené J., and Figueras M.J. Atlas of Clinical Fungi. 2nd ed. (2000), Centraalbureau voor Schimmelcultures and Universitat Rovira i Virgili, Utrecht, the Netherlands and Reus, Spain
7. Hall L., Wohlfiel S., and Roberts G.D. Experience with the MicroSeq D2 large-subunit ribosomal DNA sequencing kit for identification of filamentous fungi encountered in the clinical laboratory. J. Clin. Microbiol. 42 (2004) 622-626
8. Hinrikson H.P., Hurst S.F., Lott T.J., Warnock D.W., and Morrison C.J. Assessment of ribosomal large-subunit D1-D2, internal transcribed spacer 1, and internal transcribed spacer 2 regions as targets for molecular identification of medically important Aspergillus species. J. Clin. Microbiol. 43 (2005) 2092-2103
9. Husain S., Alexander B.D., Munoz P., Avery R.K., Houston S., Pruett T., Jacobs R., Dominguez E.A., Tollemar J.G., Baumgarten K., Yu C.M., Wagener M.M., Linden P., Kusne S., and Singh N. Opportunistic mycelial fungal infections in organ transplant recipients: emerging importance of non-Aspergillus mycelial fungi. Clin. Infect. Dis. 37 (2003) 221-229
10. Iwen P.C., Hinrichs S.H., and Rupp M.E. Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens. Med. Mycol. 40 (2002) 87-109
11. Kauffman C.A. Fungal infections in older adults. Clin. Infect. Dis. 33 (2001) 550-555
12. Kaufman D. Fungal infection in the very low birthweight infant. Curr. Opin. Infect. Dis. 17 (2004) 253-259
13. Maertens J., Vrebos M., and Boogaerts M. Assessing risk factors for systemic fungal infections. Eur J Cancer Care 10 (2001) 56-62
14. McNeil M.M., Nash S.L., Hajjeh R.A., Phelan M.A., Conn L.A., Plikaytis B.D., and Warnock D.W. Trends in mortality due to invasive mycotic diseases in the United States, 1980-1997. Clin. Infect. Dis. 33 (2001) 641-647
15. Mesa-Arango A.C., Del Rocio Reyes-Montes M., Perez-Mejia A., Navarro-Barranco H., Souza V., Zuniga G., and Toriello C. Phenotyping and genotyping of Sporothrix schenckii isolates according to geographic origin and clinical form of sporotrichosis. J. Clin. Microbiol. 40 (2002) 3004-3011
16. Patterson J.E., Peters J., Calhoon J.H., Levine S., Anzueto A., Al-Abdely H., Sanchez R., Patterson T.F., Rech M., Jorgensen J.H., Rinaldi M.G., Sako E., Johnson S., Speeg V., Halff G.A., and Trinkle J.K. Investigation and control of aspergillosis and other filamentous fungal infections in solid organ transplant recipients. Transpl. Infect. Dis. 2 (2000) 22-28
17. Perea S., and Patterson T.F. Antifungal resistance in pathogenic fungi. Clin. Infect. Dis. 35 (2002) 1073-1080
18. Pfaller M.A., and Diekema D.J. Rare and emerging opportunistic fungal pathogens: concern for resistance beyond Candida albicans and Aspergillus fumigatus. J. Clin. Microbiol. 42 (2004) 4419-4431
19. Rooney A.P., and Ward T.J. Evolution of a large ribosomal RNA multigene family in filamentous fungi: birth and death of a concerted evolution paradigm. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 5084-5089
20. Silveira F., and Nucci M. Emergence of black moulds in fungal disease: epidemiology and therapy. Curr. Opin. Infect. Dis. 14 (2001) 679-684
21. von Arx J.A. The Genera of Fungi Sporulating in Pure Culture. 3rd ed. (1981), J. Cramer, Vaduz, Switzerland
22. Walsh T.J., Groll A., Hiemenz J., Fleming R., Roilides E., and Anaissie E. Infections due to emerging and uncommon medically important fungal pathogens. Clin. Microbiol. Infect. 10 Suppl 1 (2004) 48-66
23. White T.J., Bruns T., Lee S., and Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: M.A. I., D.H. G., J.J. S., and T.J. W. (Eds). PCR Protocols: a Guide to Methods and Applications (1990), Academic Press, Inc, San Diego, CA 315-322
24. Wood V., Gwilliam R., Rajandream M.A., Lyne M., Lyne R., Stewart A., Sgouros J., Peat N., Hayles J., Baker S., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C., Collins M., Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K., Murphy L., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S., Warren T., Whitehead S., Woodward J., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schafer M., Muller-Auer S., Gabel C., Fuchs M., Dusterhoft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., and Nurse P. The genome sequence of Schizosaccharomyces pombe. Nature 415 (2002) 871-880
25. Yeo S.F., and Wong B. Current status of nonculture methods for diagnosis of invasive fungal infections. Clin. Microbiol. Rev. 15 (2002) 465-484