T uberculosis (TB) remains a major global health problem; 10 million new cases were reported in 2018 (1). In Sudan, the estimated national TB incidence in 2018 was 71/100,000 persons; a total of 20,638 cases were reported (1). However, the TB burden is by no means homogeneous across the country. For instance, in eastern Sudan, TB notifications reached 275/100,000 persons in 2012 (2,3). Prevalence of multidrug-resistant TB (MDR TB) (i.e., resistant to isoniazid and rifampin) was estimated at 2.9% in new and 13% in retreatment cases; however, studies have reported MDR TB rates of 6%-22% (1,4-10). Ongoing transmission is one of the key challenges for TB control programs, especially in countries with a high TB burden (1,11). In recent years, molecular techniques have been increasingly used to clarify and trace transmission of Mycobacterium tuberculosis complex (MTBC) strains and to direct and guide targeted TB control actions (12,13). However, availability of molecular techniques is limited in many countries in Africa with a high TB burden (11). In Sudan, drug-resistant TB often goes undetected, resulting in inadequate treatment, illness, death, and ongoing transmission (1,14). Local laboratories have limited access to mycobacterial culture and drug susceptibility testing (DST) or DNA-based techniques (14). Therefore, MDR TB rates might be underestimated in eastern Sudan. In addition, mutations that mediate drug resistance have not been investigated. Taken together, these factors indicate that, although TB is a huge health problem in eastern Sudan, precise data on the phylogeny and transmission dynamics of MTBC strains, as well as on resistance patterns, is sparsely available (2,3,7,8,15). Studies using molecular epidemiologic tools are rare and have used classical genotyping techniques, such as