Maximum likelihood phylogeny (GTR substitution model, 1000 resamples) of 277 MDR-MTBC isolates from Karakalpakstan, Uzbekistan sampled from 2001 to 2006. Columns show drug resistance associated mutations to first- and second-line drugs (different mutations represented by different colors), genetic classification of pre-XDR (purple) and XDR (pink) isolates, and putative compensatory mutations in the RNA polymerase genes rpoA, rpoB and rpoC. Transmission index represents number of isolates within a maximum range of 10 SNPs at whole genome level. MTBC lineage two isolates (Beijing genotype) are differentiated into three clades (i.e. Central Asian Outbreak (CAO), group 2 and group 3). Isolates belonging to lineage 4 (Euro-American) are colored in grey: H = isoniazid, R = rifampicin, S = streptomycin, E = ethambutol, Z = pyrazinamide, FQ = fluoroquinolone, AG = aminoglycosides, Km = kanamycin Cm = capreomycin, TA = thioamide, PAS = para aminosalicylic acid.