Molecular epidemiology of tuberculosis in the Somali region, eastern Ethiopia

Getnet Worku; Balako Gumi; Binyam Mohammedbirhan; Musse Girma; Henok Sileshi; Michael Hailu; Amanuel Wondimu; Wondimu Ashagre; Rea Tschopp; Lauren Carruth; Gobena Ameni

doi:10.3389/fmed.2022.960590

Molecular epidemiology of tuberculosis in the Somali region, eastern Ethiopia

Front Med (Lausanne). 2022 Oct 14:9:960590. doi: 10.3389/fmed.2022.960590. eCollection 2022.

Authors

Getnet Worku^{1

2}, Balako Gumi², Binyam Mohammedbirhan³, Musse Girma², Henok Sileshi¹, Michael Hailu⁴, Amanuel Wondimu⁴, Wondimu Ashagre⁵, Rea Tschopp^{5

6}, Lauren Carruth⁷, Gobena Ameni^{2

8}

Affiliations

¹ Department of Medical Laboratory Science, College of Medicine and Health Sciences, Jigjiga University, Jigjiga, Ethiopia.
² Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
³ Department of Pathology, College of Medicine and Health Sciences, Jigjiga University, Jigjiga, Ethiopia.
⁴ National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia.
⁵ One-Health Unit, Armauer Hansen Research Institute, Addis Ababa, Ethiopia.
⁶ Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.
⁷ School of International Studies, American University, Washington, DC, United States.
⁸ Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates.

Abstract

Background: Tuberculosis (TB) is one of the leading causes of morbidity and mortality in low-income countries like Ethiopia. However, because of the limited laboratory infrastructure there is a shortage of comprehensive data on the genotypes of clinical isolates of Mycobacterium tuberculosis (M. tuberculosis) complex (MTBC) in peripheral regions of Ethiopia. The objective of this study was to characterize MTBC isolates in the Somali region of eastern Ethiopia.

Methods: A cross-sectional study was conducted in three health institutions between October 2018 and December 2019 in the capital of Somali region. A total of 323 MTBC isolates (249 from pulmonary TB and 74 from extrapulmonary TB) were analyzed using regions of difference 9 (RD 9)-based polymerase chain reaction (PCR) and spoligotyping.

Results: Of the 323 MTBC isolates, 99.7% (95% CI: 99.1-100%) were M. tuberculosis while the remaining one isolate was M. bovis based on RD 9-based PCR. Spoligotyping identified 71 spoligotype patterns; 61 shared types and 10 orphans. A majority of the isolates were grouped in shared types while the remaining grouped in orphans. The M. tuberculosis lineages identified in this study were lineage 1, 2, 3, 4, and 7 with the percentages of 7.4, 2.2, 28.2, 60.4, and 0.6%, respectively. Most (87.9%) of the isolates were classified in clustered spoligotypes while the remaining 12.1% isolates were singletons. The predominant clustered spoligotypes identified were SIT 149, SIT 21, SIT 26, SIT 53, and SIT 52, each consisting of 17.6, 13.3, 8.4, 7.4, and 5%, respectively. Lineage 3 and lineage 4, as well as the age group (15-24), were associated significantly with clustering.

Conclusion: The MTBC isolated from TB patients in Somali region were highly diverse, with considerable spoligotype clustering which suggests active TB transmission. In addition, the Beijing spoligotype was isolated in relatively higher frequency than the frequencies of its isolation from the other regions of Ethiopia warranting the attention of the TB Control Program of the Somali region.

Keywords: M. tuberculosis complex; eastern Ethiopia; molecular epidemiology; spoligotyping; tuberculosis.

Grants and funding

MR/R005850/1/MRC_/Medical Research Council/United Kingdom