*4.3. Genomic Analysis*

Genomic DNA was isolated from the Rostov strain of *M. tuberculosis* using a standard extraction method [31].

Spoligotyping and 24 MIRU-VNTR typing were performed as described in references [32,33], respectively. Verification of the presence of SNP in the *sigA* gene and CAO-specific IS*6110* insertion in the *Rv1359-Rv1360* intergenic region was performed by PCR as described previously [18,34].

Whole genome sequencing was performed on Ion Torrent PGM (Life Technologies, Camarillo, CA, USA) with Ion 318 chip and Ion PGM ™ Sequencing 200 Kit v2 (Life Technologies, Camarillo, CA, USA). Raw sequence data were submitted to the NCBI under the project PRJNA269675. The genome was assembled using Newbler GS de novo assembler 2.5 (Roche, Branford, CT, USA) with standard parameters for Ion technology. SNPs were detected with Snippy v.4.3.6 (https://github.com/tseemann/ snippy) pipeline with a minimum coverage depth of 10 and an alternate fraction of 0.9. A comprehensive list of drug-resistance mutations to first- and second-line drugs was used to determine genetic resistance of the strain [35]. Functional categories and virulence factors were defined according to Mycobrowser (https://mycobrowser.epfl.ch/) and [27].
