Nucleotide Sequence Database Comparison for Routine Dermatophyte Identification by Internal Transcribed Spacer 2...

Area of Science:

• Medical Mycology
• Molecular Biology
• Fungal Taxonomy

Background:

• Conventional dermatophyte identification relies on morphology, which can be unreliable.
• Nucleotide sequencing of the rRNA internal transcribed spacer (ITS) region is proposed as a fungal identification barcode.
• Existing DNA sequence databases for fungal identification often contain mislabeled sequences, compromising accuracy.

Purpose of the Study:

• To evaluate the accuracy of five DNA databases for identifying clinical dermatophyte isolates using ITS2 sequencing.
• To assess the reliability of ITS sequencing for dermatophyte identification compared to DNA-based clustering.
• To highlight issues with database accuracy and taxonomic revisions in fungal identification.

Main Methods:

• Prospective analysis of 292 clinical dermatophyte strains using ITS2 nucleotide sequence analysis.
• Comparison of sequences against five available DNA databases.
• Identification results were compared to clusters obtained via DNA alignment, with the DNA tree serving as the identification standard.

Main Results:

• ITS2 sequencing identified the majority of strains (255/292) within the genus *Trichophyton*, with *T. rubrum* complex being most prevalent (184/292).
• Other genera identified included *Microsporum*, *Nannizzia*, and *Epidermophyton*.
• Species-level identification of the *T. rubrum* complex proved challenging, and database inaccuracies were noted.

Conclusions:

• ITS DNA sequencing is a reliable method for dermatophyte identification when using comprehensive and accurately labeled databases.
• Inaccurate data in current DNA databases necessitates frequent verification and updates aligned with fungal taxonomy revisions.
• New species or DNA references require verification of their phylogenetic position before database inclusion.