Resolving phylogenetic relationships within theTrichophyton mentagrophytescomplex: a RADseq genomic approach challenges status of “terbinafine-resistant”Trichophyton indotineaeas distinct species

Abstract

The Trichophyton (T.) mentagrophytes complex encompasses common dermatophytes causing superficial mycoses in humans and animals. The taxonomy of the complex is unstable, with conflicting views on the species status of some taxa, particularly T. indotineae and T. interdigitale. Due to presence of intermediate genotypes, MALDI-TOF MS and ITS rRNA sequencing cannot accurately distinguish all taxa in the complex, potentially contributing to clinical misdiagnoses. In order to resolve the phylogenetic relationship of T. mentagrophytes complex, we employed Restriction Site Associated DNA Sequencing (RADseq) to produce a high-resolution single nucleotide polymorphism (SNP) dataset from 95 isolates. The SNP-based analyses indicated the presence of two major genetic clusters, corresponding to T. mentagrophytes (including T. indotineae) and T. interdigitale. Our results challenge the species status of T. indotineae, because of insufficient genetic divergence from T. mentagrophytes. Therefore, we propose designating T. indotineae as T. mentagrophytes var. indotineae (or T. mentagrophytes ITS genotype VIII) to avoid further splitting of the complex and taxonomic inflation. Although T. interdigitale shows clearer genetic differentiation, its separation is incomplete and identification of some isolates is ambiguous when using routine methods, leading us to consider it a variety as well: T. mentagrophytes var. interdigitale. We recommend using T. mentagrophytes as the overarching species name for all complex isolates. Where precise molecular identification is possible, the use of variety ranks is encouraged. Since identical resistance mechanisms are not specific to any genotype or dermatophytes species, identifying antifungal resistance is more important than differentiating closely related genotypes or populations.