Comparative genomics of Mycobacterium africanum L6 from a case of tuberculosis in a cat from Italy

In 2023, following a suspect histological report, we detected a Mycobacterium tuberculosis Complex (MTBC) isolate from a skin biopsy of a 3-year-old female domestic cat with multifocal nodular cutaneous lesions and respiratory problems. Whole-genome sequencing and bioinformatics identified the isolate as M. africanum L6. Phylogeny with 633 M. africanum (L5, L6, L9) and other MTBC genomes from international repositories placed it within a West African cluster (mainly from Gambia) of the L6.1.2 sublineage. The resistome indicated the presence resistance genes intrinsic in M. tuberculosis. The cat died roughly one year later, most probably from systemic tuberculosis, but a necropsy was not requested by the owner. This represents the first report of M. africanum infection in a carnivore, and in a companion animal. The strain belongs to a lineage often considered closer to certain MTBC animal-adapted lineages. The case history reports a stray kitten collected in an area of southern Italy with first migrant reception centers and croplands where workers coming from West Africa are often employed.