Host oxidative stress primes mycobacteria for rapid antibiotic resistance evolution.

Publication Title

Nat Commun

Authors

• Evan Pepper-Tunick, Institute for Systems Biology, Seattle, WA, USA.
• Vivek Srinivas, Institute for Systems Biology, Seattle, WA, USA.Follow
• Fred D Mast
• Song Li
• Sagan Russ, Institute for Systems Biology, Seattle, WA, USA.
• Weston Hanson, Institute for Systems Biology, Seattle, WA, USA.
• Amy D Zamora, Institute for Systems Biology, Seattle, WA, USA.
• Wei-Ju Wu, Institute for Systems Biology, Seattle, WA, USA.
• Matthew Silcocks
• Dang Thi Minh Ha
• Sarah J Dunstan
• Thuong Nguyen Thuy Thuong
• Serdar Turkarslan, Institute for Systems Biology, Seattle, WA, USA.Follow
• John D Aitchison
• Mario L Arrieta-Ortiz, Institute for Systems Biology, Seattle, WA, USA.
• Nitin S Baliga, Institute for Systems Biology, Seattle, WA, USA.Follow

Document Type

Article

Publication Date

5-7-2026

Keywords

Oxidative Stress; Mycobacterium smegmatis; Isoniazid; Mycobacterium tuberculosis; Mutation; Antitubercular Agents; Bacterial Proteins; Humans; Drug Resistance, Multiple, Bacterial; Glycopeptides; Cysteine; Microbial Sensitivity Tests; Evolution, Molecular; Drug Resistance, Bacterial; Tuberculosis, Multidrug-Resistant; Inositol; washington; isb

Abstract

The rapid emergence of multidrug-resistant Mycobacterium tuberculosis (Mtb) threatens global tuberculosis (TB) control, yet the mechanisms enabling rapid evolution of resistance in Mtb remain poorly understood. Here, we show that pre-existing mutations in oxidative stress response genes create permissive genomic backgrounds that accelerate high-level isoniazid resistance (INHR), challenging the paradigm that resistance mutations must precede compensatory adaptation. Using Mycobacterium smegmatis mc2155 (Msm) as a model, we demonstrate that brief exposure to sublethal isoniazid (INH) enriches for "low-level resistance and tolerance" (LLRT) mutants in a single step. LLRT mutants, particularly those with ohrR loss-of-function mutations, acquire high-level resistance (>500× IC50) at ~6-fold higher rates than wildtype, primarily through otherwise deleterious mycothiol biosynthesis mutations that become tolerable in an oxidative stress-buffered background. Crucially, sublethal oxidative stress alone, mimicking host immune pressure, nearly tripled the rate of INHR evolution. Analysis of 1578 clinical Mtb isolates revealed significant enrichment of oxidative stress-related loci among those associated with INHR. Reanalysis of genome-wide CRISPRi data further linked oxidative stress response pathways to survival under multiple antibiotics. Together, these findings suggest that host-imposed oxidative stress and suboptimal drug exposure may prime Mtb populations for rapid resistance evolution, highlighting oxidative stress defenses as potential targets to limit resistance emergence.

Specialty/Research Institute

Infectious Diseases

DOI

10.1038/s41467-026-72496-4