resistant to 1 of 2 first-line drugs (isoniazid or rifampicin); pre-XDR, resistant to fluoroquinolones or injectable drugs in addition to MDR; XDR, resistant to fluoroquinolones and injectable drugs, in addition to MDR. Scale bar indicates nucleotide substitutions per site. MDR, multidrug resistant; XDR, extensively drug resistant.. Maximum-likelihood tree based on whole-genome analysis of 309 Mycobacterium tuberculosisstrains from Myanmar. Lineages and drug resistance status of isolates are shown. MDR indicates multidrug-resistant to 2 first-line drugs...Maximum-likelihood tree of Mycobacterium tuberculosis strains, Myanmar, within 9 clusters and their drug resistance profiles. Dotted lines indicate boundaries of individual clusters. An outgroup (#108) differs by >100 single-nucleotide polymorphisms from the strains within 9 clusters. N, E, and W indicate the North, East, and West Districts of Yangon, respectively. MDR, resistant to 2 first-line drugs (isoniazid and rifampin); pre-MDR, resistant to 1 of 2 first-line drugs (isoniazid or rifampicin); pre-XDR, resistant to fluoroquinolones or injectable drugs in addition to MDR; XDR, resistant to fluoroquinolones and injectable drugs, in addition to MDR. AMG, aminoglycosides; ETH, ethambutol; FQ, fluoroquinolones; INH, isoniazid; RIF, rifampin; STR, streptomycin. Scale bar indicates nucleotide substitutions per site. Maximum-likelihood tree of Mycobacterium tuberculosis strains, Myanmar, within 9 clusters and their drug resistance profiles. Dotted lines indicate boundaries of individual clusters. An outgroup (#108) differs by >100 single-nucleotide...Using specific SNP barcodes, we classified the M. tuberculosis isolates as either lineage 1 (73, 24%), lineage 2 (201, 65%), lineage 3 (16, 5%) or lineage 4 (19, 6%) (- 3; Appendix Table 1). Most isolates were identified as belonging to sublineage 2.2.1, Beijing strain (Appendix Table 1). Isolates linked to TB lineage 2 were more commonly drug resistant than those belonging to other lineages (175 [85%] of 207 vs. 32 [15%] of 207; p<0.0001). In contrast, the other lineages were more commonly associated with drug susceptibility (76 [75%] of 102 vs. 26 [25%] of 102; p<0.001) (Table 1; Appendix Table 2). Drug-resistant isolates were also more commonly found in the East and West districts of Yangon (124 [60%] of 207; p<0.0001) (Table 1; Appendix Table 2) and to be associated with patients who had previously received treatment (112 [54%] of 207; p<0.0001) (Appendix Table 2). A total of 181 [87%] of 207 isolates were genomically unlinked on the basis of a standard pairwise distance threshold. The remaining 26 (13%) of 207 drug-resistant isolates formed 9 potential transmission chains. Cases within most of these groups were located within the same districts (- 4), and each group contained a combination of new and previously treated TB patients. In 6 groups, all isolates had the same resistance profile; the remaining 3 (i.e., groups 5, 6, and 8) groups, had different resistance profiles. In group 6, an XDR isolate appears to have developed from an isoniazid-resistant (pre-MDR) isolate This WGS study from Myanmar provides new insights into the landscape of drug-resistant TB in the country’s largest city. A large proportion of isolates with high-level drug resistance, including pre-XDR and XDR, were identified. However, there was no resistance to new and repurposed drugs, such as bedaquiline, pretomanid, delamanid, and linezolid. Most drug-resistant cases were associated with previous