A Multimethod, Multicountry Evaluation of Breakpoints for Bedaquiline Resistance Determination

Abstract

<jats:p>Criteria defining bedaquiline resistance for tuberculosis have been proposed addressing an emerging concern. We evaluated bedaquiline phenotypic drug susceptibility testing (pDST) criteria using drug-resistant tuberculosis clinical isolates tested at five reference laboratories. Isolates were tested at the proposed bedaquiline MGIT960 and 7H11 Agar Proportion (AP) critical concentrations, and dilutions higher. The epidemiological cut-off value for the broth microdilution (BMD) plates (frozen and dry) was investigated. Any isolate testing resistant had Sanger sequencing performed (<jats:italic>atpE</jats:italic> and <jats:italic>Rv0678</jats:italic> genes). The composite reference standard (CRS) defined susceptibility or resistance as is, if all pDST methods agreed. If pDST was discordant sequencing results was used for final classification. Geographically-diverse and bedaquiline unexposed isolates were tested (N=495). The epidemiological cutoff value for BMD was confirmed to be 0.12 μg/mL. The majority of isolates were susceptible by all methods (467/495; 94.3%) and 28 were resistant by at least one method; of which 4 were resistant by all methods. 12/28 harboured Rv0678 mutations exclusively. Isolates with insertions/deletions were more likely to be resistant by more than one method (5/7) compared with isolates having a single nucleotide polymorphism (1/5). Applying the CRS to 24 discordant pDST, BMD dry correctly detected most (15/24; 63%), followed by MGIT960 and BMD frozen (13/24; 61%) and lastly AP (12/24; 50%). Applying the CRS, the prevalence of bedaquiline resistance was 2.2% and ranged from 1.4% to 3.4%, dependent on the method used. All methods performed well for bedaquiline susceptibility determination, however resistance detected should be investigated by a second alternative method.</jats:p>

Assessment of epidemiological and genetic characteristics and clinical outcomes of resistance to bedaquiline in patients treated for rifampicin-resistant tuberculosis: a cross-sectional and longitudinal study

“…However, in the longitudinal cohort, primary transmission was 6•7%, which is similar to the 7•9% observed in the cross-sectional analysis. The occurrence of bedaquiline resistance at baseline at a prevalence of 2-4% in multiple regions among patients without previous exposure, 21 which is not sufficiently explained directly by the factors we identified, suggests a generalised occurrence.…”

“…Over the surveillance period (2015-19) and under programmatic conditions, 3•8% of patients had baseline isolates resistant to bedaquiline, correlating with data from clinical trials done in South Africa (16 [4%] of 391). 11 A multicountry surveillance study using isolates from patients without exposure to bedaquiline across 28 countries showed a prevalence of 2•2% (95% CI 1•1-3•9), 21 and an identical point prevalence was observed in a multicentre study from China. 22 Bedaquiline resistance was associated with Rv0678 mutations across all studies, including our study.…”

Epidemiological cut-off values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing ofM. tuberculosis

“…This value was supported by two subsequent studies, the first of which showed that that the sensitivity and specificity is maximised with a ECOFF/ECV of 0.12 mg/L compared to 0.25 mg/L (43). The second confirmed this value, however also stated that the 99 th percentile of the wild-type population was 0.25 mg/L (44). This illustrates that the exact value can be difficult to pin down when different ECOFF/ECV definitions are used;…”

Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis

“…This value was supported by two subsequent studies, the first of which showed that that the sensitivity and specificity is maximised with a ECOFF/ECV of 0.12 mg/L compared to 0.25 mg/L (39). The second confirmed this value, however also stated that the 99 th percentile of the wild-type population was 0.25 mg/L (40). This illustrates that the exact value can be difficult to pin down when different ECOFF/ECV definitions are used; hopefully the number and diversity of samples in our study will help resolve this important question.…”