Fig. 1

Characteristics of the study population. Our study was based on serial sputum isolates obtained from 12 TB patients at 2-week intervals. We obtained three sputum samples at each time point and cultured each on Löwenstein–Jenssen solid medium (L-J) or in a mycobacterial growth indicator tube (MGIT); we chose one culture per patient per time point for deep sequencing. Eight patients (P01–P08) were treated with a combination composed of at least four effective antibiotics (sampling indicated by red circles). While four patients (P09–P12) were treated with fewer than four effective antibiotics (grey circles). Phenotypic drug susceptibility testing (Phenotypic DST) and genotypic drug susceptibility testing (Genotypic DST) results are shown for each patient with light blue dots indicating drug susceptibility (DS) and red dots reflecting drug resistance (DR). The antibiotics are abbreviated as: RIF rifampicin, INH isoniazid, EMB ethambutol, STR streptomycin, INJ injectable aminoglycosides, FQ fluoroquinolones, PZA pyrazinamide. Resistance profiles of strains are given as: DS drug susceptible, INH-R isoniazid monoresistant, MDR multidrug resistant, P-XDR pre-extensively drug resistant, XDR extensively drug resistant. MDR is defined as RIF and INH resistant, XDR is MDR with additional resistance to FQ and INJ, and P-XDR is MDR with either FQ or INJ resistance