PacBio raw sequence reads and genome assembly from Mycobacterium canettii STB-K.

PacBio raw sequence reads and genome assembly from Mycobacterium canettii STB-K used as a reference for alignment of Illumina whole genome sequencing reads from clones and populations of STB-K, obtained at different cycles of an experimental evolution study 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-K strain in a mouse model. Starting a same parental strain, four evolution lineages (A, B, C and D) were generated, which were evolved independently over 15 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-K over the course of this experimental evolution in mice, whole genome sequencing of 100 individual clones evolved from the parental strain was performed. In addition, whole genome sequencing of the bacterial population from each evolution lineage and each cycle was performed. The resulting reads were aligned against a genome assembly of Mycobacterium canettii STB-K, as referred to above, obtained by PacBio sequencing.