A Descriptive Genomic Snapshot of Seven Mycobacterium bovis Isolates from Morocco (1987–2023)

Bovine tuberculosis (bTB) remains endemic in Morocco, where a national control strategy is implemented through screening and culling of infected animals. In this study, seven Mycobacterium bovis (M. bovis) strains were analyzed. Three strains were isolated in 1987, two in 2015 and two between 2022 and 2023. Bacterial culture and isolation were performed according to the protocol recommended by the World Organization for Animal Health (WOAH). PCR confirmed isolates as M. bovis within the Mycobacterium tuberculosis complex (MTBC). Whole genome sequencing (WGS) was performed (short-read sequencing, Illumina platform), followed by phylogenetic tree construction, and determination of clonal complexes and sub-lineages. Six of the seven strains clustered within the Eu2 clonal complex (CC) and sub-lineage La1.7.1, whereas one strain belonged to the CC unknown 2 and sub-lineage La1.2. Single nucleotide polymorphism (SNP)-based analysis revealed genetic distances ranging from 0 to 204. Low SNP distances were observed between the pairs B2–EL2562 and B3–EL2562. High-impact coding SNPs showed variation, although lineage-specific patterns could not be reliably assessed due to the limited sample size. Comparison of M. bovis strains isolated in different years described the distribution of genetic lineages across time in Morocco, based on the available isolates. Within this limited set of isolates, the Eu2 CC (La1.7.1 sublineage) and the unknown2 CC (La1.2 sublineage) were identified across multiple time points; however, given the limited sample size, these findings should be considered descriptive and do not allow conclusions regarding persistence, evolutionary trends, or transmission dynamics. These findings may offer useful information to strengthen the national bTB control strategy and support One Health surveillance of this zoonotic pathogen in Morocco.