Emergence of mmpT5 Variants during Bedaquiline Treatment of Mycobacterium intracellulare Lung Disease

Abstract

Bedaquiline (BDQ), a diarylquinoline antibiotic that targets ATP synthase, is effective for the treatment of Mycobacterium tuberculosis infections that no longer respond to conventional drugs. While investigating the off-label use of BDQ as salvage therapy, seven of 13 patients with Mycobacterium intracellulare lung disease had an initial microbiological response and then relapsed. Whole-genome comparison of pretreatment and relapse isolates of M. intracellulare uncovered mutations in a previously uncharacterized locus, mmpT5. Preliminary analysis suggested similarities between mmpT5 and the mmpR5 locus, which is associated with low-level BDQ resistance in M. tuberculosis. Both genes encode transcriptional regulators and are adjacent to orthologs of the mmpS5-mmpL5 drug efflux operon. However, MmpT5 belongs to the TetR superfamily, whereas MmpR5 is a MarR family protein. Targeted sequencing uncovered nonsynonymous mmpT5 mutations in isolates from all seven relapse cases, including two pretreatment isolates. In contrast, only two relapse patient isolates had nonsynonymous changes in ATP synthase subunit c (atpE), the primary target of BDQ. Susceptibility testing indicated that mmpT5 mutations are associated with modest 2-to 8-fold increases in MICs for BDQ and clofazimine, whereas one atpE mutant exhibited a 50-fold increase in MIC for BDQ. Bedaquiline shows potential for the treatment of M. intracellulare lung disease, but optimization of treatment regimens is required to prevent the emergence of mmpT5 variants and microbiological relapse.

In Vitro Activity of Bedaquiline against Nontuberculous Mycobacteria in China

“…Numerous reports have found nucleotide substitutions in selected bedaquiline-resistant mutants, such as A63P and I66M in M. tuberculosis (20)(21)(22). Similar to those findings in M. tuberculosis, a recent study by Alexander et al indicated that one nonsynonymous mutation in the atpE gene was associated with a 50-fold increase in the bedaquiline MIC in M. intracellulare (23). However, no nonsynonymous mutations in the atpE gene that conferred bedaquiline resistance in all six NTM species were identified in our study.…”

Efflux Attenuates the Antibacterial Activity of Q203 in Mycobacterium tuberculosis

“…These nontarget-based mutants primarily harbored single nucleotide polymorphisms (SNPs) in the Rv0687 gene, which is a transcriptional repressor of mmpS5-mmpL5 (18). The involvement of MmpL5 in the resistance to bedaquiline was further evidenced in vitro (19) and supported by recent clinical data (20,21). We were unable to identify and confirm which molecular targets were involved in this efflux pump-mediated tolerance to Q203 in the present study because of the low rate of spontaneous Q203-resistant mutants (ϳ10 Ϫ8 ), with SNPs appearing exclusively in the qcrB gene (A937G leading to T313A) (13).…”

The diverse family of MmpL transporters in mycobacteria: from regulation to antimicrobial developments

“…Mutations in the mmpT5 encoded TetR repressor located ahead of the mmpS5/mmpL5 operon in Mycobacterium intracellulare were associated with modest resistance levels to bedaquiline and clofazimine (Fig. B) (Alexander et al ., ). In addition, high resistance levels to a range of thiacetazone derivatives with potent activity against M. abscessus were found in spontaneous resistant mutants harbouring SNPs or indels in the TetR upstream and divergently orientated to one of three putative mmpS5 ‐ mmpL5 operons (Fig.…”