Genetic diversity of Mycobacterium tuberculosis isolated from tuberculosis patients in the Serengeti ecosystem in Tanzania

Tuberculosis

Volumn 95, Issue 2, 2015, Pages 170-178

  Mbugi, Erasto V ^a   Katale, Bugwesa Z ^a,c   Siame, Keith K ^b   Keyyu, Julius D ^c   Kendall, Sharon L ^d   Dockrell, Hazel M ^e   Streicher, Elizabeth M ^b   Michel, Anita L ^f   Rweyemamu, Mark M ^g   Warren, Robin M ^b   Matee, Mecky I ^a   Van Helden, Paul D ^b  

^a MUHIMBILI UNIVERSITY OF HEALTH AND ALLIED SCIENCES   (Tanzania)

^b UNIVERSITY OF STELLENBOSCH   (South Africa)

^c TANZANIA WILDLIFE RESEARCH INSTITUTE   (Tanzania)

^d ROYAL VETERINARY COLLEGE   (United Kingdom)

^e LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

^f UNIVERSITY OF PRETORIA   (South Africa)

^g SOKOINE UNIVERSITY OF AGRICULTURE   (Tanzania)

Author keywords

Genotyping; Human animal interface; Mycobacterium tuberculosis; Serengeti ecosystem

Indexed keywords

ADULT; ARTICLE; BACTERIUM CULTURE; COMPARATIVE STUDY; CROSS-SECTIONAL STUDY; DNA EXTRACTION; ECOSYSTEM; GENETIC VARIABILITY; GENOTYPE; HUMAN; MINORITY GROUP; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; SPUTUM CULTURE; TANZANIA; TUBERCULOSIS; VARIABLE NUMBER OF TANDEM REPEAT; AGED; BACTERIAL GENOME; BACTERIUM IDENTIFICATION; CLASSIFICATION; GENETIC VARIATION; GENETICS; INTERSPERSED REPEAT; ISOLATION AND PURIFICATION; MICROBIOLOGY; MIDDLE AGED; PHYLOGENY; PROCEDURES; SPECIMEN HANDLING; SPUTUM; TRANSMISSION; YOUNG ADULT;

ADULT; AGED; BACTERIAL TYPING TECHNIQUES; CROSS-SECTIONAL STUDIES; ECOSYSTEM; GENETIC VARIATION; GENOME, BACTERIAL; GENOTYPE; HUMANS; INTERSPERSED REPETITIVE SEQUENCES; MIDDLE AGED; MINISATELLITE REPEATS; MYCOBACTERIUM TUBERCULOSIS; PHYLOGENY; SPECIMEN HANDLING; SPUTUM; TANZANIA; TUBERCULOSIS; YOUNG ADULT;

EID: 84924974595     PISSN: 14729792     EISSN: 1873281X     Source Type: Journal    
DOI: 10.1016/j.tube.2014.11.006     Document Type: Article

References (36)

1. WHO Global tuberculosis report 2013 World Health Organization Genever, Switzerland WHO/HTM/TB/201311
2. K.Y. Yuen, C.M. Chan, K.S. Chan, W.C. Yam, P.L. Ho, and P.Y. Chau IS6110 based amplityping assay and RFLP fingerprinting of clinical isolates of Mycobacterium tuberculosis J Clin Pathol 48 10 1995 924 928
3. J. Kamerbeek, L. Schouls, A. Kolk, M. van Agterveld, D. Van Soolingen, S. Kuijper, A. Bunschoten, H. Molhuizen, R. Shaw, and M. Goyal Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology J Clin Microbiol 35 4 1997 907 914
4. P. Supply, S. Lesjean, E. Savine, K. Kremer, D. van Soolingen, and C. Locht Automated high-throughput genotyping for study of global epidemiology of Mycobacterium tuberculosis based on mycobacterial interspersed repetitive units J Clin Microbiol 39 10 2001 3563 3571
5. A.C. Schürch, and D. van Soolingen DNA fingerprinting of Mycobacterium tuberculosis: from phage typing to whole-genome sequencing Infect Genet Evol 12 4 2012 602 609
6. C. Demay, B. Liens, T. Burguière, V. Hill, D. Couvin, J. Millet, I. Mokrousov, C. Sola, T. Zozio, and N. Rastogi SITVITWEB - a publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology Infect Genet Evol 12 4 2012 755 766
7. C. Ford, K. Yusim, T. Ioerger, S. Feng, M. Chase, M. Greene, B. Korber, and S. Fortune Mycobacterium tuberculosis - heterogeneity revealed through whole genome sequencing Tuberculosis 92 3 2012 194 201
8. J. Bryant, A. Schurch, H. van Deutekom, S. Harris, J. de Beer, V. de Jager, K. Kremer, S.A.F.T. van Hijum, R. Siezen, and M. Borgdorff Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data BMC Infect Dis 13 1 2013 110
9. J.L. Gardy, J.C. Johnston, S.J.H. Sui, V.J. Cook, L. Shah, E. Brodkin, S. Rempel, R. Moore, Y. Zhao, and R. Holt Whole-genome sequencing and social-network analysis of a tuberculosis outbreak N Eng J Med 364 8 2011 730 739
10. T.M. Walker, L.C. Camilla, R.H. Harrell, J.T. Evans, G. Kapatai, M.J. Dedicoat, D.W. Eyre, D.J. Wilson, P.M. Hawkey, and D.W. Crook Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study Lancet Infect Dis 13 2 2013 137 146
11. S.H. Gillespie, N. Kennedy, F.I. Ngowi, N.G. Fomukong, S. Al-Maamary, and J.W. Dale Restriction fragment length polymorphism analysis of Mycobacterium tuberculosis isolated from patients with pulmonary tuberculosis in northern Tanzania Trans R Soc Trop Med Hyg 89 3 1995 335 338
12. T.D. McHugh, S.L. Batt, R.J. Shorten, R.D. Gosling, L. Uiso, and S.H. Gillespie Mycobacterium tuberculosis lineage: a naming of the parts Tuberculosis 85 3 2005 127 136
13. Z.H. Yang, I. Mtoni, M. Chonde, M. Mwasekaga, K. Fuursted, D.S. Askgård, J. Bennedsen, P.E. de Haas, D. van Soolingen, and J.D. van Embden DNA fingerprinting and phenotyping of Mycobacterium tuberculosis isolates from human immunodeficiency virus (HIV)-seropositive and HIV-seronegative patients in Tanzania J Clin Microbiol 33 5 1995 1064 1069
14. V. Eldholm, M. Matee, S. Mfinanga, M. Heun, and U. Dahle A first insight into the genetic diversity of Mycobacterium tuberculosis in Dar es Salaam, Tanzania, assessed by spoligotyping BMC Microbiol 6 1 2006 76
15. G. Kibiki, B. Mulder, W. Dolmans, J. de Beer, M. Boeree, N. Sam, D. van Soolingen, C. Sola, and A.M. van der Zanden tuberculosis genotypic diversity and drug susceptibility pattern in HIV- infected and non-HIV-infected patients in northern Tanzania BMC Microbiol 7 1 2007 51
16. B. Katale, E. Mbugi, E. Karimuribo, J. Keyyu, S. Kendall, G. Kibiki, P. Godfrey-Faussett, A. Michel, R. Kazwala, and P. van Helden Prevalence and risk factors for infection of bovine tuberculosis in indigenous cattle in the Serengeti ecosystem, Tanzania BMC Vet Res 9 1 2013 267
17. M. Pardini, F. Varaine, E. Iona, E. Arzumanian, F. Checchi, M.R. Oggioni, G. Orefici, and L. Fattorini Cetyl-pyridinium chloride is useful for isolation of Mycobacterium tuberculosis from sputa subjected to long-term storage J Clin Microbiol 43 1 2005 442 444
18. K. Brudey, J. Driscoll, L. Rigouts, W. Prodinger, A. Gori, S. Al-Hajoj, C. Allix, L. Aristimuno, J. Arora, and V. Baumanis Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology BMC Microbiol 6 1 2006 23
19. A. Mihret, Y. Bekele, A.G. Loxton, A.M. Jordan, L. Yamuah, A. Aseffa, R. Howe, and G. Walzl Diversity of Mycobacterium tuberculosis isolates from new pulmonary tuberculosis cases in Addis Ababa, Ethiopia Tuberc Res Treat 2012 2012 1 7
20. C. Mulenga, I. Shamputa, D. Mwakazanga, N. Kapata, F. Portaels, and L. Rigouts Diversity of Mycobacterium tuberculosis genotypes circulating in Ndola, Zambia BMC Infect Dis 10 1 2010 177
21. E.M. Streicher, T.C. Victor, G. van der Spuy, C. Sola, N. Rastogi, P.D. van Helden, and R.M. Warren Spoligotype signatures in the Mycobacterium tuberculosis complex J Clin Microbiol 45 1 2007 237 240
22. I. Vitol, J. Driscoll, B. Kreiswirth, N. Kurepina, and K.P. Bennett Identifying Mycobacterium tuberculosis complex strain families using spoligotypes Infect Genet Evol 6 6 2006 491 504
23. P. Supply, C. Allix, S. Lesjean, M. Cardoso-Oelemann, S. Rüsch-Gerdes, E. Willery, E. Savine, P. de Haas, H. van Deutekom, and S. Roring Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis J Clin Microbiol 44 12 2006 4498 4510
24. T. Weniger, J. Krawczyk, P. Supply, S. Niemann, and D. Harmsen MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria Nucleic Acids Res 38 suppl. 2010 W326 331
25. C. Allix-Béguec, D. Harmsen, T. Weniger, P. Supply, and S. Niemann Evaluation and user-strategy of MIRU-VNTRplus, a multifunctional database for online analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates J Clin Microbiol 46 8 2008 2692 2699
26. A. Mihret, Y. Bekele, M. Aytenew, Y. Assefa, M. Abebe, L. Wassie, G.A. Loxton, L. Yamuah, A. Aseffa, and G. Walzl Modern lineages of Mycobacterium tuberculosis in Addis Ababa, Ethiopia: implications for the tuberculosis control programe Afr Health Sci 12 3 2012 339 344
27. B. Asiimwe, S. Ghebremichael, G. Kallenius, T. Koivula, and M. Joloba Mycobacterium tuberculosis spoligotypes and drug susceptibility pattern of isolates from tuberculosis patients in peri-urban Kampala, Uganda BMC Infect Dis 8 1 2008 101
28. J. Bazira, B. Asiimwe, M. Joloba, F. Bwanga, and M. Matee Mycobacterium tuberculosis spoligotypes and drug susceptibility pattern of isolates from tuberculosis patients in South-Western Uganda BMC Infect Dis 11 1 2011 81
29. J. Bazira, M. Matte, B.B. Asiimwe, and L.M. Joloba Genetic diversity of Mycobacterium tuberculosis in Mbarara, South Western Uganda Afr Health Sci 10 4 2010 306 311
30. B.C. de Jong, M. Antonio, T. Awine, K. Ogungbemi, Y.P. de Jong, S. Gagneux, K. DeRiemer, T. Zozio, N. Rastogi, and M. Borgdorff Use of spoligotyping and large sequence polymorphisms to study the population structure of the Mycobacterium tuberculosis complex in a cohort study of consecutive smear-positive tuberculosis cases in the Gambia J Clin Microbiol 47 4 2009 994 1001
31. Y. Blouin, Y. Hauck, C. Soler, M. Fabre, R. Vong, C. Dehan, G. Cazajous, P.-L. Massoure, P. Kraemer, and A. Jenkins Significance of the identification in the horn of Africa of an exceptionally deep branching Mycobacterium tuberculosis clade PLoS ONE 7 12 2012 e52841
32. S. Gagneux, and P.M. Small Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development Lancet Infect Dis 7 5 2007 328 337
33. S. Godreuil, F. Renaud, M. Choisy, J.J. Depina, E. Garnotel, M. Morillon, P. Van de Perre, and A.L. Bañuls Highly structured genetic diversity of the Mycobacterium tuberculosis population in Djibouti Clin Microbiol Infect 16 7 2009 1023 1026
34. J.R. Glynn, S. Alghamdi, K. Mallard, R. McNerney, R. Ndlovu, L. Munthali, R.M. Houben, P.E.M. Fine, N. French, and A.C. Crampin Changes in Mycobacterium tuberculosis genotype families over 20 years in a population-based study in northern Malawi PLoS ONE 5 8 2010 e12259
35. L.V. Adams, B.N. Kreiswirth, R.D. Arbeit, H. Soini, L. Mtei, M. Matee, M. Bakari, T. Lahey, W. Wieland-Alter, and E. Shashkina Molecular epidemiology of HIV-associated tuberculosis in Dar es Salaam, Tanzania: strain predominance, clustering, and polyclonal disease J Clin Microbiol 50 8 2012 2645 2650
36. H. van Deutekom, P. Supply, P.E.W. de Haas, E. Willery, S.P. Hoijng, C. Locht, R.A. Coutinho, and D. van Soolingen Molecular typing of Mycobacterium tuberculosis by mycobacterial interspersed repetitive unit-variable-number tandem repeat analysis, a more accurate method for identifying epidemiological links between patients with tuberculosis J Clin Microbiol 43 9 2005 4473 4479