title: Detection and identification of yeasts from formalin-fixed, paraffin-embedded tissue by use of PCR-electrospray ionization mass spectrometry.
abstract: Diagnosis of yeast infection is typically accomplished by fungal smear and culture, histopathologic examination, and/or serologic studies. Newer assays based on mass spectrometry may be useful for yeast identification when histologic examination is inconclusive, fungal cultures are not ordered, or cultures fail to yield a causative agent. The purpose of this study was to evaluate the ability of the PLEX-ID broad fungal assay to accurately detect and identify yeasts in formalin-fixed paraffin-embedded (FFPE) tissues. Tissue samples from 78 FFPE specimens with both histopathology and corresponding culture results for a variety of yeasts were tested using the PLEX-ID broad fungal assay. A 40-μm FFPE tissue section from each specimen was digested with proteinase K followed by nucleic acid extraction and PCR using broad-range fungal primers. Yeast DNA in amplified products was identified using electrospray ionization mass spectrometry. Discordant results were resolved by D2 rRNA gene sequencing. PLEX-ID analysis detected yeast DNA in 78.2% (61/78) of the cases, of which 91.8% (56/61) were concordant with culture results. Of the 5 discordant positive results, 4 PLEX-ID results were considered to result from environmental contaminants, while 1 clinically important discrepancy was observed (Blastomyces dermatitidis by culture and Cryptococcus neoformans by PLEX-ID). Sequencing of the discordant sample was unsuccessful. The majority of histopathology results (89.7% [70/78]) correlated with culture results. The PLEX-ID broad fungal assay identifies fungi directly from FFPE tissues and can be a useful adjunct to traditional culture and histopathology tests.
authors.affiliation: Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA.
authors.forename: Patricia J
authors.initials: PJ
authors.lastname: Simner
authors.forename: Seanne P
authors.initials: SP
authors.lastname: Buckwalter
authors.forename: James R
authors.initials: JR
authors.lastname: Uhl
authors.forename: Nancy L
authors.initials: NL
authors.lastname: Wengenack
authors.forename: Bobbi S
authors.initials: BS
authors.lastname: Pritt
mesh_terms: D004271:DNA, Fungal / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D009181:Mycoses / Q000175:diagnosis* / Q000382:microbiology; D057089:Pathology, Molecular / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods*; D013048:Specimen Handling / Q000379:methods; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D016610:Tissue Embedding; D016707:Tissue Fixation; D015003:Yeasts / Q000235:genetics / Q000302:isolation & purification*
chemical_list: D004271:DNA, Fungal