title: 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.
authors.affiliation: Department of Biochemistry, Muhimbili University of Health and Allied Sciences, P. O. Box 65001, Dar es Salaam, Tanzania.|Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania.
authors.forename: Erasto V
authors.initials: EV
authors.lastname: Mbugi
authors.affiliation: Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania.|Tanzania Wildlife Research Institute (TAWIRI), P.O. Box 661, Arusha, Tanzania.
authors.forename: Bugwesa Z
authors.initials: BZ
authors.lastname: Katale
authors.affiliation: DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ South African Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa.
authors.forename: Elizabeth M
authors.initials: EM
authors.lastname: Streicher
authors.affiliation: Tanzania Wildlife Research Institute (TAWIRI), P.O. Box 661, Arusha, Tanzania.
authors.forename: Julius D
authors.initials: JD
authors.lastname: Keyyu
authors.affiliation: Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom.
authors.forename: Sharon L
authors.initials: SL
authors.lastname: Kendall
authors.affiliation: The Royal Veterinary College, Royal College Street, London, NW1 0TU, United Kingdom.
authors.forename: Hazel M
authors.initials: HM
authors.lastname: Dockrell
authors.affiliation: Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa.
authors.forename: Anita L
authors.initials: AL
authors.lastname: Michel
authors.affiliation: Southern African Centre for Infectious Disease Surveillance, Sokoine University of Agriculture, Morogoro, Tanzania.
authors.forename: Mark M
authors.initials: MM
authors.lastname: Rweyemamu
authors.affiliation: DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ South African Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa.
authors.forename: Robin M
authors.initials: RM
authors.lastname: Warren
authors.affiliation: Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania.
authors.forename: Mecky I
authors.initials: MI
authors.lastname: Matee
authors.affiliation: DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ South African Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa.
authors.forename: Paul D
authors.initials: PD
authors.lastname: van Helden
authors.affiliation: WHO Supranational TB Reference Laboratory, Tuberculosis & Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Morne Joliviere, BP 484, 97183, Abymes, Guadeloupe.
authors.forename: David
authors.initials: D
authors.lastname: Couvin
authors.affiliation: WHO Supranational TB Reference Laboratory, Tuberculosis & Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Morne Joliviere, BP 484, 97183, Abymes, Guadeloupe.
authors.forename: Nalin
authors.initials: N
authors.lastname: Rastogi
mesh_terms: D000349:Africa; D005798:Genes, Bacterial; D014644:Genetic Variation; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D013636:Tanzania