*3.2. Genomic Analysis*

Genomic DNA was isolated from the strains using standard extraction methods [33]. To verify that the strains belong to a Beijing B0/W148 cluster, the PCR assay was performed as described previously [34]. Spoligotyping, IS*6110*-RFLP and 24-MIRU-VNTR typing were performed as described in [35], [33], and [36], respectively.

Whole genome sequencing of the strains was performed on Illumina HiSeq 2500 Sequencing Platform according to the manufacturer's instructions. Raw data were deposited in the NCBI Sequence Read Archive under accession number PRJNA421323. The circular genome of RUS\_B0 strains was assembled and deposited in the NCBI earlier (CP030093.1) [37]. WGS reads were aligned to the *M. tuberculosis* H37Rv (NC\_000962.3) and RUS\_B0 (CP030093.1) genome sequences using Bowtie 2 [38]. SAMtools (v.0.1.18) [39], FreeBayes (v.1.1.0) [40] and Snippy (v.4.3.6) [41] were used for variant calling [39,42]. For FreeBayes and Snippy SNPs with a minimum mapping quality of 20, minimum coverage of 10 and alternate fraction of 0.9 were taken.

A comprehensive list of drug-resistance mutations to first- and second-line drugs were used to determine genetically resistant strains [43]. The identification of IS*6110* integration sites was carried out using ISMapper pipeline [44].
