Mycobacterium tuberculosis genotypes isolated from clinical specimens of extrapulmonary TB

BACKGROUND Ethiopia has reported a high rate of extrapulmonary TB (EPTB). We aimed to identify the epidemiology of TB (sub-) lineages and the transmission cluster of EPTB as understanding the driving genotypes helps to implement appropriate intervention. METHODS In a cross-sectional study conducted between 2022–2023, whole genome sequencing was employed on microbiologically confirmed EPTB isolates. A bioinformatics pipeline MTBSeq was used to analyze genomic data. RESULTS The majority (98.1%) of study isolates belonged to the Mycobacterium tuberculosis (MTB) species, and the remaining 1.9% were identified as Mycobacterium bovis . The MTB species were further classified into 4 common lineages and 15 sub-lineages. The Euro-American lineage 4 (63.8%) and East African Indian lineage 3 (31.9%) were predominant. Lineage 4 was further branched into 11 sub-lineages, of which the group Clade1 (n = 78, 48.8%) was the highest, followed by the Haarlem branch (n = 19, 11.9%). The clustering rate and recent transmission index were 12.5% and 6.9% respectively. The risk of rifampicin resistance increases among (sub-)lineage 4.2.2 genotypes. CONCLUSION There was high genotype variability and low clustering rate among main MTBC genotypes and (sub-)lineages of EPTB. M.bovis was detected among EPTB patients in central urban areas.