Characterization of Drug Resistance Mutations in Mycobacterium tuberculosis Isolates from Moroccan Patients Using Deeplex Targeted Next-Generation Sequencing

Tuberculosis (TB) is a major public health concern worldwide and in Morocco, particularly considering the increasing burden of drug-resistant Mycobacterium tuberculosis (MTB) strains. In this study, we report the first nationwide molecular characterization of MTB clinical isolates using the Deeplex-MycTB targeted next-generation sequencing (tNGS) assay. A total of 71 culture-derived DNA samples from Moroccan TB patients were analyzed to detect resistance-associated mutations across 18 genes and to determine phylogenetic lineages. Of the 68 interpretable samples, 75% harbored either confirmed or uncharacterized mutations linked to drug resistance. Among these, 78% were classified as multidrug-resistant TB (MDR-TB) including 25.5% that met the criteria for pre-extensively drug-resistant TB (pre-XDR-TB). Mutations were most frequently identified in rpoB, katG, inhA, and pncA, consistent with resistance to rifampicin, isoniazid, and pyrazinamide. Phylogenetic analysis revealed a predominance of Lineage 4.3 (Euro-American) with a high representation of the LAM9 and T clades, some of which showed associations with specific resistance profiles. These findings highlight the utility of tNGS as a powerful tool for rapid resistance detection and molecular surveillance, with potential implications for guiding individualized treatment and informing national TB control strategies in Morocco.