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Detection of Trichophyton indotineae using a species-specific genomic marker: a marker identification and assay
Chao Tang1, Yuhan Zhang2, Ricardo Belmonte-Lopes3
1Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Radboudumc-CWZ Center of Expertise for Mycology, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands; Foundation Atlas of Clinical Fungi, Hilversum, Netherlands.
Background:
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.
Methods:
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.
Findings:
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.
Interpretation:
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.
Funding:
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.
