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.
