Mapping of Mycobacterium tuberculosis Complex Genetic Diversity Profiles in Tanzania and Other African Countries

Abstract

The aim of this study was to assess and characterize Mycobacterium tuberculosis complex (MTBC) genotypic diversity in Tanzania, as well as in neighbouring East and other several African countries. We used spoligotyping to identify a total of 293 M. tuberculosis clinical isolates (one isolate per patient) collected in the Bunda, Dar es Salaam, Ngorongoro and Serengeti areas in Tanzania. The results were compared with results in the SITVIT2 international database of the Pasteur Institute of Guadeloupe. Genotyping and phylogeographical analyses highlighted the predominance of the CAS, T, EAI, and LAM MTBC lineages in Tanzania. The three most frequent Spoligotype International Types (SITs) were: SIT21/CAS1-Kili (n = 76; 25.94%), SIT59/LAM11-ZWE (n = 22; 7.51%), and SIT126/EAI5 tentatively reclassified as EAI3-TZA (n = 18; 6.14%). Furthermore, three SITs were newly created in this study (SIT4056/EAI5 n = 2, SIT4057/T1 n = 1, and SIT4058/EAI5 n = 1). We noted that the East-African-Indian (EAI) lineage was more predominant in Bunda, the Manu lineage was more common among strains isolated in Ngorongoro, and the Central-Asian (CAS) lineage was more predominant in Dar es Salaam (p-value<0.0001). No statistically significant differences were noted when comparing HIV status of patients vs. major lineages (p-value = 0.103). However, when grouping lineages as Principal Genetic Groups (PGG), we noticed that PGG2/3 group (Haarlem, LAM, S, T, and X) was more associated with HIV-positive patients as compared to PGG1 group (Beijing, CAS, EAI, and Manu) (p-value = 0.03). This study provided mapping of MTBC genetic diversity in Tanzania (containing information on isolates from different cities) and neighbouring East African and other several African countries highlighting differences as regards to MTBC genotypic distribution between Tanzania and other African countries. This work also allowed underlining of spoligotyping patterns tentatively grouped within the newly designated EAI3-TZA lineage (remarkable by absence of spacers 2 and 3, and represented by SIT126) which seems to be specific to Tanzania. However, further genotyping information would be needed to confirm this specificity.

NewMycobacterium tuberculosisComplex Sublineage, Brazzaville, Congo

“…These findings are in accordance with most recent studies from the other African countries reporting a predominance of M. tuberculosis strains ( 25 – 28 ). The high prevalence of M. tuberculosis detected in our investigation suggests that this predominance of M. tuberculosis strains might equally be the case for Congo, mainly driven by the newly described Congo-type sublineage.…”

Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania

“…We found that, the Central Asian strains (CAS) genotype (lineage 3) were the predominant lineages (Table 5), with no evidence of any change in terms of the CAS dominance over the past few years in Tanzania [50]. The CAS is among the prevalent lineage in the Indian subcontinent, South-East Asia, the Middle-East and East-Africa [51], showing a North-South divide along the Tropic of Cancer in the Eastern hemispheremainly in Asia, and partly prolonged along the horn of Africa [51,52]. The dominance of CAS lineages in our local settings might be attributed to early contact due to migration and trade between people in Asian and East Africa countries.…”

Insights into the genetic diversity ofMycobacterium tuberculosisin Tanzania

“…This illustrates the ability of “modern” lineages to thrive in co-existence with the pre-existing “ancient” (TbD1+) lineages such as Lineage 1 in our case, perhaps because of the comparably higher virulence [16,37]. The neighboring countries of Tanzania on the other hand show comparable M. tuberculosis lineage composition [38,39], indicating common demographic histories and ongoing exchanges that resulted into distinct M. tuberculosis populations. The frequency of Lineage 2–Beijing in Tanzania, like in most parts of the continent except for South Africa [38,39] is relatively low, despite the long-standing African- Asian contacts [39].…”

“…The neighboring countries of Tanzania on the other hand show comparable M. tuberculosis lineage composition [38,39], indicating common demographic histories and ongoing exchanges that resulted into distinct M. tuberculosis populations. The frequency of Lineage 2–Beijing in Tanzania, like in most parts of the continent except for South Africa [38,39] is relatively low, despite the long-standing African- Asian contacts [39]. Evidence from recent studies show that Lineage 2-Beijing was only recently introduced into Africa [15,40].…”