3.3 M. bovis from the safari park and cattle farms
We then evaluated the 18 M. bovis genomes of deer and llamas in the context of 71 additional genomes obtained from cattle herds located from 37 to 308 km away of the safari park. The phylogenetic tree and associated CCs, lineages and spoligotype patterns are shown in figure 4. While 17 genomes of M. bovis from the safari park were part of the same clade (includes clusters 1, 2 and 3 of the safari park), the most distantly related genome TB013S13L branched into a separated clade with other M. bovis isolates from cattle. In contrast, threeM. bovis genomes from cattle herds appeared within the same main clade of the deer from the safari park. Both lineages Lb3 and Lb4, represented by CC markers of Eu2 and Eu1, respectively, were detected in the dataset, with Lb4 constituted by M. bovis isolates from cattle farms only. In addition, the phylogenetic clustering did not follow spoligotype patterns, as these appeared dispersed throughout the phylogenetic tree. This includes both llamas and three cattle isolates with SB0295 clustering with M. bovis isolates obtained from deer with SB1401. The phylogenetic relatedness of M. bovis genomes from cattle farms and the safari park indicates the safari park was affected by strains already circulating in the region during some point in time.