SQLE mutations and antifungal susceptibility profile of Trichophyton species isolated from patients with recalcitrant dermatophytosis: A laboratory-based study from Pakistan

This study evaluated squalene epoxidase (SQLE) mutations, and the antifungal susceptibility profile of Trichophyton species isolated from patients with recalcitrant dermatophytosis in Pakistan. The study was conducted at the Aga Khan University Hospital Laboratory, Karachi, between January 2023 and February 2024. Identification of the isolates was performed through sequencing of the internal transcribed spacer (ITS) region. Antifungal susceptibility testing for terbinafine, itraconazole, and voriconazole was performed using the broth microdilution method based on modified European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. Minimum inhibitory concentrations (MICs) were interpreted using EUCAST epidemiological cutoff values to classify isolates as wild-type or non-wild-type. DNA extraction was carried out using the QIAamp DNA Mini Kit, and ITS and SQLE gene regions were amplified and sequenced via Sanger sequencing. A total of 37 Trichophyton isolates were included, of which 17 (45.9%) were Trichophyton mentagrophytes, 16 (43.2%) were T. indotineae, 2 (5.40%) were T. rubrum, and 2 (5.40%) were T. interdigitale identified through ITS sequencing. Non-wild-type MICs to terbinafine were observed in 28 (75.7%) isolates, while eight isolates (21.6%) also showed non-wild-type MICs to itraconazole; no isolates demonstrated non-wild-type MICs to voriconazole. The most prevalent SQLE gene mutations were F397L (54%), Q408R (32.4%), and A448T (21.6%). This study represents the first report from Pakistan of antifungal resistance and SQLE gene mutations in Trichophyton strains from patients with recalcitrant dermatophytosis. The high prevalence of resistance underscores the urgent need for capacity building in antifungal susceptibility testing and highlights the importance of guiding appropriate treatment strategies to manage resistant dermatophytosis in the region effectively.