Common Variants in the Glycerol Kinase Gene Reduce Tuberculosis Drug Efficacy

Abstract

Despite the administration of multiple drugs that are highly effective <i>in vitro</i>, tuberculosis (TB) treatment requires prolonged drug administration and is confounded by the emergence of drug-resistant strains. To understand the mechanisms that limit antibiotic efficacy, we performed a comprehensive genetic study to identify <i>Mycobacterium tuberculosis</i> genes that alter the rate of bacterial clearance in drug-treated mice. Several functionally distinct bacterial genes were found to alter bacterial clearance, and prominent among these was the <i>glpK</i> gene that encodes the glycerol-3-kinase enzyme that is necessary for glycerol catabolism. Growth on glycerol generally increased the sensitivity of <i>M. tuberculosis</i> to antibiotics <i>in vitro</i>, and <i>glpK</i>-deficient bacteria persisted during antibiotic treatment <i>in vivo</i>, particularly during exposure to pyrazinamide-containing regimens. Frameshift mutations in a hypervariable homopolymeric region of the <i>glpK</i> gene were found to be a specific marker of multidrug resistance in clinical <i>M. tuberculosis</i> isolates, and these loss-of-function alleles were also enriched in extensively drug-resistant clones. These data indicate that frequently observed variation in the <i>glpK</i> coding sequence produces a drug-tolerant phenotype that can reduce antibiotic efficacy and may contribute to the evolution of resistance.<b>IMPORTANCE</b> TB control is limited in part by the length of antibiotic treatment needed to prevent recurrent disease. To probe mechanisms underlying survival under antibiotic pressure, we performed a genetic screen for <i>M. tuberculosis</i> mutants with altered susceptibility to treatment using the mouse model of TB. We identified multiple genes involved in a range of functions which alter sensitivity to antibiotics. In particular, we found glycerol catabolism mutants were less susceptible to treatment and that common variation in a homopolymeric region in the <i>glpK</i> gene was associated with drug resistance in clinical isolates. These studies indicate that reversible high-frequency variation in carbon metabolic pathways can produce phenotypically drug-tolerant clones and have a role in the development of resistance.