Mammalian tuberculosis (TB) is a chronic granulomatous disease that affects both animals and humans and is caused by bacteria within the Mycobacterium tuberculosis complex (MTBC). MTBC members belong to the family Mycobacteriaceae and are Gram-positive, acid-fast bacilli. The taxonomy of organisms in the MTBC is in a state of constant evolution (World Organisation for Animal Health, 2022). Recent genomic analyses suggest that all MTBC members belong to a single species, M. tuberculosis, with Mycobacterium africanum, Mycobacterium bovis, Mycobacterium caprae, Mycobacterium microti, and Mycobacterium pinnipedii considered heterotypic synonyms (variants) of M. tuberculosis, and Mycobacterium canettii, Mycobacterium mungi, and Mycobacterium orygis are recognized as strains of M. tuberculosis (World Organisation for Animal Health, 2022; Riojas et al., 2018). To retain linkage with historical nomenclature, the more widely recognized designations are commonly used instead of infra-subspecific designations (World Organisation for Animal Health, 2022). Hence, throughout the paper, we used the historical nomenclature (e.g., M. africanum) designations instead of M. tuberculosis var. africanum for ease of prior association.

All MTBC members share remarkable genomic similarity, with more than 99.95% nucleotide identity. Although all mammalian species are considered susceptible to tuberculosis, they vary considerably in their host tropism and ability to cause disease (Silva-Pereira et al., 2019). Single nucleotide polymorphisms (SNPs) and deletions of genomic regions ranging from 2 to 12.7 Kb, denominated “regions of difference (RDs),” allow for species differentiation (Brosch et al., 2002; Cousins et al., 2003); World lineage-wise classification of MTBC was also achieved using restriction fragment length polymorphism (RFLP) and PCR, such as mycobacterial interspersed repetitive units – variable number of tandem repeats (MIRU-VNTR) spoligotyping (Brosch et al., 2002).

M. tuberculosis and M. africanum are primarily human pathogens, but are also known to infect animals, and are considered pathogens of high Public-Health and One-Health relevance (Comín et al., 2021; World Organisation for Animal Health, 2022). M. tuberculosis is widely spread, while M. africanum, first described in 1968 from TB patients in Senegal (Castets et al., 1968), is more ecologically restricted to Africa and, in particular, West Africa, where it is responsible for almost half of all the TB cases (Comín et al., 2021; World Organisation for Animal Health, 2022; Silva et al., 2022). TB caused by M. africanum strains outside West Africa, although rare, has been described in several countries, mostly found in migrants from endemic areas (Yeboah-Manu et al., 2017; Comín et al., 2021; Silva et al., 2022).

Ten human-adapted lineages (L) belong to the MTBC. In particular, L1–L4 and L7 and L8 comprise M. tuberculosis sensu stricto (which majorly infects humans), while L5, L6, L9, and L10 consist of M. africanum (Blouin et al., 2012; Firdessa et al., 2013; Riojas et al., 2018; Gagneux, 2018; Ngabonziza et al., 2020; Coscolla et al., 2021; Balamurugan et al., 2022; Silva et al., 2022; Guyeux et al., 2024). L6 is known to be geographically restricted to West Africa, and L5 is known to have moved from West Africa to Central Africa (Coscolla et al., 2021; Balamurugan et al., 2022). In contrast, L9 belongs to a sister clade of L6, being placed between L6 and the animal-adapted lineages (Coscolla et al., 2021). Recently, a proposed L10 was also described, a sister lineage of L6 and L9 associated with Central Africa. Phylogenetic reconstruction suggests L10 could represent a missing link in the evolutionary and geographic migration histories of M. africanum (Guyeux et al., 2024).

Historically, M. africanum shows “intermediate” phenotypic characteristics between M. tuberculosis and M. bovis based on biochemical testing (Castets et al., 1968; Meyer and David, 1979; Thorel, 1980); however, lineage classification based on genotypic differences is more accurate than one based on phenotypic assays, also because phenotypic diversity among isolates of the same lineage or even sublineage cannot be excluded (Silva et al., 2022). Compared to M. tuberculosis, L5 and L6 are reported to have slower growth in culture, along with lower bacterial load and delayed disease progression (Cá et al., 2019; Baya et al., 2020; Balamurugan et al., 2022).

Phylogenetically, L5, L6, L9, L10, and the animal-adapted lineages share a common ancestor lacking the RD9, but L5 split from the common phylogenetic branch before the others. Some L5 genomes (L5.1.1) have also undergone RD711 deletion, while L6 has lost RD702 (Mostowy et al., 2004; De Jong et al., 2010; Ates et al., 2018; Coscolla et al., 2021; Comín et al., 2021). L6 has also undergone deletion of RD7, RD8, and RD10 regions (Gagneux, 2018; Comín et al., 2021; Balamurugan et al., 2022). L9 shares some genomic deletions with those of strains belonging to L6, such as RD702, but not with others, which are also present in the genomes of strains of animal-associated lineages, such as RD1 and RD5 (Coscolla et al., 2021; Silva et al., 2022). L10 lacks RD9, RD7, RD8, and RD10, and it harbors a specific large 9,134-no turning (nt) deletion (Rv0613c–Rv0622) in M. tuberculosis H37Rv (NC\_000962.3:706602–715,736) not observed in any other lineage (Guyeux et al., 2024).

Recently, whole-genome sequencing (WGS) analyses allowed the construction of detailed MTBC phylogenetic trees also based on several specific SNPs (Brites et al., 2018; Ates et al., 2018; Otchere et al., 2018; Sanoussi et al., 2021; Coscolla et al., 2021; Balamurugan et al., 2022). WGS has now become a fundamental tool for resolving epidemiological relationships, phylogeny, host adaptation, resistance and virulence determinants, etc. (Coscolla et al., 2021; Balamurugan et al., 2022). Phylogenetically, L5 is placed closer to the human-adapted MTBC and L6 closer to the animal-adapted strains (Gagneux, 2018). The proposed evolutionary scenario is that the L6 ancestor was a generalist pathogen that subsequently adapted to different host species, with the possible hypothesis that L6 strains may have originated from an animal reservoir (Silva et al., 2022). L6 also shows a more differentiated population structure than L5, with three distinct monophyletic main sublineages (L6.1, L6.2, and L6.3) that can be further subdivided into at least three other subgroups/sublineages each (Coscolla et al., 2021; Balamurugan et al., 2022).

The objectives of the present study were: to describe the tuberculosis case that occurred in a domestic cat and its etiology; to perform an in-depth genomics characterization by WGS and bioinformatic analysis of the isolate for identification at the lineage/subspecies level, and to compare it with other genomes available in public repositories, gaining an insight into phylogenetic aspects.

We report, for the first time, an infection due to M. africanum in a domestic cat. The histopathological skin lesions observed resembled those of other cutaneous mycobacteriosis in cats (Malik et al., 2000; Lloret et al., 2013; Gunn-Moore, 2014; Sykes, 2025). Unfortunately, no further samples in addition to the skin nodules were made available for our laboratory, and the owner declined to perform a necropsy on the deceased animal. The lack of postmortem examination prevented the possibility of testing additional tissue samples to fully characterize the disease progression and systemic involvement. In any case, the reported clinical history and the computed tomography (CT) scan, with respiratory/pulmonary and lymph nodes involvement, were indicative of a generalized form consistent with a systemic TB case. The isolation of a S. aureus from the biopsy is probably attributable to a secondary infection that might have contributed to the cutaneous lesions.

In animals, M. africanum has been seldom reported in monkeys (Thorel, 1980; Coscolla et al., 2013), cattle (Weber et al., 1998; Rahim et al., 2007), pigs (Alfredsen and Saxegaard, 1992), and in hyrax (Procavia capensis) (Gudan et al., 2008). However, no animal reservoir has ever been postulated (Silva et al., 2022), and it is accepted that the epidemiology of infection basically relies on inter-human transmission. To the best of our knowledge, this represents the first report of M. africanum infection in a carnivore and in a companion animal. Recently, we have already witnessed zoonotic exposure of a M. pinnipedii from a captive sea lion (Alba et al., 2023). Indeed, the zoonotic risk of disease caused by MTBC from domestic or captive-bred carnivores should be taken into consideration (World Organisation for Animal Health, 2022; Gunn-Moore, 2014; Sykes, 2025; Rüfenacht et al., 2011; O’Halloran et al., 2024; Commandeur et al., 2025), and our findings highlight the need for awareness of potential MTBC transmission between species, including the potential role of humans as a reservoir. To the best of our knowledge, at the time of paper submission, no human TB cases in the cat household were reported.

The genomic investigation demonstrated that the implicated isolate was a M. africanum L6, and our isolate, together with an L6 isolated from a wild Chimpanzee in Côte d’Ivoire in 2013 (Coscolla et al., 2013), is at present the only fully genetically characterized M. africanum isolated from an animal.

This identification was further confirmed by the high similarity with other L6 genomes in the SNP-based phylogenomic approach, conducted as in the study by Coscolla et al. (2021), which placed the cat Italian isolate (ERR14161356) in a cluster together with isolates belonging to the L6.1.2 sublineage, a sublineage representing genomes originating in West Africa, mostly The Gambia (Coscolla et al., 2021). In particular, the closest genome to our isolate is a historical isolate detected in France (Ates et al., 2018). Unfortunately, no further information on the patient’s geographical origin is available about this French isolate, although a likely association with a West African exposure or origin has been suggested (R. Brosch, personal communication). TB caused by M. africanum strains is prevalent in West Africa, while outside it has been found mostly—but not only—in migrants from endemic areas (Silva et al., 2022). Indeed, inter-human transmission has also been reported in TB low-incidence European countries (Eldholm et al., 2021), where immigration and travel patterns from endemic areas facilitate local exposure. However, most of the sublineages within L6 have been reported to originate from West Africa, and only a few L6 strains were found in Central Africa or outside Africa (Coscolla et al., 2021). The cat was taken as a stray kitten at a camping site located on the Ionian coast of southern Italy, where in the nearby area are present two first migrant reception centers and several croplands, where workers coming from West Africa are often employed. Although the exact source of the infection in our case remains unknown, it might be speculated that the cat was initially exposed to infected humans/animals/fomites originally from West Africa, possibly including The Gambia. M. africanum geographical restriction, which contrasts with the widespread distribution of M. tuberculosis strains, remains largely unexplained. Regarding this, there are basically three main hypotheses: M. africanum is not able to compete with modern M. tuberculosis lineages; it is adapted to the African population, perhaps mediated through differential modulation of the immune response; and there could be an animal reservoir, making it a zoonotic disease (Comín et al., 2021; Silva et al., 2022). Furthermore, the true incidence of M. africanum infection may be underestimated whenever accurate laboratory differentiation within the MTBC isolates is not performed routinely on human cases (Comín et al., 2021). Based on human infections and experimental models, several Authors suggested that M. africanum strains and L6 may be less transmissible or virulent than M. tuberculosis strains (Sharma et al., 2016; Cá et al., 2019; Baya et al., 2020; Coscolla et al., 2021; Silva et al., 2022). Still, in our case, the cat became infected and likely died from TB. Some studies showed a high proportion of extrapulmonary TB caused by M. africanum, suggesting that these strains might show a different ability to cause pulmonary disease than M. tuberculosis sensu stricto (Ates et al., 2018; Comín et al., 2021). In our animal case, the cat likely had a generalized type of disease, with involvement of the skin and a clinical picture resembling those of other systemic mycobacteriosis in cats (Gunn-Moore, 2014).

The scientific interest in understanding the variation of M. africanum with respect to epidemiology and virulence is high (Yeboah-Manu et al., 2017; Gagneux, 2018; Ates et al., 2018; Coscolla et al., 2021; Balamurugan et al., 2022). Since the resistome and virulome found in our isolate are considered intrinsic/common features of M. tuberculosis, their presence in our cat M. africanum isolate could also be considered intrinsic and indicators of its zoonotic potential.

In conclusion, we report for the first time an infection due to M. africanum in a cat that most likely died from TB. Our molecular data show that the isolated strain belongs to L6, a lineage that has been considered closer (Silva et al., 2022) to certain animal-adapted lineages.

Although MTBC comprises host-adapted taxa, inter-species transmission between wild, captive, and domesticated animals and humans has been frequently reported, thanks to the plasticity of many of the MTBC taxa, posing a worldwide threat to both human and animal health (Vågene et al., 2022).

Indeed, the finding of tuberculosis caused by M. africanum in a carnivore further raises the possibility of the existence of non-human reservoirs, which may contribute to the main pattern of inter-human transmission in endemic areas, at least for some sublineages. TB-infected people who live in close contact with pets should be aware of the possibility of human-to-animal transmission, as proposed in our study. Conversely, citizens should be informed about the hazards posed by some well-known zoonotic lineages within the MTBC. In this regard, rapid and reliable etiological identification and characterization are of paramount importance, not only for an accurate diagnosis, but also for a correct approach to treatment and management options. Indeed, nowadays, the accuracy has greatly improved by genomics, which also allowed phylogenetic and phylogeographic insights.

In any case, suspected or confirmed tuberculosis cases in companion animals, in addition to an appropriate clinical case management, should also rapidly prompt prevention and control action within the household settings.