Molecular Epidemiology of Pulmonary Tuberculosis in Southern Ethiopia

Background Understanding the epidemiology of tuberculosis (TB) is limited by lack of genotyping data. We sought to characterize the drug susceptibility testing (DST) patterns and genetic diversity of M. tuberculosis (Mtb) isolates in Southern Ethiopia. Methodology A cross-sectional study was conducted among newly diagnosed sputum smear positive patients with TB visiting nine health facilities in southern Ethiopia from June 2015 to May 2016. Three consecutive sputum samples (spot-morning-spot) per patient were examined using acid-fast bacilli (AFB) smear microscopy with all smear positive specimens having AFB cultures performed. Mtb isolates had DST performed using indirect proportion method and were genotyped with RD9 deletion typing and spoligotyping. Spoligotyping International Types (SIT) and sub-lineages (clades) were assigned according to the SITVITWEB data base. Results Among 250 newly diagnosed patients with TB, 154 (52%) were male and 143 (57%) from rural areas. The prevalence of HIV co-infection was 4%. Of the 250 AFB positive sputum samples, 230 (92%) were culture positive. All 230 isolates were M. tuberculosis strains belonging to three lineages: Euro-American, 187 (81%); East-African-Indian, 31 (14%); and Lineage 7 (Ethiopian lineage), 8 (4%). The 230 isolates could be categorized into 65 different spoligotype patterns, of which 84% fell into 29 clusters. The dominant spoligotypes were SIT149 (21%), SIT53 (19%) and new strains (16%). Mtb strains were clustered by districts. DST revealed that 14% of Mtb isolates were resistant to > 1 first line anti-TB drugs including 11% to isoniazid. SIT 149 was the most prevalent genotype among drug resistant isolates (20%). Conclusion The study revealed several clusters including lineage 7 strains circulating in southern Ethiopia. SIT 149 (T3-ETH) was the most dominant circulating strain in the study area including among drug-resistant cases.