CinA mediates multidrug tolerance in Mycobacterium tuberculosis

Abstract

The ability of Mycobacterium tuberculosis (Mtb) to resist and tolerate antibiotics complicates the development of improved tuberculosis (TB) chemotherapies. Here we define the Mtb protein CinA as a major determinant of drug tolerance and as a potential target to shorten TB chemotherapy. By reducing the fraction of drug-tolerant persisters, genetic inactivation of cinA accelerated killing of Mtb by four antibiotics in clinical use: isoniazid, ethionamide, delamanid and pretomanid. Mtb ΔcinA was killed rapidly in conditions known to impede the efficacy of isoniazid, such as during nutrient starvation, during persistence in a caseum mimetic, in activated macrophages and during chronic mouse infection. Deletion of CinA also increased in vivo killing of Mtb by BPaL, a combination of pretomanid, bedaquiline and linezolid that is used to treat highly drug-resistant TB. Genetic and drug metabolism studies suggest that CinA mediates drug tolerance via cleavage of NAD-drug adducts.

Mycobacterium tuberculosis functional genetic diversity, altered drug sensitivity, and precision medicine

“…We can start by exploring mutations noted in a 2021 WHO catalogue of mutations associated with drug resistance, but in order to improve upon the growing collection of Mtb mutations with diagnostic potential, we should diversify our repertoire of phenotypes of clinical interest beyond just MIC ( Walker et al., 2022 ). For example, further exploration into prevalent mutations in Mtb clinical isolates that modulate MBC, rather than just MIC, could reveal interesting predictors of host-relevant antibiotic tolerance phenotypes ( Kalia et al., 2017 ; Sarathy et al., 2018 ; Dutta et al., 2019 ; Kreutzfeldt et al., 2022 ). Further, we should integrate Mtb strain characteristics with information regarding patient factors such as genetics, metabolism, environment, and geographic location to find novel ways to optimize treatment regimens and dosing.…”

Unraveling the mechanisms of intrinsic drug resistance in Mycobacterium tuberculosis

“…Despite the strong GC bias in the Mtb genome, the overwhelming majority of Mtb genes are sufficiently susceptible to transposition for this technique to work efficiently at genome scale ( Dejesus et al., 2017 ). Transposon sequencing (TnSeq) has been used to study chemical-genetic interactions in axenic culture ( Xu et al., 2017 ; Furió et al., 2021 ; Thiede et al., 2022 ) as well as in macrophage and mouse models of infection ( Bellerose et al., 2020 ; Kreutzfeldt et al., 2022 ).…”

“…The classic example of this can be seen with the use of beta lactamase inhibitors to prevent the degradation of beta lactam antibiotics. In addition to the Mtb beta lactamase, BlaC, two other well-characterized examples which modify drugs or drug adducts are Eis and CinA ( Zaunbrecher et al., 2009 ; Kreutzfeldt et al., 2022 ). Many more drug-modifying enzymes likely remain to be discovered ( Zaunbrecher et al., 2009 ; Kreutzfeldt et al., 2022 ).…”

Mycobacterium tuberculosis requires the outer membrane lipid phthiocerol dimycocerosate for starvation-induced antibiotic tolerance

“…The copyright holder for this preprint (which this version posted July 8, 2022. ; https://doi.org/10.1101/2022.07.07.499240 doi: bioRxiv preprint Genetic approaches including identification of genes expressed in the drug-tolerant population (25,26) and screens for strains exhibiting altered drug tolerance in vitro (27,28) or during infection of macrophages or mice (29)(30)(31)(32) have revealed some molecular mechanisms underlying M. tuberculosis drug tolerance. Specific metabolic pathways and toxins of toxinantitoxin (TA) systems induce M. tuberculosis drug tolerance by slowing growth.…”

“…Drug tolerant M. tuberculosis have been observed within infected mouse lungs (20), in interferon-gamma (IFN-g) activated macrophages (21), in the hypoxic caseum of necrotic granulomas (22) and in human sputum (23,24). Genetic approaches including identification of genes expressed in the drug-tolerant population (25,26) and screens for strains exhibiting altered drug tolerance in vitro (27,28) or during infection of macrophages or mice (29)(30)(31)(32) have revealed some molecular mechanisms underlying M. tuberculosis drug tolerance. Specific metabolic pathways and toxins of toxinantitoxin (TA) systems induce M. tuberculosis drug tolerance by slowing growth.…”