Spoligotyping of Clinical Isolates of Mycobacterium tuberculosis Complex Species in the Oromia Region of Ethiopia

Abstract

BackgroundTuberculosis (TB) is a leading cause of morbidity and mortality in Ethiopia. Investigation of the Mycobacterium tuberculosis complex (MTBC) species circulating in the Ethiopian population would contribute to the efforts made to control TB in the country. Therefore, this study was conducted to investigate the MTBC species and spoligo patterns in the Oromia region (central) of Ethiopia.MethodsA cross-sectional study design was used to recruit 450 smear positive pulmonary TB (PTB) cases from the Oromia region between September 2017 and August 2018. Mycobacteria were isolated from sputum samples on the Lowenstein Jensen (LJ) medium. Molecular identification of the isolates was performed by spoligotyping. The results of spoligotyping were transferred into a query box in the SITVIT2 database and Run TB-Lineage in the TB Insight website for the identification of spoligo international type (SIT) number and linages of the isolates, respectively. Statistical Product and Service Solutions (SPSS) 20 was applied for statistical analysis.ResultsThree hundred and fifteen isolates were grouped under 181 different spoligotype patterns. The most dominantly isolated spoligotype pattern was SIT149 and it consisted of 23 isolates. The majority of the isolates were grouped under Euro-American (EA), East-African-Indian (EAI), and Indo-Oceanic (IO) lineages. These lineages consisted of 79.4, 9.8, and 9.8% of the isolates, respectively. One hundred and sixty-five of the isolates were classified under 31 clustered spoligotypes whereas the remaining 150 were singleton types. Furthermore, 91.1% of the total isolates were classified as orphan types. Clustering of spoligotypes was associated (p < 0.001) with EAI lineage.ConclusionSIT149 and EA lineage were predominantly isolated from the Oromia region substantiating the findings of the similar studies conducted in other regions of Ethiopia. The observation of significant number of singleton and orphan spoligotypes warrants for additional genetic typing of the isolates using method(s) with a better discriminatory power than spoligotyping.

Genetic diversity of Mycobacterium tuberculosis strains isolated from spiritual holy water site attendees in Northwest Ethiopia. A cross-sectional study

“…Consistent with earlier research conducted in various regions of Ethiopia [ 25 , [31] , [32] , [33] , [34] , [35] , 62 , 66 , 67 ], the SIT149/T3-ETH sub-lineage, which has been found to be more likely in a cluster [ 13 , 20 , 65 ], was the most common in our study, followed by the SIT52/T2 spoligotype. In the current study region, SIT149/T3-ETH sublineage [ 39 ] was reported as a predominant TB strain.…”

“…The genetic diversity and geographic distribution of MTB lineages have been studied across different settings and regions of Ethiopia [ [20] , [21] , [22] , [23] , [24] , [25] , [26] , [27] , [28] , [29] , [30] , [31] ] and revealed the presence of diverse MTBC sublineages. The Ethiopian-specific lineage (SIT149/T3-ETH sublineages) was reported as a predominant TB strain in the country [ 25 , [31] , [32] , [33] , [34] , [35] ], while lineage 3/CAS1-DELHI sublineages was another widespread strain in certain regions of Ethiopia [ 20 , 26 , 27 , 36 ]. In the current study region, lineage 3/CAS1-DELHI [ 20 , 21 , 37 , 38 ], and lineage 4/T3-ETH sublineages [ 39 ] were identified as the most abundant TB strains.…”

Genetic diversity of Mycobacterium tuberculosis isolates from the central, eastern and southeastern Ethiopia

“…A relatively large cluster (n = 11) of the SIT41 spoligotype, which is phylogeographically specific to Turkey [ 44 ], was reported in this study with the majority (10/11) being from patients in southeastern (Borena and Guji) Ethiopia. This sub-lineage, although in small numbers (n ≤ 5), was previously reported [ 23 , 28 , 30 , 32 , 43 , [45] , [46] , [47] , [48] ] in different parts of Ethiopia. Similarly, it was reported to be less common in the African continent [ 49 ].…”

“…Consistent with other investigations carried out in Ethiopia [ [11] , [12] , [13] ], the T3-ETH sub-lineage/SIT149 spoligotype, reported to be more likely in a cluster [ 36 , 41 , 42 ], was the most frequent in our study, followed by the T1 sub-lineage/SIT53 spoligotype. A study conducted in Oromia region [ 43 ], which included the zones from which two-thirds of our isolates were obtained, found a high proportion of clustered ST149 spoligotype followed by orphan spoligotypes rather than the commonly reported T or CAS sub-lineages. This could be attributed to several factors including differences in sampling techniques, the broad geographic area and high population of the region and the relatively small sample size used in the current study.…”