Molecular Epidemiology of Mycobacterium tuberculosis strains isolated from pulmonary tuberculosis patients in south Ethiopia

Abstract

Introduction: Understanding the epidemiology of tuberculosis is limited by lack of genotyping data. We sought to characterize the drug susceptibility testing patterns and genetic diversity of M. tuberculosis isolates in southern Ethiopia.

Methodology: A cross-sectional study was conducted among newly diagnosed sputum smear positive patients with tuberculosis 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 smear microscopy with all smear positive specimens having acid-fast bacilli cultures performed. M. tuberculosis isolates had drug susceptibility testing performed using indirect proportion method and were genotyped with RD9 deletion analysis and spoligotyping. Mapping of strain was made using geographic information system.

Results: Among 250 newly diagnosed patients with tuberculosis, 4% were HIV co-infected. All 230 isolates tested were M. tuberculosis strains belonging to three lineages: Euro-American, 187 (81%), East-African-Indian, 31 (14%), and Lineage 7 (Ethiopian lineage), 8 (4%); categorized into 63 different spoligotype patterns, of which 85% fell into 28 clusters. M. tuberculosis strains were clustered by geographic localities. The dominant spoligotypes were SIT149 (21%) and SIT53 (19%). Drug susceptibility testing found that 14% of isolates tested were resistant to > 1 first line anti- tuberculosis drugs and 11% to INH. SIT 149 was dominant among drug resistant isolates.

Conclusions: The study revealed several clusters and drug resistant strains of M. tuberculosis in the study area, suggesting recent transmission including of drug resistant tuberculosis. Wider monitoring of drug susceptibility testing and geospatial analysis of transmission trends is required to control tuberculosis in southern Ethiopia.

Keywords: Ethiopia; Molecular epidemiology; Tuberculosis; drug susceptibility testing; geospatial cluster.

Figure 1.

Map of the study area (East Arisi Zone districts, Oromia and Wondo Genet of Sidama Regional State) A: Map of Ethiopia; B: Map of Oromia Regional State; C: Map of districts of Oromia Regional state and Wondogenet district from Sidama Regional State; D: Map of districts involved in the study.

Figure 2.

Study Diagram. DST: drug susceptibility testing; RD9: region of difference-9.

Figure 3.

Spoligotype pattern of M. tuberculosis strains isolated from pulmonary tuberculosis patients in southern Ethiopia. The black squares represent positive hybridization signals and white squares represent a lack of hybridization. EA: Euro-American; EAI: East-African-Indian; EL: Ethiopian lineage (L7); SIT: Spoligotype international type; NA: Not assigned; Un: unknown.

Figure 4.

Spatial distribution of TB lineages; West Arisi zone and Wondogenet district. A: East-African-Indian (L3); B: Euro-American lineage (L4); C: Lineage 7 (Ethiopian lineage).

Figure 5.

Spatial distribution of clustered strains by district; West Arisi zone and Wondogenet district. SIT: Spoligotype international type. A: SIT 149; B: SIT 53; C:SIT 25; D:SIT 26; E: SIT 910; F:SIT 699; G:SIT 777; H: SIT 37; I: SIT 4.