Abstract
BackgroundTuberculosis (TB) is caused by Mycobacterium tuberculosis complex (MTBC). Mapping the genetic diversity of MTBC in high TB burden country like Ethiopia is important to understand principles of the disease transmission and to strengthen the regional TB control program. The aim of this study was to investigate the genetic diversity of Mycobacterium tuberculosis complex (MTBC) isolates circulating in the South Omo, southern Ethiopia.MethodsMTBC isolates (N = 156) were genetically analyzed using spacer oligotyping (spoligotyping) and mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing. Major lineages and lineages were identified using MTBC databases. Logistic regression was used to correlate patient characteristics with strain clustering.ResultsThe study identified Euro-American (EA), East-African-Indian (EAI), Indo-Oceanic (IO), Lineage_7/Aethiops vertus, Mycobacterium bovis and Mycobacterium africanum major lineages in proportions of 67.3% (105/156), 22.4% (35/156), 6.4% (10/156), 1.9% (3/156), 1.3% (2/156) and 0.6% (1/156), respectively. Lineages identified were Delhi/CAS 23.9% (37/155), Ethiopia_2 20.6% (32/155), Haarlem 14.2% (22/155), URAL 14.2%(22/155), Ethiopia_3 8.4% (13/155), TUR 6.5% (10/155), Lineage_7/Aethiops vertus 1.9% (3/155), Bovis 1.3% (2/155), LAM 1.3% (2/155), EAI 0.6% (1/155), X 0.6% (1/155) and Ethiopia H37Rv-like strain 0.6% (1/155). Of the genotyped isolates 5.8% (9/155) remained unassigned. The recent transmission index (RTI) was 3.9%. Orphan strains compared to shared types (AOR: 0.09, 95% CI: 0.04–0.25) were associated with reduced odds of clustering. The dominant TB lineage in pastoral areas was EAI and in non-pastoral areas was EA.ConclusionThe epidemiological data, highly diverse MTBC strains and a low RTI in South Omo, provide information contributing to the TB Control Program of the country.
Highlights
Tuberculosis (TB) is caused by Mycobacterium tuberculosis complex (MTBC)
Orphan strains compared to shared types (AOR: 0.09, 95% Confidence interval (CI): 0.04–0.25) were associated with reduced odds of clustering
The epidemiological data, highly diverse MTBC strains and a low recent transmission index (RTI) in South Omo, provide information contributing to the TB Control Program of the country
Summary
Tuberculosis (TB) is caused by Mycobacterium tuberculosis complex (MTBC). Mapping the genetic diversity of MTBC in high TB burden country like Ethiopia is important to understand principles of the disease transmission and to strengthen the regional TB control program. The aim of this study was to investigate the genetic diversity of Mycobacterium tuberculosis complex (MTBC) isolates circulating in the South Omo, southern Ethiopia. The Mycobacterium tuberculosis complex (MTBC) constitutes a group of mycobacteria which are 99.9% similar at the nucleotide level and the causative agents for tuberculosis (TB) [11]. Ethiopia stands 12th in the world and 4th in Africa among the high TB burden countries with 24,000 TB deaths and 165,000 new TB cases in 2018 [39]. Understanding the molecular epidemiology of TB is important for regional disease control. Distinct strains may be linked to outbreaks [10], high virulence [42], emergency of drug resistance [44], disease progression [43], and can point to the geographic origin of a strain [20, 33] as well as identify new lineages [17, 28]
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