Fig. 2: Pathway analysis identifies diverse functions that are more vulnerable to inhibition in INH^R-katG.

a Pathway analysis identifies functional classifications of genes with increased vulnerability in INH^R-katG (i.e., Fig. 1g). The bubble plot represents data from day 14. The x-axis quantifies the proportion of genes called “more vulnerable” over the total number of M. tuberculosis genes per functional pathway, and the y-axis shows the name of each functional pathway with the total number of genes in each class labelled in brackets. Within each functional class, the dot size indicates the average ratio of gRNAs targeting each gene that is more depleted in INH^R-katG. The dot colour denotes the ATc concentration from which the amplicon sequencing was performed. b Scatter plot illustrating experimental validation of each of the 30 gRNAs. Data is plotted as the difference in gRNA abundance between INH^R-katG and the DS-parent from WG-CRISPRi screens (Day14+ATc-300) (x-axis) against the fold change in ATc MIC between INH^R-katG and the DS-parent from ATc dose response assays (y-axis). The vertical dotted line indicates the cut-off for a gRNA to be significantly depleted, whilst the horizontal dotted indicates a two-fold change in ATc MIC. c–e Growth of M. tuberculosis DS-parent and INH^R-katG expressing for gRNA targeting (c) gyrB, (d) atpD and atpF and (e) clpC1 in ATc dose response assays (mean ± extrema of two biological replicates, n=3 independent experiments). The (gx) after each gRNA denotes the specific gRNA targeting each gene. f Viability plots of M. tuberculosis DS-parent and INH^R-katG expressing for gRNA targeting atpD (mean ± extrema of two biological replicates, n=3 independent experiments). g M. tuberculosis survival in macrophages. THP-1 macrophage cells were infected with M. tuberculosis DS-parent and INH^R-katG cells expressing the stated gRNA (mean ± SD of three biological replicates, n = 2 independent experiments). h, i The susceptibility of M. tuberculosis DS-parent and INH^R-katG to increasing concentrations of (h) levofloxacin (mean ± extrema of two biological replicates, n=3 independent experiments) and (i) SQ109 (mean ± extrema of two biological replicates, n = 3 independent experiments). f, h, i Inoc denotes the starting CFU/ml and no-cpd denotes the detected CFU/ml in the absence of compound Dashed line represents the lower detection limit. Source data are provided as a Source Data file.