Abstract
<title>Abstract</title> <p> Background Tuberculosis (TB) remains a major public health challenge in Morocco, with marked regional disparities shaped by social and environmental conditions. We investigated the molecular epidemiology of Mycobacterium tuberculosis complex (MTBC) strains circulating in Tétouan, Morocco, focusing on strain diversity, lineage distribution, transmission dynamics, and associated sociodemographic factors using 24-locus MIRU-VNTR genotyping. Methods In this prospective cross-sectional study, 103 MTBC isolates from bacteriologically confirmed pulmonary TB patients diagnosed in Tétouan between 2020 and 2023 were analyzed using the 24-locus MIRU-VNTR scheme. Genetic diversity was assessed using the Hunter–Gaston Discriminatory Index (HGDI) and locus-level allelic diversity ( <italic>h</italic> ). Phylogenetic relationships were analyzed using UPGMA dendrograms and minimum spanning tree (MST) analysis <italic>via</italic> the MIRU-VNTR <italic>plus</italic> platform and recent transmission was estimated using the n − 1 method. Associations between clonal complex (CC) assignment and sociodemographic variables were evaluated using binary logistic regression. To explore the evolutionary context of the locally dominant Beijing and LAM strains, their profiles were compared to representative global datasets. Results The 24-locus MIRU-VNTR scheme demonstrated excellent discriminatory power (HGDI = 0.9896). Among the 103 isolates, 52 (50.5%) were assigned to established lineages: LAM (29.1%), Beijing (9.7%), Ghana (3.9%), S (2.9%), Haarlem (1.9%), West African 1 (1.9%), and West African 2 (1.0%). UPGMA analysis identified 17 (16.5%) isolates grouped into five identical-profile clusters, translating to a recent transmission rate of 11.6%. MST analysis revealed 10 CCs encompassing 40 (38.8%) isolates. Residence in the Old Medina slum area was the only independent predictor of CC membership ( <italic>p</italic> =.001). Conclusion The MTBC population in Tétouan is characterized by high genetic diversity and limited evidence of recent transmission, with residence in informal urban settlements (slums) emerging as a potential predictor of transmission. The first reported detection of Ghana, West African 1, and West African 2 lineages in Morocco suggests recent strain introductions, while the phylogeographic structure of Beijing and LAM strains reflects multiple historical dissemination routes involving Northern Eurasia, the Mediterranean basin, Africa, and possibly South America, followed by local diversification. Our findings support strengthening molecular surveillance through high-resolution genomic approaches and implementing geographically targeted public health interventions to interrupt TB transmission in lower-middle-income countries such as Morocco. </p>