Extended Data Fig. 2: Experimental evolution in mice selects M. canettii clones with enhanced persistence.

Persistence phenotypes of individual STB-K clones recovered from STB-K evolution lineages A-D after cycles a) 6, b) 12 and c) 15. Mice were i.n. infected with 103 c.f.u. of a) KC6A1, KC6A2, KC6B1, KC6B2, KC6C1, KC6C2, KC6D1, and KC6D2, b) KC12A1, KC12B1, KC12C1, and KC12D1, or c) KC15A1, KC15B1, KC15C1, and KC15D1. Parental STB-K and control MTB H37Rv strains were included in all three experiments. The bacterial burden in the lungs and spleen was assessed at various intervals post infection by plating serial dilutions of organ homogenates on 7H11 agar plates. Data are shown as log10 c.f.u. for individual mice and the mean. n = 4 individual mice for each time point and each strain over one experiment (when only 3 values are visible in the figure, it indicates that an animal died or had to be euthanized due to health issues prior to the end point). When bacteria were undetectable, the c.f.u. value was set at the limit of detection (log10 1.7; indicated by the broken horizontal line).