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

Yared Merid,Abraham Aseffa,Getnet Habtamu,Markos Abebe,Daniel Gemechu Datiko,Yimtubezinash Woldeamanuel,Melaku Tilahun,Mesay Hailu,Tsegaye Hailu,Elena Hailu

doi:10.3855/jidc.14742

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.

Highlights

Understanding the epidemiology of tuberculosis is limited by lack of genotyping data
Ethiopia has a long history of TB [2] and is still hugely affected by the disease and it is one of fourteen countries appearing in all three WHO high burden country lists for TB, TB/HIV and MDR-TB [1]
A high proportion of INH resistance was reported in the current study and Spoligotyping International Types (SIT) 149 (T3-ETH) was the most dominant circulating strain in the study area including among drug-resistant cases

Summary

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. M. tuberculosis isolates had drug susceptibility testing performed using indirect proportion method and were genotyped with RD9 deletion analysis and spoligotyping. 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. Wider monitoring of drug susceptibility testing and geospatial analysis of transmission trends is required to control tuberculosis in southern Ethiopia. Data from different parts of the country show that drug-resistant TB is a major public health concern that demands attention [4,5]

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Conclusion