High prevalence of Ethiopian and Indo-Oceanic Mycobacterium tuberculosis lineages among pulmonary tuberculosis cases in East Gojjam, Northwest Ethiopia: insights from genomic characterization

Abstract

IntroductionMycobacterium tuberculosis (Mtb) strains in Ethiopia exhibit significant genetic and regional variation, highlighting the need for further research across diverse geographic areas. ObjectiveWe employed a molecular tool to characterize Mtb isolates from predominantly rural patients at two public hospitals in East Gojjam, Amhara Region, northwest Ethiopia. MethodsMolecular typing, including the region of difference 9 (RD9)-based polymerase chain reaction (PCR) and spoligotyping, was performed on stored sputum samples at Armauer Hansen Research Institute (AHRI) in Addis Ababa. ResultsOut of 120 Mtb, 116 yielded interpretable spoligotyping results, revealing four major lineages. The Euro-American (Lineage 4) was most common (42.6%), followed by the Ethiopian (Lineage 7, 20.8%), Indo-Oceanic (Lineage 1, 20.0%), and East African-Indian (Lineage 3, 16.5%). The dominant sublineages were ETH1 (Lineage 7, 20.8%), T (Lineage 4, 15.6%), and CAS1-Delhi (Lineage 3, 13.9%). In total, 39 spoligotype patterns were identified, including 19 shared types (48.7%) comprising 90 strains from the SITVIT2 database. The most frequent spoligotypes were SIT 910 (23.3%) and SIT 53 (14.4%), followed by SIT 54 and SIT 149 (10.0% each). Overall, 82.7% of the strains were clustered. ConclusionThis study reveals substantial genetic diversity among Mtb strains in a rural area of Ethiopia, with a notably high prevalence of Lineage 7 and Indo-Oceanic strains. The high clustering rate (82.7%) suggests ongoing local transmission, particularly involving the ETH1, CAS1-Delhi, and Manu2 sublineages. Due to the distinct strain distribution, whole-genome sequencing is essential to better understand Mtb diversity and inform targeted TB control strategies.