First report of Mycobacterium africanum Lineage 6 from a case of tuberculosis in a cat from Italy: genomic characterization and phylogenetic analysis

Patricia Alba¹Andrea Caprioli^1*Cristiano Cocumelli¹Claudia Eleni¹Valentina Galietta¹Angelo Giacomi¹Luigi Sorbara¹Fiorentino Stravino¹Fabiola Feltrin¹Roberta Amoruso¹Angela Ianzano¹Francesco Ceccaroni²Mario Frega³Virginia Carfora¹Alessia Franco¹Antonio Battisti¹

• ¹Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, General Diagnostic Department, Rome, Italy
• ²Veterinary practitioner, Rome, Italy
• ³Azienda Sanitaria Roma 1, Servizi Veterinari, Rome, Italy

Tuberculosis in humans is mainly caused by 2 highly related bacteria within the Mycobacterium tuberculosis complex (MTBC), M. tuberculosis and M. africanum. M. tuberculosis is widely spread, while M. africanum is more ecologically restricted to Africa. In 2023 we examined a skin biopsy from a 3-year-old female domestic cat with multifocal nodular cutaneous lesions and respiratory problems. The animal was an indoor cat kept in Rome, reportedly taken as a stray kitten in a village in the south of Italy (Central Calabria Region). Skin histology with Ziehl-Neelsen staining were consistent with suspected mycobacteriosis. Bacterial cultures for Mycobacterium spp. yielded an isolate, identified by PCR as a MTBC. Whole-genome sequencing and bioinformatics further identified the isolate as M. africanum lineage 6 and phylogeny with 634 other MTBC genomes placed it within a West African cluster (mainly from Gambia) of the L6.1.2 sublineage. Resistome analysis indicated the presence of resistance genes intrinsic in M. tuberculosis and point mutations not associated with resistance. 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 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, consistently with our phylogenetic evidence.