Mycobacterium tuberculosis Raw sequence reads

We assessed bedaquiline resistance in patients with Xpert MTB/RIF Ultra (Xpert)-diagnosed rifampicin-resistant tuberculosis in the Western Cape during South Africa's scale-up of the bedaquiline-pretomanid-linezolid regimen. This study provides updated evidence on resistance patterns during a crucial period of programmatic change and highlights challenges in detecting bedaquiline resistance under routine conditions. Whole-genome sequencing (WGS) was performed for isolates showing phenotypic resistance but without a Deeplex Myc-TB PCR-indicated mmpR5 mutation. Four baseline isolates reported as resistant to bedaquiline by Deeplex but without a specific variant call were also phenotypically resistant; WGS revealed IS6110 insertions in mmpR5 in two of these four isolates (the two remaining isolates were non-viable).