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∇

Journal of Clinical Microbiology

Volumn 47, Issue 4, 2009, Pages 994-1001

  De Jong, Bouke C ^a,b   Antonio, Martin ^a   Awine, Timothy ^a   Ogungbemi, Kunle ^a   De Jong, Ype P ^a   Gagneux, Sebastien ^c   Deriemer, Kathryn ^d   Zozio, Thierry ^e   Rastogi, Nalin ^e   Borgdorff, Martien ^f,g   Hill, Philip C ^a   Adegbola, Richard A ^a  

^a MEDICAL RESEARCH COUNCIL LABORATORIES   (Gambia)

^b NEW YORK UNIVERSITY   (United States)

^c NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e Institut Pasteur de Guadeloupe   (Guadeloupe)

^f UNIVERSITY OF AMSTERDAM   (Netherlands)

^g KNCV TUBERCULOSIS FOUNDATION   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIUM ISOLATE; COHORT ANALYSIS; ENDEMIC DISEASE; GAMBIA; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHIC DISTRIBUTION; GUINEA-BISSAU; LARGE SEQUENCE POLYMORPHISM; LUNG TUBERCULOSIS; MOLECULAR EPIDEMIOLOGY; MYCOBACTERIUM AFRICANUM; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; POLYMERASE CHAIN REACTION; POPULATION STRUCTURE; PRIORITY JOURNAL; SENEGAL; SPUTUM SMEAR; ADOLESCENT; ADULT; AGED; BACTERIUM IDENTIFICATION; CLASSIFICATION; CLUSTER ANALYSIS; DNA FINGERPRINTING; FEMALE; GENETICS; HUMAN; ISOLATION AND PURIFICATION; MALE; METHODOLOGY; MICROBIOLOGY; MIDDLE AGED; TUBERCULOSIS;

MYCOBACTERIUM AFRICANUM; MYCOBACTERIUM TUBERCULOSIS; MYCOBACTERIUM TUBERCULOSIS COMPLEX;

BACTERIAL DNA;

ADOLESCENT; ADULT; AGED; AGED, 80 AND OVER; BACTERIAL TYPING TECHNIQUES; CLUSTER ANALYSIS; COHORT STUDIES; DNA FINGERPRINTING; DNA, BACTERIAL; FEMALE; GAMBIA; GENOTYPE; GUINEA-BISSAU; HUMANS; MALE; MIDDLE AGED; MYCOBACTERIUM TUBERCULOSIS; POLYMORPHISM, GENETIC; TUBERCULOSIS; YOUNG ADULT;

EID: 65249155889     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.01216-08     Document Type: Article

References (28)

1. Anonymous. 2004. National Leprosy and Tuberculosis Programme. Annual Report. The Gambia. KNCV Tuberculosis Foundation, The Hague, The Netherlands.
2. Brosch, R., S. V. Gordon, M. Marmiesse, P. Brodin, C. Buchrieser, K. Eiglmeier, T. Garnier, C. Gutierrez, G. Hewinson, K. Kremer, L. M. Parsons, A. S. Pym, S. Samper, D. van Soolingen, and S. T. Cole. 2002. A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc. Natl. Acad. Sci. USA 99:3684-3689.
3. Brudey, K., J. R. Driscoll, L. Rigouts, W. M. Prodinger, A. Gori, S. A. Al-Hajoj, C. Allix, L. Aristimuno, J. Arora, V. Baumanis, L. Binder, P. Cafrune, A. Cataldi, S. Cheong, R. Diel, C. Ellermeier, J. T. Evans, M. Fauville-Dufaux, S. Ferdinand, D. Garcia de Viedma, C. Garzelli, L. Gaz-zola, H. M. Gomes, M. C. Guttierez, P. M. Hawkey, P. D. van Helden, G. V. Kadival, B. N. Kreiswirth, K. Kremer, M. Kubin, S. P. Kulkarni, B. Liens, T. Lillebaek, M. L. Ho, C. Martin, I. Mokrousov, O. Narvskaia, Y. F. Ngeow, L. Naumann, S. Niemann, I. Parwati, Z. Rahim, V. Rasolofo-Razanam-parany, T. Rasolonavalona, M. L. Rossetti, S. Rusch-Gerdes, A. Sajduda, S. Samper, I. G. Shemyakin, U. B. Singh, A. Somoskovi, R. A. Skuce, D. van Soolingen, E. M. Streicher, P. N. Suffys, E. Tortoli, T. Tracevska, V. Vincent, T. C. Victor, R. M. Warren, S. F. Yap, K. Zaman, F. Portaels, N. Rastogi, and C. Sola. 2006. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol. 6:23.
4. Corbett, E. L., C. J. Watt, N. Walker, D. Maher, B. G. Williams, M. C. Raviglione, and C. Dye. 2003. The growing burden of tuberculosis: global trends and interactions with the HIV epidemic. Arch. Intern. Med. 163: 1009-1021.
5. de Jong, B. C., P. C. Hill, A. Aiken, D. J. Jeffries, A. Onipede, P. M. Small, R. A. Adegbola, and T. P. Corrah. 2007. Clinical presentation and outcome of tuberculosis patients infected by M. africanum versus M. tuberculosis. Int. J. Tuberc. Lung Dis. 11:450-456.
6. de Jong, B. C., P. C. Hill, R. H. Brookes, S. Gagneux, D. J. Jeffries, J. K. Otu, S. A. Donkor, A. Fox, K. P. McAdam, P. M. Small, and R. A. Adegbola. 2006. Mycobacterium africanum elicits an attenuated T cell response to early secreted antigenic target, 6 kDa, in patients with tuberculosis and their household contacts. J. Infect. Dis. 193:1279-1286.
7. de Jong, B. C., P. C. Hill, R. H. Brookes, J. K. Otu, K. L. Peterson, P. M. Small, and R. A. Adegbola. 2005. Mycobacterium africanum: a new opportunistic pathogen in HIV infection? AIDS 19:1714-1715.
8. Desmond, E., A. T. Ahmed, W. S. Probert, J. Ely, Y. Jang, C. A. Sanders, S. Y. Lin, and J. Flood. 2004. Mycobacterium africanum cases, California. Emerg. Infect. Dis. 10:921-923.
9. Diop, S., D. de Medeiros, G. de Medeiros, R. Baylet, and M. Sankale. 1976. Incidence and geographic distribution of Mycobacterium africanum in Senegal. Bull. Soc. Med. Afr. Noire Lang Fr. 21:50-56. (In French.)
10. Gagneux, S., K. DeRiemer, T. Van, M. Kato-Maeda, B. C. de Jong, S. Narayanan, M. Nicol, S. Niemann, K. Kremer, M. C. Gutierrez, M. Hilty, P. C. Hopewell, and P. M. Small. 2006. Variable host-pathogen compatibility in Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 103:2869-2873.
11. Gagneux, S., and P. M. Small. 2007. Global phylogeography of Mycobacte-rium tuberculosis and implications for tuberculosis product development. Lancet Infect. Dis. 7:328-337.
12. Hershberg, R., M. Lipatov, P. M. Small, H. Sheffer, S. Niemann, S. Ho-molka, J. C. Roach, K. Kremer, D. A. Petrov, M. W. Feldman, and S. Gagneux. 2008. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol. 6:e311.
13. Huard, R. C., L. C. de Oliveira Lazzarini, W. R. Butler, D. van Soolingen, and J. L. Ho. 2003. PCR-based method to differentiate the subspecies of the Mycobacterium tuberculosis complex on the basis of genomic deletions. J. Clin. Microbiol. 41:1637-1650.
14. Hunter, P. R., and M. A. Gaston. 1988. Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J. Clin. Microbiol. 26:2465-2466.
15. Kallenius, G., T. Koivula, S. Ghebremichael, S. E. Hoffner, R. Norberg, E. Svensson, F. Dias, B. I. Marklund, and S. B. Svenson. 1999. Evolution and clonal traits of Mycobacterium tuberculosis complex in Guinea-Bissau. J. Clin. Microbiol. 37:3872-3878.
16. Kamerbeek, J., L. Schouls, A. Kolk, M. van Agterveld, D. van Soolingen, S. Kuijper, A. Bunschoten, H. Molhuizen, R. Shaw, M. Goyal, and J. van Embden. 1997. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J. Clin. Microbiol. 35:907-914.
17. Marmiesse, M., P. Brodin, C. Buchrieser, C. Gutierrez, N. Simoes, V. Vincent, P. Glaser, S. T. Cole, and R. Brosch. 2004. Macro-array and bioinfor-matic analyses reveal mycobacterial 'core' genes, variation in the ESAT-6 gene family and new phylogenetic markers for the Mycobacterium tuberculosis complex. Microbiology 150:483-496.
18. Mostowy, S., A. Onipede, S. Gagneux, S. Niemann, K. Kremer, E. P. Desmond, M. Kato-Maeda, and M. Behr. 2004. Genomic analysis distinguishes Mycobacterium africanum. J. Clin. Microbiol. 42:3594-3599.
19. Niobe-Eyangoh, S. N., C. Kuaban, P. Sorlin, P. Cunin, J. Thonnon, C. Sola, N. Rastogi, V. Vincent, and M. C. Gutierrez. 2003. Genetic biodiversity of Mycobacterium tuberculosis complex strains from patients with pulmonary tuberculosis in Cameroon. J. Clin. Microbiol. 41:2547-2553.
20. Niobe-Eyangoh, S. N., C. Kuaban, P. Sorlin, J. Thonnon, V. Vincent, and M. C. Gutierrez. 2004. Molecular characteristics of strains of the Cameroon family, the major group of Mycobacterium tuberculosis in a country with a high prevalence of tuberculosis. J. Clin. Microbiol. 42:5029-5035.
21. Small, P. M., P. C. Hopewell, S. P. Singh, A. Paz, J. Parsonnet, D. C. Ruston, G. F. Schecter, C. L. Daley, and G. K. Schoolnik. 1994. The epidemiology of tuberculosis in San Francisco. A population-based study using conventional and molecular methods. N. Engl. J. Med. 330:1703-1709.
22. Sola, C., N. Rastogi, M. C. Gutierrez, V. Vincent, R. Brosch, and L. Parsons. 2003. Is Mycobacterium africanum subtype II (Uganda I and Uganda II) a genetically well-defined subspecies of the Mycobacterium tuberculosis complex? J. Clin. Microbiol. 41:1345-1346. (Author reply, 41:1346-1348.)
23. Tanaka, M. M., and A. R. Francis. 2006. Detecting emerging strains of tuberculosis by using spoligotypes. Proc. Natl. Acad. Sci. USA 103:1526615271.
24. Tsolaki, A. G., A. E. Hirsh, K. DeRiemer, J. A. Enciso, M. Z. Wong, M. Hannan, Y. O. Goguet de la Salmoniere, K. Aman, M. Kato-Maeda, and P. M. Small. 2004. Functional and evolutionary genomics of Mycobacterium tuberculosis: insights from genomic deletions in 100 strains. Proc. Natl. Acad. Sci. USA 101:4865-4870.
25. van Embden, J. D., M. D. Cave, J. T. Crawford, J. W. Dale, K. D. Eisenach, B. Gicquel, P. Hermans, C. Martin, R. McAdam, T. M. Shinnick, et al. 1993. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J. Clin. Microbiol. 31: 406-409.
26. Verver, S., R. M. Warren, Z. Munch, M. Richardson, G. D. van der Spuy, M. W. Borgdorff, M. A. Behr, N. Beyers, and P. D. van Helden. 2004. Proportion of tuberculosis transmission that takes place in households in a high-incidence area. Lancet 363:212-214.
27. Voskuil, M. I., D. Schnappinger, K. C. Visconti, M. I. Harrell, G. M. Dol-ganov, D. R. Sherman, and G. K. Schoolnik. 2003. Inhibition of respiration by nitric oxide induces a Mycobacterium tuberculosis dormancy program. J. Exp. Med. 198:705-713.
28. Zink, A. R., C. Sola, U. Reischl, W. Grabner, N. Rastogi, H. Wolf, and A. G. Nerlich. 2003. Characterization of Mycobacterium tuberculosis complex DNAs from Egyptian mummies by spoligotyping. J. Clin. Microbiol. 41:359367.