Fig 1.
Map showing the slaughterhouse locations from where tissue samples with evidence of bTB-like lesions were collected from cattle. The brown outline shows the Sahara Desert. We used the rnaturalearth package in R to download world country polygons from Natural Earth, sub-setting to Northern Africa. We produced the map using the sf and ggplot packages in R, plotting Oujda, Rabat, and Casablanca points using latitude and longitude data [46–48]. The data to build the map in Fig 1 came from here: https://www.rdocumentation.org/packages/rnaturalearth/versions/1.0.1/topics/countries.
Fig 2.
Distribution of Mycobacterium bovis isolates from North Africa and Sub-Saharan Africa based on clonal complexes/lineages.
Fig 3.
Maximum-likelihood phylogenetic tree with all Mycobacterium bovis isolates used in this study.
The phylogenetic tree was generated using the GTR-CAT substitution model and presents all the analyzed M. bovis isolates used in the study (n = 725), with information about countries (inner circle), clonal complex (middle circle) and lineages (outer circle) color coded. Moroccan isolates are indicated with bold marked tree branches, and human isolates are indicated with a red dot. The areas filled with a light grey shade indicate the groups that include Moroccan isolates.
Fig 4.
High-resolution maximum-likelihood phylogenetic tree of groups 1–8.
The legend indicates country of origin based on the highlighted isolate color. The scale bar represents the branch length in SNPs. Within this figure, eight panels illustrate the genetic relationships among M. bovis isolates. Fig 4A highlights the genetic connection between Moroccan and Spanish M. bovis isolates from cattle, alongside one of the seven Canadian M. bovis isolates analyzed. Fig 4B reveals genetic relationships between M. bovis isolates from Moroccan cattle and UK human in the top red box, while the bottom red box showcases the close genetic proximity of M. bovis isolates between Moroccan and Spanish cattle. Fig 4C emphasizes genetic proximity between M. bovis isolates from Moroccan and Spanish cattle in the top red box, with the second box displaying clustering of M. bovis isolates between Moroccan and Portuguese cattle. The third and fourth red boxes in Panel 3 show that M. bovis from Moroccan cattle are genetically related with M. bovis isolates collected from humans in Germany (including one that shares their Most Recent Common Ancestor with 20 SNPs apart). The bottom box also highlights another closely related relationship between a M. bovis isolate from Moroccan cattle a M. bovis isolate from human in Germany, as well as between M. bovis in Moroccan cattle and M. bovis in Algerian cattle. Fig 4D demonstrates the close genetic relationship between M. bovis cattle isolates from Morocco, Spain, and Portugal. Fig 4E displays genetic relationships between M. bovis isolates from Moroccan cattle and Spanish cattle and Moroccan cattle and humans in Germany. Fig 4F does not show close genetic links between M. bovis isolates from Morrocan cattle and cattle or humans from other countries. Fig 4G shows a close genetic relationship between M. bovis from Moroccan cattle and three humans from Germany. Fig 4H’s red box illustrates the genetic clustering of M. bovis isolates between cattle from Morocco and humans from Italy and Switzerland. The bottom red box highlights the close genetic relationship of M. bovis isolates between cattle in Morocco and a human in Italy, as well as the close relationship of these isolates with one from cattle in Algeria.