Integrating Machine Learning and Molecular Methods for Trichophyton indotineae Identification and Resistance Profiling Using MALDI-TOF Spectra

Trichophyton indotineae is an emerging dermatophyte species responsible for recalcitrant and terbinafine-resistant dermatophytosis, raising concerns over diagnostic accuracy and treatment efficacy. This study aimed to improve the identification and resistance profiling of T. indotineae by integrating molecular methods with machine learning-assisted analysis of MALDI-TOF mass spectra. A total of 56 clinical isolates within the Trichophyton mentagrophytes complex were analyzed using ITS and ERG1 gene sequencing, antifungal susceptibility testing, and MALDI-TOF MS profiling. Terbinafine resistance was detected in 23 isolates and correlated with specific ERG1 mutations, including F397L, L393S, F415C, and A448T. While conventional MALDI-TOF MS failed to reliably distinguish T. indotineae from closely related species, unsupervised statistical methods (PCA and hierarchical clustering) revealed distinct spectral groupings. Supervised machine learning algorithms, particularly PLS-DA and SVM, achieved 100% balanced accuracy in species classification using 10-fold cross-validation. Biomarker analysis identified discriminatory spectral peaks for both T. indotineae and T. mentagrophytes (3417.29 m/z and 3423.53 m/z). These results demonstrate that combining MALDI-TOF MS with multivariate analysis and machine learning improves diagnostic resolution and may offer a practical alternative to sequencing in resource-limited settings. This approach could enhance the routine detection of terbinafine-resistant T. indotineae and support more targeted antifungal therapy.