Summary of the applied drug treatments and their phenotypic consequences

Cell volume distribution of M. smegmatis treated with different drugs. Various drug treatments are color-coded. Numerical values along with the used and obtained statistical parameters are shown in Table S1.

Mutation rates of wild-type M. smegmatis mc2155 strains under antibiotic pressure and DNA damaging stress in the mutation accumulation assay. Error bars represent standard deviations.

Mutation rates measured in the wild-type M. smegmatis mc2155 at the conclusion of the mutation accumulation assay

Changes in the expression of DNA repair genes upon stress treatments. Gene expression changes are normalized to the mock treated control using the SigA and Ffh reference genes. Upregulation is interpreted as fold change; downregulation is interpreted as −1/ (fold change). * p<0.1; ** p<0.05.

First line antituberculotic treatments and DNA damaging agents alter dNTP concentrations in the cell. A-F) Cellular dNTP concentrations of drug treated M. smegmatis. dNTP quantities were measured in cellular extracts and normalized to the average cell volume in each treatment to obtain the shown concentrations. Each drug treatment and dNTP quantitation included its own control to account for potential fluctuations in growth and experimental conditions. Note the different scales on the Y axis. Data bars represent the averages of three biological replicates each carried out in three technical replicates; error bars represent SE. The p-values of the t-tests calculated for the measured differences are shown in Table S5. G) dNTP pool compositions of drug treated bacteria. The large error bars in the control data arise from the combination of individual controls measured for each treatment. H) The observed levels of dNTP concentration in the cells (all four dNTPs combined) show a comparable trend to changes in cell size under different treatments. All data is compared to the mock treatment.

Phenotypic CIP tolerance assay. A) Scheme of the fluctuation test used in the study. B) Development of phenotypic resistance to a selecting CIP concentration following preincubation with a sublethal CIP concentration for various time periods. Data bars represent the averages of three biological replicates each carried out in three technical replicates; error bars represent SE.