VBNR and TB treatment failure. Drug susceptible clinical isolates from individuals who failed treatment have increased potential to form viable but non-replicating populations of Mycobacterium tuberculosis

The current standard treatment for tuberculosis (TB) is typically effective against drug susceptible Mycobacterium tuberculosis infections, however, treatment failure can result from acquired drug resistance or phenotypic resistance. M. tuberculosis persisters, a sub-population of viable but non-replicating (VBNR) antibiotic tolerant bacteria, are thought to contribute to poor treatment outcomes of TB patients. In this study we investigated the ability of treatment-naïve drug susceptible clinical isolates collected from people with TB who subsequently had unsuccessful treatment outcomes (or recurrent TB infections) to form VBNR sub-populations. We hypothesized that these isolates may have increased potential for VBNR M. tuberculosis formation. We demonstrate that these drug susceptible clinical isolates from individuals with unfavorable treatment outcomes form larger sub-populations of VBNR M. tuberculosis following infection of THP-1 macrophages than clinical isolates from cured cases. Whole genome sequencing confirmed genetic drug susceptibility of clinical isolates and identified 23 non-synonymous genomic variants shared by treatment failure clinical isolates, and not present in isolates from cured cases. These variants included those in genes previously associated with M. tuberculosis persisters. This study, for the first time, highlights the ability of treatment-naïve clinical isolates to form heterogeneous populations of VBNR containing M. tuberculosis whilst demonstrating the ability of clinical isolates from patients with unsuccessful treatment outcomes to form higher percentages of VBNR M. tuberculosis. These findings suggest that increased VBNR sub-populations may impact TB treatment outcome.