2.4.1. Spoligotyping

The genotypes of the isolates were determined by spoligotyping as previously described by Kamerbeek et al. [20] and Mogashoa et al. [17]. The *M.tb* families and lineages of the isolates were assigned based on the spoligotyping results.

### 2.4.2. Hain Genotype MTBDRsl Version 2

The second line drug resistance profiles were determined by using the Hain GenoType MTBDR*sl* assay (Hain Lifescience, Germany). The steps were performed as per the manufacturer's instructions [12]. The culture based second line phenotypic DST was not performed for this study since the test was unavailable at the reference laboratory.
