MRC National Institute for Medical Research, London

Sebastien Gagneux Publications

• Bentley, SD; Comas, I; Bryant, JM; Walker, D; Smith, NH; Harris, SR; Thurston, S; Gagneux, S; Wood, J; Antonio, M; Quail, MA; Gehre, F; Adegbola, RA; Parkhill, J and de Jong, BC (2012)
  The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex.
  PLoS Neglected Tropical Diseases 6, e1552
• Comas, I; Borrell, S; Roetzer, A; Rose, G; Malla, B; Kato-Maeda, M; Galagan, J; Niemann, S and Gagneux, S (2012)
  Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes.
  Nature Genetics 44, 106-110 PubMed abstract
• Weiner, B; Gomez, J; Victor, TC; Warren, RM; Sloutsky, A; Plikaytis, BB; Posey, JE; van Helden, PD; Gey van Pittius, NC; Koehrsen, M; Sisk, P; Stolte, C; White, J; Gagneux, S; Birren, B; Hung, D; Murray, M and Galagan, J (2012)
  Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region.
  PLoS ONE 7, e26038 PubMed abstract
• Comas, I and Gagneux, S (2011)
  A role for systems epidemiology in tuberculosis research.
  Trends in Microbiology 19, 492-500 PubMed abstract
• Fenner, L; Malla, B; Ninet, B; Dubuis, O; Stucki, D; Borrell, S; Huna, T; Bodmer, T; Egger, M and Gagneux, S (2011)
  "Pseudo-Beijing": evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis.
  PLoS ONE 6, e24737 PubMed abstract
• Kato-Maeda, M; Gagneux, S; Flores, LL; Kim, EY; Small, PM; Desmond, EP and Hopewell, PC (2011)
  Strain classification of Mycobacterium tuberculosis: congruence between large sequence polymorphisms and spoligotypes.
  International Journal of Tuberculosis and Lung Disease 15, 131-133 PubMed abstract
• Portevin, D; Gagneux, S; Comas, I and Young, D (2011)
  Human macrophage responses to clinical isolates from the Mycobacterium tuberculosis complex discriminate between ancient and modern lineages.
  PLoS Pathogens 7, e1001307 PubMed abstract
• Yeboah-Manu, D; Asante-Poku, A; Bodmer, T; Stucki, D; Koram, K; Bonsu, F; Pluschke, G and Gagneux, S (2011)
  Genotypic diversity and drug susceptibility patterns among M. tuberculosis complex isolates from South-Western Ghana.
  PLoS ONE 6, e21906 PubMed abstract
• Comas, I; Chakravartti, J; Small, PM; Galagan, J; Niemann, S; Kremer, K; Ernst, JD and Gagneux, S (2010)
  Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved.
  Nature Genetics 42, 498-503 PubMed abstract
• Coscolla, M and Gagneux, S (2010)
  Does M. tuberculosis genomic diversity explain disease diversity?
  Drug Discovery Today: Disease Mechanisms 7, e43-e59 PubMed abstract
• de Jong, BC; Antonio, M and Gagneux, S (2010)
  Mycobacterium africanum--review of an important cause of human tuberculosis in West Africa.
  PLoS Neglected Tropical Diseases 4, e744 PubMed abstract
• Nahid, P; Bliven, EE; Kim, EY; Mac Kenzie, WR; Stout, JE; Diem, L; Johnson, JL; Gagneux, S; Hopewell, PC; Kato-Maeda, M and The Tuberculosis Trials Consortium (2010)
  Influence of M. tuberculosis lineage variability within a clinical trial for pulmonary tuberculosis.
  PLoS ONE 5, e10753 PubMed abstract
• Borrell, S and Gagneux, S (2009)
  Infectiousness, reproductive fitness and evolution of drug-resistant Mycobacterium tuberculosis.
  International Journal of Tuberculosis and Lung Disease 13, 1456-1466 PubMed abstract
• Comas, I and Gagneux, S (2009)
  The past and future of tuberculosis research.
  PLoS Pathogens 5, e1000600 PubMed abstract
• Comas, I; Homolka, S; Niemann, S and Gagneux, S (2009)
  Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies.
  PLoS ONE 4, e7815 PubMed abstract
• de Jong, BC; Antonio, M; Awine, T; Ogungbemi, K; de Jong, YP; Gagneux, S; DeRiemer, K; Zozio, T; Rastogi, N; Borgdorff, M; Hill, PC and Adegbola, RA (2009)
  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 47, 994-1001 PubMed abstract
• Fenner, L; Egger, M and Gagneux, S (2009)
  Annie Darwin's death, the evolution of tuberculosis and the need for systems epidemiology.
  International Journal of Epidemiology 38, 1425-1428 PubMed abstract
• Gagneux, S (2009)
  Fitness cost of drug resistance in Mycobacterium tuberculosis.
  Clinical Microbiology and Infection 15, 66-68 PubMed abstract
• Gagneux, S (2009)
  Strain variation and evolution.
  In: Mycobacterium: Genomics and Molecular Biology. Edited by Brown, A and Parish, T.
  Norwich, Caister Academic Press, 2009. 1-19.
• Niemann, S; Köser, CU; Gagneux, S; Plinke, C; Homolka, S; Bignell, H; Carter, RJ; Cheetham, RK; Cox, A; Gormley, NA; Kokko-Gonzales, P; Murray, LJ; Rigatti, R; Smith, VP; Arends, FPM; Cox, HS; Smith, G and Archer, JAC (2009)
  Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints.
  PLoS ONE 4, e7407 PubMed abstract
• Xu, P; Li, X; Zhao, M; Gui, X; DeRiemer, K; Gagneux, S; Mei, J and Gao, Q (2009)
  Prevalence of fluoroquinolone resistance among tuberculosis patients in Shanghai, China.
  Antimicrobial Agents and Chemotherapy 53, 3170-3172 PubMed abstract
• Caws, M; Thwaites, G; Dunstan, S; Hawn, TR; Thi Ngoc Lane, N; Thuong, NTT; Stepniewska, K; Huyen, MNT; Bang, ND; Huu Loc, T; Gagneux, S; van Soolingen, D; Kremer, K; van der Sande, M; Small, P; Thi Hoang Anh, P; Chinh, NT; Thi Quy, H; Thi Hong Duyen, N; Quang Tho, D; Hieu, NT; Torok, E; Hien, TT; Dung, NH; Thi Quynh Nhu, N; Duy, PM; van Vinh Chau, N and Farrar, J (2008)
  The influence of host and bacterial genotype on the development of disseminated disease with Mycobacterium tuberculosis.
  PLoS Pathogens 4, e1000034 PubMed abstract
• de Jong, BC; Hill, PC; Aiken, A; Awine, T; Antonio, M; Adetifa, IM; Jackson-Sillah, DJ; Fox, A; DeRiemer, K; Gagneux, S; Borgdorff, MW; McAdam, KPWJ; Corrah, T; Small, PM and Adegbola, RA (2008)
  Progression to active tuberculosis, but not transmission, varies by Mycobacterium tuberculosis lineage in The Gambia.
  Journal of Infectious Diseases 198, 1037-1043 PubMed abstract
• Gagneux, S and Small, PM (2008)
  Molecular evolution of mycobacteria.
  In: Handbook of Tuberculosis: Molecular Biology and Biochemistry. Edited by Rubin, E and Kaufmann, SHE.
  Weinheim, Wiley-VCH, 2008. 1, 393-416.
• Hershberg, R; Lipatov, M; Small, PM; Sheffer, H; Niemann, S; Homolka, S; Roach, JC; Kremer, K; Petrov, DA; Feldman, MW and Gagneux, S (2008)
  High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography.
  PLoS Biology 6, 2658-2671 e2311 PubMed abstract
• Narayanan, S; Gagneux, S; Hari, L; Tsolaki, AG; Rajasekhar, S; Narayanan, PR; Small, PM; Holmes, S and DeRiemer, K (2008)
  Genomic interrogation of ancestral Mycobacterium tuberculosis from south India.
  Infection, Genetics and Evolution 8, 474-483 PubMed abstract
• Thwaites, G; Caws, M; Chau, TTH; D'Sa, A; Lan, NTN; Huyen, MNT; Gagneux, S; Anh, PTH; Tho, DQ; Torok, E; Nhu, NTQ; Duyen, NTH; Duy, PM; Richenberg, J; Simmons, C; Hien, TT and Farrar, J (2008)
  Relationship between Mycobacterium tuberculosis genotype and the clinical phenotype of pulmonary and meningeal tuberculosis.
  Journal of Clinical Microbiology 46, 1363-1368 PubMed abstract
• Flores, L; Van, T; Narayanan, S; DeRiemer, K; Kato-Maeda, M and Gagneux, S (2007)
  Large sequence polymorphisms classify Mycobacterium tuberculosis strains with ancestral spoligotyping patterns.
  Journal of Clinical Microbiology 45, 3393-3395 PubMed abstract
• Gagneux, S and Small, PM (2007)
  The global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development.
  Lancet Infectious Diseases 7, 328-337 PubMed abstract
• Leimkugel, J; Forgor, AA; Dangy, J-P; Pflüger, V; Gagneux, S; Hodgson, A and Pluschke, G (2007)
  Genetic diversification of Neisseria meningitidis during waves of colonization and disease in the meningitis belt of sub-Saharan Africa.
  Vaccine 25, A18-23 PubMed abstract
• Leimkugel, J; Hodgson, A; Forgor, AA; Pflüger, V; Dangy, J-P; Smith, T; Achtman, M; Gagneux, S and Pluschke, G (2007)
  Clonal waves of Neisseria colonisation and disease in the African meningitis belt: eight-year longitudinal study in northern Ghana.
  PLoS Medicine 4, e101 PubMed abstract
• Reed, MB; Gagneux, S; Deriemer, K; Small, PM and Barry, CE, 3rd (2007)
  The W-Beijing lineage of Mycobacterium tuberculosis overproduces triglycerides and has the DosR dormancy regulon constitutively upregulated.
  Journal of Bacteriology 189, 2583-2589 PubMed abstract
• De Jong, BC; Hill, PH; Brookes, RH; Gagneux, S; Jeffries, D, J.; Otu, JK; Donker, SA; Fox, A; McAdam, KPW; Small, PM and Adegbola, RA (2006)
  Mycobacterium africanum elicits an attenuated T cell response to early secreted antigenic target, 6 kDa, in patients with tuberculosis and their household contacts.
  Journal of Infectious Diseases 193, 1279-1286 PubMed abstract
• Gagneux, S; Burgos, MV; DeRiemer, K; Enciso, A; Muñoz, S; Hopewell, PC; Small, PM and Pym, AS (2006)
  Impact of bacterial genetics on the transmission of isoniazid-resistant Mycobacterium tuberculosis.
  PLoS Pathogens 2, e61 PubMed abstract
• Gagneux, S; DeRiemer, K; Van, T; Kato-Maeda, M; de Jong, BC; Narayanan, S; Nicol, M; Niemann, S; Kremer, K; Gutierrez, MC; Hilty, M; Hopewell, PC and Small, PM (2006)
  Variable host-pathogen compatibility in Mycobacterium tuberculosis.
  Proceedings of the National Academy of Sciences of the United States of America 103, 2869-2873 PubMed abstract
• Gagneux, S; Long, CD; Small, PM; Van, T; Schoolnik, GK and Bohannan, BJM (2006)
  The competitive cost of antibiotic resistance in Mycobacterium tuberculosis.
  Science 312, 1944-1946 PubMed abstract

[Page last updated 1 May 2012]