The Ethiopian Third National Tuberculosis Drug Resistance Survey Incorporating Whole Genome Sequencing

Background. Drug-resistant tuberculosis (DR-TB) is a major challenge hindering global tuberculosis control. Ethiopia conducted a third national antituberculosis (TB) drug resistance survey, and this is the first survey to report on drug resistance using whole genome sequencing (WGS) in addition to genotypic and phenotypic test results. The aim of this study was to obtain up-to-date information regarding the magnitude and pattern of drug resistance in Ethiopia. Methods. A nationwide cross-sectional study was conducted in 217 health facilities across all Ethiopian regional states from August 2017 to January 2019. Sputum specimens were collected from patients with bacteriologically confirmed pulmonary TB to detect resistance to anti-TB drugs with Xpert MTB/RIF assay, culture-based phenotypic drug susceptibility testing (DST), and WGS with phylogenetic analysis. Results. The prevalence of rifampicin-resistant TB (RR-TB) was 1.07% (95% confidence interval [CI], .65%–1.74%) among new cases and 6.89% (95% CI, 4.02%–11.57%) among previously treated cases. The prevalence of isoniazid-resistant, rifampicin-susceptible TB was 4.15% (95% CI, 3.11%–5.53%) among new cases and 4.41% (95% CI, 1.97%–9.57%) among previously treated cases. While resistance to fluoroquinolones was detected in 1 RR-TB case, resistance to bedaquiline and linezolid was not detected in RR-TB cases. Mycobacterium tuberculosis lineage 4 was the most common, followed by lineage 3 and lineage 1, with sublineage 4.2.2 being the most frequent. Conclusions. The level of RR-TB remained low. Expanding baseline DST for isoniazid may help further lower the burden of DR-TB in Ethiopia.