Bedaquiline resistance-associated genetic mutations and minimum inhibitory concentrations in drug-resistant tuberculosis clinical isolates from Limpopo province, South Africa

Abstract

Background Bedaquiline (BDQ) resistance is a significant threat to tuberculosis (TB) control efforts, particularly in areas with a high burden of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis, such as South Africa. Determining the minimum inhibitory concentration (MIC) of BDQ and identifying the associated resistance-conferring mutations are critical for understanding resistance patterns and guiding therapeutic decisions. This study investigated BDQ resistance in Mycobacterium tuberculosis isolates across five districts in Limpopo, South Africa, by analyzing the relationship between minimum inhibitory concentrations (MICs) and resistance-conferring mutations. Method This study is a cross-sectional study including 147 drug-resistant (DR-TB) isolates obtained from the Polokwane laboratory, Limpopo province, South Africa. The study used phenotypic MIC drug susceptibility testing and whole-genome sequencing (WGS) to investigate BDQ susceptibility patterns. MIC determination and genetic analysis were performed on all isolates with an MIC of >1 μg/mL and a subset of those with an MIC of <1 μg/mL as a control for sequencing. Results Of the 147 DR-TB isolates included, 128 (87.1%) had an MIC of ≤1 μg/mL (susceptible), while 19 (12.9%) had an MIC of >1 μg/mL (resistant). Whole-genome sequencing revealed that mutations in Rv0678 (89.1%), including frameshift and codon substitution variants, were mainly associated with drug resistance, while mutations in the atpE (5.1%) and Rv1979c (5.1%) were also identified. Of the BDQ-R strains, the Euro-American (L4) lineage was dominant, accounting for 62.5%. Conclusion In this study, BDQ resistance was primarily driven by Rv0678 mutations. As BDQ is one of the few potent drugs available for treating DR-TB, there is a critical need for early detection and continuous surveillance to prevent the spread of resistance.