Rapid and Specific Identification of Emerging Trichophyton mentagrophytes Genotype VII Using an In-House Developed and Validated Real-Time PCR Assay

Trichophyton mentagrophytes genotype VII (Tm VII ) is an emerging sexually transmitted dermatophyte that causes skin infections characterized by inflammatory, erythematous-squamous, painful, and persistent lesions. This genotype is part of the T. interdigitale/T. mentagrophytes Species Complex ( TiTm SC), which comprises 28 genotypes. To enable rapid and specific differentiation of Tm VII from other genotypes, a real-time polymerase chain reaction (rt-PCR) assay was developed targeting three unique single-nucleotide polymorphisms in the ITS1 region of Tm VII. Assay specificity was further improved by introducing an additional mismatch at the 3’ ends of both forward and reverse primers. The rt-PCR assay demonstrated high sensitivity, with a detection limit of 0.0002 ng of Tm VII genomic DNA. The assay was highly specific, with no cross-reactivity observed with either closely or distantly related fungal pathogens when a cycle threshold (Ct) cutoff of 37 was applied. Among 497 mold isolates tested, 47 were confirmed as Tm VII by rt-PCR, and the results were fully concordant with conventional ITS-PCR/Sanger sequencing. The rt-PCR assay demonstrated high sensitivity, specificity, reproducibility, and speed, with a turnaround time of one day after DNA extraction, compared with seven to ten days for Sanger sequencing. The first rapid molecular assay developed using TaqMan chemistry for Tm VII identification is expected to enhance patient care and support infection control measures.