Skip to main content
Top
Published in: BMC Infectious Diseases 1/2008

Open Access 01-12-2008 | Research article

Use of cluster-graphs from spoligotyping data to study genotype similarities and a comparison of three indices to quantify recent tuberculosis transmission among culture positive cases in French Guiana during a eight year period

Authors: Vanina Guernier, Christophe Sola, Karine Brudey, Jean-François Guégan, Nalin Rastogi

Published in: BMC Infectious Diseases | Issue 1/2008

Login to get access

Abstract

Background

French Guiana has the highest tuberculosis (TB) burden among all French departments, with a strong increase in the TB incidence over the last few years. It is now uncertain how best to explain this incidence. The objective of this study was to compare three different methods evaluating the extent of recent TB transmission in French Guiana.

Methods

We conducted a population-based molecular epidemiology study of tuberculosis in French Guiana based on culture-positive TB strains (1996 to 2003, n = 344) to define molecular relatedness between isolates, i.e. potential transmission events. Phylogenetic relationships were inferred by comparing two methods: a "cluster-graph" method based on spoligotyping results, and a minimum spanning tree method based on both spoligotyping and variable number of tandem DNA repeats (VNTR). Furthermore, three indices attempting to reflect the extent of recent TB transmission (RTIn, RTIn-1 and TMI) were compared.

Results

Molecular analyses showed a total amount of 120 different spoligotyping patterns and 273 clinical isolates (79.4%) that were grouped in 49 clusters. The comparison of spoligotypes from French Guiana with an international spoligotype database (SpolDB4) showed that the majority of isolates belonged to major clades of M. tuberculosis (Haarlem, 22.6%; Latin American-Mediterranean, 23.3%; and T, 32.6%). Indices designed to quantify transmission of tuberculosis gave the following values: RTIn = 0.794, RTIn-1 = 0.651, and TMI = 0.146.

Conclusion

Our data showed a high number of Mycobacterium tuberculosis clusters, suggesting a high level of recent TB transmission, nonetheless an estimation of transmission rate taking into account cluster size and mutation rate of genetic markers showed a low ongoing transmission rate (14.6%). Our results indicate an endemic mode of TB transmission in French Guiana, with both resurgence of old spatially restricted genotypes, and a significant importation of new TB genotypes by migration of TB infected persons from neighgouring high-incidence countries.
Appendix
Available only for authorised users
Literature
1.
go back to reference Hopewell PC: Tuberculosis control: how the world has changed since 1990. Bulletin of the World Health Organization. 2002, 80 (6): 427-PubMedPubMedCentral Hopewell PC: Tuberculosis control: how the world has changed since 1990. Bulletin of the World Health Organization. 2002, 80 (6): 427-PubMedPubMedCentral
2.
go back to reference Barnes PF, El-Hajj H, Preston-Martin S, Cave MD, Jones BE, Otaya M, Pogoda J, Eisenach KD: Transmission of tuberculosis among the urban homeless. JAMA. 1996, 275: 305-307. 10.1001/jama.275.4.305.CrossRefPubMed Barnes PF, El-Hajj H, Preston-Martin S, Cave MD, Jones BE, Otaya M, Pogoda J, Eisenach KD: Transmission of tuberculosis among the urban homeless. JAMA. 1996, 275: 305-307. 10.1001/jama.275.4.305.CrossRefPubMed
3.
go back to reference Lukacs J, Tubak V, Mester J, David S, Bartfai Z, Kubica T, Niemann S, Somoskovi A: Conventional and Molecular Epidemiology of Tuberculosis in Homeless Patients in Budapest, Hungary. J Clin Microbiol. 2004, 42 (12): 5931-5934. 10.1128/JCM.42.12.5931-5934.2004.CrossRefPubMedPubMedCentral Lukacs J, Tubak V, Mester J, David S, Bartfai Z, Kubica T, Niemann S, Somoskovi A: Conventional and Molecular Epidemiology of Tuberculosis in Homeless Patients in Budapest, Hungary. J Clin Microbiol. 2004, 42 (12): 5931-5934. 10.1128/JCM.42.12.5931-5934.2004.CrossRefPubMedPubMedCentral
4.
go back to reference Reichler MR, Bur S, Reves R, Mangura B, Thompson V, Ford J, Castro KG: Results of testing for human immunodeficiency virus infection among recent contacts of infectious tuberculosis cases in the United States. Int J Tuberc Lung Dis. 2003, 7 (12 Suppl 3): S471-8.PubMed Reichler MR, Bur S, Reves R, Mangura B, Thompson V, Ford J, Castro KG: Results of testing for human immunodeficiency virus infection among recent contacts of infectious tuberculosis cases in the United States. Int J Tuberc Lung Dis. 2003, 7 (12 Suppl 3): S471-8.PubMed
5.
go back to reference Schaaf HS, Krook S, Hollemans DW, Warren RM, Donald PR, Hesseling AC: Recurrent culture-confirmed tuberculosis in human immunodeficiency virus-infected children. Pediatr Infect Dis J. 2005, 24 (8): 685-691. 10.1097/01.inf.0000172933.22481.36.CrossRefPubMed Schaaf HS, Krook S, Hollemans DW, Warren RM, Donald PR, Hesseling AC: Recurrent culture-confirmed tuberculosis in human immunodeficiency virus-infected children. Pediatr Infect Dis J. 2005, 24 (8): 685-691. 10.1097/01.inf.0000172933.22481.36.CrossRefPubMed
6.
go back to reference Monot M, Honore N, Garnier T, Araoz R, Coppée JY, Lacroix C, Sow S, Spencer JS, Truman RW, Williams DL, Gelber R, Virmond M, Flageul B, Cho S-N, Ji B, Paniz-Mondolfi A, Convit J, Young S, Fine PE, Rasolofo V, Brennan PJ, Cole ST: On the origin of leprosy. Science. 2005, 308 (5724): 1040-1042. 10.1126/science/1109759.CrossRefPubMed Monot M, Honore N, Garnier T, Araoz R, Coppée JY, Lacroix C, Sow S, Spencer JS, Truman RW, Williams DL, Gelber R, Virmond M, Flageul B, Cho S-N, Ji B, Paniz-Mondolfi A, Convit J, Young S, Fine PE, Rasolofo V, Brennan PJ, Cole ST: On the origin of leprosy. Science. 2005, 308 (5724): 1040-1042. 10.1126/science/1109759.CrossRefPubMed
7.
go back to reference Small P, Behr M: Molecular fingerprinting of Mycobacterium tuberculosis: how can it help the clinician?. Clinical Infectious Diseases. 1997, 25: 806-810. 10.1086/515550.CrossRefPubMed Small P, Behr M: Molecular fingerprinting of Mycobacterium tuberculosis: how can it help the clinician?. Clinical Infectious Diseases. 1997, 25: 806-810. 10.1086/515550.CrossRefPubMed
8.
go back to reference Crawford JT, Braden CR, Schable BA, Onorato IM: National Tuberculosis Genotyping and Surveillance Network: design and methods. Emerg Infect Dis. 2002, 8 (11): 1192-1196.CrossRefPubMedPubMedCentral Crawford JT, Braden CR, Schable BA, Onorato IM: National Tuberculosis Genotyping and Surveillance Network: design and methods. Emerg Infect Dis. 2002, 8 (11): 1192-1196.CrossRefPubMedPubMedCentral
9.
go back to reference Moström P, Gordon M, Sola C, Ridell M, Rastogi N: Methods used in the molecular epidemiology of tuberculosis. Clin Microbiol Infect. 2002, 8 (11): 694-704. 10.1046/j.1469-0691.2002.00460.x.CrossRefPubMed Moström P, Gordon M, Sola C, Ridell M, Rastogi N: Methods used in the molecular epidemiology of tuberculosis. Clin Microbiol Infect. 2002, 8 (11): 694-704. 10.1046/j.1469-0691.2002.00460.x.CrossRefPubMed
10.
go back to reference Alland D, Kalkut G, Moss A, McAdam R, Hahn JA, Bosworth W, Drucker E, Bloom BR: Transmission of tuberculosis in New York City. An analysis by DNA fingerprinting and conventional epidemiologic methods. N Engl J Med. 1994, 330 (24): 1710-1716. 10.1056/NEJM199406163302403.CrossRefPubMed Alland D, Kalkut G, Moss A, McAdam R, Hahn JA, Bosworth W, Drucker E, Bloom BR: Transmission of tuberculosis in New York City. An analysis by DNA fingerprinting and conventional epidemiologic methods. N Engl J Med. 1994, 330 (24): 1710-1716. 10.1056/NEJM199406163302403.CrossRefPubMed
11.
go back to reference 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. 10.1056/NEJM199406163302402.CrossRefPubMed 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. 10.1056/NEJM199406163302402.CrossRefPubMed
12.
go back to reference Seidler A, Nienhaus A, Diel R: The transmission of tuberculosis in the light of new molecular biological approaches. Occup Environ Med. 2004, 61 (2): 96-102. 10.1136/oem.2003.008573.CrossRefPubMedPubMedCentral Seidler A, Nienhaus A, Diel R: The transmission of tuberculosis in the light of new molecular biological approaches. Occup Environ Med. 2004, 61 (2): 96-102. 10.1136/oem.2003.008573.CrossRefPubMedPubMedCentral
13.
go back to reference Kulaga S, Behr MA, Schwartzman K: Genetic fingerprinting in the study of tuberculosis transmission. CMAJ. 1999, 161 (9): 1165-1169.PubMedPubMedCentral Kulaga S, Behr MA, Schwartzman K: Genetic fingerprinting in the study of tuberculosis transmission. CMAJ. 1999, 161 (9): 1165-1169.PubMedPubMedCentral
14.
go back to reference Tanaka MM, Francis AR: Methods of quantifying and visualising outbreaks of tuberculosis using genotypic information. Infect Genet Evol. 2005, 5 (1): 35-43. 10.1016/j.meegid.2004.06.001.CrossRefPubMed Tanaka MM, Francis AR: Methods of quantifying and visualising outbreaks of tuberculosis using genotypic information. Infect Genet Evol. 2005, 5 (1): 35-43. 10.1016/j.meegid.2004.06.001.CrossRefPubMed
15.
go back to reference Guernier V, Guegan JF, Deparis X: An evaluation of the actual incidence of tuberculosis in French Guiana using a capture-recapture model. Microbes Infect. 2006, 8 (3): 721-727. 10.1016/j.micinf.2005.09.009.CrossRefPubMed Guernier V, Guegan JF, Deparis X: An evaluation of the actual incidence of tuberculosis in French Guiana using a capture-recapture model. Microbes Infect. 2006, 8 (3): 721-727. 10.1016/j.micinf.2005.09.009.CrossRefPubMed
16.
go back to reference Filliol I, Ferdinand S, Negroni L, Sola C, Rastogi N: Molecular typing of Mycobacterium tuberculosis based on variable number of tandem DNA repeats used alone and in association with spoligotyping. J Clin Microbiol. 2000, 38 (7): 2520-2524.PubMedPubMedCentral Filliol I, Ferdinand S, Negroni L, Sola C, Rastogi N: Molecular typing of Mycobacterium tuberculosis based on variable number of tandem DNA repeats used alone and in association with spoligotyping. J Clin Microbiol. 2000, 38 (7): 2520-2524.PubMedPubMedCentral
17.
go back to reference Sola C, Filliol I, Legrand E, Lesjean S, Locht C, Supply P, Rastogi N: Genotyping of the Mycobacterium tuberculosis complex using MIRUs: association with VNTR and spoligotyping for molecular epidemiology and evolutionary genetics. Infect Genet Evol. 2003, 3 (2): 125-133. 10.1016/S1567-1348(03)00011-X.CrossRefPubMed Sola C, Filliol I, Legrand E, Lesjean S, Locht C, Supply P, Rastogi N: Genotyping of the Mycobacterium tuberculosis complex using MIRUs: association with VNTR and spoligotyping for molecular epidemiology and evolutionary genetics. Infect Genet Evol. 2003, 3 (2): 125-133. 10.1016/S1567-1348(03)00011-X.CrossRefPubMed
18.
go back to reference Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rüsch-Gerdes S, Willery E, Savine E, de Haas P, van Deutekom H, Roring S, Bifani P, Kurepina N, Kreiswirth B, Sola C, Rastogi N, Vatin V, Gutierrez MC, Fauville M, Niemann S, Skuce R, Kremer K, Locht C, van Soolingen D: Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol. 2006, 44 (12): 4498-4510. 10.1128/JCM.01392-06.CrossRefPubMedPubMedCentral Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rüsch-Gerdes S, Willery E, Savine E, de Haas P, van Deutekom H, Roring S, Bifani P, Kurepina N, Kreiswirth B, Sola C, Rastogi N, Vatin V, Gutierrez MC, Fauville M, Niemann S, Skuce R, Kremer K, Locht C, van Soolingen D: Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol. 2006, 44 (12): 4498-4510. 10.1128/JCM.01392-06.CrossRefPubMedPubMedCentral
19.
go back to reference van Soolingen D, de Haas PE, Hermans PWM, van Embden JDA: DNA fingerprinting of Mycobacterium tuberculosis. Methods Enzymol. 1994, 235: 196-205.CrossRefPubMed van Soolingen D, de Haas PE, Hermans PWM, van Embden JDA: DNA fingerprinting of Mycobacterium tuberculosis. Methods Enzymol. 1994, 235: 196-205.CrossRefPubMed
20.
go back to reference Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S, Bunschoten A, Molhuizen H, Shaw R, Goyal M, van Embden J: Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol. 1997, 35: 907-914.PubMedPubMedCentral Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S, Bunschoten A, Molhuizen H, Shaw R, Goyal M, van Embden J: Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol. 1997, 35: 907-914.PubMedPubMedCentral
21.
go back to reference Goguet de la Salmoniere YO, Li HM, Torrea G, Bunschoten A, van Embden J, Gicquel B: Evaluation of spoligotyping in a study of the transmission of Mycobacterium tuberculosis. J Clin Microbiol. 1997, 35: 2210-2214.PubMedPubMedCentral Goguet de la Salmoniere YO, Li HM, Torrea G, Bunschoten A, van Embden J, Gicquel B: Evaluation of spoligotyping in a study of the transmission of Mycobacterium tuberculosis. J Clin Microbiol. 1997, 35: 2210-2214.PubMedPubMedCentral
22.
go back to reference Brudey K, Filliol I, Ferdinand S, Guernier V, Duval P, Maubert P, Sola S, Rastogi N: Long-term population-based genotyping study of Mycobacterium tuberculosis complex isolates in the French Departments of the Americas. J Clin Microbiol. 2006, 44 (1): 183-191. 10.1128/JCM.44.1.183-191.2006.CrossRefPubMedPubMedCentral Brudey K, Filliol I, Ferdinand S, Guernier V, Duval P, Maubert P, Sola S, Rastogi N: Long-term population-based genotyping study of Mycobacterium tuberculosis complex isolates in the French Departments of the Americas. J Clin Microbiol. 2006, 44 (1): 183-191. 10.1128/JCM.44.1.183-191.2006.CrossRefPubMedPubMedCentral
23.
go back to reference Frothingham R, Meeker-O'Connell WA: Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats. Microbiology. 1998, 144: 1189-1196.CrossRefPubMed Frothingham R, Meeker-O'Connell WA: Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats. Microbiology. 1998, 144: 1189-1196.CrossRefPubMed
24.
go back to reference Brudey K, Driscoll JR, Rigouts L, Prodinger WM, Gori A, Al-Hajoj SA, Allix C, Aristimuño L, Arora J, Baumanis V, Binder L, Cafrune P, Cataldi A, Cheong S, Diel R, Ellermeier C, Evans JT, Fauville-Dufaux M, Ferdinand S, Garcia de Viedma D, Garzelli C, Gazzola L, Gomes HM, Guttierez MC, Hawkey PM, van Helden PD, Kadival GV, Kreiswirth BN, Kremer K, Kubin M, Kulkarni SP, Liens B, Lillebaek T, Ho ML, Martin C, Martin C, Mokrousov I, Narvskaïa O, Ngeow YF, Naumann L, Niemann S, Parwati I, Rahim Z, Rasolofo-Razanamparany V, Rasolonavalona T, Rossetti ML, Rüsch-Gerdes S, Sajduda A, Samper S, Shemyakin IG, Singh UB, Somoskovi A, Skuce RA, van Soolingen D, Streicher EM, Suffys PN, Tortoli E, Tracevska T, Vincent V, Victor TC, Warren RM, Yap SF, Zaman K, Portaels F, Rastogi N, Sola C: Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics, and epidemiology. BMC Microbiol. 2006, 6: 23-10.1186/1471-2180-6-23.CrossRefPubMedPubMedCentral Brudey K, Driscoll JR, Rigouts L, Prodinger WM, Gori A, Al-Hajoj SA, Allix C, Aristimuño L, Arora J, Baumanis V, Binder L, Cafrune P, Cataldi A, Cheong S, Diel R, Ellermeier C, Evans JT, Fauville-Dufaux M, Ferdinand S, Garcia de Viedma D, Garzelli C, Gazzola L, Gomes HM, Guttierez MC, Hawkey PM, van Helden PD, Kadival GV, Kreiswirth BN, Kremer K, Kubin M, Kulkarni SP, Liens B, Lillebaek T, Ho ML, Martin C, Martin C, Mokrousov I, Narvskaïa O, Ngeow YF, Naumann L, Niemann S, Parwati I, Rahim Z, Rasolofo-Razanamparany V, Rasolonavalona T, Rossetti ML, Rüsch-Gerdes S, Sajduda A, Samper S, Shemyakin IG, Singh UB, Somoskovi A, Skuce RA, van Soolingen D, Streicher EM, Suffys PN, Tortoli E, Tracevska T, Vincent V, Victor TC, Warren RM, Yap SF, Zaman K, Portaels F, Rastogi N, Sola C: Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics, and epidemiology. BMC Microbiol. 2006, 6: 23-10.1186/1471-2180-6-23.CrossRefPubMedPubMedCentral
25.
go back to reference Enright AJ, Ouzounis CA: BioLayout – an automatic graph layout algorithm for similarity visualization. Bioinformatics. 2001, 17 (9): 853-854. 10.1093/bioinformatics/17.9.853.CrossRefPubMed Enright AJ, Ouzounis CA: BioLayout – an automatic graph layout algorithm for similarity visualization. Bioinformatics. 2001, 17 (9): 853-854. 10.1093/bioinformatics/17.9.853.CrossRefPubMed
26.
go back to reference Goldovsky L, Cases I, Enright AJ, Ouzounis CA: BioLayoutJava: versatile network visualisation of structural and functional relationships. Applied Bioinformatics. 2005, 4 (1): 71-74. 10.2165/00822942-200504010-00009.CrossRefPubMed Goldovsky L, Cases I, Enright AJ, Ouzounis CA: BioLayoutJava: versatile network visualisation of structural and functional relationships. Applied Bioinformatics. 2005, 4 (1): 71-74. 10.2165/00822942-200504010-00009.CrossRefPubMed
27.
go back to reference Glynn JR, Vynnycky E, Fine PE: Influence of sampling on estimates of clustering and recent transmission of Mycobacterium tuberculosis derived from DNA fingerprinting techniques. Am J Epidemiol. 1999, 149: 366-371.CrossRefPubMed Glynn JR, Vynnycky E, Fine PE: Influence of sampling on estimates of clustering and recent transmission of Mycobacterium tuberculosis derived from DNA fingerprinting techniques. Am J Epidemiol. 1999, 149: 366-371.CrossRefPubMed
29.
go back to reference Rosenberg NA, Tsolaki AG, Tanaka MM: Estimating change rates of genetic markers using serial samples: applications to the transposon IS 611O in Mycobacterium tuberculosis. Theor Popul Biol. 2003, 63 (4): 347-363. 10.1016/S0040-5809(03)00010-8.CrossRefPubMed Rosenberg NA, Tsolaki AG, Tanaka MM: Estimating change rates of genetic markers using serial samples: applications to the transposon IS 611O in Mycobacterium tuberculosis. Theor Popul Biol. 2003, 63 (4): 347-363. 10.1016/S0040-5809(03)00010-8.CrossRefPubMed
30.
go back to reference Filliol I, Driscoll JR, van Soolingen D, Kreiswirth BN, Kremer K, Valétudie G, Dang DA, Barlow R, Banerjee D, Bifani PJ, Brudey K, Cataldi A, Cooksey RC, Cousins DV, Dale JW, Dellagostin OA, Drobniewski F, Engelmann G, Ferdinand S, Gascoyne-Binzi D, Gordon M, Gutierrez MC, Haas WH, Heersma H, Kassa-Kelembho E, Ho ML, Makristathis A, Mammina C, Martin G, Moström P, Mokrousov I, Narbonne V, Narvskaya O, Nastasi A, Niobe-Eyangoh SN, Pape JW, Rasolofo-Razanamparany V, Ridell M, Rossetti ML, Stauffer F, Suffys PN, Takiff H, Texier-Maugein J, Vincent V, de Waard JH, Sola C, Rastogi N: Snapshot of moving and expanding clones of Mycobacterium tuberculosis and their global distribution assessed by spoligotyping in an international study. J Clin Microbiol. 2003, 41 (5): 1963-1970. 10.1128/JCM.41.5.1963-1970.2003.CrossRefPubMedPubMedCentral Filliol I, Driscoll JR, van Soolingen D, Kreiswirth BN, Kremer K, Valétudie G, Dang DA, Barlow R, Banerjee D, Bifani PJ, Brudey K, Cataldi A, Cooksey RC, Cousins DV, Dale JW, Dellagostin OA, Drobniewski F, Engelmann G, Ferdinand S, Gascoyne-Binzi D, Gordon M, Gutierrez MC, Haas WH, Heersma H, Kassa-Kelembho E, Ho ML, Makristathis A, Mammina C, Martin G, Moström P, Mokrousov I, Narbonne V, Narvskaya O, Nastasi A, Niobe-Eyangoh SN, Pape JW, Rasolofo-Razanamparany V, Ridell M, Rossetti ML, Stauffer F, Suffys PN, Takiff H, Texier-Maugein J, Vincent V, de Waard JH, Sola C, Rastogi N: Snapshot of moving and expanding clones of Mycobacterium tuberculosis and their global distribution assessed by spoligotyping in an international study. J Clin Microbiol. 2003, 41 (5): 1963-1970. 10.1128/JCM.41.5.1963-1970.2003.CrossRefPubMedPubMedCentral
31.
go back to reference Warren RM, Streicher EM, Sampson SL, van der Spuy GD, Richardson M, Nguyen D, Behr MA, Victor TC, van Helden PD: Microevolution of the Direct Repeat region of Mycobacterium tuberculosis: implications for interpretation of spoligotyping data. J Clin Microbiol. 2002, 40 (12): 4457-4465. 10.1128/JCM.40.12.4457-4465.2002.CrossRefPubMedPubMedCentral Warren RM, Streicher EM, Sampson SL, van der Spuy GD, Richardson M, Nguyen D, Behr MA, Victor TC, van Helden PD: Microevolution of the Direct Repeat region of Mycobacterium tuberculosis: implications for interpretation of spoligotyping data. J Clin Microbiol. 2002, 40 (12): 4457-4465. 10.1128/JCM.40.12.4457-4465.2002.CrossRefPubMedPubMedCentral
32.
go back to reference Filliol I, Driscoll JR, Van Soolingen D, Kreiswirth BN, Kremer K, Valétudie G, Anh DD, Barlow R, Banerjee D, Bifani PJ, Brudey K, Cataldi A, Cooksey RC, Cousins DV, Dale JW, Dellagostin OA, Drobniewski F, Engelmann G, Ferdinand S, Gascoyne-Binzi D, Gordon M, Gutierrez MC, Haas WH, Heersma H, Källenius G, Kassa-Kelembho E, Koivula T, Ly HM, Makristathis A, Mammina C, Martin G, Moström P, Mokrousov I, Narbonne V, Narvskaya O, Nastasi A, Niobe-Eyangoh SN, Pape JW, Rasolofo-Razanamparany V, Ridell M, Rossetti ML, Stauffer F, Suffys PN, Takiff H, Texier-Maugein J, Vincent V, De Waard JH, Sola C, Rastogi N: Global distribution of Mycobacterium tuberculosis spoligotypes. Emerg Infect Dis. 2002, 8: 1347-1349.CrossRefPubMedPubMedCentral Filliol I, Driscoll JR, Van Soolingen D, Kreiswirth BN, Kremer K, Valétudie G, Anh DD, Barlow R, Banerjee D, Bifani PJ, Brudey K, Cataldi A, Cooksey RC, Cousins DV, Dale JW, Dellagostin OA, Drobniewski F, Engelmann G, Ferdinand S, Gascoyne-Binzi D, Gordon M, Gutierrez MC, Haas WH, Heersma H, Källenius G, Kassa-Kelembho E, Koivula T, Ly HM, Makristathis A, Mammina C, Martin G, Moström P, Mokrousov I, Narbonne V, Narvskaya O, Nastasi A, Niobe-Eyangoh SN, Pape JW, Rasolofo-Razanamparany V, Ridell M, Rossetti ML, Stauffer F, Suffys PN, Takiff H, Texier-Maugein J, Vincent V, De Waard JH, Sola C, Rastogi N: Global distribution of Mycobacterium tuberculosis spoligotypes. Emerg Infect Dis. 2002, 8: 1347-1349.CrossRefPubMedPubMedCentral
33.
go back to reference Singh UB, Suresh N, Bhanu NV, Arora J, Pant H, Sinha S, Aggarwal RC, Singh S, Pande JN, Sola C, Rastogi N, Seth P: Predominant tuberculosis spoligotypes, Delhi, India. Emerg Infect Dis. 2004, 10: 1138-1142.CrossRefPubMedPubMedCentral Singh UB, Suresh N, Bhanu NV, Arora J, Pant H, Sinha S, Aggarwal RC, Singh S, Pande JN, Sola C, Rastogi N, Seth P: Predominant tuberculosis spoligotypes, Delhi, India. Emerg Infect Dis. 2004, 10: 1138-1142.CrossRefPubMedPubMedCentral
34.
go back to reference Sola C, Filliol I, Guttierez C, Mokrousov I, Vincent V, Rastogi N: Spoligotype database of Mycobacterium tuberculosis: biogeographical distribution of shared types and epidemiological and phylogenetic perspectives. Emerg Infect Dis. 2001, 7: 390-396.CrossRefPubMedPubMedCentral Sola C, Filliol I, Guttierez C, Mokrousov I, Vincent V, Rastogi N: Spoligotype database of Mycobacterium tuberculosis: biogeographical distribution of shared types and epidemiological and phylogenetic perspectives. Emerg Infect Dis. 2001, 7: 390-396.CrossRefPubMedPubMedCentral
35.
go back to reference Kremer K, van Soolingen D, Frothingham R, Haas WH, Hermans PW, Martín C, Palittapongarnpim P, Plikaytis BB, Riley LW, Yakrus MA, Musser JM, van Embden JD: Comparison of methods based on different molecular epidemiological markers for typing of Mycobacterium tuberculosis complex strains: interlaboratory study of discriminatory power and reproducibility. J Clin Microbiol. 1999, 37: 2607-2618.PubMedPubMedCentral Kremer K, van Soolingen D, Frothingham R, Haas WH, Hermans PW, Martín C, Palittapongarnpim P, Plikaytis BB, Riley LW, Yakrus MA, Musser JM, van Embden JD: Comparison of methods based on different molecular epidemiological markers for typing of Mycobacterium tuberculosis complex strains: interlaboratory study of discriminatory power and reproducibility. J Clin Microbiol. 1999, 37: 2607-2618.PubMedPubMedCentral
36.
go back to reference Barret J, (Dir): Atlas illustré de la Guyane. 2001, Limoges: IRD, 2 Barret J, (Dir): Atlas illustré de la Guyane. 2001, Limoges: IRD, 2
37.
go back to reference Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P: CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007, 315 (5819): 1709-1712. 10.1126/science.1138140.CrossRefPubMed Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P: CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007, 315 (5819): 1709-1712. 10.1126/science.1138140.CrossRefPubMed
38.
go back to reference Filliol I, Motiwala AS, Cavatore M, Qi W, Hazbón MH, Bobadilla del Valle M, Fyfe J, García-García L, Rastogi N, Sola C, Zozio T, Guerrero MI, León CI, Crabtree J, Angiuoli S, Eisenach KD, Durmaz R, Joloba ML, Rendón A, Sifuentes-Osornio J, Ponce de León A, Cave MD, Fleischmann R, Whittam TS, Alland D: Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set. J Bacteriol. 2006, 188 (2): 759-772. 10.1128/JB.188.2.759-772.2006.CrossRefPubMedPubMedCentral Filliol I, Motiwala AS, Cavatore M, Qi W, Hazbón MH, Bobadilla del Valle M, Fyfe J, García-García L, Rastogi N, Sola C, Zozio T, Guerrero MI, León CI, Crabtree J, Angiuoli S, Eisenach KD, Durmaz R, Joloba ML, Rendón A, Sifuentes-Osornio J, Ponce de León A, Cave MD, Fleischmann R, Whittam TS, Alland D: Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set. J Bacteriol. 2006, 188 (2): 759-772. 10.1128/JB.188.2.759-772.2006.CrossRefPubMedPubMedCentral
39.
go back to reference 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 (1): 121-128. 10.1086/498574.CrossRefPubMed 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 (1): 121-128. 10.1086/498574.CrossRefPubMed
Metadata
Title
Use of cluster-graphs from spoligotyping data to study genotype similarities and a comparison of three indices to quantify recent tuberculosis transmission among culture positive cases in French Guiana during a eight year period
Authors
Vanina Guernier
Christophe Sola
Karine Brudey
Jean-François Guégan
Nalin Rastogi
Publication date
01-12-2008
Publisher
BioMed Central
Published in
BMC Infectious Diseases / Issue 1/2008
Electronic ISSN: 1471-2334
DOI
https://doi.org/10.1186/1471-2334-8-46

Other articles of this Issue 1/2008

BMC Infectious Diseases 1/2008 Go to the issue
Live Webinar | 27-06-2024 | 18:00 (CEST)

Keynote webinar | Spotlight on medication adherence

Live: Thursday 27th June 2024, 18:00-19:30 (CEST)

WHO estimates that half of all patients worldwide are non-adherent to their prescribed medication. The consequences of poor adherence can be catastrophic, on both the individual and population level.

Join our expert panel to discover why you need to understand the drivers of non-adherence in your patients, and how you can optimize medication adherence in your clinics to drastically improve patient outcomes.

Prof. Kevin Dolgin
Prof. Florian Limbourg
Prof. Anoop Chauhan
Developed by: Springer Medicine
Obesity Clinical Trial Summary

At a glance: The STEP trials

A round-up of the STEP phase 3 clinical trials evaluating semaglutide for weight loss in people with overweight or obesity.

Developed by: Springer Medicine

Highlights from the ACC 2024 Congress

Year in Review: Pediatric cardiology

Watch Dr. Anne Marie Valente present the last year's highlights in pediatric and congenital heart disease in the official ACC.24 Year in Review session.

Year in Review: Pulmonary vascular disease

The last year's highlights in pulmonary vascular disease are presented by Dr. Jane Leopold in this official video from ACC.24.

Year in Review: Valvular heart disease

Watch Prof. William Zoghbi present the last year's highlights in valvular heart disease from the official ACC.24 Year in Review session.

Year in Review: Heart failure and cardiomyopathies

Watch this official video from ACC.24. Dr. Biykem Bozkurt discusses last year's major advances in heart failure and cardiomyopathies.