Degradation of fungal DNA in formalin-fixed paraffin-embedded sinus fungal balls hampers reliable sequence-based identification of fungi

Medical Mycology

Volumn 49, Issue 3, 2011, Pages 329-332

  Cabaret, Odile ^a,b   Toussain, Guillaume ^b   Abermil, Nassera ^b   Alsamad, Issam Abd ^b   Botterel, Françoise ^a,b   Costa, Jean Marc ^b,c   Papon, Jean François ^b,d   Bretagne, Stéphane ^a,b,e  

^a ECOLE NATIONALE VÉTÉRINAIRE D ALFORT   (France)

^b HENRI MONDOR HOSPITAL   (France)

^c LABORATOIRE CERBA   (France)

^d FACULTÉ DE MÉDECINE   (France)

^e INSTITUT PASTEUR   (France)

Author keywords

fungus identifi cation; ITS sequencing; real time quantitative PCR; Sinus fungal ball

Indexed keywords

DNA FRAGMENT; FORMALDEHYDE; FUNGAL DNA; INTERNAL TRANSCRIBED SPACER; MITOCHONDRIAL DNA; PARAFFIN;

ARTICLE; ASPERGILLUS FUMIGATUS; CONTROLLED STUDY; DIAGNOSTIC ACCURACY; DNA DEGRADATION; DNA EXTRACTION; DNA SEQUENCE; FUNGAL STRAIN; FUNGUS; FUNGUS CULTURE; FUNGUS IDENTIFICATION; GENE AMPLIFICATION; HUMAN; HUMAN TISSUE; LEWIA; MAJOR CLINICAL STUDY; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RELIABILITY; SINUS FUNGUS BALL; SYSTEMIC MYCOSIS;

DNA, FUNGAL; FORMALDEHYDE; FUNGI; HUMANS; MYCOSES; PARAFFIN; PARANASAL SINUS DISEASES; PATHOLOGY, MOLECULAR; SENSITIVITY AND SPECIFICITY; TISSUE FIXATION;

ASPERGILLUS; ASPERGILLUS FUMIGATUS; FUNGI; LEWIA;

EID: 79952637550     PISSN: 13693786     EISSN: 14602709     Source Type: Journal    
DOI: 10.3109/13693786.2010.525537     Document Type: Article

References (14)

1. Chakrabarti A, Denning DW, Ferguson BJ, et al. Fungal rhinosinusi-tis: a categorization and def nitional schema addressing current con-troversies. Laryngoscope 2009; 119: 1809-1818.
2. Grosjean P, Weber R. Fungus balls of the paranasal sinuses: a review. Eur Arch Otorhinolaryngol 2007; 264: 461-470. (Pubitemid 46569964)
3. Dufour X, Kauffmann-Lacroix C, Ferrie JC, et al. Paranasal sinus fungus ball: epidemiology, clinical features and diagnosis. A retro-spective analysis of 173 cases from a single medical center in France, 1989-2002. Med Mycol 2006; 44: 61-67. (Pubitemid 43135557)
4. Costa C, Costa JM, Desterke C, et al. 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 2002; 40: 2224-2227. (Pubitemid 34596412)
5. Costa JM, Ernault P, Gautier E, Bretagne S. Prenatal diagnosis of congenital toxoplasmosis by duplex real-time PCR using f uorescence resonance energy transfer hybridization probes. Prenat Diagn 2001; 21: 85-88.
6. White TJ, Bruns T, Lee S, Taylor JW. Amplif cation and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds. PCR Protocols: A Guide to Methods and Applications. San Diego: Academic Press, 1990: 315-322.
7. 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 2007; 45: 380-385.
8. Willinger B, Obradovic A, Selitsch B, et al. Detection and identif ca-tion of fungi from fungus balls of the maxillary sinus by molecular techniques. J Clin Microbiol 2003; 41: 581-585. (Pubitemid 36184165)
9. Bialek R, Konrad F, Kern J, et al. PCR based identif cation and dis-crimination of agents of mucormycosis and aspergillosis in paraff n wax embedded tissue. J Clin Pathol 2005; 58: 1180-1184. (Pubitemid 41566463)
10. Hata DJ, Buckwalter SP, Pritt BS, Roberts GD, Wengenack NL. Real-time PCR method for detection of zygomycetes. J Clin Microbiol 2008; 46: 2353-2358.
11. Hewitt SM, Lewis FA, Cao Y, et al. Tissue handling and specimen preparation in surgical pathology: issues concerning the recovery of nucleic acids from formalin-f xed, paraff n-embedded tissue. Arch Pathol Lab Med 2008; 132: 1929-1935.
12. Dannaoui E, Schwarz P, Slany M, et al. Molecular detection and iden-tif cation of zygomycetes species from paraff n-embedded tissues in a murine model of disseminated zygomycosis: a collaborative European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Fungal Infection Study Group (EFISG) evaluation. J Clin Microbiol 2010; 48: 2043-2046.
13. Badali H, De Hoog GS, Curfs-Breuker I, Andersen B, Meis JF. In vitro activities of eight antifungal drugs against 70 clinical and environmen-tal isolates of Alternaria species. J Antimicrob Chemother 2009; 63: 1295-1297.
14. Balajee SA, Borman AM, Brandt ME, et al. Sequence-based identif-cation of Aspergillus, Fusarium, and mucorales species in the clinical mycology laboratory: where are we and where should we go from here? J Clin Microbiol 2009; 47: 877-884.