Fig. 1.

Phylogeny of M. tuberculosis strains isolated from HIV-1 coinfected and HIV-1 uninfected individuals. A maximum likelihood phylogenetic tree was constructed using RAxML (Stamatakis 2014). A reference set of strains (annotated as “Ref” on the tree) representative of the known global diversity of M. tuberculosis (Comas et al. 2010) was included to provide phylogenetic context for strains isolated in Khayelitsha, South Africa. M. canettii is included as an outgroup. Blue and red branches indicate strains belonging to lineage 2 and 4, respectively. Other lineage branches are coloured as in (Comas et al. 2010). Strains isolated from HIV-1 uninfected individuals (N) are indicated in light blue, and those from HIV-1 coinfected individuals (P) in orange. The scale bar indicates SNP differences. The tree with associated bootstrap values is available in the supporting information (supplementary fig. 1, Supplementary Material online).