isoniazid or rifampin); multidrug-resistant TB (MDR TB, resistant to 2 first-line drugs: isoniazid and rifampin); pre‒extensively drug-resistant (pre-XDR, resistant to either fluoroquinolones or injectable drugs in addition to MDR); and extensively drug-resistant TB (XDR TB, resistant to fluoroquinolones and injectable drugs in addition to MDR) (1). An estimated 0.5 million cases of MDR TB were reported in patients worldwide during 2018, but only one third had access to effective treatment, resulting in 56% of patients being successfully treated (1). In addition, an estimated 6% of diagnosed case of MDR TB cases are actually cases of XDR TB (1). Myanmar is recognized by the World Health Organization (WHO) as having high burdens of TB (338 cases/100,000 population), MDR TB (21 cases/100,000 population), and co-infections of TB and HIV (29 cases/100,000 population) (1). A nationwide drug-resistant TB survey was conducted during 2012–2013 by the Myanmar National Tuberculosis Programme (NTP) to identify the drug susceptibility profile for first-line drugs (phenotypic drug susceptibility testing for second-line drugs was established during 2016) (2). This survey identified MDR TB among 5% of new cases and 27.1% of previously treated cases, and the Yangon region was identified as a hotspot for drug-resistant TB (3). Having an estimated population of 8 million persons, Yangon is the most populous city in Myanmar. All patients with suspected pulmonary TB are referred to a TB diagnostic center run by the NTP for testing by using the GeneXpert platform (https://www.cepheid.comExternal Link). Routine, phenotypic drug-susceptibility testing (DST) of first-line or second-line drugs is rarely performed for new patients, and currently testing is based solely on the Xpert MTB/RIF (M. tuberculosis/rifampin) assay. Therefore, clinical decisions reflect the detection of rifampin resistance and national therapeutic guidelines on the basis of WHO recommendations. Technological advances in next-generation, whole-genome sequencing (WGS) and downstream bioinformatic analyses now enable comprehensive detection of drug resistance and provide an alternative to existing approaches (3–5). Such sequence-based, drug-resistant profiles have high concordance with phenotypic DST (3,4). In addition, phylogenetic analyses of sequence data can be used to identify transmission patterns in the absence of epidemiologic data, which is often lacking in high-burden settings such as Myanmar (3,6). We combined clinical, genomic, and phenotypic drug-resistance data to provide insights into drug resistance and transmission patterns in Yangon. In this study, we used WGS analyses of 309 M. tuberculosis isolates to determine how the increasing burden of MDR TB has been driven in Yangon. Methods Study Design and Participants This population-based, cross-sectional study included consenting participants >15 years of age who had GeneXpert-confirmed positive pulmonary TB at 3 major NTP TB diagnostic centers (Aung San, Latha, and North Oakkalapa) in Yangon during July 2016‒June 2018. We aimed to recruit 250 patients consecutively given a diagnosis of infection with rifampin-resistant (RR) M. tuberculosis and 200 patients infected with rifampin-susceptible (RS) M. tuberculosis. Recruitment numbers at each facility reflected the relative numbers of patients given a diagnosis during the previous year. Patients were eligible to be included in the study if they had lived in Yangon at the time of