Abstract
The global health burden caused by Mycobacterium tuberculosis is aggravated by the emergence and spread of drug resistance. Mutations that cause drug resistance can have collateral effects that increase the vulnerability of downstream pathways to inhibition. Here, using genome scale CRISPR interference we identified collateral effects associated with different drug-resistant genotypes of M. tuberculosis. We demonstrate that drug resistance generated shared vulnerabilities in several overlapping functional pathways. Most drug-resistant strains were more sensitive to tRNA synthetase knockdowns than the parental drug-sensitive strain, highlighting the potential of tRNA synthetases as high-value drug targets. Additionally, the rifampicin-resistant mutant RpoB(S450L) had increased sensitivity to the dysregulation of sulphur metabolism due to transcriptional dysregulation. This increased vulnerability did not translate to all rpoB genotypes but was linked to predicted effects on transcriptional dynamics. Amongst clinical isolates, non-synonymous mutations in sulphur metabolism genes have evolved in a geographic lineage specific manner to mitigate fitness costs associated with the collateral phenotypes of drug resistance. Combined, our findings highlight the power of functional genomics in pinpointing highly vulnerable drug targets across drug-resistant strains.
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Acknowledgements
We acknowledge the use of New Zealand eScience Infrastructure (NeSI) high performance computing facilities services as part of this research. We thank members of the Department of Microbiology and Immunology 6th floor for helpful discussions.
Funding
This research was supported by project grants awarded by the Health Research Council of New Zealand (20/459 and 22/323) and by Te Niwha, the Infectious Diseases Research Platform – co-hosted by PHF Science and the University of Otago and provisioned by the Ministry of Business, Innovation and Employment, New Zealand (Project number TN/DDC/48/UOOJK) awarded to MM. Sir Charles Hercus Health Research Fellowships supported MM and SAJ (grants 22/156 and 23/228, respectively). PCF was supported by a James Cook Research Fellowship (RSNZ, Te Apārangi). GMC was supported by the Marsden Fund, Royal Society, New Zealand.
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Wang, X., Jowsey, W.J., Cheung, CY. et al. Genome scale CRISPRi reveals both shared and strain-specific vulnerabilities in genetically diverse drug-resistant strains of Mycobacterium tuberculosis. Nat Commun (2026). https://doi.org/10.1038/s41467-026-73952-x
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DOI: https://doi.org/10.1038/s41467-026-73952-x
