Barcode identifiers as a practical tool for reliable species assignment of medically important black yeast species.
Herpotrichiellaceous black yeasts and relatives comprise severe pathogens flanked by nonpathogenic environmental siblings. Reliable identification by conventional methods is notoriously difficult. Molecular identification is hampered by the sequence variability in the internal transcribed spacer (ITS) domain caused by difficult-to-sequence homopolymeric regions and by poor taxonomic attribution of sequences deposited in GenBank. Here, we present a potential solution using short barcode identifiers (27 to 50 bp) based on ITS2 ribosomal DNA (rDNA), which allows unambiguous definition of species-specific fragments. Starting from proven sequences of ex-type and authentic strains, we were able to describe 103 identifiers. Multiple BLAST searches of these proposed barcode identifiers in GenBank revealed uniqueness for 100 taxonomic entities, whereas the three remaining identifiers each matched with two entities, but the species of these identifiers could easily be discriminated by differences in the remaining ITS regions. Using the proposed barcode identifiers, a 4.1-fold increase of 100% matches in GenBank was achieved in comparison to the classical approach using the complete ITS sequences. The proposed barcode identifiers will be made accessible for the diagnostic laboratory in a permanently updated online database, thereby providing a highly practical, reliable, and cost-effective tool for identification of clinically important black yeasts and relatives.
Institut für Medizinische Mikrobiologie, RWTH Aachen University Hospital, Aachen, Germany.
Guido
G
Heinrichs
G Sybren
GS
de Hoog
Gerhard
G
Haase
D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D004271:DNA, Fungal / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D030541:Databases, Genetic; D006801:Humans; D009181:Mycoses / Q000175:diagnosis / Q000382:microbiology; D015003:Yeasts / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification
D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer