Kaplan Engin, Bingöl Oğuzhan, Kandemir Hazal, Karakoyun Ayşe Sultan, Durdu Murat, Ilkit Macit
Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Istanbul University-Cerrahpaşa, Istanbul, Türkiye.
Division of Mycology, Department of Microbiology, Faculty of Medicine, Çukurova University, Adana, Türkiye.
Mycopathologia. 2025 Apr 3;190(2):32. doi: 10.1007/s11046-025-00939-5.
Trichophyton indotineae, formerly known as T. mentagrophytes internal transcribed spacer (ITS) genotype VIII, has been recognized over the last decade due to its high virulence and resistance to treatment. Its accurate identification in routine mycology laboratories remains challenging, as it shares phenotypic traits and substantial rDNA ITS similarity with T. mentagrophytes and T. interdigitale. This study aimed to identify more divergent and stable sequences via whole-genome comparisons between T. indotineae and T. interdigitale to facilitate highly specific targeting of T. indotineae using a validated quantitative polymerase chain reaction (qPCR)-based method. Our whole-genome comparison revealed at least 22 unique sequences of T. indotineae compared to T. interdigitale and revealed the divergence of the former from the reference genomes of other Trichophyton species. Among these, a 499 bp segment was identified as the most genetically distinct sequence within the T. indotineae genome. Seventy-three dermatophyte strains [T. indotineae (n = 66), non-T. indotineae (n = 7)], were tested using our qPCR assay targeting the above-mentioned stable 499-bp region. Regarding analytical performance, our T. indotineae-specific qPCR assay exhibited high sensitivity (93.3%) and specificity (100%), with a detection limit of ~ 15 genomic copies. Our approach has the potential to establish highly sensitive and specific qPCR assays without relying on specialized assay designs for single nucleotide polymorphisms in the ITS or other loci. This approach offers a practical solution for updating molecular diagnostics, particularly for novel taxa such as T. indotineae, for which limited gene data are available in public databases.
印多蒂内毛癣菌，以前称为须癣毛癣菌内转录间隔区（ITS）基因型VIII，在过去十年中因其高毒力和耐药性而被人们所认识。在常规真菌学实验室中对其进行准确鉴定仍然具有挑战性，因为它与须癣毛癣菌和指间毛癣菌具有共同的表型特征和大量的核糖体DNA ITS相似性。本研究旨在通过印多蒂内毛癣菌和指间毛癣菌之间的全基因组比较来鉴定更多不同且稳定的序列，以便使用经过验证的基于定量聚合酶链反应（qPCR）的方法对印多蒂内毛癣菌进行高度特异性靶向检测。我们的全基因组比较显示，与指间毛癣菌相比，印多蒂内毛癣菌至少有22个独特序列，并揭示了前者与其他毛癣菌属参考基因组的差异。其中，一个499 bp的片段被确定为印多蒂内毛癣菌基因组中最具遗传差异的序列。使用我们针对上述稳定的499 bp区域的qPCR检测方法对73株皮肤癣菌菌株[印多蒂内毛癣菌（n = 66），非印多蒂内毛癣菌（n = 7）]进行了检测。关于分析性能，我们的印多蒂内毛癣菌特异性qPCR检测方法表现出高灵敏度（93.3%）和特异性（100%），检测限约为15个基因组拷贝。我们的方法有可能建立高度灵敏和特异的qPCR检测方法，而无需依赖针对ITS或其他位点单核苷酸多态性的专门检测设计。这种方法为更新分子诊断提供了一个切实可行的解决方案，特别是对于像印多蒂内毛癣菌这样的新分类群，公共数据库中可用的基因数据有限。
