Abstract:
BACKGROUND : The genetic diversity of Mycobacterium tuberculosis complex (MTBC) strains was characterized
among isolates from individuals with pulmonary tuberculosis (PTB) symptoms attended holy water sites (HWSs)
in the Amhara region, Ethiopia.
METHODS : A cross-sectional study was done from June 2019 to March 2020 to describe the genetic diversity and
drug-resistance profiles of MTBC isolates. Sputum specimens were collected and cultured in the L¨owenstein-
Jensen culture medium. Line Probe Assay, MTBDRplus VER 2.0, and MTBDRsl VER 2.0 were used to detect firstand
second-line anti-TB drug-resistance patterns. A spoligotyping technique was utilized to characterize the
genetic diversity. Statistical analysis was performed using STATA 15.
RESULTS : Of 560 PTB-symptomatic participants, 122 (21.8%) were culture-positive cases. Spoligotyping of 116
isolates revealed diverse MTBC sublineages, with four major lineages: Euro-American (EA) (Lineage 4), East-
African-Indian (EAI) (Lineage 3), Ethiopian (ETH) (Lineage 7), East Asian (EA) (Lineage 2). The majority
(96.6%) of the isolates were EA (lineage 4) and EAI, with proportions of 54.3% and 42.2%, respectively. A total
of 31 spoligotype patterns were identified, 26 of which were documented in the SITVIT2 database. Of these, there
were 15 unique spoligotypes, while eleven were grouped with 2-17 isolates. SIT149/T3-ETH (n = 17), SIT26/
CAS1-DELHI (n = 16), SIT25/CAS1-DELHI (n = 12), and SIT52/T2 (n = 11) spoligotypes were predominant.
A rare spoligotype pattern: SIT41/Turkey and SIT1/Beijing, has also been identified in North Shewa. The overall
clustering rate of sub-lineages with known SIT was 76.4%.
Of the 122 culture-positive isolates tested, 16.4% were resistant to rifampicin (RIF) and/or isoniazid (INH).
Multidrug-resistant TB (MDR-TB) was detected in 12.3% of isolates, five of which were fluoroquinolones (FLQs)
resistant. SIT149/T3-ETH and SIT21/CAS1-KILI sublineages showed a higher proportion of drug resistance.
CONCLUSIONS : Diverse MTBC spoligotypes were identified, with the T and CAS families and EA (lineage 4) predominating.
A high prevalence of drug-resistant TB, with SIT149/T3-ETH and CAS1-KILI sublineages comprising
a greater share, was observed. A study with large sample size and a sequencing method with stronger
discriminatory power is warranted to understand better the genetic diversity of circulating MTBC in this cohort
of study, which would help to adopt targeted interventions.
