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.
Highlights
Human tuberculosis remains a global leading devastating, often severe and contagious chronic respiratory disease
This work allowed underlining of spoligotyping patterns tentatively grouped within the newly designated EAI3-TZA lineage which seems to be specific to Tanzania
Our findings suggest that a high proportion of strains belonging to the newly defined EAI3-TZA sublineage were misclassified as EAI5 sublineage by SITVIT2
Summary
Human tuberculosis remains a global leading devastating, often severe and contagious chronic respiratory disease. In Tanzania various studies have been conducted using both conventional and nonconventional means to characterize the disease and its spread. None of the studies compared Tanzanian strain patterns with those prevailing in neighbouring countries and sub-regions to underline differences relating to the presence of specific lineages. All this information is important in establishing phylogenetical relatedness of the strains causing disease within and between countries as well as establishing transmission links between individuals. This study aimed to describe the genotypic diversity of Mycobacterium tuberculosis complex (MTBC) in Tanzania, as well as neighbouring and other countries in Africa (having spoligotyping data deposited in SITVIT database), with reference to their global distribution. This paper tentatively proposes a sublineage which seems to be phylogeographically specific for Tanzania
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