Description of study isolates.

The 337 clinical study isolates derived from five patient cohorts and were both prospectively and retrospectively collected from all 11 districts of KwaZulu-Natal from 2008 to 2013. Culture conditions describe the initial M. tuberculosis isolation method from sputum. If subsequent single colony isolation (SCI) was performed prior to DNA extraction on the entire study cohort or a subset of the cohort, then this is denoted. Drugs for which DST was performed are abbreviated as follows: rifampicin (R), isoniazid (H), nicotinamide (N), pyrazinamide (P), ethambutol (E), streptomycin (S), kanamycin (K), ofloxacin (O), ethionamide (Et), and capreomycin (C).