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

A C Normand¹, A Packeu², C Cassagne³

¹Service de Parasitologie/Mycologie, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France annececile.normand@aphp.fr.

Journal of Clinical Microbiology

|March 2, 2018

Summary

This summary is machine-generated.

DNA sequencing of the internal transcribed spacer (ITS) region reliably identifies dermatophytes. However, inaccurate fungal DNA databases hinder accurate identification, necessitating frequent verification and updates for reliable species identification.

Keywords:

ITS barcode dermatophyte fungi hospital sequencing

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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.