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

Mulualem Agonafir; Gurja Belay; Nontuthuko E Maningi; Adey Feleke; Melese Abate Reta; Sharon L Olifant; Mohammed Suaudi Hassen; Tewodros Girma; P Bernard Fourie

doi:10.1016/j.heliyon.2023.e22898

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

Heliyon. 2023 Nov 29;9(12):e22898. doi: 10.1016/j.heliyon.2023.e22898. eCollection 2023 Dec.

Authors

Mulualem Agonafir¹, Gurja Belay¹, Nontuthuko E Maningi², Adey Feleke¹, Melese Abate Reta^{2

3}, Sharon L Olifant², Mohammed Suaudi Hassen⁴, Tewodros Girma⁵, P Bernard Fourie²

Affiliations

¹ Department of Microbial, Cellular and Molecular Biology, College of Natural Sciences, Addis Ababa University, Ethiopia.
² Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
³ Department of Medical Laboratory Sciences, College of Health Sciences, Woldia University, Woldia, Ethiopia.
⁴ Adama Public Health Research and Referral Laboratory Center, Adama, Ethiopia.
⁵ Harar Health Research and Regional Laboratory, Harar, 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.