KatG inactivation generates vulnerabilities in isoniazid resistant strains of Mycobacterium tuberculosis

Drug-resistant strains of Mycobacterium tuberculosis are a major global health problem. Resistance to the front-line anti-tubercular isoniazid is often associated with mutations in the katG encoded bifunctional catalase-peroxidase. We hypothesised that perturbed KatG activity would generate in collateral vulnerabilities in INH-resistant katG mutants, providing new pathways to combat isoniazid resistance. Here using whole genome CRISPRi screens, transcriptomics, and metabolomics we have generated a genome-wide map of cellular vulnerabilities in a M. tuberculosis katG mutants. Specifically, we discovered that metabolic and transcriptional remodelling is used to compensate for the loss of KatG, generating vulnerabilities in ribosome biogenesis, and nucleotide and amino acid metabolism. These vulnerabilities were more sensitive to inhibition in an isoniazid-resistant katG mutant under in vitro and host-relevant conditions and translated to clinical isolates. These findings provide a framework for developing novel strategies to combat antimicrobial resistance in M. tuberculosis and other bacterial pathogens.