Comparison of DermaGenius and In-House qPCR Methods for Detection of Recalcitrant Dermatophyte Infections: A Practical Approach for Dermatologists and Mycologists.

Abstract

Background: Chronic and recalcitrant dermatophytosis has become increasingly problematic in dermatology practice, largely due to emerging antifungal resistance, affecting not only terbinafine but also azoles. Among the causative agents, Trichophyton indotineae has emerged as a key pathogen associated with treatment failure, extensive disease, and frequent relapse, even in immunocompetent patients.

Objective: This study aimed to evaluate and compare two rapid molecular diagnostic approaches: A commercial multiplex qPCR assay (DermaGenius Resistance Multiplex PCR, DermaGenius RMP) and a T. indotineae-specific in-house qPCR assay, focusing on their practical value for early detection of recalcitrant dermatophyte infections and terbinafine resistance in routine dermatology practice.

Methods: Sixty-four dermatophyte isolates obtained from patients with chronic or treatment-resistant dermatophytosis in Türkiye wereanalysed. Species identification and detection of squalene epoxidase (SQLE) gene mutations associated with terbinafine resistance were performed using DermaGenius RMP and the in-house T. indotineae-specific qPCR assay, with confirmatory ITS/SQLE sequencing and CLSI microbroth dilution antifungal susceptibility testing.

Results: Overall concordance between the two qPCR methods was 93.8% (κ = 0.74, z = 5.99, p < 0.001) for T. indotineae identification. Most recalcitrant cases were caused by T. indotineae, and SQLE mutations were detected in > 90% of these isolates, consistent with the observed clinical resistance. DermaGenius RMP enabled rapid, standardised detection of terbinafine resistance-associated mutations suitable for routine diagnostics, whereas the in-house qPCR provided highly specific identification of T. indotineae. Notably, 10 T. indotineae isolates harboured the SQLE F397L substitution despite terbinafine susceptibility.

Conclusions: Rapid molecular diagnostics, particularly qPCR-based assays, provide actionable information early in the course of infection. In this study, both assays showed comparable performance for T. indotineae detection. Prompt identification of T. indotineae and associated resistance mutations may help avoid ineffective antifungal therapy, reduce chronicity, and support rational treatment decisions in routine clinical practice.