Distinct genotypic profiles of the two major clades of Mycobacterium africanum

go back to reference Brosch R, Gordon SV, Marmiesse M, Brodin P, Buchrieser C, Eiglmeier K, Garnier T, Gutierrez C, Hewinson G, Kremer K, Parsons LM, Pym AS, Samper S, van Soolingen D, Cole ST: A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc Natl Acad Sci USA. 2002, 99 (6): 3684-3689. 10.1073/pnas.052548299.CrossRefPubMedPubMedCentral Brosch R, Gordon SV, Marmiesse M, Brodin P, Buchrieser C, Eiglmeier K, Garnier T, Gutierrez C, Hewinson G, Kremer K, Parsons LM, Pym AS, Samper S, van Soolingen D, Cole ST: A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc Natl Acad Sci USA. 2002, 99 (6): 3684-3689. 10.1073/pnas.052548299.CrossRefPubMedPubMedCentral

go back to reference Huard RC, Lazzarini LCO, Butler W, van Soolingen D, Ho JL: PCR-based method to differentiate the subspecies of the Mycobacterium tuberculosis complex on the basis of genomic deletions. J Clin Microbiol. 2003, 41 (4): 1637-1650. 10.1128/JCM.41.4.1637-1650.2003.CrossRefPubMedPubMedCentral Huard RC, Lazzarini LCO, Butler W, van Soolingen D, Ho JL: PCR-based method to differentiate the subspecies of the Mycobacterium tuberculosis complex on the basis of genomic deletions. J Clin Microbiol. 2003, 41 (4): 1637-1650. 10.1128/JCM.41.4.1637-1650.2003.CrossRefPubMedPubMedCentral

go back to reference Mostowy S, Cousins D, Brinkman J, Aranaz A, Behr M: Genomic deletions suggest a phylogeny for the Mycobacterium tuberculosis complex. J Infect Dis. 2002, 186 (1): 74-80. 10.1086/341068.CrossRefPubMed Mostowy S, Cousins D, Brinkman J, Aranaz A, Behr M: Genomic deletions suggest a phylogeny for the Mycobacterium tuberculosis complex. J Infect Dis. 2002, 186 (1): 74-80. 10.1086/341068.CrossRefPubMed

go back to reference Aranaz A, Cousins D, Mateos A, Domínguez L: Elevation of Mycobacterium tuberculosis subsp. caprae Aranaz et al. 1999 to species rank as Mycobacterium caprae comb. nov., sp. nov. Int J Syst Evol Microbiol. 2003, 53 (6): 1785-1789. 10.1099/ijs.0.02532-0.CrossRefPubMed Aranaz A, Cousins D, Mateos A, Domínguez L: Elevation of Mycobacterium tuberculosis subsp. caprae Aranaz et al. 1999 to species rank as Mycobacterium caprae comb. nov., sp. nov. Int J Syst Evol Microbiol. 2003, 53 (6): 1785-1789. 10.1099/ijs.0.02532-0.CrossRefPubMed

go back to reference Cousins D, Bastida R, Cataldi A, Quse V, Redrobe S, Dow S, Duignan P, Murray A, Dupont C, Ahmed N, Collins D, Butler W, Dawson D, Rodríguez D, Loureiro J, Romano M, Alito A, Zumarraga M, Bernardelli A: Tuberculosis in seals caused by a novel member of the Mycobacterium tuberculosis complex: Mycobacterium pinnipedii sp. nov. Int J Syst Evol Microbiol. 2003, 53 (5): 1305-1314. 10.1099/ijs.0.02401-0.CrossRefPubMed Cousins D, Bastida R, Cataldi A, Quse V, Redrobe S, Dow S, Duignan P, Murray A, Dupont C, Ahmed N, Collins D, Butler W, Dawson D, Rodríguez D, Loureiro J, Romano M, Alito A, Zumarraga M, Bernardelli A: Tuberculosis in seals caused by a novel member of the Mycobacterium tuberculosis complex: Mycobacterium pinnipedii sp. nov. Int J Syst Evol Microbiol. 2003, 53 (5): 1305-1314. 10.1099/ijs.0.02401-0.CrossRefPubMed

go back to reference Cousins D, Peet R, Gaynor W, Williams S, Gow B: Tuberculosis in imported hyrax (Procavia capensis) caused by an unusual variant belonging to the Mycobacterium tuberculosis complex. Vet Microbiol. 1994, 42 (2-3): 135-145. 10.1016/0378-1135(94)90013-2.CrossRefPubMed Cousins D, Peet R, Gaynor W, Williams S, Gow B: Tuberculosis in imported hyrax (Procavia capensis) caused by an unusual variant belonging to the Mycobacterium tuberculosis complex. Vet Microbiol. 1994, 42 (2-3): 135-145. 10.1016/0378-1135(94)90013-2.CrossRefPubMed

go back to reference Huard RC, Fabre M, de Haas P, Lazzarini LCO, van Soolingen D, Cousins D, Ho JL: Novel genetic polymorphisms that further delineate the phylogeny of the Mycobacterium tuberculosis complex. J Bacteriol. 2006, 188 (12): 4271-4287. 10.1128/JB.01783-05.CrossRefPubMedPubMedCentral Huard RC, Fabre M, de Haas P, Lazzarini LCO, van Soolingen D, Cousins D, Ho JL: Novel genetic polymorphisms that further delineate the phylogeny of the Mycobacterium tuberculosis complex. J Bacteriol. 2006, 188 (12): 4271-4287. 10.1128/JB.01783-05.CrossRefPubMedPubMedCentral

go back to reference van Soolingen D, Hoogenboezem T, de Haas P, Hermans P, Koedam M, Teppema K, Brennan P, Besra G, Portaels F, Top J, Schouls L, van Embden J: A novel pathogenic taxon of the Mycobacterium tuberculosis complex, Canetti: characterization of an exceptional isolate from Africa. Int J Syst Bacteriol. 1997, 47 (4): 1236-1245. 10.1099/00207713-47-4-1236.CrossRefPubMed van Soolingen D, Hoogenboezem T, de Haas P, Hermans P, Koedam M, Teppema K, Brennan P, Besra G, Portaels F, Top J, Schouls L, van Embden J: A novel pathogenic taxon of the Mycobacterium tuberculosis complex, Canetti: characterization of an exceptional isolate from Africa. Int J Syst Bacteriol. 1997, 47 (4): 1236-1245. 10.1099/00207713-47-4-1236.CrossRefPubMed

go back to reference Scorpio A, Zhang Y: Mutations in pncA, a gene encoding pyrazinamidase/nicotinamidase, cause resistance to the antituberculous drug pyrazinamide in the tubercle bacillus. Nat Med. 1996, 2 (6): 662-667. 10.1038/nm0696-662.CrossRefPubMed Scorpio A, Zhang Y: Mutations in pncA, a gene encoding pyrazinamidase/nicotinamidase, cause resistance to the antituberculous drug pyrazinamide in the tubercle bacillus. Nat Med. 1996, 2 (6): 662-667. 10.1038/nm0696-662.CrossRefPubMed

go back to reference Niemann S, Richter E, Rüsch-Gerdes S: Differentiation among members of the Mycobacterium tuberculosis complex by molecular and biochemical features: evidence for two pyrazinamide-susceptible subtypes of M. bovis. J Clin Microbiol. 2000, 38 (1): 152-157.PubMedPubMedCentral Niemann S, Richter E, Rüsch-Gerdes S: Differentiation among members of the Mycobacterium tuberculosis complex by molecular and biochemical features: evidence for two pyrazinamide-susceptible subtypes of M. bovis. J Clin Microbiol. 2000, 38 (1): 152-157.PubMedPubMedCentral

go back to reference Goh K, Legrand E, Sola C, Rastogi N: Rapid differentiation of "Mycobacterium canettii" from other Mycobacterium tuberculosis complex organisms by PCR-restriction analysis of the hsp65 gene. J Clin Microbiol. 2001, 39 (10): 3705-3708. 10.1128/JCM.39.10.3705-3708.2001.CrossRefPubMedPubMedCentral Goh K, Legrand E, Sola C, Rastogi N: Rapid differentiation of "Mycobacterium canettii" from other Mycobacterium tuberculosis complex organisms by PCR-restriction analysis of the hsp65 gene. J Clin Microbiol. 2001, 39 (10): 3705-3708. 10.1128/JCM.39.10.3705-3708.2001.CrossRefPubMedPubMedCentral

go back to reference Parsons L, Brosch R, Cole S, Somoskövi A, Loder A, Bretzel G, Van Soolingen D, Hale Y, Salfinger M: Rapid and simple approach for identification of Mycobacterium tuberculosis complex isolates by PCR-based genomic deletion analysis. J Clin Microbiol. 2002, 40 (7): 2339-2345. 10.1128/JCM.40.7.2339-2345.2002.CrossRefPubMedPubMedCentral Parsons L, Brosch R, Cole S, Somoskövi A, Loder A, Bretzel G, Van Soolingen D, Hale Y, Salfinger M: Rapid and simple approach for identification of Mycobacterium tuberculosis complex isolates by PCR-based genomic deletion analysis. J Clin Microbiol. 2002, 40 (7): 2339-2345. 10.1128/JCM.40.7.2339-2345.2002.CrossRefPubMedPubMedCentral

go back to reference Warren R, Gey van Pittius N, Barnard M, Hesseling A, Engelke E, de Kock M, Gutierrez M, Chege G, Victor T, Hoal E, van Helden P: Differentiation of Mycobacterium tuberculosis complex by PCR amplification of genomic regions of difference. Int J Tuberc Lung Dis. 2006, 10 (7): 818-822.PubMed Warren R, Gey van Pittius N, Barnard M, Hesseling A, Engelke E, de Kock M, Gutierrez M, Chege G, Victor T, Hoal E, van Helden P: Differentiation of Mycobacterium tuberculosis complex by PCR amplification of genomic regions of difference. Int J Tuberc Lung Dis. 2006, 10 (7): 818-822.PubMed

go back to reference Richter E, Weizenegger M, Fahr A, Rüsch-Gerdes S: Usefulness of the GenoType MTBC assay for differentiating species of the Mycobacterium tuberculosis complex in cultures obtained from clinical specimens. J Clin Microbiol. 2004, 42 (9): 4303-4306. 10.1128/JCM.42.9.4303-4306.2004.CrossRefPubMedPubMedCentral Richter E, Weizenegger M, Fahr A, Rüsch-Gerdes S: Usefulness of the GenoType MTBC assay for differentiating species of the Mycobacterium tuberculosis complex in cultures obtained from clinical specimens. J Clin Microbiol. 2004, 42 (9): 4303-4306. 10.1128/JCM.42.9.4303-4306.2004.CrossRefPubMedPubMedCentral

go back to reference Richter E, Weizenegger M, Rüsch-Gerdes S, Niemann S: Evaluation of GenoType MTBC assay for differentiation of clinical Mycobacterium tuberculosis complex isolates. J Clin Microbiol. 2003, 41 (6): 2672-2675. 10.1128/JCM.41.6.2672-2675.2003.CrossRefPubMedPubMedCentral Richter E, Weizenegger M, Rüsch-Gerdes S, Niemann S: Evaluation of GenoType MTBC assay for differentiation of clinical Mycobacterium tuberculosis complex isolates. J Clin Microbiol. 2003, 41 (6): 2672-2675. 10.1128/JCM.41.6.2672-2675.2003.CrossRefPubMedPubMedCentral

go back to reference Somoskovi A, Dormandy J, Rivenburg J, Pedrosa M, McBride M, Salfinger M: Direct comparison of the GenoType MTBC and genomic deletion assays in terms of ability to distinguish between members of the Mycobacterium tuberculosis Complex in clinical isolates and in clinical specimens. J Clin Microbiol. 2008, 46 (5): 1854-1857. 10.1128/JCM.00105-07.CrossRefPubMedPubMedCentral Somoskovi A, Dormandy J, Rivenburg J, Pedrosa M, McBride M, Salfinger M: Direct comparison of the GenoType MTBC and genomic deletion assays in terms of ability to distinguish between members of the Mycobacterium tuberculosis Complex in clinical isolates and in clinical specimens. J Clin Microbiol. 2008, 46 (5): 1854-1857. 10.1128/JCM.00105-07.CrossRefPubMedPubMedCentral

go back to reference Viana-Niero C, Gutierrez C, Sola C, Filliol I, Boulahbal F, Vincent V, Rastogi N: Genetic diversity of Mycobacterium africanum clinical isolates based on IS6110-restriction fragment length polymorphism analysis, spoligotyping, and variable number of tandem DNA repeats. J Clin Microbiol. 2001, 39 (1): 57-65. 10.1128/JCM.39.1.57-65.2001.CrossRefPubMedPubMedCentral Viana-Niero C, Gutierrez C, Sola C, Filliol I, Boulahbal F, Vincent V, Rastogi N: Genetic diversity of Mycobacterium africanum clinical isolates based on IS6110-restriction fragment length polymorphism analysis, spoligotyping, and variable number of tandem DNA repeats. J Clin Microbiol. 2001, 39 (1): 57-65. 10.1128/JCM.39.1.57-65.2001.CrossRefPubMedPubMedCentral

go back to reference Haas W, Bretzel G, Amthor B, Schilke K, Krommes G, Rüsch-Gerdes S, Sticht-Groh V, Bremer H: Comparison of DNA fingerprint patterns of isolates of Mycobacterium africanum from east and west Africa. J Clin Microbiol. 1997, 35 (3): 663-666.PubMedPubMedCentral Haas W, Bretzel G, Amthor B, Schilke K, Krommes G, Rüsch-Gerdes S, Sticht-Groh V, Bremer H: Comparison of DNA fingerprint patterns of isolates of Mycobacterium africanum from east and west Africa. J Clin Microbiol. 1997, 35 (3): 663-666.PubMedPubMedCentral

go back to reference Niemann S, Rüsch-Gerdes S, Joloba M, Whalen C, Guwatudde D, Ellner J, Eisenach K, Fumokong N, Johnson J, Aisu T, Mugerwa R, Okwera A, Schwander S: Mycobacterium africanum subtype II is associated with two distinct genotypes and is a major cause of human tuberculosis in Kampala, Uganda. J Clin Microbiol. 2002, 40 (9): 3398-3405. 10.1128/JCM.40.9.3398-3405.2002.CrossRefPubMedPubMedCentral Niemann S, Rüsch-Gerdes S, Joloba M, Whalen C, Guwatudde D, Ellner J, Eisenach K, Fumokong N, Johnson J, Aisu T, Mugerwa R, Okwera A, Schwander S: Mycobacterium africanum subtype II is associated with two distinct genotypes and is a major cause of human tuberculosis in Kampala, Uganda. J Clin Microbiol. 2002, 40 (9): 3398-3405. 10.1128/JCM.40.9.3398-3405.2002.CrossRefPubMedPubMedCentral

go back to reference Sola C, Rastogi N, Gutierrez M, Vincent V, Brosch R, Parsons L: Is Mycobacterium africanum subtype II (Uganda I and Uganda II) a genetically well-defined subspecies of the Mycobacterium tuberculosis complex?. J Clin Microbiol. 2003, 41 (3): 1345-1346. 10.1128/JCM.41.3.1345-1348.2003.CrossRefPubMedPubMedCentral Sola C, Rastogi N, Gutierrez M, Vincent V, Brosch R, Parsons L: Is Mycobacterium africanum subtype II (Uganda I and Uganda II) a genetically well-defined subspecies of the Mycobacterium tuberculosis complex?. J Clin Microbiol. 2003, 41 (3): 1345-1346. 10.1128/JCM.41.3.1345-1348.2003.CrossRefPubMedPubMedCentral

go back to reference Asiimwe B, Koivula T, Källenius G, Huard R, Ghebremichael S, Asiimwe J, Joloba M: Mycobacterium tuberculosis Uganda genotype is the predominant cause of TB in Kampala, Uganda. Int J Tuberc Lung Dis. 2008, 12 (4): 386-391.PubMed Asiimwe B, Koivula T, Källenius G, Huard R, Ghebremichael S, Asiimwe J, Joloba M: Mycobacterium tuberculosis Uganda genotype is the predominant cause of TB in Kampala, Uganda. Int J Tuberc Lung Dis. 2008, 12 (4): 386-391.PubMed

go back to reference Niemann S, Kubica T, Bange F, Adjei O, Browne E, Chinbuah M, Diel R, Gyapong J, Horstmann R, Joloba M, Meyer C, Mugerwa R, Okwera A, Osei I, Owusu-Darbo E, Schwander S, Rüsch-Gerdes S: The species Mycobacterium africanum in the light of new molecular markers. J Clin Microbiol. 2004, 42 (9): 3958-3962. 10.1128/JCM.42.9.3958-3962.2004.CrossRefPubMedPubMedCentral Niemann S, Kubica T, Bange F, Adjei O, Browne E, Chinbuah M, Diel R, Gyapong J, Horstmann R, Joloba M, Meyer C, Mugerwa R, Okwera A, Osei I, Owusu-Darbo E, Schwander S, Rüsch-Gerdes S: The species Mycobacterium africanum in the light of new molecular markers. J Clin Microbiol. 2004, 42 (9): 3958-3962. 10.1128/JCM.42.9.3958-3962.2004.CrossRefPubMedPubMedCentral

go back to reference Mostowy S, Onipede A, Gagneux S, Niemann S, Kremer K, Desmond E, Kato-Maeda M, Behr M: Genomic analysis distinguishes Mycobacterium africanum. J Clin Microbiol. 2004, 42 (8): 3594-3599. 10.1128/JCM.42.8.3594-3599.2004.CrossRefPubMedPubMedCentral Mostowy S, Onipede A, Gagneux S, Niemann S, Kremer K, Desmond E, Kato-Maeda M, Behr M: Genomic analysis distinguishes Mycobacterium africanum. J Clin Microbiol. 2004, 42 (8): 3594-3599. 10.1128/JCM.42.8.3594-3599.2004.CrossRefPubMedPubMedCentral

go back to reference Wirth T, Hildebrand F, Allix-Béguec C, Wölbeling F, Kubica T, Kremer K, van Soolingen D, Rüsch-Gerdes S, Locht C, Brisse S, Meyer A, Supply P, Niemann S: Origin, spread and demography of the Mycobacterium tuberculosis complex. PLoS Pathog. 2008, 4 (9): e1000160-10.1371/journal.ppat.1000160.CrossRefPubMedPubMedCentral Wirth T, Hildebrand F, Allix-Béguec C, Wölbeling F, Kubica T, Kremer K, van Soolingen D, Rüsch-Gerdes S, Locht C, Brisse S, Meyer A, Supply P, Niemann S: Origin, spread and demography of the Mycobacterium tuberculosis complex. PLoS Pathog. 2008, 4 (9): e1000160-10.1371/journal.ppat.1000160.CrossRefPubMedPubMedCentral

go back to reference Gagneux S, DeRiemer K, Van T, Kato-Maeda M, de Jong B, Narayanan S, Nicol M, Niemann S, Kremer K, Gutierrez M, Hilty M, Hopewell P, Small P: Variable host-pathogen compatibility in Mycobacterium tuberculosis. Proc Natl Acad Sci USA. 2006, 103 (8): 2869-2873. 10.1073/pnas.0511240103.CrossRefPubMedPubMedCentral Gagneux S, DeRiemer K, Van T, Kato-Maeda M, de Jong B, Narayanan S, Nicol M, Niemann S, Kremer K, Gutierrez M, Hilty M, Hopewell P, Small P: Variable host-pathogen compatibility in Mycobacterium tuberculosis. Proc Natl Acad Sci USA. 2006, 103 (8): 2869-2873. 10.1073/pnas.0511240103.CrossRefPubMedPubMedCentral

go back to reference Smith N, Kremer K, Inwald J, Dale J, Driscoll J, Gordon S, van Soolingen D, Hewinson R, Smith J: Ecotypes of the Mycobacterium tuberculosis complex. J Theor Biol. 2006, 239 (2): 220-225. 10.1016/j.jtbi.2005.08.036.CrossRefPubMed Smith N, Kremer K, Inwald J, Dale J, Driscoll J, Gordon S, van Soolingen D, Hewinson R, Smith J: Ecotypes of the Mycobacterium tuberculosis complex. J Theor Biol. 2006, 239 (2): 220-225. 10.1016/j.jtbi.2005.08.036.CrossRefPubMed

go back to reference Allix-Béguec C, Harmsen D, Weniger T, Supply P, Niemann S: Evaluation and strategy for use of MIRU-VNTRplus, a multifunctional database for online analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates. J Clin Microbiol. 2008, 46 (8): 2692-2699. 10.1128/JCM.00540-08.CrossRefPubMedPubMedCentral Allix-Béguec C, Harmsen D, Weniger T, Supply P, Niemann S: Evaluation and strategy for use of MIRU-VNTRplus, a multifunctional database for online analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates. J Clin Microbiol. 2008, 46 (8): 2692-2699. 10.1128/JCM.00540-08.CrossRefPubMedPubMedCentral

go back to reference Kremer K, van Soolingen D, Frothingham R, Haas W, Hermans P, Martín C, Palittapongarnpim P, Plikaytis B, Riley L, Yakrus M, Musser J, van Embden J: 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 (8): 2607-2618.PubMedPubMedCentral Kremer K, van Soolingen D, Frothingham R, Haas W, Hermans P, Martín C, Palittapongarnpim P, Plikaytis B, Riley L, Yakrus M, Musser J, van Embden J: 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 (8): 2607-2618.PubMedPubMedCentral

go back to reference Sreevatsan S, Pan X, Stockbauer K, Connell N, Kreiswirth B, Whittam T, Musser J: Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc Natl Acad Sci USA. 1997, 94 (18): 9869-9874. 10.1073/pnas.94.18.9869.CrossRefPubMedPubMedCentral Sreevatsan S, Pan X, Stockbauer K, Connell N, Kreiswirth B, Whittam T, Musser J: Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc Natl Acad Sci USA. 1997, 94 (18): 9869-9874. 10.1073/pnas.94.18.9869.CrossRefPubMedPubMedCentral

go back to reference Frothingham R, Strickland P, Bretzel G, Ramaswamy S, Musser J, Williams D: Phenotypic and genotypic characterization of Mycobacterium africanum isolates from West Africa. J Clin Microbiol. 1999, 37 (6): 1921-1926.PubMedPubMedCentral Frothingham R, Strickland P, Bretzel G, Ramaswamy S, Musser J, Williams D: Phenotypic and genotypic characterization of Mycobacterium africanum isolates from West Africa. J Clin Microbiol. 1999, 37 (6): 1921-1926.PubMedPubMedCentral

go back to reference Lazzarini LCO, Huard RC, Boechat N, Gomes H, Oelemann M, Kurepina N, Shashkina E, Mello F, Gibson A, Virginio M, Marsico A, Butler W, Kreiswirth B, Suffys P, Lapa E, Silva JR, Ho JL: Discovery of a novel Mycobacterium tuberculosis lineage that is a major cause of tuberculosis in Rio de Janeiro, Brazil. J Clin Microbiol. 2007, 45 (12): 3891-3902. 10.1128/JCM.01394-07.CrossRefPubMedPubMedCentral Lazzarini LCO, Huard RC, Boechat N, Gomes H, Oelemann M, Kurepina N, Shashkina E, Mello F, Gibson A, Virginio M, Marsico A, Butler W, Kreiswirth B, Suffys P, Lapa E, Silva JR, Ho JL: Discovery of a novel Mycobacterium tuberculosis lineage that is a major cause of tuberculosis in Rio de Janeiro, Brazil. J Clin Microbiol. 2007, 45 (12): 3891-3902. 10.1128/JCM.01394-07.CrossRefPubMedPubMedCentral

go back to reference Gibson A, Huard R, Gey van Pittius N, Lazzarini L, Driscoll J, Kurepina N, Zozio T, Sola C, Spindola S, Kritski A, Fitzgerald D, Kremer K, Mardassi H, Chitale P, Brinkworth J, Garcia de Viedma D, Gicquel B, Pape J, van Soolingen D, Kreiswirth B, Warren R, van Helden P, Rastogi N, Suffys P, Lapa e Silva J, Ho J: Application of sensitive and specific molecular methods to uncover global dissemination of the major RDRio Sublineage of the Latin American-Mediterranean Mycobacterium tuberculosis spoligotype family. J Clin Microbiol. 2008, 46 (4): 1259-1267. 10.1128/JCM.02231-07.CrossRefPubMedPubMedCentral Gibson A, Huard R, Gey van Pittius N, Lazzarini L, Driscoll J, Kurepina N, Zozio T, Sola C, Spindola S, Kritski A, Fitzgerald D, Kremer K, Mardassi H, Chitale P, Brinkworth J, Garcia de Viedma D, Gicquel B, Pape J, van Soolingen D, Kreiswirth B, Warren R, van Helden P, Rastogi N, Suffys P, Lapa e Silva J, Ho J: Application of sensitive and specific molecular methods to uncover global dissemination of the major RD^Rio Sublineage of the Latin American-Mediterranean Mycobacterium tuberculosis spoligotype family. J Clin Microbiol. 2008, 46 (4): 1259-1267. 10.1128/JCM.02231-07.CrossRefPubMedPubMedCentral

go back to reference Goh K, Rastogi N, Berchel M, Huard R, Sola C: Molecular evolutionary history of tubercle bacilli assessed by study of the polymorphic nucleotide within the nitrate reductase (narGHJI) operon promoter. J Clin Microbiol. 2005, 43 (8): 4010-4014. 10.1128/JCM.43.8.4010-4014.2005.CrossRefPubMedPubMedCentral Goh K, Rastogi N, Berchel M, Huard R, Sola C: Molecular evolutionary history of tubercle bacilli assessed by study of the polymorphic nucleotide within the nitrate reductase (narGHJI) operon promoter. J Clin Microbiol. 2005, 43 (8): 4010-4014. 10.1128/JCM.43.8.4010-4014.2005.CrossRefPubMedPubMedCentral

go back to reference Constant P, Perez E, Malaga W, Laneelle MA, Saurel O, Daffe M, Guilhot C: Role of the pks15/1 gene in the biosynthesis of phenolglycolipids in the Mycobacterium tuberculosis complex - Evidence that all strains synthesize glycosylated p-hydroxybenzoic methyl esters and that strains devoid of phenolglycolipids harbor a frameshift mutation in the pks15/1 gene. Journal of Biological Chemistry. 2002, 277 (41): 38148-38158. 10.1074/jbc.M206538200.CrossRefPubMed Constant P, Perez E, Malaga W, Laneelle MA, Saurel O, Daffe M, Guilhot C: Role of the pks15/1 gene in the biosynthesis of phenolglycolipids in the Mycobacterium tuberculosis complex - Evidence that all strains synthesize glycosylated p-hydroxybenzoic methyl esters and that strains devoid of phenolglycolipids harbor a frameshift mutation in the pks15/1 gene. Journal of Biological Chemistry. 2002, 277 (41): 38148-38158. 10.1074/jbc.M206538200.CrossRefPubMed

go back to reference Huard R, Chitale S, Leung M, Lazzarini L, Zhu H, Shashkina E, Laal S, Conde M, Kritski A, Belisle J, Kreiswirth B, Lapa e Silva J, Ho J: The Mycobacterium tuberculosis complex-restricted gene cfp32 encodes an expressed protein that is detectable in tuberculosis patients and is positively correlated with pulmonary interleukin-10. Infect Immun. 2003, 71 (12): 6871-6883. 10.1128/IAI.71.12.6871-6883.2003.CrossRefPubMedPubMedCentral Huard R, Chitale S, Leung M, Lazzarini L, Zhu H, Shashkina E, Laal S, Conde M, Kritski A, Belisle J, Kreiswirth B, Lapa e Silva J, Ho J: The Mycobacterium tuberculosis complex-restricted gene cfp32 encodes an expressed protein that is detectable in tuberculosis patients and is positively correlated with pulmonary interleukin-10. Infect Immun. 2003, 71 (12): 6871-6883. 10.1128/IAI.71.12.6871-6883.2003.CrossRefPubMedPubMedCentral

go back to reference Sholto-Douglas-Vernon C, Sandy J, Victor T, Sim E, Helden P: Mutational and expression analysis of tbnat and its response to isoniazid. J Med Microbiol. 2005, 54 (12): 1189-1197. 10.1099/jmm.0.46153-0.CrossRefPubMed Sholto-Douglas-Vernon C, Sandy J, Victor T, Sim E, Helden P: Mutational and expression analysis of tbnat and its response to isoniazid. J Med Microbiol. 2005, 54 (12): 1189-1197. 10.1099/jmm.0.46153-0.CrossRefPubMed

go back to reference Källenius G, Koivula T, Ghebremichael S, Hoffner S, Norberg R, Svensson E, Dias F, Marklund B, Svenson S: Evolution and clonal traits of Mycobacterium tuberculosis complex in Guinea-Bissau. J Clin Microbiol. 1999, 37 (12): 3872-3878.PubMedPubMedCentral Källenius G, Koivula T, Ghebremichael S, Hoffner S, Norberg R, Svensson E, Dias F, Marklund B, Svenson S: Evolution and clonal traits of Mycobacterium tuberculosis complex in Guinea-Bissau. J Clin Microbiol. 1999, 37 (12): 3872-3878.PubMedPubMedCentral

go back to reference de Jong B, Hill P, Brookes R, Gagneux S, Jeffries D, Otu J, Donkor S, Fox A, McAdam K, Small P, Adegbola R: 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. 2006, 193 (9): 1279-1286. 10.1086/502977.CrossRefPubMed de Jong B, Hill P, Brookes R, Gagneux S, Jeffries D, Otu J, Donkor S, Fox A, McAdam K, Small P, Adegbola R: 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. 2006, 193 (9): 1279-1286. 10.1086/502977.CrossRefPubMed

go back to reference Homolka S, Post E, Oberhauser B, George A, Westman L, Dafae F, Rüsch-Gerdes S, Niemann S: High genetic diversity among Mycobacterium tuberculosis complex strains from Sierra Leone. BMC Microbiol. 2008, 8: 103-10.1186/1471-2180-8-103.CrossRefPubMedPubMedCentral Homolka S, Post E, Oberhauser B, George A, Westman L, Dafae F, Rüsch-Gerdes S, Niemann S: High genetic diversity among Mycobacterium tuberculosis complex strains from Sierra Leone. BMC Microbiol. 2008, 8: 103-10.1186/1471-2180-8-103.CrossRefPubMedPubMedCentral

go back to reference Ledru S, Cauchoix B, Yaméogo M, Zoubga A, Lamandé-Chiron J, Portaels F, Chiron J: Impact of short-course therapy on tuberculosis drug resistance in South-West Burkina Faso. Tuber Lung Dis. 1996, 77 (5): 429-436. 10.1016/S0962-8479(96)90116-1.CrossRefPubMed Ledru S, Cauchoix B, Yaméogo M, Zoubga A, Lamandé-Chiron J, Portaels F, Chiron J: Impact of short-course therapy on tuberculosis drug resistance in South-West Burkina Faso. Tuber Lung Dis. 1996, 77 (5): 429-436. 10.1016/S0962-8479(96)90116-1.CrossRefPubMed

go back to reference Niobe-Eyangoh S, Kuaban C, Sorlin P, Cunin P, Thonnon J, Sola C, Rastogi N, Vincent V, Gutierrez M: Genetic biodiversity of Mycobacterium tuberculosis complex strains from patients with pulmonary tuberculosis in Cameroon. J Clin Microbiol. 2003, 41 (6): 2547-2553. 10.1128/JCM.41.6.2547-2553.2003.CrossRefPubMedPubMedCentral Niobe-Eyangoh S, Kuaban C, Sorlin P, Cunin P, Thonnon J, Sola C, Rastogi N, Vincent V, Gutierrez M: Genetic biodiversity of Mycobacterium tuberculosis complex strains from patients with pulmonary tuberculosis in Cameroon. J Clin Microbiol. 2003, 41 (6): 2547-2553. 10.1128/JCM.41.6.2547-2553.2003.CrossRefPubMedPubMedCentral

go back to reference Cadmus S, Palmer S, Okker M, Dale J, Gover K, Smith N, Jahans K, Hewinson R, Gordon S: Molecular analysis of human and bovine tubercle bacilli from a local setting in Nigeria. J Clin Microbiol. 2006, 44 (1): 29-34. 10.1128/JCM.44.1.29-34.2006.CrossRefPubMedPubMedCentral Cadmus S, Palmer S, Okker M, Dale J, Gover K, Smith N, Jahans K, Hewinson R, Gordon S: Molecular analysis of human and bovine tubercle bacilli from a local setting in Nigeria. J Clin Microbiol. 2006, 44 (1): 29-34. 10.1128/JCM.44.1.29-34.2006.CrossRefPubMedPubMedCentral

go back to reference Brudey K, Driscoll J, Rigouts L, Prodinger W, Gori A, Al-Hajoj S, Allix C, Aristimuño L, Arora J, Baumanis V, Binder L, Cafrune P, Cataldi A, Cheong S, Diel R, Ellermeier C, Evans J, Fauville-Dufaux M, Ferdinand S, Garcia de Viedma D, Garzelli C, Gazzola L, Gomes H, Guttierez M, Hawkey P, van Helden P, Kadival G, Kreiswirth B, Kremer K, Kubin M, Kulkarni S, Liens B, Lillebaek T, Ho M, Martin C, Mokrousov I, Narvskaïa O, Ngeow Y, Naumann L, Niemann S, Parwati I, Rahim Z, Rasolofo-Razanamparany V, Rasolonavalona T, Rossetti M, Rüsch-Gerdes S, Sajduda A, Samper S, Shemyakin I, Singh U, Somoskovi A, Skuce R, van Soolingen D, Streicher E, Suffys P, Tortoli E, Tracevska T, Vincent V, Victor T, Warren R, Yap S, Zaman K, Portaels F, Rastogi N, Sola C: 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 J, Rigouts L, Prodinger W, Gori A, Al-Hajoj S, Allix C, Aristimuño L, Arora J, Baumanis V, Binder L, Cafrune P, Cataldi A, Cheong S, Diel R, Ellermeier C, Evans J, Fauville-Dufaux M, Ferdinand S, Garcia de Viedma D, Garzelli C, Gazzola L, Gomes H, Guttierez M, Hawkey P, van Helden P, Kadival G, Kreiswirth B, Kremer K, Kubin M, Kulkarni S, Liens B, Lillebaek T, Ho M, Martin C, Mokrousov I, Narvskaïa O, Ngeow Y, Naumann L, Niemann S, Parwati I, Rahim Z, Rasolofo-Razanamparany V, Rasolonavalona T, Rossetti M, Rüsch-Gerdes S, Sajduda A, Samper S, Shemyakin I, Singh U, Somoskovi A, Skuce R, van Soolingen D, Streicher E, Suffys P, Tortoli E, Tracevska T, Vincent V, Victor T, Warren R, Yap S, Zaman K, Portaels F, Rastogi N, Sola C: 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

go back to reference de Jong B, Hill P, Aiken A, Jeffries D, Onipede A, Small P, Adegbola R, Corrah T: Clinical presentation and outcome of tuberculosis patients infected by M. africanum versus M. tuberculosis. Int J Tuberc Lung Dis. 2007, 11 (4): 450-456.PubMed de Jong B, Hill P, Aiken A, Jeffries D, Onipede A, Small P, Adegbola R, Corrah T: Clinical presentation and outcome of tuberculosis patients infected by M. africanum versus M. tuberculosis. Int J Tuberc Lung Dis. 2007, 11 (4): 450-456.PubMed

go back to reference Koivula T, Ekman M, Leitner T, Löfdahl S, Ghebremicahel S, Mostowy S, Behr M, Svenson S, Källenius G: Genetic characterization of the Guinea-Bissau family of Mycobacterium tuberculosis complex strains. Microbes Infect. 2004, 6 (3): 272-278. 10.1016/j.micinf.2003.12.006.CrossRefPubMed Koivula T, Ekman M, Leitner T, Löfdahl S, Ghebremicahel S, Mostowy S, Behr M, Svenson S, Källenius G: Genetic characterization of the Guinea-Bissau family of Mycobacterium tuberculosis complex strains. Microbes Infect. 2004, 6 (3): 272-278. 10.1016/j.micinf.2003.12.006.CrossRefPubMed

go back to reference Brudey K, Gutierrez M, Vincent V, Parsons L, Salfinger M, Rastogi N, Sola C: Mycobacterium africanum genotyping using novel spacer oligonucleotides in the direct repeat locus. J Clin Microbiol. 2004, 42 (11): 5053-5057. 10.1128/JCM.42.11.5053-5057.2004.CrossRefPubMedPubMedCentral Brudey K, Gutierrez M, Vincent V, Parsons L, Salfinger M, Rastogi N, Sola C: Mycobacterium africanum genotyping using novel spacer oligonucleotides in the direct repeat locus. J Clin Microbiol. 2004, 42 (11): 5053-5057. 10.1128/JCM.42.11.5053-5057.2004.CrossRefPubMedPubMedCentral

go back to reference Niang M, de la Salmoniere Y, Samb A, Hane A, Cisse M, Gicquel B, Perraut R: Characterization of M. tuberculosis strains from west African patients by spoligotyping. Microbes Infect. 1999, 1 (14): 1189-1192. 10.1016/S1286-4579(99)00243-9.CrossRefPubMed Niang M, de la Salmoniere Y, Samb A, Hane A, Cisse M, Gicquel B, Perraut R: Characterization of M. tuberculosis strains from west African patients by spoligotyping. Microbes Infect. 1999, 1 (14): 1189-1192. 10.1016/S1286-4579(99)00243-9.CrossRefPubMed

go back to reference de Jong B, Antonio M, Awine T, Ogungbemi K, de Jong Y, Gagneux S, De Riemer K, Zozio T, Rastogi N, Borgdorff M, Hill P, Adegbola R: 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. 2009, 47 (4): 994-1001. 10.1128/JCM.01216-08.CrossRefPubMedPubMedCentral de Jong B, Antonio M, Awine T, Ogungbemi K, de Jong Y, Gagneux S, De Riemer K, Zozio T, Rastogi N, Borgdorff M, Hill P, Adegbola R: 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. 2009, 47 (4): 994-1001. 10.1128/JCM.01216-08.CrossRefPubMedPubMedCentral

go back to reference Desmond E, Ahmed A, Probert W, Ely J, Jang Y, Sanders C, Lin S, Flood J: Mycobacterium africanum cases, California. Emerg Infect Dis. 2004, 10 (5): 921-923.CrossRefPubMed Desmond E, Ahmed A, Probert W, Ely J, Jang Y, Sanders C, Lin S, Flood J: Mycobacterium africanum cases, California. Emerg Infect Dis. 2004, 10 (5): 921-923.CrossRefPubMed

go back to reference Gutiérrez M, Galán J, Blázquez J, Bouvet E, Vincent V: Molecular markers demonstrate that the first described multidrug-resistant Mycobacterium bovis outbreak was due to Mycobacterium tuberculosis. J Clin Microbiol. 1999, 37 (4): 971-975.PubMedPubMedCentral Gutiérrez M, Galán J, Blázquez J, Bouvet E, Vincent V: Molecular markers demonstrate that the first described multidrug-resistant Mycobacterium bovis outbreak was due to Mycobacterium tuberculosis. J Clin Microbiol. 1999, 37 (4): 971-975.PubMedPubMedCentral

go back to reference Comas I, Homolka S, Niemann S, Gagneux S: Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies. PLoS ONE. 2009, 4 (11): e7815-10.1371/journal.pone.0007815.CrossRefPubMedPubMedCentral Comas I, Homolka S, Niemann S, Gagneux S: Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies. PLoS ONE. 2009, 4 (11): e7815-10.1371/journal.pone.0007815.CrossRefPubMedPubMedCentral

go back to reference Gagneux S, Small P: Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infect Dis. 2007, 7 (5): 328-337. 10.1016/S1473-3099(07)70108-1.CrossRefPubMed Gagneux S, Small P: Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infect Dis. 2007, 7 (5): 328-337. 10.1016/S1473-3099(07)70108-1.CrossRefPubMed

go back to reference Filliol I, Motiwala A, Cavatore M, Qi W, Hazbón M, Bobadilla del Valle M, Fyfe J, García-García L, Rastogi N, Sola C, Zozio T, Guerrero M, León C, Crabtree J, Angiuoli S, Eisenach K, Durmaz R, Joloba M, Rendón A, Sifuentes-Osornio J, Ponce de León A, Cave M, Fleischmann R, Whittam T, 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 A, Cavatore M, Qi W, Hazbón M, Bobadilla del Valle M, Fyfe J, García-García L, Rastogi N, Sola C, Zozio T, Guerrero M, León C, Crabtree J, Angiuoli S, Eisenach K, Durmaz R, Joloba M, Rendón A, Sifuentes-Osornio J, Ponce de León A, Cave M, Fleischmann R, Whittam T, 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

go back to reference Gutacker M, Smoot J, Migliaccio C, Ricklefs S, Hua S, Cousins D, Graviss E, Shashkina E, Kreiswirth B, Musser J: Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains. Genetics. 2002, 162 (4): 1533-1543.PubMedPubMedCentral Gutacker M, Smoot J, Migliaccio C, Ricklefs S, Hua S, Cousins D, Graviss E, Shashkina E, Kreiswirth B, Musser J: Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains. Genetics. 2002, 162 (4): 1533-1543.PubMedPubMedCentral

go back to reference Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, Homolka S, Roach JC, Kremer K, Petrov DA, Feldman MW, Gagneux S: High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol. 2008, 6 (12): e311-10.1371/journal.pbio.0060311.CrossRefPubMedPubMedCentral Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, Homolka S, Roach JC, Kremer K, Petrov DA, Feldman MW, Gagneux S: High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol. 2008, 6 (12): e311-10.1371/journal.pbio.0060311.CrossRefPubMedPubMedCentral

go back to reference Reed M, Pichler V, McIntosh F, Mattia A, Fallow A, Masala S, Domenech P, Zwerling A, Thibert L, Menzies D, Schwartzman K, Behr M: Major Mycobacterium tuberculosis lineages associate with patient country of origin. J Clin Microbiol. 2009, 47 (4): 1119-1128. 10.1128/JCM.02142-08.CrossRefPubMedPubMedCentral Reed M, Pichler V, McIntosh F, Mattia A, Fallow A, Masala S, Domenech P, Zwerling A, Thibert L, Menzies D, Schwartzman K, Behr M: Major Mycobacterium tuberculosis lineages associate with patient country of origin. J Clin Microbiol. 2009, 47 (4): 1119-1128. 10.1128/JCM.02142-08.CrossRefPubMedPubMedCentral

go back to reference Gutierrez MC, Brisse S, Brosch R, Fabre M, Omaïs B, Marmiesse M, Supply P, Vincent V: Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis. PLoS Pathog. 2005, 1 (1): e5-10.1371/journal.ppat.0010005.CrossRefPubMedPubMedCentral Gutierrez MC, Brisse S, Brosch R, Fabre M, Omaïs B, Marmiesse M, Supply P, Vincent V: Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis. PLoS Pathog. 2005, 1 (1): e5-10.1371/journal.ppat.0010005.CrossRefPubMedPubMedCentral