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Is the extraction by Whatman FTA filter matrix technology and sequencing of large ribosomal subunit D1–D2 region sufficient for identification of clinical fungi?
Author(s) -
Kiraz Nuri,
Oz Yasemin,
Aslan Huseyin,
Erturan Zayre,
Ener Beyza,
Arikan Akdagli Sevtap,
Muslumanoglu Hamza,
Cetinkaya Zafer
Publication year - 2015
Publication title -
mycoses
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.13
H-Index - 69
eISSN - 1439-0507
pISSN - 0933-7407
DOI - 10.1111/myc.12365
Subject(s) - biology , ribosomal rna , dna sequencing , yeast , dna extraction , ribosomal dna , identification (biology) , gene , mycology , protein subunit , filter paper , internal transcribed spacer , dna , microbiology and biotechnology , polymerase chain reaction , genetics , computational biology , phylogenetics , botany , chromatography , chemistry
Summary Although conventional identification of pathogenic fungi is based on the combination of tests evaluating their morphological and biochemical characteristics, they can fail to identify the less common species or the differentiation of closely related species. In addition these tests are time consuming, labour‐intensive and require experienced personnel. We evaluated the feasibility and sufficiency of DNA extraction by Whatman FTA filter matrix technology and DNA sequencing of D1–D2 region of the large ribosomal subunit gene for identification of clinical isolates of 21 yeast and 160 moulds in our clinical mycology laboratory. While the yeast isolates were identified at species level with 100% homology, 102 (63.75%) clinically important mould isolates were identified at species level, 56 (35%) isolates at genus level against fungal sequences existing in DNA databases and two (1.25%) isolates could not be identified. Consequently, Whatman FTA filter matrix technology was a useful method for extraction of fungal DNA ; extremely rapid, practical and successful. Sequence analysis strategy of D1–D2 region of the large ribosomal subunit gene was found considerably sufficient in identification to genus level for the most clinical fungi. However, the identification to species level and especially discrimination of closely related species may require additional analysis.