Molecular epidemiology of Mycobacterium tuberculosis among South African gold miners

Annals of the American Thoracic Society

Volumn 12, Issue 1, 2015, Pages 12-20

  Mathema, Barun ^a,b   Lewis, James J ^c   Connors, Jeremy ^b   Chihota, Violet N ^d,e   Shashkina, Elena ^b   Van Der Meulen, Minty ^d   Graviss, Edward A ^f   Ha, Ngan P ^f   Kreiswirth, Barry N ^b   Grant, Alison D ^c   Fielding, Katherine L ^c   Dorman, Susan E ^g   Churchyard, Gavin J ^c,d,e  

^a Department of Medicine   (United States)

^b PUBLIC HEALTH RESEARCH INSTITUTE   (United States)

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

^d AURUM INSTITUTE   (South Africa)

^e UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^f HOUSTON METHODIST RESEARCH INSTITUTE   (United States)

^g JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Gold mines; Molecular epidemiology; South africa; Tuberculosis

Indexed keywords

ADULT; ARTICLE; BACTERIAL STRAIN; BACTERIAL TRANSMISSION; BACTERIUM CULTURE; BACTERIUM ISOLATE; FEMALE; GENETIC VARIABILITY; GENOTYPE; GOLD MINER; GOLD MINING; HIGH RISK POPULATION; HUMAN; MAJOR CLINICAL STUDY; MALE; MIDDLE AGED; MINER; MINING; MOLECULAR EPIDEMIOLOGY; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RISK FACTOR; SOUTH AFRICAN; YOUNG ADULT; CLINICAL TRIAL; CROSS-SECTIONAL STUDY; GENETICS; INCIDENCE; ISOLATION AND PURIFICATION; MICROBIOLOGY; MULTICENTER STUDY; PROCEDURES; SOUTH AFRICA; TUBERCULOSIS;

BACTERIAL DNA; GOLD;

ADULT; CROSS-SECTIONAL STUDIES; DNA, BACTERIAL; FEMALE; GENOTYPE; GOLD; HUMANS; INCIDENCE; MALE; MINING; MOLECULAR EPIDEMIOLOGY; MYCOBACTERIUM TUBERCULOSIS; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; SOUTH AFRICA; TUBERCULOSIS;

EID: 84922467475     PISSN: 23256621     EISSN: None     Source Type: Journal    
DOI: 10.1513/AnnalsATS.201404-150OC     Document Type: Article

References (49)

1. World Health Organization (WHO). Global tuberculosis control: a short update to the 2009 report. Geneva: WHO; 2009.
2. Corbett EL, Watt CJ, Walker N, Maher D, Williams BG, Raviglione MC, Dye C. The growing burden of tuberculosis: global trends and interactions with the HIV epidemic. Arch Intern Med 2003;163:1009-1021.
3. Lewis JJ, Charalambous S, Day JH, Fielding KL, Grant AD, Hayes RJ, Corbett EL, Churchyard GJ. HIV infection does not affect active case finding of tuberculosis in South African gold miners. Am J Respir Crit Care Med 2009;180:1271-1278.
4. Corbett EL, Churchyard GJ, Clayton TC, Williams BG, Mulder D, Hayes RJ, De Cock KM. HIV infection and silicosis: the impact of two potent risk factors on the incidence of mycobacterial disease in South African miners. AIDS 2000;14:2759-2768.
5. Corbett EL, Churchyard GJ, Charalambos S, Samb B, Moloi V, Clayton TC, Grant AD, Murray J, Hayes RJ, De Cock KM. Morbidity and mortality in South African gold miners: impact of untreated disease due to human immunodeficiency virus. Clin Infect Dis 2002;34:1251-1258.
6. Glynn JR, Murray J, Bester A, Nelson G, Shearer S, Sonnenberg P. Effects of duration of HIV infection and secondary tuberculosis transmission on tuberculosis incidence in the South African gold mines. AIDS 2008;22:1859-1867.
7. Bifani PJ, Mathema B, Liu Z, Moghazeh SL, Shopsin B, Tempalski B, Driscol J, Frothingham R, Musser JM, Alcabes P, et al. Identification of a W variant outbreak of Mycobacterium tuberculosis via population-based molecular epidemiology. JAMA 1999;282:2321-2327.
8. Braden CR, Templeton GL, Stead WW, Bates JH, Cave MD, Valway SE. Retrospective detection of laboratory cross-contamination of Mycobacterium tuberculosis cultures with use of DNA fingerprint analysis. Clin Infect Dis 1997;24:35-40.
9. Mathema B, Bifani PJ, Driscoll J, Steinlein L, Kurepina N, Moghazeh SL, Shashkina E, Marras SA, Campbell S, Mangura B, et al. Identification and evolution of an IS6110 low-copy-number Mycobacterium tuberculosis cluster. J Infect Dis 2002;185:641-649.
10. Caws M, Thwaites G, Dunstan S, Hawn TR, Lan NT, Thuong NT, Stepniewska K, Huyen MN, Bang ND, Loc TH, et al. The influence of host and bacterial genotype on the development of disseminated disease with Mycobacterium tuberculosis. PLoS Pathog 2008;4: e1000034.
11. Godfrey-Faussett P, Sonnenberg P, Shearer SC, Bruce MC, Mee C, Morris L, Murray J. Tuberculosis control and molecular epidemiology in a South African gold-mining community. Lancet 2000;356:1066-1071.
12. Middelkoop K, Bekker LG, Mathema B, Shashkina E, Kurepina N, Whitelaw A, Fallows D, Morrow C, Kreiswirth B, Kaplan G, et al. Molecular epidemiology of Mycobacterium tuberculosis in a South African community with high HIV prevalence. J Infect Dis 2009;200:1207-1211.
13. Sonnenberg P, Murray J, Glynn JR, Shearer S, Kambashi B, Godfrey-Faussett P. HIV-1 and recurrence, relapse, and reinfection of tuberculosis after cure: a cohort study in South African mineworkers. Lancet 2001;358:1687-1693.
14. Streicher EM, Warren RM, Kewley C, Simpson J, Rastogi N, Sola C, van der Spuy GD, van Helden PD, Victor TC. Genotypic and phenotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from rural districts of the Western Cape Province of South Africa. J Clin Microbiol 2004;42:891-894.
15. van Rie A, Warren R, Richardson M, Victor TC, Gie RP, Enarson DA, Beyers N, van Helden PD. Exogenous reinfection as a cause of recurrent tuberculosis after curative treatment. N Engl J Med 1999;341:1174-1179.
16. Churchyard GJ, Fielding KL, Lewis JJ, Coetzee L, Corbett EL, Godfrey-Faussett P, Hayes RJ, Chaisson RE, Grant AD; Thibela TB Study Team. A trial of mass isoniazid preventive therapy for tuberculosis control. N Engl J Med 2014;370:301-310.
17. Chihota VN, Grant AD, Fielding K, Ndibongo B, van Zyl A, Muirhead D, Churchyard GJ. Liquid vs. solid culture for tuberculosis: performance and cost in a resource-constrained setting. Int J Tuberc Lung Dis 2010;14:1024-1031.
18. Kent PT, Kubica GP. Public health mycobacteriology: a guide for the level III laboratory. Atlanta, GA: Centers for Disease Control and Prevention; 1985.
19. van Embden JD, Cave MD, Crawford JT, Dale JW, Eisenach KD, Gicquel B, Hermans P, Martin C, McAdam R, Shinnick TM, et al. Strain identification of Mycobacterium tuberculosis DNA by DNA fingerprinting: recommendations for a standardized methodology. J Clin Microbiol 1993;31:406-409. (see comments).
20. Brudey K, Driscoll JR, Rigouts L, Prodinger WM, Gori A, Al-Hajoj SA, Allix C, Aristimuño L, Arora J, Baumanis V, et al. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol 2006;6:23.
21. Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S, Bunschoten A, Molhuizen H, Shaw R, Goyal M, et al. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol 1997;35:907-914.
22. Gutacker MM, Mathema B, Soini H, Shashkina E, Kreiswirth BN, Graviss EA, Musser JM. Single-nucleotide polymorphism-based population genetic analysis of Mycobacterium tuberculosis strains from 4 geographic sites. J Infect Dis 2006;193:121-128.
23. Small PM, Hopewell PC, Singh SP, Paz A, Parsonnet J, Ruston DC, Schecter GF, Daley CL, Schoolnik GK. The epidemiology of tuberculosis in San Francisco: a population-based study using conventional and molecular methods. N Engl J Med 1994;330:1703-1709. (see comments).
24. Richardson M, van Lill SW, van der Spuy GD, Munch Z, Booysen CN, Beyers N, van Helden PD, Warren RM. Historic and recent events contribute to the disease dynamics of Beijing-like Mycobacterium tuberculosis isolates in a high incidence region. Int J Tuberc Lung Dis 2002;6:1001-1011.
25. Chihota V, Apers L, Mungofa S, Kasongo W, Nyoni IM, Tembwe R, Mbulo G, Tembo M, Streicher EM, van der Spuy GD, et al. Predominance of a single genotype of Mycobacterium tuberculosis in regions of Southern Africa. Int J Tuberc Lung Dis 2007;11:311-318.
26. Gandhi NR, Weissman D, Moodley P, Ramathal M, Elson I, Kreiswirth BN, Mathema B, Shashkina E, Rothenberg R, Moll AP, et al. Nosocomial transmission of extensively drug-resistant tuberculosis in a rural hospital in South Africa. J Infect Dis 2013;207:9-17.
27. Mlambo CK, Warren RM, Poswa X, Victor TC, Duse AG, Marais E. Genotypic diversity of extensively drug-resistant tuberculosis (XDRTB) in South Africa. Int J Tuberc Lung Dis 2008;12:99-104.
28. Nicol MP, Sola C, February B, Rastogi N, Steyn L, Wilkinson RJ. Distribution of strain families of Mycobacterium tuberculosis causing pulmonary and extrapulmonary disease in hospitalized children in Cape Town, South Africa. J Clin Microbiol 2005;43:5779-5781.
29. Warren RM, Victor TC, Streicher EM, Richardson M, van der Spuy GD, Johnson R, Chihota VN, Locht C, Supply P, van Helden PD. Clonal expansion of a globally disseminated lineage of Mycobacterium tuberculosis with low IS6110 copy numbers. J Clin Microbiol 2004; 42:5774-5782.
30. Glynn JR, Crampin AC, Traore H, Chaguluka S, Mwafulirwa DT, Alghamdi S, Ngwira BM, Yates MD, Drobniewski FD, Fine PE. Determinants of cluster size in large, population-based molecular epidemiology study of tuberculosis, northern Malawi. Emerg Infect Dis 2008;14:1060-1066.
31. Verver S, Warren RM, Munch Z, Vynnycky E, van Helden PD, Richardson M, van der Spuy GD, Enarson DA, Borgdorff MW, Behr MA, et al. Transmission of tuberculosis in a high incidence urban community in South Africa. Int J Epidemiol 2004;33:351-357.
32. Rees D, Murray J, Nelson G, Sonnenberg P. Oscillating migration and the epidemics of silicosis, tuberculosis, and HIV infection in South African gold miners. Am J Ind Med 2010;53:398-404.
33. Pillay M, Sturm AW. Evolution of the extensively drug-resistant F15/LAM4/KZN strain of Mycobacterium tuberculosis in KwaZulu-Natal, South Africa. Clin Infect Dis 2007;45:1409-1414.
34. McEvoy CR, Falmer AA, Gey van Pittius NC, Victor TC, van Helden PD, Warren RM. The role of IS6110 in the evolution of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2007;87:393-404.
35. van der Spuy GD, Kremer K, Ndabambi SL, Beyers N, Dunbar R, Marais BJ, van Helden PD, Warren RM. Changing Mycobacterium tuberculosis population highlights clade-specific pathogenic characteristics. Tuberculosis (Edinb) 2009;89:120-125.
36. Victor TC, de Haas PE, Jordaan AM, van der Spuy GD, Richardson M, van Soolingen D, van Helden PD, Warren R. Molecular characteristics and global spread of Mycobacterium tuberculosis with a Western Cape F11 genotype. J Clin Microbiol 2004;42:769-772.
37. Bifani PJ, Mathema B, Kurepina NE, Kreiswirth BN. Global dissemination of the Mycobacterium tuberculosis W-Beijing family strains. Trends Microbiol 2002;10:45-52.
38. Cowley D, Govender D, February B, Wolfe M, Steyn L, Evans J, Wilkinson RJ, Nicol MP. Recent and rapid emergence of W-Beijing strains of Mycobacterium tuberculosis in Cape Town, South Africa. Clin Infect Dis 2008;47:1252-1259.
39. Victor TC, Streicher EM, Kewley C, Jordaan AM, van der Spuy GD, Bosman M, Louw H, Murray M, Young D, van Helden PD, et al. Spread of an emerging Mycobacterium tuberculosis drug-resistant strain in the Western Cape of South Africa. Int J Tuberc Lung Dis 2007;11:195-201.
40. Hu Y, Mathema B, Jiang W, Kreiswirth B, Wang W, Xu B. Transmission pattern of drug-resistant tuberculosis and its implication for tuberculosis control in eastern rural China. PLoS ONE 2011;6:e19548.
41. Murray M, Alland D. Methodological problems in the molecular epidemiology of tuberculosis. Am J Epidemiol 2002;155:565-571.
42. Vynnycky E, Nagelkerke N, Borgdorff MW, van Soolingen D, van Embden JD, Fine PE. The effect of age and study duration on the relationship between 'clustering' of DNA fingerprint patterns and the proportion of tuberculosis disease attributable to recent transmission. Epidemiol Infect 2001;126:43-62.
43. Mathema B, Kurepina NE, Bifani PJ, Kreiswirth BN. Molecular epidemiology of tuberculosis: current insights. Clin Microbiol Rev 2006;19:658-685.
44. Chihota VN, Popane F, Churchyard GJ, Lewis JJ, Fielding KL, Vynnycky E, White RG, Grant AD; Thibela TB Study Team. Community-wide isoniazid preventive therapy among gold miners in South Africa: the Thibela TB study. Presented at the Third South African Tuberculosis Conference. Durban, South Africa; June 12, 2012, Durban, South Africa [accessed 2014 Dec 5]. Available from: http://www.auruminstitute.org/thibela-TB/Thibela-SA-TB-conf-12-06-12.pdf
45. Driver CR, Kreiswirth B, Macaraig M, Clark C, Munsiff SS, Driscoll J, Zhao B. Molecular epidemiology of tuberculosis after declining incidence, New York City, 2001-2003. Epidemiol Infect 2007;135:634-643.
46. Stuckler D, Basu S, McKee M, Lurie M. Mining and risk of tuberculosis in sub-Saharan Africa. Am J Public Health 2011;101:524-530.
47. van Halsema CL, Fielding KL, Chihota VN, Lewis JJ, Churchyard GJ, Grant AD. Trends in drug-resistant tuberculosis in a gold-mining workforce in South Africa, 2002-2008. Int J Tuberc Lung Dis 2012;16:967-973.
48. Nardell E, Churchyard G. What is thwarting tuberculosis prevention in high-burden settings? N Engl J Med 2011;365:79-81.
49. Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med 2011;364:730-739.