Phase variation in <i>Mycobacterium tuberculosis glpK</i> produces transiently heritable drug tolerance

Abstract

The length and complexity of tuberculosis (TB) therapy, as well as the propensity of <i>Mycobacterium tuberculosis</i> to develop drug resistance, are major barriers to global TB control efforts. <i>M. tuberculosis</i> is known to have the ability to enter into a drug-tolerant state, which may explain many of these impediments to TB treatment. We have identified a mechanism of genetically encoded but rapidly reversible drug tolerance in <i>M. tuberculosis</i> caused by transient frameshift mutations in a homopolymeric tract (HT) of 7 cytosines (7C) in the <i>glpK</i> gene. Inactivating frameshift mutations associated with the 7C HT in <i>glpK</i> produce small colonies that exhibit heritable multidrug increases in minimal inhibitory concentrations and decreases in drug-dependent killing; however, reversion back to a fully drug-susceptible large-colony phenotype occurs rapidly through the introduction of additional insertions or deletions in the same <i>glpK</i> HT region. These reversible frameshift mutations in the 7C HT of <i>M. tuberculosis glpK</i> occur in clinical isolates, accumulate in <i>M. tuberculosis</i>-infected mice with further accumulation during drug treatment, and exhibit a reversible transcriptional profile including induction of <i>dosR</i> and <i>sigH</i> and repression of <i>kstR</i> regulons, similar to that observed in other in vitro models of <i>M. tuberculosis</i> tolerance. These results suggest that GlpK phase variation may contribute to drug tolerance, treatment failure, and relapse in human TB. Drugs effective against phase-variant <i>M. tuberculosis</i> may hasten TB treatment and improve cure rates.