Detection of Trichophyton indotineae using a species-specific genomic marker: a marker identification and assay validation study.
Trichophyton indotineae is an emerging dermatophyte associated with extensive inflammatory tinea and terbinafine resistance. Routine laboratory methods often fail to distinguish T indotineae from related lineages in the Trichophyton mentagrophytes-interdigitale complex, hindering surveillance and delaying resistance testing. We aimed to define the public internal transcribed spacer (ITS) haplotypes of T indotineae and develop novel molecular assays for accurate identification.
We conducted a marker identification and assay validation study by recurating GenBank ITS records (annotated as T mentagrophytes, T interdigitale, and T indotineae) from database inception to March 10, 2026, and performing haplotype analysis based on a 540 bp ITS region. We excluded records lacking complete coverage of this region or containing degenerate bases or alignment gaps from the primary network. We analysed Trichophyton genomes to identify a T indotineae-specific single-copy marker, OG7443, and developed duplex endpoint PCR and TaqMan real-time PCR assays. These assays were validated using culture isolates and direct skin-scraping specimens across two centres in China and one in the Netherlands.
Of 5584 ITS records retrieved, 4744 were retained for haplotype analysis after curation. The type-associated haplotype H002 comprised 1576 records, and a type-strain-anchored T indotineae cluster comprised 1698 records across 75 haplotypes. Duplex endpoint PCR identified all T indotineae and non-T indotineae isolates (sensitivity 100% [57/57; 95% CI 93·7-100·0]; specificity 100% [105/105; 96·5-100·0]). The TaqMan assay identified all culture isolates and direct skin scrapings, with sensitivity 100% (53/53; 93·3-100·0) and specificity 100% (160/160; 97·7-100·0). Estimated consumable costs were US$0·39 per sample for duplex endpoint PCR and $4·24 for TaqMan PCR.
OG7443 is a species-specific genomic marker for T indotineae that supports two assay formats. These assays could aid surveillance, case recognition, and triage for downstream resistance testing, but direct-specimen performance requires confirmation in larger prospective cohorts.
Noncommunicable Chronic Diseases-National Science and Technology Major Project; Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences; 111 Project; Brazilian Council for Scientific and Technological Development.
We conducted a marker identification and assay validation study by recurating GenBank ITS records (annotated as T mentagrophytes, T interdigitale, and T indotineae) from database inception to March 10, 2026, and performing haplotype analysis based on a 540 bp ITS region. We excluded records lacking complete coverage of this region or containing degenerate bases or alignment gaps from the primary network. We analysed Trichophyton genomes to identify a T indotineae-specific single-copy marker, OG7443, and developed duplex endpoint PCR and TaqMan real-time PCR assays. These assays were validated using culture isolates and direct skin-scraping specimens across two centres in China and one in the Netherlands.
Of 5584 ITS records retrieved, 4744 were retained for haplotype analysis after curation. The type-associated haplotype H002 comprised 1576 records, and a type-strain-anchored T indotineae cluster comprised 1698 records across 75 haplotypes. Duplex endpoint PCR identified all T indotineae and non-T indotineae isolates (sensitivity 100% [57/57; 95% CI 93·7-100·0]; specificity 100% [105/105; 96·5-100·0]). The TaqMan assay identified all culture isolates and direct skin scrapings, with sensitivity 100% (53/53; 93·3-100·0) and specificity 100% (160/160; 97·7-100·0). Estimated consumable costs were US$0·39 per sample for duplex endpoint PCR and $4·24 for TaqMan PCR.
OG7443 is a species-specific genomic marker for T indotineae that supports two assay formats. These assays could aid surveillance, case recognition, and triage for downstream resistance testing, but direct-specimen performance requires confirmation in larger prospective cohorts.
Noncommunicable Chronic Diseases-National Science and Technology Major Project; Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences; 111 Project; Brazilian Council for Scientific and Technological Development.
Authors
Tang Tang, Zhang Zhang, Belmonte-Lopes Belmonte-Lopes, Buil Buil, Pas Pas, van der Maas van der Maas, Kong Kong, Luo Luo, Xu Xu, Rezaei-Matehkolaei Rezaei-Matehkolaei, Xie Xie, Liu Liu, Brasch Brasch, Vicente Vicente, Li Li, Tsui Tsui, Kang Kang, Xu Xu, Liang Liang, de Hoog de Hoog
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