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

Abstract

Introduction: The population structure of Mycobacterium tuberculosis complex (MTBC) in Ethiopia is diverse but dominated by Euro-American (Lineage 4) and East-African-Indian (Lineage 3) lineages. The objective of this study was to describe the genetic diversity of MTBC isolates in Central, Eastern and Southeastern Ethiopia.

Methods: A total of 223 MTBC culture isolates obtained from patients referred to Adama and Harar TB reference laboratories were spoligotyped. Demographic and clinical characteristics were collected.

Results: Six major lineages: Euro-American (Lineage 4), East-African-Indian (Lineage 3), East Asian (Lineage 2), Indo-Oceanic (Lineage 1), Mycobacterium africanum (Lineage 5 and Lineage 6) and Ethiopian (Lineage 7) were identified. The majority (94.6 %) of the isolates were Euro-American and East-African-Indian, with proportions of 75.3 % and 19.3 %, respectively. Overall, 77 different spoligotype patterns were identified of which 42 were registered in the SITVIT2 database. Of these, 27 spoligotypes were unique, while 15 were clustered with 2-49 isolates. SIT149/T3_ETH (n = 49), SIT53/T1 (n = 33), SIT21/CAS1_Kili (n = 24) and SIT41/Turkey (n = 11) were the dominant spoligotypes. A rare Beijing spoligotype pattern, SIT541, has also been identified in Eastern Ethiopia. The overall clustering rate of sub-lineages with known SIT was 71.3 %. Age group (25-34) was significantly associated with clustering.

Conclusion: We found a heterogeneous population structure of MTBC dominated by T and CAS families, and the Euro-American lineage. The identification of the Beijing strain, particularly the rare SIT541 spoligotype in Eastern Ethiopia, warrants a heightened surveillance plan, as little is known about this genotype. A large-scale investigation utilizing a tool with superior discriminatory power, such as whole genome sequencing, is necessary to gain a thorough understanding of the genetic diversity of MTBC in the nation, which would help direct the overall control efforts.

Keywords: Ethiopia; Genetic diversity; Lineage; Mycobacterium tuberculosis complex; Spoligotyping; Sub-lineage.

Fig. 1

Radial UPGMA tree based on spoligotyping data of 223 MTB isolates from central, eastern and southeastern Ethiopia. Annotations with similar colored fonts in the outer ring represent clustered sub-lineages/spoligotypes. The ones written in black fonts are unique/orphan isolates. The colors of branches in the inner circle indicate the major lineages. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2

Distribution of major lineages in central, eastern and southeastern Ethiopia. Pie charts show the proportions of the six lineages among MTBC isolates in each zone from where isolates were obtained. The size of the circle does not correspond to the number of isolates analyzed. The actual numbers are shown in Supplementary material 2: color codes are as in Fig. 2. A total of 223 MTBC isolates were included. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3

Distribution of MTBC sub-lineages in central, eastern and southeastern Ethiopia. Pie charts show the proportions of the sub-lineages among MTBC isolates in each zone from where isolates were obtained. The size of the circle does not correspond to the number of isolates analyzed. The actual numbers are shown in Supplementary material 4: color codes are as shown in Fig. 3. A total of 223 MTBC isolates were included. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

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