The emergence of superficial dermatophytosis due to <i>Trichophyton indotineae</i> and <i>Trichophyton mentagrophytes</i> genotypes VII and II* in New York: a need for comprehensive testing approaches

ABSTRACT We report a rapid increase in dermatophyte infections in New York City and surrounding counties from 2022 to 2024. Reported cases include 135 of Trichophyton indotineae ( Ti ), 39 of Trichophyton mentagrophytes genotype VII ( Tm VII), and 14 of T. mentagrophytes genotype II* ( Tm II*). These numbers highlight the urgent need for rapid, high-throughput identification, drug-resistance testing, and surveillance of these pathogens. To address these challenges, an automated deep learning model was developed using internal transcribed spacer (ITS) sequences from 28 well-defined genotypes of Trichophyton interdigitale/T. mentagrophytes Species Complex ( TiTm SC). Ti , previously classified as T. mentagrophytes genotype VIII, is now recognized as a distinct species. The model enabled rapid and accurate identification of all 28 genotypes directly from Sanger sequencing output files. In vitro antifungal susceptibility testing (AFST) demonstrated that 57% of Ti isolates exhibited high minimum inhibitory concentrations (MICs) to the first-line drug terbinafine, and 38%–52% showed elevated MICs to azoles. In contrast, all Tm VII and Tm II* isolates had low MICs to both terbinafine and azoles. Whole-genome sequencing (WGS) of a subset of Ti , Tm VII, and Tm II* isolates revealed evidence of both clonal transmission and independent introductions. This integrated approach, combining rapid identification, drug resistance testing, and transmission analysis, is expected to improve patient care and infection control measures. IMPORTANCE This report presents a comprehensive laboratory investigation into the emergence and rapid spread of Trichophyton indotineae ( Ti ), Trichophyton mentagrophytes genotype VII ( Tm VII), and T. mentagrophytes genotype II* ( Tm II*) in New York City and its surrounding counties. A high-throughput pipeline for the identification of Trichophyton species and genotypes is described. Approximately 57% of Ti isolates exhibited elevated minimum inhibitory concentrations (MICs) to terbinafine, while 38%–52% demonstrated elevated MICs to azoles, raising significant concern. Whole-genome sequencing revealed evidence of both clonal spread and independent introductions of Ti , Tm VII, and Tm II*. These findings have important implications for patient care and infection control measures.