Genetic diversity of the Mycobacterium tuberculosis complex strains from newly diagnosed tuberculosis patients in Northwest Ethiopia reveals a predominance of East-African-Indian and Euro-American lineages

Abstract

This study described the population structure of M. tuberculosis complex (MTBc) strains among patients with pulmonary or lymph node tuberculosis (TB) in Northwest Ethiopia and tested the performance of culture isolation and MPT64-based speciation for Lineage 7 (L7). Methods: Patients were recruited between April 2017 and June 2019 in North Gondar, Ethiopia. The MPT64 assay was used to confirm MTBc, and spoligotyping was used to characterize mycobacterial lineages. Line probe assay (LPA) was used to detect resistance to rifampicin and isoniazid. Results: Among 274 MTBc genotyped isolates, there were five MTBc lineages: L1-L4 and L7 were identified, with predominant East-African-Indian (L3) (53.6%) and Euro-American (L4) (40.1%) strains, and low prevalence (2.6%) of Ethiopia L7. The genotypes were similarly distributed between pulmonary and lymph node TB, and all lineages were equally isolated by culture and recognized as MTBc by the MPT64 assay. Additionally, LPA showed that 259 (94.5%) MTBc were susceptible to both rifampicin and isoniazid, and one (0.4%) was multi-drug resistant (resistant to both rifampicin and isoniazid). Conclusion: These findings show that TB in North Gondar, Ethiopia, is mainly caused by L3 and L4 strains, with low rates of L7, confirmed as MTBc by MPT64 assay and with limited resistance to rifampicin and isoniazid.

Molecular Epidemiology of Mycobacterium tuberculosis Complex Strains in Urban and Slum Settings of Nairobi, Kenya

“…Strains of L4 and L3 are the main causative agents of TB comprising 55.8% and 25.7% of the investigated strains, respectively. These findings mirror reports from neighboring countries, such as Ethiopia [ 33 ], Tanzania [ 34 ], and Uganda [ 35 ] but are in contrast to the findings from Shuaib et al [ 12 ] and Ejo et al [ 36 ] in Eastern Sudan and Northwest Ethiopia where L3 strains were the main etiological agent of TB.…”

“…Therefore, the high prevalence of the strains of the generalist LAM sublineage might explain the dominance of L4 strains in Nairobi in Kenya. Another possible explanation for the success of L4 might be related to the observation that some L4 strains are capable of evading the host immune response and rapidly progressing to TB disease and thus are more often transmitted [ 15 , 36 ].…”

“…It’s been previously suggested that L3 strains have an evolutionary origin in South Asia. However, L3 strains have frequently been isolated from TB patients in East and North Africa [ 12 , 34 , 36 , 38 ], and one could speculate if these strains have co-evolved with and adapted to their East African hosts and consequently developed specific biological/phenotypic traits in this particular host population [ 12 ]. The high prevalence of L3 strains in Kenya could also be related to recent and/or past movements of people from the Indian subcontinent (i.e., migration, tourism, and trade).…”

Mycobacterial Lineages Associated with Drug Resistance in Patients with Extrapulmonary Tuberculosis in Addis Ababa, Ethiopia

“…Likewise, the INH mono-resistance was predominantly identified in the T3-ETH sublineage. Previous studies from Ethiopia conducted using direct spoligotyping have also reported similar detection rates of INH monoresistant isolates belonged to diverse families within Euro-American (L4) [37]. As a consequence, it is necessary to develop a closer surveillance system in the country, with a particular emphasis on isolates where resistance to isoniazid is observed, and to reduce the evolution of DR to MDR and subsequent dispersion within the population.…”

Genetic diversity of Mycobacterium tuberculosis strains isolated from spiritual holy water site attendees in Northwest Ethiopia. A cross-sectional study

“…Molecular genotyping tools, like spoligotyping and other PCR-based sequencing methods, help us to understand MTBC epidemiology in a specific geographical region, predict disease transmission, and identify prominent genotypes and TB strains that are likely to spread [ 19 ]. The genetic diversity and geographic distribution of MTB lineages have been studied across different settings and regions of Ethiopia [ [20] , [21] , [22] , [23] , [24] , [25] , [26] , [27] , [28] , [29] , [30] , [31] ] and revealed the presence of diverse MTBC sublineages. The Ethiopian-specific lineage (SIT149/T3-ETH sublineages) was reported as a predominant TB strain in the country [ 25 , [31] , [32] , [33] , [34] , [35] ], while lineage 3/CAS1-DELHI sublineages was another widespread strain in certain regions of Ethiopia [ 20 , 26 , 27 , 36 ].…”