Defining Bedaquiline Susceptibility, Resistance, Cross-Resistance and Associated Genetic Determinants: A Retrospective Cohort Study

Abstract

BackgroundBedaquiline (BDQ) is a novel agent approved for use in combination treatment of multi-drug resistant tuberculosis (MDR-TB). We sought to determine BDQ epidemiological cut-off values (ECVs), define and assess interpretive criteria against putative resistance associated variants (RAVs), microbiological outcomes and cross resistance with clofazimine (CFZ).MethodsA retrospective cohort study was conducted. Minimal inhibitory concentrations (MIC) to BDQ were determined using 7H9 broth microdilution (BMD) and MGIT960. RAVs were genetically characterised using whole genome sequencing. BDQ ECVs were determined using ECOFFinder and compared with 6-month culture conversion status and CFZ MICs.FindingsA total of 391 isolates were analysed. Susceptible and intermediate categories were determined to have MICs of ≤ 0.125 μg/ml and 0.25 μg/ml using BMD and ≤ 1 μg/ml and 2 μg/ml using MGIT960 respectively. Microbiological failures occurred among BDQ exposed patients with a non-susceptible BDQ MIC, an Rv0678 mutation and ≤ 2 active drug classes. The Rv0678 RAVs were not the dominant mechanism of CFZ resistance and cross resistance was limited to isolates with an Rv0678 mutation.InterpretationCriteria for BDQ susceptibility are defined and will facilitate improved early detection of resistance. Cross- resistance between BDQ and CFZ is an emerging concern but in this study was primarily among those with an Rv0678 mutation.

Acquisition of cross-resistance to Bedaquiline and Clofazimine following treatment for Tuberculosis in Pakistan

“…In this study, we show that the increase of MIC to bedaquiline and clofazimine could be explained by mutations emerging during therapy in Rv0678 . As reported in table 1 we observed four different mutations and three of these (138-139_Ins-G, 141-142_Ins-C, 192-193_Ins-G) were previously reported as associated to bedaquiline resistance in MTB clinical strains (8). We show that the same mutations are associated to Clofazimine resistance.…”

“…The genetic basis of resistance to bedaquiline is still the subject of much uncertainty. WGS analysis in different studies showed that bedaquiline-clofazimine cross resistance arises through mutations in Rv0678 (6,7,8) and pepQ (9). In this study, we show that the increase of MIC to bedaquiline and clofazimine could be explained by mutations emerging during therapy in Rv0678 .…”

Validation of Bedaquiline Phenotypic Drug Susceptibility Testing Methods and Breakpoints: a Multilaboratory, Multicountry Study

“…Characterized RAVs include mutations in BDQ target gene atpE (3), efflux pump regulator gene Rv0678 (8)(9)(10), gene pepQ (11,12), and gene Rv1979c (12). atpE RAVs that reduce BDQ activity have been observed previously in vitro (13) but rarely in patient clinical isolates (14,15). In contrast, mutations in Rv0678 have led to low-level resistance in isolates obtained both in vitro and in the clinic (15).…”

Contribution of pretomanid to novel regimens containing bedaquiline with either linezolid or moxifloxacin and pyrazinamide in murine models of tuberculosis

“…As such, it exerts strong selection pressure and bactericidal and sterilizing companion drugs are necessary to restrict the selective amplification of spontaneous BDQ-resistant mutants. Previous studies have identified BDQ-resistant mutants selected in vitro , in mice and in TB patients (13, 29–31). In most cases in which it emerged in vivo , resistance was attributable to mutations in the transcriptional repressor Rv0678 or in the predicted proline aminopeptidase pepQ , although the latter mutation target has yet to be confirmed in BDQ-resistant clinical isolates.…”