Raw sequence reads from Mycobacterium canettii STB-D clones from experimental evolution in mice.

Raw sequence reads from clones obtained at different cycles of experimental evolution of the Mycobacterium canettii STB-D parental strain in a mouse infection model.M. canettii strains represent evolutionarily early branching lineages of tubercle bacilli. Although they can cause disease clinically indistinguishable from classical tuberculosis, epidemiological data indicate that, in contrast to M. tuberculosis complex strains, these strains are not fully adapted for infection and transmission in the human host, and they are believed to have an environmental reservoir. Consistently, M. canettii strains are less able to persist and cause disease in animal models than the M. tuberculosis complex strains.The objective of the study was to select M. canettii mutants with enhanced persistence in vivo in order to identify what adaptations are associated with this phenotypic gain. A positive selection strategy was implemented based on unbiased experimental evolution of 4 populations of M. canettii STB-D strain in a mouse model. Four evolution lineages (A, B, C and D) were generated, which were evolved independently over 6 cycles and were never mixed. At each cycle, the lung and spleen bacterial loads were evaluated at days 1, 28 and 56 post-infection, and a persistence index, corresponding to the log ratio of lung bacterial burden at day 56 vs day 28, was calculated. An increase in persistence index was observed throughout the cycles indicating that mutants with enhanced abilities to persist emerged. This was confirmed by evaluating the persistence of clones randomly collected from agar plates used to measure the bacterial burden in the lungs during the experimental evolution cycles.To identify the mutations that putatively arose in STB-D over the course of this experimental evolution in mice, whole genome sequencing of 40 individual clones evolved from the parental strain was performed. Five clones from each of the four evolution lineages, collected after cycles 3 and 6 were analyzed. The files containing the corresponding sequence reads are coded as follows: DCxZy where Cx indicates cycle number (i.e. 3 or 6), Z one of the four evolution lineages (i.e. A, B, C or D) and y the clone number. The parental strain from which the evolved clones were directly derived is coded Di00.