title: Genetic diversity of Mycobacterium tuberculosis isolated from tuberculosis patients in the Serengeti ecosystem in Tanzania.
abstract: This study was part of a larger cross-sectional survey that was evaluating tuberculosis (TB) infection in humans, livestock and wildlife in the Serengeti ecosystem in Tanzania. The study aimed at evaluating the genetic diversity of Mycobacterium tuberculosis isolates from TB patients attending health facilities in the Serengeti ecosystem. DNA was extracted from 214 sputum cultures obtained from consecutively enrolled newly diagnosed untreated TB patients aged ≥18 years. Spacer oligonucleotide typing (spoligotyping) and Mycobacterium Interspersed Repetitive Units and Variable Number Tandem Repeat (MIRU-VNTR) were used to genotype M. tuberculosis to establish the circulating lineages. Of the214 M. tuberculosis isolates genotyped, 55 (25.7%) belonged to the Central Asian (CAS) family, 52 (24.3%) were T family (an ill-defined family), 38 (17.8%) belonged to the Latin American Mediterranean (LAM) family, 25 (11.7%) to the East-African Indian (EAI) family, 25 (11.7%) comprised of different unassigned ('Serengeti') strain families, while 8 (3.7%) belonged to the Beijing family. A minority group that included Haarlem, X, U and S altogether accounted for 11 (5.2%) of all genotypes. MIRU-VNTR typing produced diverse patterns within and between families indicative of unlinked transmission chains. We conclude that, in the Serengeti ecosystem only a few successful families predominate namely CAS, T, LAM and EAI families. Other types found in lower prevalence are Beijing, Haarlem, X, S and MANU. The Haarlem, EAI_Somalia, LAM3 and S/convergent and X2 subfamilies found in this study were not reported in previous studies in Tanzania.
authors.affiliation: Department of Biochemistry, Muhimbili University of Health and Allied Sciences, P. O. Box 65001 Dar es Salaam, Tanzania; Departments of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001 Dar es Salaam, Tanzania. Electronic address: rerasto@yahoo.com.
authors.forename: Erasto V
authors.initials: EV
authors.lastname: Mbugi
authors.affiliation: Departments 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. Electronic address: bugwesa2002@yahoo.co.uk.
authors.forename: Bugwesa Z
authors.initials: BZ
authors.lastname: Katale
authors.affiliation: DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P. O. Box 19063, Tygerberg, 7505, South Africa. Electronic address: kksiame@sun.ac.za.
authors.forename: Keith K
authors.initials: KK
authors.lastname: Siame
authors.affiliation: Tanzania Wildlife Research Institute (TAWIRI), P.O. Box 661, Arusha, Tanzania. Electronic address: julius.keyyu@gmail.com.
authors.forename: Julius D
authors.initials: JD
authors.lastname: Keyyu
authors.affiliation: The Royal Veterinary College, Royal College Street, London, NW1 0TU, United Kingdom. Electronic address: skendall@rvc.ac.uk.
authors.forename: Sharon L
authors.initials: SL
authors.lastname: Kendall
authors.affiliation: Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom. Electronic address: hazel.dockrell@lshtm.ac.uk.
authors.forename: Hazel M
authors.initials: HM
authors.lastname: Dockrell
authors.affiliation: DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P. O. Box 19063, Tygerberg, 7505, South Africa. Electronic address: lizma@sun.ac.za.
authors.forename: Elizabeth M
authors.initials: EM
authors.lastname: Streicher
authors.affiliation: Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, South Africa. Electronic address: Anita.Michel@up.ac.za.
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. Electronic address: mark.rweyemamu@sacids.org.
authors.forename: Mark M
authors.initials: MM
authors.lastname: Rweyemamu
authors.affiliation: DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P. O. Box 19063, Tygerberg, 7505, South Africa. Electronic address: rw1@sun.ac.za.
authors.forename: Robin M
authors.initials: RM
authors.lastname: Warren
authors.affiliation: Departments of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001 Dar es Salaam, Tanzania. Electronic address: mateemecky@yahoo.com.
authors.forename: Mecky I
authors.initials: MI
authors.lastname: Matee
authors.affiliation: DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ Medical Research Council (MRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P. O. Box 19063, Tygerberg, 7505, South Africa. Electronic address: pvh@sun.ac.za.
authors.forename: Paul D
authors.initials: PD
authors.lastname: van Helden
mesh_terms: D000328:Adult; D000368:Aged; D015373:Bacterial Typing Techniques; D003430:Cross-Sectional Studies; D017753:Ecosystem; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D020071:Interspersed Repetitive Sequences / Q000235:genetics; D008875:Middle Aged; D018598:Minisatellite Repeats / Q000235:genetics; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D010802:Phylogeny; D013048:Specimen Handling / Q000379:methods; D013183:Sputum / Q000382:microbiology; D013636:Tanzania / Q000453:epidemiology; D014376:Tuberculosis / Q000453:epidemiology / Q000382:microbiology* / Q000635:transmission; D055815:Young Adult
keywords: Genotyping; Human–animal interface; Mycobacterium tuberculosis; Serengeti ecosystem