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2023Hall, M. B. and Rabodoarivelo, M. S. and Koch, A. and Dippenaar, A. and George, S. and Grobbelaar, M. and Warren, R. and Walker, T. M. and Cox, H. and Gagneux, S. and Crook, D. and Peto, T. and Rakotosamimanana, N. and Grandjean Lapierre, S. and Iqbal, Z.. (2023) Evaluation of nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis. Lancet Microbe, 4 (2). e84-e92. Domínguez, J. and Boeree, M. J. and Cambau, E. and Chesov, D. and Conradie, F. and Cox, V. and Dheda, K. and Dudnyk, A. and Farhat, M. R. and Gagneux, S. and Grobusch, M. P. and Gröschel, M. I. and Guglielmetti, L. and Kontsevaya, I. and Lange, B. and van Leth, F. and Lienhardt, C. and Mandalakas, A. M. and Maurer, F. P. and Merker, M. and Miotto, P. and Molina-Moya, B. and Morel, F. and Niemann, S. and Veziris, N. and Whitelaw, A. and Horsburgh, C. R. and Jr., and Lange, C. and TBnet, and Resist-TB networks, . (2023) Clinical implications of molecular drug resistance testing for Mycobacterium tuberculosis: a 2023 TBnet/RESIST-TB consensus statement. The Lancet infectious diseases, 23 (4). e122-e137. Loiseau, C. and Windels, E. M. and Gygli, S. M. and Jugheli, L. and Maghradze, N. and Brites, D. and Ross, A. and Goig, G. and Reinhard, M. and Borrell, S. and Trauner, A. and Dötsch, A. and Aspindzelashvili, R. and Denes, R. and Reither, K. and Beisel, C. and Tukvadze, N. and Avaliani, Z. and Stadler, T. and Gagneux, S.. (2023) The relative transmission fitness of multidrug-resistant; Mycobacterium tuberculosis; in a drug resistance hotspot. Nat Commun, 14. p. 1988. Zwyer, M. and Rutaihwa, L. K. and Windels, E. and Hella, J. and Menardo, F. and Sasamalo, M. and Sommer, G. and Schmülling, L. and Borrell, S. and Reinhard, M. and Dötsch, A. and Hiza, H. and Stritt, C. and Sikalengo, G. and Fenner, L. and De Jong, B. C. and Kato-Maeda, M. and Jugheli, L. and Ernst, J. D. and Niemann, S. and Jeljeli, L. and Ballif, M. and Egger, M. and Rakotosamimanana, N. and Yeboah-Manu, D. and Asare, P. and Malla, B. and Dou, H. Y. and Zetola, N. and Wilkinson, R. J. and Cox, H. and Carter, E. J. and Gnokoro, J. and Yotebieng, M. and Gotuzzo, E. and Abimiku, A. and Avihingsanon, A. and Xu, Z. M. and Fellay, J. and Portevin, D. and Reither, K. and Stadler, T. and Gagneux, S. and Brites, D.. (2023) Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania. PLoS Pathog, 19 (4). e1010893. Hailu, E. and Cantillon, D. and Madrazo, C. and Rose, G. and Wheeler, P. R. and Golby, P. and Adnew, B. and Gagneux, S. and Aseffa, A. and Gordon, S. V. and Comas, I. and Young, D. B. and Waddell, S. J. and Larrouy-Maumus, G. and Berg, S.. (2023) Lack of methoxy-mycolates characterizes the geographically restricted lineage 7 of Mycobacterium tuberculosis complex. Microb Genom, 9 (5). 001011. Goig, G. A. and Menardo, F. and Salaam-Dreyer, Z. and Dippenaar, A. and Streicher, E. M. and Daniels, J. and Reuter, A. and Borrell, S. and Reinhard, M. and Doetsch, A. and Beisel, C. and Warren, R. M. and Cox, H. and Gagneux, S.. (2023) Effect of compensatory evolution in the emergence and transmission of rifampicin-resistant Mycobacterium tuberculosis in Cape Town, South Africa: a genomic epidemiology study. Lancet Microbe, 4 (7). e506-e515. 2022Cox, H. and Goig, G. A. and Salaam-Dreyer, Z. and Dippenaar, A. and Reuter, A. and Mohr-Holland, E. and Daniels, J. and Cudahy, P. G. T. and Nicol, M. P. and Borrell, S. and Reinhard, M. and Doetsch, A. and Beisel, C. and Gagneux, S. and Warren, R. M. and Furin, J.. (2022) Whole genome sequencing has the potential to improve treatment for rifampicin-resistant tuberculosis in high burden settings: a retrospective cohort study. Journal of clinical microbiology, 60 (3). e0236221. Hiza, H. and Hella, J. and Arbués, A. and Sasamalo, M. and Misana, V. and Fellay, J. and Gagneux, S. and Reither, K. and Portevin, D.. (2022) CD38 expression by antigen-specific CD4 t cells is significantly restored 5 months after treatment initiation independently of sputum bacterial load at the time of tuberculosis diagnosis. Front Med, 9. p. 821776. Maghradze, N. and Jugheli, L. and Borrell, S. and Tukvadze, N. and Kempker, R. R. and Blumberg, H. M. and Gagneux, S.. (2022) Developing customized stepwise MIRU-VNTR typing for tuberculosis surveillance in Georgia. PLoS One, 17 (3). e0264472. Merker, M. and Rasigade, J. P. and Barbier, M. and Cox, H. and Feuerriegel, S. and Kohl, T. A. and Shitikov, E. and Klaos, K. and Gaudin, C. and Antoine, R. and Diel, R. and Borrell, S. and Gagneux, S. and Nikolayevskyy, V. and Andres, S. and Crudu, V. and Supply, P. and Niemann, S. and Wirth, T.. (2022) Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis. Nat Commun, 13. p. 5105. Vera-Cabrera, L. and Ramos-Cavazos, C. J. and Youssef, N. A. and Pearce, C. M. and Molina-Torres, C. A. and Avalos-Ramirez, R. and Gagneux, S. and Ocampo-Candiani, J. and Gonzalez-Juarrero, M. and Mayorga-Rodriguez, J. A. and Mayorga-Garibaldi, L. and Spencer, J. S. and Jackson, M. and Avanzi, C.. (2022) Mycobacterium leprae Infection in a Wild Nine-Banded Armadillo, Nuevo Leon, Mexico. Emerg Infect Dis, 28 (3). pp. 747-749. Xu, Z. M. and Rüeger, S. and Zwyer, M. and Brites, D. and Hiza, H. and Reinhard, M. and Rutaihwa, L. and Borrell, S. and Isihaka, F. and Temba, H. and Maroa, T. and Naftari, R. and Hella, J. and Sasamalo, M. and Reither, K. and Portevin, D. and Gagneux, S. and Fellay, J.. (2022) Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations. PLoS Comput Biol, 18 (1). e1009628. Van Rie, A. and Walker, T. and de Jong, B. and Rupasinghe, P. and Riviere, E. and Dartois, V. and Sonnenkalb, L. and Machado, D. and Gagneux, S. and Supply, P. and Dreyer, V. and Niemann, S. and Goig, G. and Meehan, C. and Tagliani, E. and Cirillo, D. M.. (2022) Balancing access to BPaLM regimens and risk of resistance. The Lancet infectious diseases, S1473-3099 (22). 00543-00546. Otchere, I. D. and Morgan, P. A. and Asare, P. and Osei-Wusu, S. and Aboagye, S. Y. and Yirenkyi, S. O. and Musah, A. B. and Danso, E. K. and Tetteh-Ocloo, G. and Afum, T. and Asante-Poku, A. and Laryea, C. and Poku, Y. A. and Bonsu, F. and Gagneux, S. and Yeboah-Manu, D.. (2022) Analysis of drug resistance among difficult-to-treat tuberculosis patients in Ghana identifies several pre-XDR TB cases. Front Microbiol, 13. p. 1069292. 2021Asare, P. and Osei-Wusu, S. and Baddoo, N. A. and Bedeley, E. and Otchere, I. D. and Brites, D. and Loiseau, C. and Asante-Poku, A. and Prah, D. A. and Borrell, S. and Reinhard, M. and Omari, M. A. and Forson, A. and Koram, K. A. and Gagneux, S. and Yeboah-Manu, D.. (2021) Genomic epidemiological analysis identifies high relapse among individuals with recurring tuberculosis and provides evidence of household recent TB transmission in Ghana. Int J Infect Dis, 106. pp. 13-22. Alagna, R. and Cabibbe, A. M. and Miotto, P. and Saluzzo, F. and Köser, C. U. and Niemann, S. and Gagneux, S. and Rodrigues, C. and Rancoita, P. V. M. and Cirillo, D. M.. (2021) Is the new WHO definition of extensively drug-resistant tuberculosis easy to apply in practice? The European respiratory journal, 58. p. 2100959. Castro, R. A. D. and Borrell, S. and Gagneux, S.. (2021) The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis. FEMS microbiology reviews, 45 (4). fuaa071. Cox, H. and Salaam-Dreyer, Z. and Goig, G. A. and Nicol, M. P. and Menardo, F. and Dippenaar, A. and Mohr-Holland, E. and Daniels, J. and Cudahy, P. G. T. and Borrell, S. and Reinhard, M. and Dötsch, A. and Beisel, C. and Reuter, A. and Furin, J. and Gagneux, S. and Warren, R. M.. (2021) Potential contribution of HIV during first-line tuberculosis treatment to subsequent rifampicin-monoresistant tuberculosis and acquired tuberculosis drug resistance in South Africa: a retrospective molecular epidemiology study. Lancet Microbe, 2 (11). e584-e593. Coscolla, M. and Gagneux, S. and Menardo, F. and Loiseau, C. and Ruiz-Rodriguez, P. and Borrell, S. and Otchere, I. D. and Asante-Poku, A. and Asare, P. and Sanchez-Buso, L. and Gehre, F. and Sanoussi, C. N. and Antonio, M. and Affolabi, D. and Fyfe, J. and Beckert, P. and Niemann, S. and Alabi, A. S. and Grobusch, M. P. and Kobbe, R. and Parkhill, J. and Beisel, C. and Fenner, L. and Bottger, E. C. and Meehan, C. J. and Harris, S. R. and de Jong, B. C. and Yeboah-Manu, D. and Brites, D.. (2021) Phylogenomics of; Mycobacterium africanum; reveals a new lineage and a complex evolutionary history. Microb Genom, 7 (2). 000477. Hockings, K. J. and Mubemba, B. and Avanzi, C. and Pleh, K. and Dux, A. and Bersacola, E. and Bessa, J. and Ramon, M. and Metzger, S. and Patrono, L. V. and Jaffe, J. E. and Benjak, A. and Bonneaud, C. and Busso, P. and Couacy-Hymann, E. and Gado, M. and Gagneux, S. and Johnson, R. C. and Kodio, M. and Lynton-Jenkins, J. and Morozova, I. and Mätz-Rensing, K. and Regalla, A. and Said, A. R. and Schuenemann, V. J. and Sow, S. O. and Spencer, J. S. and Ulrich, M. and Zoubi, H. and Cole, S. T. and Wittig, R. M. and Calvignac-Spencer, S. and Leendertz, F. H.. (2021) Leprosy in wild chimpanzees. Nature, 598 (7882). pp. 652-656. Hiza, H. and Hella, J. and Arbués, A. and Magani, B. and Sasamalo, M. and Gagneux, S. and Reither, K. and Portevin, D.. (2021) Case-control diagnostic accuracy study of a non-sputum CD38-based TAM-TB test from a single milliliter of blood. Sci Rep, 11 (1). p. 13190. Haraka, F. and Kakolwa, M. and Schumacher, S. G. and Nathavitharana, R. R. and Denkinger, C. M. and Gagneux, S. and Reither, K. and Ross, A.. (2021) Impact of the diagnostic test Xpert MTB/RIF on patient outcomes for tuberculosis (Review). Cochrane Database Syst Rev, 2021 (4). CD012972. Guimarães, A. E. D. S. and Sharma, A. and Furlaneto, I. P. and Rutaihwa, L. and Cardoso, J. F. and da Conceição, M. L. and Spinassé, L. B. and Machado, E. and Lopes, M. L. and Duarte, R. S. and Gagneux, S. and Suffys, P. N. and Lima, K. V. B. and Conceição, E. C.. (2021) Evaluation of drug susceptibility profile of; Mycobacterium tuberculosis; lineage 1 from Brazil based on whole genome sequencing and phenotypic methods. MemoÌ�rias do Instituto Oswaldo Cruz, 115. e200520. Ley, S. D. and Pillay, S. and Streicher, E. M. and van der Heijden, Y. F. and Sirgel, F. and Derendinger, B. and de Kock, M. and Gagneux, S. and Warren, R. M. and Theron, G. and de Vos, M.. (2021) Melting the eis: non-detection of kanamycin resistance markers by routine diagnostic tests and identification of new eis-promoter variants. Antimicrob Agents Chemother, 65 (7). e0250220. Menardo, F. and Rutaihwa, L. K. and Zwyer, M. and Borrell, S. and Comas, I. and Conceicao, E. C. and Coscolla, M. and Cox, H. and Joloba, M. and Dou, H. Y. and Feldmann, J. and Fenner, L. and Fyfe, J. and Gao, Q. and Garcia de Viedma, D. and Garcia-Basteiro, A. L. and Gygli, S. M. and Hella, J. and Hiza, H. and Jugheli, L. and Kamwela, L. and Kato-Maeda, M. and Liu, Q. and Ley, S. D. and Loiseau, C. and Mahasirimongkol, S. and Malla, B. and Palittapongarnpim, P. and Rakotosamimanana, N. and Rasolofo, V. and Reinhard, M. and Reither, K. and Sasamalo, M. and Silva Duarte, R. and Sola, C. and Suffys, P. and Batista Lima, K. V. and Yeboah-Manu, D. and Beisel, C. and Brites, D. and Gagneux, S.. (2021) Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim. F1000Res, 10. p. 60. Menardo, F. and Gagneux, S. and Freund, F.. (2021) Multiple merger genealogies in outbreaks of Mycobacterium tuberculosis. Molecular biology and evolution, 38 (1). pp. 290-306. Moreno-Molina, M. and Shubladze, N. and Khurtsilava, I. and Avaliani, Z. and Bablishvili, N. and Torres-Puente, M. and Villamayor, L. and Gabrielian, A. and Rosenthal, A. and Vilaplana, C. and Gagneux, S. and Kempker, R. R. and Vashakidze, S. and Comas, I.. (2021) Genomic analyses of Mycobacterium tuberculosis from human lung resections reveal a high frequency of polyclonal infections. Nat Commun, 12. p. 2716. Minja, L. T. and Hella, J. and Mbwambo, J. and Nyandindi, C. and Omary, U. S. and Levira, F. and Mpagama, S. and Shimwela, M. and Okuma, J. and Gagneux, S. and Bruce, R. D. and Reither, K.. (2021) High burden of tuberculosis infection and disease among people receiving medication-assisted treatment for substance use disorder in Tanzania. PLoS One, 16 (4). e0250038. Pečerska, J. and Kuhnert, D. and Meehan, C. J. and Coscolla, M. and de Jong, B. C. and Gagneux, S. and Stadler, T.. (2021) Quantifying transmission fitness costs of multi-drug resistant tuberculosis. Epidemics, 36. p. 100471. Osei-Wusu, S. and Otchere, I. D. and Morgan, P. and Musah, A. B. and Siam, I. M. and Asandem, D. and Afum, T. and Asare, P. and Asante-Poku, A. and Kusi, K. A. and Gagneux, S. and Yeboah-Manu, D.. (2021) Genotypic and phenotypic diversity of Mycobacterium tuberculosis complex genotypes prevalent in West Africa. PLoS One, 16 (8). e0255433. Sanoussi, C. N. and Coscolla, M. and Ofori-Anyinam, B. and Otchere, I. D. and Antonio, M. and Niemann, S. and Parkhill, J. and Harris, S. and Yeboah-Manu, D. and Gagneux, S. and Rigouts, L. and Affolabi, D. and de Jong, B. C. and Meehan, C. J.. (2021) Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv. Microb Genom, 7 (7). 000437. Salaam-Dreyer, Z. and Streicher, E. M. and Sirgel, F. A. and Menardo, F. and Borrell, S. and Reinhard, M. and Doetsch, A. and Cudahy, P. G. T. and Mohr-Holland, E. and Daniels, J. and Dippenaar, A. and Nicol, M. P. and Gagneux, S. and Warren, R. M. and Cox, H.. (2021) Rifampicin mono-resistant tuberculosis is not the same as multidrug-resistant tuberculosis: a descriptive study from Khayelitsha, South Africa. Antimicrob Agents Chemother, 65 (11). e0036421. Trauner, A. and Banaei-Esfahani, A. and Gygli, S. M. and Warmer, P. and Feldmann, J. and Zampieri, M. and Borrell, S. and Collins, B. C. and Beisel, C. and Aebersold, R. and Gagneux, S.. (2021) Expression dysregulation as a mediator of fitness costs in antibiotic resistance. Antimicrob Agents Chemother, 65 (9). e0050421. Zürcher, K. and Reichmuth, M. L. and Ballif, M. and Loiseau, C. and Borrell, S. and Reinhard, M. and Skrivankova, V. and Hömke, R. and Sander, P. and Avihingsanon, A. and Abimiku, A. G. and Marcy, O. and Collantes, J. and Carter, E. J. and Wilkinson, R. J. and Cox, H. and Yotebieng, M. and Huebner, R. and Fenner, L. and Böttger, E. C. and Gagneux, S. and Egger, M.. (2021) Mortality from drug-resistant tuberculosis in high-burden countries comparing routine drug susceptibility testing with whole-genome sequencing: a multicentre cohort study. Lancet Microbe, 2. e320-30. Ticlla, M. R. and Hella, J. and Hiza, H. and Sasamalo, M. and Mhimbira, F. and Rutaihwa, L. K. and Droz, S. and Schaller, S. and Reither, K. and Hilty, M. and Comas, I. and Beisel, C. and Schmid, C. D. and Fenner, L. and Gagneux, S.. (2021) The sputum microbiome in pulmonary tuberculosis and its association with disease manifestations: a cross-sectional study. Front Microbiol, 12. p. 633396. Gygli, S. M. and Loiseau, C. and Jugheli, L. and Adamia, N. and Trauner, A. and Reinhard, M. and Ross, A. and Borrell, S. and Aspindzelashvili, R. and Maghradze, N. and Reither, K. and Beisel, C. and Tukvadze, N. and Avaliani, Z. and Gagneux, S.. (2021) Publisher Correction: Prisons as ecological drivers of fitness-compensated multidrug-resistant Mycobacterium tuberculosis. Nat Med, 27 (7). p. 1308. Gygli, S. M. and Loiseau, C. and Jugheli, L. and Adamia, N. and Trauner, A. and Reinhard, M. and Ross, A. and Borrell, S. and Aspindzelashvili, R. and Maghradze, N. and Reither, K. and Beisel, C. and Tukvadze, N. and Avaliani, Z. and Gagneux, S.. (2021) Prisons as ecological drivers of fitness-compensated multidrug-resistant Mycobacterium tuberculosis. Nat Med, 27. pp. 1171-1177. 2020Castro, Rhastin A. D. and Ross, Amanda and Kamwela, Lujeko and Reinhard, Miriam and Loiseau, Chloé and Feldmann, Julia and Borrell, Sonia and Trauner, Andrej and Gagneux, Sebastien. (2020) The genetic background modulates the evolution of fluoroquinolone-resistance in Mycobacterium tuberculosis. Molecular biology and evolution, 37 (1). pp. 195-207. Ezewudo, M. and Borens, A. and Chiner-Oms, A. and Miotto, P. and Chindelevitch, L. and Starks, A. M. and Hanna, D. and Liwski, R. and Zignol, M. and Gilpin, C. and Niemann, S. and Kohl, T. A. and Warren, R. M. and Crook, D. and Gagneux, S. and Hoffner, S. and Rodrigues, C. and Comas, I. and Engelthaler, D. M. and Alland, D. and Rigouts, L. and Lange, C. and Dheda, K. and Hasan, R. and McNerney, R. and Cirillo, D. M. and Schito, M. and Rodwell, T. C. and Posey, J.. (2020) Author correction: Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase. Scientific Reports, 10 (1). p. 3531. Loiseau, Chloé and Menardo, Fabrizio and Aseffa, Abraham and Hailu, Elena and Gumi, Balako and Ameni, Gobena and Berg, Stefan and Rigouts, Leen and Robbe-Austerman, Suelee and Zinsstag, Jakob and Gagneux, Sebastien and Brites, Daniela. (2020) An African origin for Mycobacterium bovis. Evolution, medicine, and public health, 2020. pp. 49-59. Øyås, Ove and Borrell, Sonia and Trauner, Andrej and Zimmermann, Michael and Feldmann, Julia and Liphardt, Thomas and Gagneux, Sebastien and Stelling, Jörg and Sauer, Uwe and Zampieri, Mattia. (2020) Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences of the United States of America, 117 (15). pp. 8494-8502. Sousa, Jeremy and Cá, Baltazar and Maceiras, Ana Raquel and Simões-Costa, Luisa and Fonseca, Kaori L. and Fernandes, Ana Isabel and Ramos, Angélica and Carvalho, Teresa and Barros, Leandro and Magalhães, Carlos and Chiner-Oms, Álvaro and Machado, Henrique and Veiga, Maria Isabel and Singh, Albel and Pereira, Rui and Amorim, António and Vieira, Jorge and Vieira, Cristina P. and Bhatt, Apoorva and Rodrigues, Fernando and Rodrigues, Pedro N. S. and Gagneux, Sebastien and Castro, António Gil and Guimarães, João Tiago and Bastos, Helder Novais and Osório, Nuno S. and Comas, Iñaki and Saraiva, Margarida. (2020) Mycobacterium tuberculosis associated with severe tuberculosis evades cytosolic surveillance systems and modulates IL-1β production. Nature Communications, 11. p. 1949. McHenry, Michael L. and Bartlett, Jacquelaine and Igo, Robert P. and Wampande, Eddie M. and Benchek, Penelope and Mayanja-Kizza, Harriet and Fluegge, Kyle and Hall, Noemi B. and Gagneux, Sebastien and Tishkoff, Sarah A. and Wejse, Christian and Sirugo, Giorgio and Boom, W. Henry and Joloba, Moses and Williams, Scott M. and Stein, Catherine M.. (2020) Interaction between host genes and Mycobacterium tuberculosis lineage can affect tuberculosis severity: evidence for coevolution? PLoS genetics, 16 (4). e1008728. Asare, Prince and Otchere, Isaac Darko and Bedeley, Edmund and Brites, Daniela and Loiseau, Chloé and Baddoo, Nyonuku Akosua and Asante-Poku, Adwoa and Osei-Wusu, Stephen and Prah, Diana Ahu and Borrell, Sonia and Reinhard, Miriam and Forson, Audrey and Koram, Kwadwo Ansah and Gagneux, Sebastien and Yeboah-Manu, Dorothy. (2020) Whole genome sequencing and spatial analysis identifies recent tuberculosis transmission hotspots in Ghana. Frontiers in medicine, 7. p. 161. Ngabonziza, Jean Claude Semuto and Loiseau, Chloé and Marceau, Michael and Jouet, Agathe and Menardo, Fabrizio and Tzfadia, Oren and Antoine, Rudy and Niyigena, Esdras Belamo and Mulders, Wim and Fissette, Kristina and Diels, Maren and Gaudin, Cyril and Duthoy, Stéphanie and Ssengooba, Willy and André, Emmanuel and Kaswa, Michel K. and Habimana, Yves Mucyo and Brites, Daniela and Affolabi, Dissou and Mazarati, Jean Baptiste and de Jong, Bouke Catherine and Rigouts, Leen and Gagneux, Sebastien and Meehan, Conor Joseph and Supply, Philip. (2020) A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region. Nature Communications, 11. p. 2917. Haraka, F. and Schumacher, S. G. and Ross, A. and Mantsoki, A. and Gagneux, S. and Reither, K. and Denkinger, C. M.. (2020) Effect of history of tuberculosis on specificity of Xpert MTB/RIF. Eur Respir J, 56 (3). p. 2000343. Loiseau, C. and Brites, D. and Reinhard, M. and Zurcher, K. and Borrell, S. and Ballif, M. and Fenner, L. and Cox, H. and Rutaihwa, L. K. and Wilkinson, R. J. and Yotebieng, M. and Carter, E. J. and Abimiku, A. and Marcy, O. and Gotuzzo, E. and Avihingsanon, A. and Zetola, N. and Doulla, B. and Bottger, E. C. and Egger, M. and Gagneux, S.. (2020) HIV coinfection is associated with low fitness rpoB variants in rifampicin-resistant Mycobacterium tuberculosis. Antimicrobial agents and chemotherapy, 64 (10). e00782-20. Reichmuth, M. L. and Homke, R. and Zürcher, K. and Sander, P. and Avihingsanon, A. and Collantes, J. and Loiseau, C. and Borrell, S. and Reinhard, M. and Wilkinson, R. J. and Yotebieng, M. and Fenner, L. and Böttger, E. C. and Gagneux, S. and Egger, M. and Keller, P. M. and International epidemiology Databases to Evaluate Aids, . (2020) Natural polymorphisms in Mycobacterium tuberculosis conferring resistance to delamanid in drug-naïve patients. Antimicrob Agents Chemother, 64 (11). e00513-20. 2019Mhimbira, F. and Hiza, H. and Mbuba, E. and Hella, J. and Kamwela, L. and Sasamalo, M. and Ticlla, M. and Said, K. and Mhalu, G. and Chiryamkubi, M. and Schindler, C. and Reither, K. and Gagneux, S. and Fenner, L.. (2019) Prevalence and clinical significance of respiratory viruses and bacteria detected in tuberculosis patients compared to household contact controls in Tanzania: a cohort study. Clinical microbiology and infection, 25 (1). 107.e1-107.e7. Asante-Poku, Adwoa and Asare, Prince and Baddoo, Nyonuku Akosua and Forson, Audrey and Klevor, Pius and Otchere, Isaac Darko and Aboagye, Sammy Yaw and Osei-Wusu, Stephen and Danso, Emelia Konadu and Koram, Kwadwo and Gagneux, Sebastien and Yeboah-Manu, Dorothy. (2019) TB-diabetes co-morbidity in Ghana : the importance of Mycobacterium africanum infection. PLoS ONE, 14 (2). e0211822. Zürcher, Kathrin and Ballif, Marie and Fenner, Lukas and Borrell, Sonia and Keller, Peter M. and Gnokoro, Joachim and Marcy, Olivier and Yotebieng, Marcel and Diero, Lameck and Carter, E. Jane and Rockwood, Neesha and Wilkinson, Robert J. and Cox, Helen and Ezati, Nicholas and Abimiku, Alash'le G. and Collantes, Jimena and Avihingsanon, Anchalee and Kawkitinarong, Kamon and Reinhard, Miriam and Hömke, Rico and Huebner, Robin and Gagneux, Sebastien and Böttger, Erik C. and Egger, Matthias and International epidemiology Databases to Evaluate Aids consortium, . (2019) Drug susceptibility testing and mortality in patients treated for tuberculosis in high-burden countries : a multicentre cohort study. The Lancet infectious diseases, 19 (3). pp. 298-307. Otchere, Isaac Darko and van Tonder, Andries J. and Asante-Poku, Adwoa and Sánchez-Busó, Leonor and Coscollá, Mireia and Osei-Wusu, Stephen and Asare, Prince and Aboagye, Samuel Yaw and Ekuban, Samuel Acquah and Yahayah, Abdallah Iddrisu and Forson, Audrey and Baddoo, Akosua and Laryea, Clement and Parkhill, Julian and Harris, Simon R. and Gagneux, Sebastien and Yeboah-Manu, Dorothy. (2019) Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana. PLoS ONE, 14 (3). e0209395. Borrell, Sònia and Trauner, Andrej and Brites, Daniela and Rigouts, Leen and Loiseau, Chloe and Coscolla, Mireia and Niemann, Stefan and De Jong, Bouke and Yeboah-Manu, Dorothy and Kato-Maeda, Midori and Feldmann, Julia and Reinhard, Miriam and Beisel, Christian and Gagneux, Sebastien. (2019) Reference set of Mycobacterium tuberculosis clinical strains: a tool for research and product development. PLoS ONE, 14 (3). e0214088. Gygli, Sebastian M. and Keller, Peter M. and Ballif, Marie and Blöchliger, Nicolas and Hömke, Rico and Reinhard, Miriam and Loiseau, Chloé and Ritter, Claudia and Sander, Peter and Borrell, Sonia and Collantes Loo, Jimena and Avihingsanon, Anchalee and Gnokoro, Joachim and Yotebieng, Marcel and Egger, Matthias and Gagneux, Sebastien and Böttger, Erik C.. (2019) Whole-genome sequencing for drug resistance profile prediction in Mycobacterium tuberculosis. Antimicrobial agents and chemotherapy, 63 (4). e02175-18. Rutaihwa, Liliana K. and Sasamalo, Mohamed and Jaleco, Aladino and Hella, Jerry and Kingazi, Ally and Kamwela, Lujeko and Kingalu, Amri and Malewo, Bryceson and Shirima, Raymond and Doetsch, Anna and Feldmann, Julia and Reinhard, Miriam and Borrell, Sonia and Brites, Daniela and Reither, Klaus and Doulla, Basra and Fenner, Lukas and Gagneux, Sebastien. (2019) Insights into the genetic diversity of Mycobacterium tuberculosis in Tanzania. PLoS ONE, 14 (4). e0206334. Mhalu, Grace and Hella, Jerry and Mhimbira, Francis and Said, Khadija and Mosabi, Thomas and Mlacha, Yeromin P. and Schindler, Christian and Gagneux, Sébastien and Reither, Klaus and de Hoogh, Kees and Weiss, Mitchell G. and Zemp, Elisabeth and Fenner, Lukas. (2019) Pathways and associated costs of care in patients with confirmed and presumptive tuberculosis in Tanzania : a cross-sectional study. BMJ Open, 9 (4). e025079. Payne, Joshua L. and Menardo, Fabrizio and Trauner, Andrej and Borrell, Sonia and Gygli, Sebastian M. and Loiseau, Chloe and Gagneux, Sebastien and Hall, Alex R.. (2019) Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis. PLoS Biology, 17 (5). e3000265. Rutaihwa L, Menardo F. and Stucki D, Gygli S. M. and Ley SD, Malla B. and Feldmann J, Borrell S. and Beisel C, Middelkoop K. and Carter JE, Diero L. and Ballif M, Jugheli L. and Reither K, Fenner L. and Brites D, Gagneux S.. (2019) Multiple introductions of Mycobacterium tuberculosis lineage 2-Beijing into Africa over centuries. Frontiers in Ecology and Evolution, 7. p. 112. Loiseau, Chloé and Brites, Daniela and Moser, Irmgard and Coll, Francesc and Pourcel, Christine and Robbe-Austerman, Suelee and Escuyer, Vincent and Musser, Kimberlee A. and Peacock, Sharon J. and Feuerriegel, Silke and Kohl, Thomas A. and Niemann, Stefan and Gagneux, Sebastien and Köser, Claudio U.. (2019) Revised interpretation of the Hain Lifescience GenoType MTBC to differentiate Mycobacterium canettii and members of the M. tuberculosis complex. Antimicrobial agents and chemotherapy, 63 (6). e00159-19. Conceição, Emilyn Costa and Refregier, Guislaine and Gomes, Harrison Magdinier and Olessa-Daragon, Xavier and Coll, Francesc and Ratovonirina, Noël Harijaona and Rasolofo-Razanamparany, Voahangy and Lopes, Maria Luiza and van Soolingen, Dick and Rutaihwa, Liliana and Gagneux, Sebastien and Bollela, Valdes Roberto and Suffys, Philip Noel and Duarte, Rafael Silva and Lima, Karla Valéria Batista and Sola, Christophe Noel. (2019) Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 73. pp. 337-341. Chiner-Oms, A. and Sánchez-Busó, L. and Corander, J. and Gagneux, S. and Harris, S. R. and Young, D. and González-Candelas, F. and Comas, I.. (2019) Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex. Science Advances, 5 (6). eaaw3307. Chiner-Oms, Álvaro and Berney, Michael and Boinett, Christine and González-Candelas, Fernando and Young, Douglas B. and Gagneux, Sebastien and Jacobs, William R. and Parkhill, Julian and Cortes, Teresa and Comas, Iñaki. (2019) Genome-wide mutational biases fuel transcriptional diversity in the Mycobacterium tuberculosis complex. Nature Communications, 10. p. 3994. Meehan, Conor J. and Goig, Galo A. and Kohl, Thomas A. and Verboven, Lennert and Dippenaar, Anzaan and Ezewudo, Matthew and Farhat, Maha R. and Guthrie, Jennifer L. and Laukens, Kris and Miotto, Paolo and Ofori-Anyinam, Boatema and Dreyer, Viola and Supply, Philip and Suresh, Anita and Utpatel, Christian and van Soolingen, Dick and Zhou, Yang and Ashton, Philip M. and Brites, Daniela and Cabibbe, Andrea M. and de Jong, Bouke C. and de Vos, Margaretha and Menardo, Fabrizio and Gagneux, Sebastien and Gao, Qian and Heupink, Tim H. and Liu, Qingyun and Loiseau, Chloé and Rigouts, Leen and Rodwell, Timothy C. and Tagliani, Elisa and Walker, Timothy M. and Warren, Robin M. and Zhao, Yanlin and Zignol, Matteo and Schito, Marco and Gardy, Jennifer and Cirillo, Daniela M. and Niemann, Stefan and Comas, Inaki and Van Rie, Annelies. (2019) Whole genome sequencing of Mycobacterium tuberculosis : current standards and open issues. Nature Reviews Microbiology, 17 (9). pp. 533-545. Menardo, Fabrizio and Duchêne, Sebastian and Brites, Daniela and Gagneux, Sebastien. (2019) The molecular clock of Mycobacterium tuberculosis. PLoS Pathogens, 15 (9). e1008067. Wampande, Eddie M. and Naniima, Peter and Mupere, Ezekiel and Kateete, David P. and Malone, LaShaunda L. and Stein, Catherine M. and Mayanja-Kizza, Harriet and Gagneux, Sebastien and Boom, W. Henry and Joloba, Moses L.. (2019) Genetic variability and consequence of Mycobacterium tuberculosis lineage 3 in Kampala-Uganda. PLoS ONE, 14 (9). e0221644. Maghradze, Nino and Jugheli, Levan and Borrell, Sonia and Tukvadze, Nestani and Aspindzelashvili, Rusudan and Avaliani, Zaza and Reither, Klaus and Gagneux, Sebastien. (2019) Classifying recurrent Mycobacterium tuberculosis cases in Georgia using MIRU-VNTR typing. PLoS ONE, 14 (10). e0223610. Mulholland, C. V. and Shockey, A. C. and Aung, H. L. and Cursons, R. T. and O'Toole , R. F. and Gautam, S. S. and Brites, D. and Gagneux, S. and Roberts, A. R. and Karalus, N. and Cook, G. M. and Pepperell, C. S. and Arcus, V. L.. (2019) Dispersal of Mycobacterium tuberculosis driven by historical European trade in the South Pacific. Frontiers in Microbiology, 10 (4). p. 2778. 2018Bastos, Helder Novais and Osório, Nuno S. and Gagneux, Sebastien and Comas, Iñaki and Saraiva, Margarida. (2018) The troika host-pathogen-extrinsic factors in Tuberculosis: modulating inflammation and clinical outcomes. Frontiers in Immunology, 8. p. 1948. Carey, Allison F. and Rock, Jeremy M. and Krieger, Inna V. and Chase, Michael R. and Fernandez-Suarez, Marta and Gagneux, Sebastien and Sacchettini, James C. and Ioerger, Thomas R. and Fortune, Sarah M.. (2018) TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities. PLoS Pathogens, 14 (3). e1006939. Zampieri, Mattia and Szappanos, Balazs and Buchieri, Maria Virginia and Trauner, Andrej and Piazza, Ilaria and Picotti, Paola and Gagneux, Sébastien and Borrell, Sonia and Gicquel, Brigitte and Lelievre, Joel and Papp, Balazs and Sauer, Uwe. (2018) High-throughput metabolomic analysis predicts mode of action of uncharacterized antimicrobial compounds. Science Translational Medicine, 10 (429). eaal3973. Sikalengo, George and Hella, Jerry and Mhimbira, Francis and Rutaihwa, Liliana K. and Bani, Farida and Ndege, Robert and Sasamalo, Mohamed and Kamwela, Lujeko and Said, Khadija and Mhalu, Grace and Mlacha, Yeromin and Hatz, Christoph and Knopp, Stefanie and Gagneux, Sébastien and Reither, Klaus and Utzinger, Jürg and Tanner, Marcel and Letang, Emilio and Weisser, Maja and Fenner, Lukas. (2018) Distinct clinical characteristics and helminth co-infections in adult tuberculosis patients from urban compared to rural Tanzania. Infectious Diseases of Poverty, 7. p. 24. Hella, Jerry and Cercamondi, Colin I. and Mhimbira, Francis and Sasamalo, Mohamed and Stoffel, Nicole and Zwahlen, Marcel and Bodmer, Thomas and Gagneux, Sebastien and Reither, Klaus and Zimmermann, Michael B. and Risch, Lorenz and Fenner, Lukas. (2018) Anemia in tuberculosis cases and household controls from Tanzania: contribution of disease, coinfections, and the role of hepcidin. PLoS ONE, 13 (4). e0195985. Boillat-Blanco, Noémie and Tumbo, Anneth-Mwasi N. and Perreau, Matthieu and Amelio, Patrizia and Ramaiya, Kaushik L. and Mganga, Maliwaza and Schindler, Christian and Gagneux, Sebastien and Reither, Klaus and Probst-Hensch, Nicole and Pantaleo, Giuseppe and Daubenberger, Claudia and Portevin, Damien. (2018) Hyperglycaemia is inversely correlated with live M. bovis BCG-specific CD4; +; T cell responses in Tanzanian adults with latent or active tuberculosis. Immunity, inflammation and disease, 6 (2). pp. 345-353. Gagneux, Sebastien. (2018) Ecology and evolution of Mycobacterium tuberculosis. Nature Reviews Microbiology, 16 (4). pp. 202-213. Nahid, P. and Jarlsberg, L. G. and Kato-Maeda, M. and Segal, M. R. and Osmond, D. H. and Gagneux, S. and Dobos, K. and Gold, M. and Hopewell, P. C. and Lewinsohn, D. M.. (2018) Interplay of strain and race/ethnicity in the innate immune response to M. tuberculosis. PLoS ONE, 13 (5). e0195392. Otchere, Isaac Darko and Coscollá, Mireia and Sánchez-Busó, Leonor and Asante-Poku, Adwoa and Brites, Daniela and Loiseau, Chloe and Meehan, Conor and Osei-Wusu, Stephen and Forson, Audrey and Laryea, Clement and Yahayah, Abdallah Iddrisu and Baddoo, Akosua and Ansa, Gloria Akosua and Aboagye, Samuel Yaw and Asare, Prince and Borrell, Sonia and Gehre, Florian and Beckert, Patrick and Kohl, Thomas A. and N'dira, Sanoussi and Beisel, Christian and Antonio, Martin and Niemann, Stefan and de Jong, Bouke C. and Parkhill, Julian and Harris, Simon R. and Gagneux, Sebastien and Yeboah-Manu, Dorothy. (2018) Comparative genomics of Mycobacterium africanum lineage 5 and lineage 6 from Ghana suggests distinct ecological niches. Scientific reports, 8. p. 11269. Asare, Prince and Asante-Poku, Adwoa and Prah, Diana Ahu and Borrell, Sonia and Osei-Wusu, Stephen and Otchere, Isaac Darko and Forson, Audrey and Adjapong, Gloria and Koram, Kwadwo Ansah and Gagneux, Sebastien and Yeboah-Manu, Dorothy. (2018) Reduced transmission of Mycobacterium africanum compared to Mycobacterium tuberculosis in urban West Africa. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, 73. pp. 30-42. Ezewudo, Matthew and Borens, Amanda and Chiner-Oms, Álvaro and Miotto, Paolo and Chindelevitch, Leonid and Starks, Angela M. and Hanna, Debra and Liwski, Richard and Zignol, Matteo and Gilpin, Christopher and Niemann, Stefan and Kohl, Thomas Andreas and Warren, Robin M. and Crook, Derrick and Gagneux, Sebastien and Hoffner, Sven and Rodrigues, Camilla and Comas, Iñaki and Engelthaler, David M. and Alland, David and Rigouts, Leen and Lange, Christoph and Dheda, Keertan and Hasan, Rumina and McNerney, Ruth and Cirillo, Daniela M. and Schito, Marco and Rodwell, Timothy C. and Posey, James. (2018) Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase. Scientific Reports, 8 (1). p. 15382. Conceição, E. C. and Guimarães, A. E. D. S. and Lopes, M. L. and Furlaneto, I. P. and Rodrigues, Y. C. and da Conceição, M. L. and Barros, W. A. and Cardoso, N. C. and Sharma, A. and Lima, L. N. G. C. and Gomes, H. M. and Duarte, R. S. and Frota, C. and Rutaihwa, L. K. and Gagneux, S. and Suffys, P. N. and Lima, K. V. B.. (2018) Analysis of potential household transmission events of tuberculosis in the city of Belem, Brazil. Tuberculosis, 113. pp. 125-129. Merker, Matthias and Barbier, Maxime and Cox, Helen and Rasigade, Jean-Philippe and Feuerriegel, Silke and Kohl, Thomas Andreas and Diel, Roland and Borrell, Sonia and Gagneux, Sebastien and Nikolayevskyy, Vladyslav and Andres, Sönke and Nübel, Ulrich and Supply, Philip and Wirth, Thierry and Niemann, Stefan. (2018) Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia. eLife, 7. e38200. Kühnert, Denise and Coscolla, Mireia and Brites, Daniela and Stucki, David and Metcalfe, John and Fenner, Lukas and Gagneux, Sebastien and Stadler, Tanja. (2018) Tuberculosis outbreak investigation using phylodynamic analysis. Epidemics, 25. pp. 47-53. Sanoussi, C. N'Dira and de Jong, Bouke C. and Odoun, Mathieu and Arekpa, Karamatou and Ali Ligali, Moulikatou and Bodi, Ousman and Harris, Simon and Ofori-Anyinam, Boatema and Yeboah-Manu, Dorothy and Otchere, Isaac Darko and Asante-Poku, Adwoa and Anagonou, Severin and Gagneux, Sebastien and Coscolla, Mireia and Rigouts, Leen and Affolabi, Dissou. (2018) Low sensitivity of the MPT64 identification test to detect lineage 5 of the Mycobacterium tuberculosis complex. Journal of medical microbiology, 67 (12). pp. 1718-1727. Liu, Qingyun and Ma, Aijing and Wei, Lanhai and Pang, Yu and Wu, Beibei and Luo, Tao and Zhou, Yang and Zheng, Hong-Xiang and Jiang, Qi and Gan, Mingyu and Zuo, Tianyu and Liu, Mei and Yang, Chongguang and Jin, Li and Comas, Iñaki and Gagneux, Sebastien and Zhao, Yanlin and Pepperell, Caitlin S. and Gao, Qian. (2018) China's tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis. Nature ecology & evolution, 2 (12). pp. 1982-1992. Seth-Smith, Helena M. B. and Imkamp, Frank and Tagini, Florian and Cuénod, Aline and Hömke, Rico and Jahn, Kathleen and Tschacher, Anne and Grendelmeier, Peter and Bättig, Veronika and Erb, Stefan and Reinhard, Miriam and Rütimann, Gottfried and Borrell, Sonia and Gagneux, Sebastien and Casanova, Carlo and Droz, Sara and Osthoff, Michael and Tamm, Michael and Nübel, Ulrich and Greub, Gilbert and Keller, Peter M. and Egli, Adrian. (2018) Discovery and characterization of Mycobacterium basiliense sp. nov., a nontuberculous mycobacterium isolated from human lungs. Frontiers in Microbiology, 9. p. 3184. Menardo, Fabrizio and Loiseau, Chloé and Brites, Daniela and Coscolla, Mireia and Gygli, Sebastian M. and Rutaihwa, Liliana K. and Trauner, Andrej and Beisel, Christian and Borrell, Sonia and Gagneux, Sebastien. (2018) Treemmer : a tool to reduce large phylogenetic datasets with minimal loss of diversity. BMC bioinformatics, 19 (1). p. 164. 2017Andre, E. and Goeminne, L. and Cabibbe, A. and Beckert, P. and Kabamba Mukadi, B. and Mathys, V. and Gagneux, S. and Niemann, S. and Van Ingen, J. and Cambau, E.. (2017) Consensus numbering system for the rifampicin resistance-associated rpoB gene mutations in pathogenic mycobacteria. Clinical microbiology and infection, 23 (3). pp. 167-172. Mhimbira, Francis and Hella, Jerry and Said, Khadija and Kamwela, Lujeko and Sasamalo, Mohamed and Maroa, Thomas and Chiryamkubi, Magreth and Mhalu, Grace and Schindler, Christian and Reither, Klaus and Knopp, Stefanie and Utzinger, Jürg and Gagneux, Sébastien and Fenner, Lukas. (2017) Prevalence and clinical relevance of helminth co-infections among tuberculosis patients in urban Tanzania. PLoS Neglected Tropical Diseases, 11 (2). e0005342. Ofori-Anyinam, B. and Dolganov, G. and Van, T. and Davis, J. L. and Walter, N. D. and Garcia, B. J. and Voskuil, M. and Fissette, K. and Diels, M. and Driesen, M. and Meehan, C. J. and Yeboah-Manu, D. and Coscolla, M. and Gagneuyx, S. and Antonio, M. and Schoolnik, G. K. and Gehre, F. and de Jong, B. C.. (2017) Significant under expression of the DosR regulon in M. tuberculosis complex lineage 6 in sputum. Tuberculosis, 104. pp. 58-64. Trauner, Andrej and Liu, Qingyun and Via, Laura E. and Liu, Xin and Ruan, Xianglin and Liang, Lili and Shi, Huimin and Chen, Ying and Wang, Ziling and Liang, Ruixia and Zhang, Wei and Wei, Wang and Gao, Jingcai and Sun, Gang and Brites, Daniela and England, Kathleen and Zhang, Guolong and Gagneux, Sebastien and Barry, Clifton E. and Gao, Qian. (2017) The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy. Genome biology, 18. p. 71. Gygli, Sebastian M. and Borrell, Sonia and Trauner, Andrej and Gagneux, Sebastien. (2017) Antimicrobial resistance in Mycobacterium tuberculosis : mechanistic and evolutionary perspectives. FEMS Microbiology Reviews, 41 (3). pp. 354-373. Koch, Anastasia S. and Brites, Daniela and Stucki, David and Evans, Joanna C. and Seldon, Ronnett and Heekes, Alexa and Mulder, Nicola and Nicol, Mark and Oni, Tolu and Mizrahi, Valerie and Warner, Digby F. and Parkhill, Julian and Gagneux, Sebastien and Martin, Darren P. and Wilkinson, Robert J.. (2017) The influence of HIV on the evolution of Mycobacterium tuberculosis. Molecular biology and evolution, 34 (7). pp. 1654-1668. Hiza, Hellen and Doulla, Basra and Sasamalo, Mohamed and Hella, Jerry and Kamwela, Lujeko and Mhimbira, Francis and Reither, Klaus and Gagneux, Sebastien and Jugheli, Levan and Fenner, Lukas. (2017) Preservation of sputum samples with cetylpyridinium chloride (CPC) for tuberculosis cultures and Xpert MTB/RIF in a low-income country. BMC Infectious Diseases, 17. p. 542. Hella, Jerry and Morrow, Carl and Mhimbira, Francis and Ginsberg, Samuel and Chitnis, Nakul and Gagneux, Sebastien and Mutayoba, Beatrice and Wood, Robin and Fenner, Lukas. (2017) Tuberculosis transmission in public locations in Tanzania: A novel approach to studying airborne disease transmission. Journal of Infection, 75 (3). pp. 191-197. Yahyaoui-Azami, Hind and Aboukhassib, Hamid and Bouslikhane, Mohammed and Berrada, Jaouad and Rami, Soukaina and Reinhard, Miriam and Gagneux, Sebastien and Feldmann, Julia and Borrell, Sonia and Zinsstag, Jakob. (2017) Molecular characterization of bovine tuberculosis strains in two slaughterhouses in Morocco. BMC Veterinary Research, 13. p. 272. Ghielmetti, Giovanni and Coscolla, Mireia and Ruetten, Maja and Friedel, Ute and Loiseau, Chloé and Feldmann, Julia and Steinmetz, Hanspeter W. and Stucki, David and Gagneux, Sebastien. (2017) Tuberculosis in Swiss captive Asian elephants: microevolution of Mycobacterium tuberculosis characterized by multilocus variable-number tandem-repeat analysis and whole-genome sequencingle-number tandem-repeat analysis and whole-genome sequencing. Scientific reports, 7 (1). p. 14647. Brites, Daniela and Gagneux, Sebastien. (2017) The nature and evolution of genomic diversity in the Mycobacterium tuberculosis complex. Advances in experimental medicine and biology, 1019. pp. 1-26. Miotto, Paolo and Tessema, Belay and Tagliani, Elisa and Chindelevitch, Leonid and Starks, Angela M. and Emerson, Claudia and Hanna, Debra and Kim, Peter S. and Liwski, Richard and Zignol, Matteo and Gilpin, Christopher and Niemann, Stefan and Denkinger, Claudia M. and Fleming, Joy and Warren, Robin M. and Crook, Derrick and Posey, James and Gagneux, Sebastien and Hoffner, Sven and Rodrigues, Camilla and Comas, Iñaki and Engelthaler, David M. and Murray, Megan and Alland, David and Rigouts, Leen and Lange, Christoph and Dheda, Keertan and Hasan, Rumina and Ranganathan, Uma Devi K. and McNerney, Ruth and Ezewudo, Matthew and Cirillo, Daniela M. and Schito, Marco and Köser, Claudio U. and Rodwell, Timothy C.. (2017) A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis. The European respiratory journal, 50 (6). p. 1701354. Gagneux, S., ed. (2017) Strain variation in the Mycobacterium tuberculosis complex: its role in biology, epidemiology and control. Advances in Experimental Medicine and Biology. Cham. Rasoahanitralisoa, Rondroarivelo and Rakotosamimanana, Niaina and Stucki, David and Sola, Christophe and Gagneux, Sebastien and Rasolofo Razanamparany, Voahangy. (2017) Evaluation of spoligotyping, SNPs and customised MIRU-VNTR combination for genotyping Mycobacterium tuberculosis clinical isolates in Madagascar. PLoS ONE, 12 (10). e0186088. 2016Domínguez, J. and Boettger, E. C. and Cirillo, D. and Cobelens, F. and Eisenach, K. D. and Gagneux, S. and Hillemann, D. and Horsburgh, R. and Molina-Moya, B. and Niemann, S. and Tortoli, E. and Whitelaw, A. and Lange, C. and Tbnet, and Resist-TB networks, . (2016) Clinical implications of molecular drug resistance testing for Mycobacterium tuberculosis : a TBNET/RESIST-TB consensus statement. The international journal of tuberculosis and lung disease, 20 (1). pp. 24-42. Stucki, David and Ballif, Marie and Egger, Matthias and Furrer, Hansjakob and Altpeter, Ekkehardt and Battegay, Manuel and Droz, Sara and Bruderer, Thomas and Coscolla, Mireia and Borrell, Sonia and Zürcher, Kathrin and Janssens, Jean-Paul and Calmy, Alexandra and Mazza Stalder, Jesica and Jaton, Katia and Rieder, Hans L. and Pfyffer, Gaby E. and Siegrist, Hans H. and Hoffmann, Matthias and Fehr, Jan and Dolina, Marisa and Frei, Reno and Schrenzel, Jacques and Böttger, Erik C. and Gagneux, Sebastien and Fenner, Lukas. (2016) Standard genotyping overestimates transmission of Mycobacterium tuberculosis among immigrants in a low-incidence country. Journal of clinical microbiology, 54 (7). pp. 1862-1870. Boillat-Blanco, Noémie and Ramaiya, Kaushik L. and Mganga, Maliwasa and Minja, Lilian T. and Bovet, Pascal and Schindler, Christian and Von Eckardstein, Arnold and Gagneux, Sebastien and Daubenberger, Claudia and Reither, Klaus and Probst-Hensch, Nicole. (2016) Transient hyperglycemia in patients with tuberculosis in Tanzania : implications for diabetes screening algorithms. Journal of Infectious Diseases, 213 (7). pp. 1163-1172. Asante-Poku, Adwoa and Otchere, Isaac Darko and Osei-Wusu, Stephen and Sarpong, Esther and Baddoo, Akosua and Forson, Audrey and Laryea, Clement and Borrell, Sonia and Bonsu, Frank and Hattendorf, Jan and Ahorlu, Collins and Koram, Kwadwo A. and Gagneux, Sebastien and Yeboah-Manu, Dorothy. (2016) Molecular epidemiology of Mycobacterium africanum in Ghana. BMC Infectious Diseases, 16. p. 385. Yeboah-Manu, Dorothy and Asare, P. and Asante-Poku, A. and Otchere, I. D. and Osei-Wusu, S. and Danso, E. and Forson, A. and Koram, K. A. and Gagneux, Sebastien. 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PLoS ONE, 11 (8). e0161171. Otchere, I. D. and Asante-Poku, A. and Osei-Wusu, S. and Baddoo, A. and Sarpong, E. and Ganiyu, A. H. and Aboagye, S. Y. and Forson, A. and Bonsu, F. and Yahayah, A. I. and Koram, K. and Gagneux, S. and Yeboah-Manu, D.. (2016) Detection and characterization of drug-resistant conferring genes in Mycobacterium tuberculosis complex strains : a prospective study in two distant regions of Ghana. Tuberculosis, 99. pp. 147-154. Boillat-Blanco, Noémie and Bovet, Pascal and Ramaiya, Kaushik L. and Mganga, Maliwasa and Minja, Lilian T. and Saleh, Lanja and Imboden, Medea and Schindler, Christian and Gagneux, Sebastien and Daubenberger, Claudia and Reither, Klaus and Probst-Hensch, Nicole. (2016) Association between tuberculosis, diabetes and 25 hydroxyvitamin D in Tanzania: a longitudinal case control study. BMC Infectious Diseases, 16 (1). p. 626. 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(2016) Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nature genetics, 48 (12). pp. 1535-1543. 2015Asante-Poku, Adwoa and Yeboah-Manu, Dorothy and Otchere, Isaac Darko and Aboagye, Samuel Y. and Stucki, David and Hattendorf, Jan and Borrell, Sonia and Feldmann, Julia and Danso, Emelia and Gagneux, Sebastien. (2015) Mycobacterium africanum is associated with patient ethnicity in Ghana. PLoS neglected tropical diseases, Vol. 9, H. 1, e3370. Brites, Daniela and Gagneux, Sebastien. (2015) Co-evolution of Mycobacterium tuberculosis and Homo sapiens. Immunological reviews, Vol. 264, H. 1. pp. 6-24. Merker, Matthias and Blin, Camille and Mona, Stefano and Duforet-Frebourg, Nicolas and Lecher, Sophie and Willery, Eve and Blum, Michael G. 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(2015) Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nature genetics, Vol. 47, H. 3. pp. 242-249. Young, David C. and Layre, Emilie and Pan, Shih-Jung and Tapley, Asa and Adamson, John and Seshadri, Chetan and Wu, Zhongtao and Buter, Jeffrey and Minnaard, Adriaan J. and Coscolla, Mireia and Gagneux, Sebastien and Copin, Richard and Ernst, Joel D. and Bishai, William R. and Snider, Barry B. and Moody, D. Branch. (2015) In vivo biosynthesis of terpene nucleosides provides unique chemical markers of Mycobacterium tuberculosis infection. Chemistry & biology, Vol. 22, H. 4. pp. 516-526. Stucki, David and Ballif, Marie and Bodmer, Thomas and Coscolla, Mireia and Maurer, Anne-Marie and Droz, Sara and Butz, Christa and Borrell, Sonia and Längle, Christel and Feldmann, Julia and Furrer, Hansjakob and Mordasini, Carlo and Helbling, Peter and Rieder, Hans L. and Egger, Matthias and Gagneux, Sébastien and Fenner, Lukas. (2015) Tracking a tuberculosis outbreak over 21 years : strain-specific single-nucleotide polymorphism typing combined with targeted whole-genome sequencing. Journal of infectious diseases, Vol. 211, H. 8. pp. 1306-1316. Rock, Jeremy M. and Lang, Ulla F. and Chase, Michael R. and Ford, Christopher B. and Gerrick, Elias R. and Gawande, Richa and Coscolla, Mireia and Gagneux, Sebastien and Fortune, Sarah M. and Lamers, Meindert H.. (2015) DNA replication fidelity in Mycobacterium tuberculosis is mediated by an ancestral prokaryotic proofreader. Nature genetics, Vol. 47, H. 6. pp. 677-681. Asante-Poku, A. and Otchere, I. D. and Danso, E. and Mensah, D. D. and Bonsu, F. and Gagneux, S. and Yeboah-Manu, D.. (2015) Evaluation of geno type(®) MTBDRplus for the rapid detection of drug-resistant tuberculosis in Ghana. The international journal of tuberculosis and lung disease, Vol. 19, H. 8. pp. 954-959. Coscolla, Mireia and Barry, Pennan M. and Oeltmann, John E. and Koshinsky, Heather and Shaw, Tambi and Cilnis, Martin and Posey, Jamie and Rose, Jordan and Weber, Terry and Fofanov, Viacheslav Y. and Gagneux, Sebastien and Kato-Maeda, Midori and Metcalfe, John Z.. (2015) Genomic epidemiology of multidrug-resistant Mycobacterium tuberculosis during transcontinental spread. Journal of infectious diseases, Vol. 212, H. 2. pp. 302-310. Wampande, Eddie M. and Mupere, Ezekiel and Jaganath, Devan and Nsereko, Mary and Mayanja, Harriet K. and Eisenach, Kathleen and Boom, W. Henry and Gagneux, Sebastien and Joloba, Moses L. and Tuberculosis Research Unit, . (2015) Distribution and transmission of mycobacterium tuberculosis complex lineages among children in peri-urban Kampala, Uganda. BMC pediatrics, Vol. 15 , 140. Wampande, Eddie M. and Hatzios, Stavroula K. and Achan, Beatrice and Mupere, Ezekiel and Nsereko, Mary and Mayanja, Harriet K. and Eisenach, Kathleen and Boom, W. 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Bloemberg, Guido V. and Keller, Peter M. and Stucki, David and Stuckia, David and Trauner, Andrej and Borrell, Sonia and Latshang, Tsogyal and Coscolla, Mireia and Rothe, Thomas and Hömke, Rico and Ritter, Claudia and Feldmann, Julia and Schulthess, Bettina and Gagneux, Sebastien and Böttger, Erik C.. (2015) Acquired resistance to bedaquiline and delamanid in therapy for tuberculosis. The New England journal of medicine, 373 (20). pp. 1986-1988. Comas, Iñaki and Hailu, Elena and Kiros, Teklu and Bekele, Shiferaw and Mekonnen, Wondale and Gumi, Balako and Tschopp, Rea and Ameni, Gobena and Hewinson, R. Glyn and Robertson, Brian D. and Goig, Galo A. and Stucki, David and Gagneux, Sebastien and Aseffa, Abraham and Young, Douglas and Berg, Stefan. (2015) Population genomics of Mycobacterium tuberculosis in Ethiopia contradicts the virgin soil hypothesis for human tuberculosis in sub-saharan Africa. Current biology, 25 (24). pp. 3260-3206. Coscolla, Mireia and Copin, Richard and Sutherland, Jayne and Gehre, Florian and de Jong, Bouke and Owolabi, Olumuiya and Mbayo, Georgetta and Giardina, Federica and Ernst, Joel D. and Gagneux, Sebastien. (2015) M. tuberculosis T cell epitope analysis reveals paucity of antigenic variation and identifies rare variable TB antigens. Cell host & microbe, 18 (5). pp. 538-548. Zumla, Alimuddin and Maeurer, Markus and Host-Directed Therapies Network Consortium, . (2015) Host-directed therapies for tackling multi-drug resistant tuberculosis : learning from the pasteur-bechamp debates. Clinical infectious diseases, 61 (9). pp. 1432-1438. 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Coll, Francesc and Preston, Mark and Guerra-Assunção, José Afonso and Hill-Cawthorn, Grant and Harris, David and Perdigão, João and Viveiros, Miguel and Portugal, Isabel and Drobniewski, Francis and Gagneux, Sebastien and Glynn, Judith R. and Pain, Arnab and Parkhill, Julian and McNerney, Ruth and Martin, Nigel and Clark, Taane G.. (2014) PolyTB : a genomic variation map for Mycobacterium tuberculosis. Tuberculosis, Vol. 94, H. 3. pp. 346-354. Trauner, Andrej and Borrell, Sonia and Reither, Klaus and Gagneux, Sebastien. (2014) Evolution of drug resistance in tuberculosis : recent progress and implications for diagnosis and therapy. Drugs, Vol. 74, H. 10. pp. 1063-1072. Gagneux, S.. (2014) Interactions between mycobacterial and human genetic diversity and implications for new TB vaccines. In: The art & science of Tuberculosis vaccine development. - 2nd ed.. Shah Alam, pp. 337-349. Köser, C. U. and Bryant, J. M. and Comas, I. and Feuerriegel, S. and Niemann, S. and Gagneux, S. and Parkhill, J. and Peacock, S. J.. (2014) Comment on: Characterization of the embB gene in Mycobacterium tuberculosis isolates from Barcelona and rapid detection of main mutations related to ethambutol resistance using a low-density DNA array. The journal of antimicrobial chemotherapy, Vol. 69, H. 8. pp. 2298-2299. Köser, C. U. and Bryant, J. M. and Comas, I. and Feuerriegel, S. and Niemann, S. and Gagneux, S. and Parkhill, J. and Peacock, S. J.. (2014) Genetic diversity within Mycobacterium tuberculosis complex impacts on the accuracy of genotypic pyrazinamide drug-susceptibility assay. Tuberculosis, Vol. 94. pp. 451-453. Copin, Richard and Coscollá, Mireia and Efstathiadis, Efstratios and Gagneux, Sebastien and Ernst, Joel D.. (2014) Impact of in vitro evolution on antigenic diversity of Mycobacterium bovis bacillus Calmette-Guerin (BCG). 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BMC microbiology, Vol. 14 , 307. 2013Fenner, Lukas and Egger, Matthias and Bodmer, Thomas and Furrer, Hansjakob and Ballif, Marie and Battegay, Manuel and Helbling, Peter and Fehr, Jan and Gsponer, Thomas and Rieder, Hans L. and Zwahlen, Marcel and Hoffmann, Matthias and Bernasconi, Enos and Cavassini, Matthias and Calmy, Alexandra and Dolina, Marisa and Frei, Reno and Janssens, Jean-Paul and Borrell, Sonia and Stucki, David and Schrenzel, Jacques and Böttger, Erik C. and Gagneux, Sebastien and Swiss HIV Cohort, and Molecular Epidemiology of Tuberculosis Study Groups, . (2013) HIV infection disrupts the sympatric host-pathogen relationship in human tuberculosis. PLoS genetics, Vol. 9, H. 3 , e1003318. Coscolla, Mireia and Lewin, Astrid and Metzger, Sonja and Maetz-Rennsing, Kerstin and Calvignac-Spencer, Sébastien and Nitsche, Andreas and Dabrowski, Pjotr Wojtek and Radonic, Aleksandar and Niemann, Stefan and Parkhill, Julian and Couacy-Hymann, Emmanuel and Feldman, Julia and Comas, Iñaki and Boesch, Christophe and Gagneux, Sebastien and Leendertz, Fabian H.. (2013) Novel Mycobacterium tuberculosis complex isolate from a wild chimpanzee. Emerging infectious diseases, Vol. 19, H. 6. pp. 969-976. Aseffa, A. and Mihret, A. and Habte, A. and Abebe, M. and Wassie, L. and Tschopp, R. and Beyene, D. and Ameni, G. and Berg, S. and Doherty, T. M. and Gagneux, S. and Young, D. and Howe, R.. (2013) Advances in tuberculosis. African journal of microbiology research, Vol. 7, H. 2. pp. 73-81. Firdessa, R. and Berg, S. and Hailu, E. and Schelling, E. and Gumi, B. and Erenso, G. and Gadisa, E. and Kiros, T. and Habtamu, M. and Hussein, J. and Zinsstag, J. and Robertson, B. D. and Ameni, G. and Lohan, A. J. and Loftus, B. and Comas, I. and Gagneux, S. and Tschopp, R. and Yamuah, L. and Hewinson, G. and Gordon, S. V. and Young, D. B. and Aseffa, A.. (2013) Mycobacterial lineages causing pulmonary and extrapulmonary tuberculosis, Ethiopia. Emerging infectious diseases, Vol. 19, H. 3. pp. 460-463. de Vos, M. and Müller, B. and Borrell, S. and Black, P. and van Helden, P. and Warren, R. and Gagneux, S. and Victor, T.. (2013) Putative compensatory mutations in the rpoC gene of rifampicin-resistant Mycobacterium tuberculosis are associated with ongoing transmission. Antimicrobial agents and chemotherapy : AAC, Vol. 57, H. 2. pp. 827-832. Kato-Maeda, M. and Ho, C. and Passarelli, B. and Banaei, N. and Grinsdale, J. and Flores, L. and Anderson, J. and Murray, M. and Rose, G. and Kawamura, L. M. and Pourmand, N. and Tariq, M. A. and Gagneux, S. and Hopewell, P. C.. (2013) Use of whole genome sequencing to determine the microevolution of Mycobacterium tuberculosis during an outbreak. PLoS ONE, Vol. 8, H. 3 , e58235. Müller, B. and Borrell, S. and Rose, G. and Gagneux, S.. (2013) The heterogeneous evolution of multidrug-resistant Mycobacterium tuberculosis. Trends in genetics : DNA, differentiation and development, Vol. 29, H. 3. pp. 160-169. Stucki, D. and Gagneux, S.. (2013) Single nucleotide polymorphisms in Mycobacterium tuberculosis and the need for a curated database. Tuberculosis, Vol. 93, H. 1. pp. 30-39. Rose, Graham and Cortes, Teresa and Comas, Iñaki and Coscolla, Mireia and Gagneux, Sebastien and Young, Douglas B.. (2013) Mapping of genotype-phenotype diversity among clinical isolates of Mycobacterium tuberculosis by sequence-based transcriptional profiling. Genome biology and evolution, Vol. 5, H. 10. pp. 1849-1862. Osório, Nuno S. and Rodrigues, Fernando and Gagneux, Sebastien and Pedrosa, Jorge and Pinto-Carbó, Marta and Castro, António G. and Young, Douglas and Comas, Iñaki and Saraiva, Margarida. (2013) Evidence for diversifying selection in a set of Mycobacterium tuberculosis genes in response to antibiotic- and nonantibiotic-related pressure. Molecular biology and evolution, Vol. 30, no. 6. pp. 1326-1336. Farhat, Maha R. and Shapiro, B. Jesse and Kieser, Karen J. and Sultana, Razvan and Jacobson, Karen R. and Victor, Thomas C. and Warren, Robin M. and Streicher, Elizabeth M. and Calver, Alistair and Sloutsky, Alex and Kaur, Devinder and Posey, Jamie E. and Plikaytis, Bonnie and Oggioni, Marco R. and Gardy, Jennifer L. and Johnston, James C. and Rodrigues, Mabel and Tang, Patrick K. C. and Kato-Maeda, Midori and Borowsky, Mark L. and Muddukrishna, Bhavana and Kreiswirth, Barry N. and Kurepina, Natalia and Galagan, James and Gagneux, Sebastien and Birren, Bruce and Rubin, Eric J. and Lander, Eric S. and Sabeti, Pardis C. and Murray, Megan. (2013) Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nature genetics, Vol. 45, H. 10. pp. 1183-1189. Comas, Iñaki and Coscolla, Mireia and Luo, Tao and Borrell, Sonia and Holt, Kathryn E. and Kato-Maeda, Midori and Parkhill, Julian and Malla, Bijaya and Berg, Stefan and Thwaites, Guy and Yeboah-Manu, Dorothy and Bothamley, Graham and Mei, Jian and Wei, Lanhai and Bentley, Stephen and Harris, Simon R. and Niemann, Stefan and Diel, Roland and Aseffa, Abraham and Gao, Qian and Young, Douglas and Gagneux, Sebastien. (2013) Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nature genetics, Vol. 45, H. 10. pp. 1176-1182. Borrell, Sònia and Teo, Youjin and Giardina, Federica and Streicher, Elizabeth M. and Klopper, Marisa and Feldmann, Julia and Müller, Borna and Victor, Tommie C. and Gagneux, Sebastien. (2013) Epistasis between antibiotic resistance mutations drives the evolution of extensively drug-resistant tuberculosis. Evolution, medicine, and public health, H. 1. pp. 65-74. Ford, Christopher B. and Shah, Rupal R. and Maeda, Midori Kato and Gagneux, Sebastien and Murray, Megan B. and Cohen, Ted and Johnston, James C. and Gardy, Jennifer and Lipsitch, Marc and Fortune, Sarah M.. (2013) Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis. Nature genetics, Vol. 45, H. 7. pp. 784-790. Via, Laura E. and Weiner, Danielle M. and Schimel, Daniel and Lin, Philana Ling and Dayao, Emmanuel and Tankersley, Sarah L. and Cai, Ying and Coleman, M. 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Ballif, M. and Harino, P. and Ley, S. and Carter, R. and Coulter, C. and Niemann, S. and Borrell, S. and Fenner, L. and Siba, P. and Phuanukoonnon, S. and Gagneux, S. and Beck, H. P.. (2012) Genetic diversity of Mycobacterium tuberculosis in Madang, Papua New Guinea. The international journal of tuberculosis and lung disease, Vol. 16, H. 8. pp. 1100-1107. Ballif, M. and Harino, P. and Ley, S. and Coscolla, M. and Niemann, S. and Carter, R. and Coulter, C. and Borrell, S. and Siba, P. and Phuanukoonnon, S. and Gagneux, S. and Beck, H. P.. (2012) Drug resistance-conferring mutations in Mycobacterium tuberculosis from Madang, Papua New Guinea. BMC microbiology, Vol. 12 , 191. Weiner, B. and Gomez, J. and Victor, T. C. and Warren, R. M. and Sloutsky, A. and Plikaytis, B. B. and Posey, J. E. and van Helden, P. D. and Gey van Pittius, N. C. and Koehrsen, M. and Sisk, P. and Stolte, C. and White, J. and Gagneux, S. and Birren, B. and Hung, D. and Murray, M. and Galagan, J.. (2012) Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region. PLoS ONE, Vol. 7, H. 2 , e26038. Bentley, S. D. and Comas, I. and Bryant, J. M. and Walker, D. and Smith, N. H. and Harris, S. R. and Thurston, S. and Gagneux, S. and Wood, J. and Antonio, M. and Quail, M. A. and Gehre, F. and Adegbola, R. A. and Parkhill, J. and de Jong, B. C.. (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, Vol. 6, H. 2 , e1552. Malla, B. and Stucki, D. and Borrell, S. and Feldmann, J. and Maharjan, B. and Shrestha, B. and Fenner, L. and Gagneux, S.. (2012) First insights into the phylogenetic diversity of Mycobacterium tuberculosis in Nepal. PLoS ONE, Vol. 7, H. 12 , e52297. McEvoy, C. R. and Cloete, R. and Müller, B. and Schurch, A. C. and van Helden, P. D. and Gagneux, S. and Warren, R. M. and Gey van Pittius, N. C.. (2012) Comparative analysis of Mycobacterium tuberculosis pe and ppe genes reveals high sequence variation and an apparent absence of selective constraints. PLoS ONE, Vol. 7, H. 4 , e30593. Kato-Maeda, M. and Shanley, C. A. and Ackart, D. and Jarlsberg, L. G. and Shang, S. and Obregon-Henao, A. and Harton, M. and Basaraba, R. J. and Henao-Tamayo, M. and Barrozo, J. C. and Rose, J. and Kawamura, L. M. and Coscolla, M. and Fofanov, V. Y. and Koshinsky, H. and Gagneux, S. and Hopewell, P. C. and Ordway, D. J. and Orme, I. M.. (2012) Beijing sublineages of Mycobacterium tuberculosis differ in pathogenicity in the Guinea pig. Clinical and vaccine immunology, Vol. 19, H. 8. pp. 1227-1237. Fenner, L. and Gagneux, S. and Janssens, J. P. and Fehr, J. and Cavassini, M. and Hoffmann, M. and Bernasconi, E. and Schrenzel, J. and Bodmer, T. and Bottger, E. C. and Helbling, P. and Egger, M.. (2012) Tuberculosis in HIV-negative and HIV-infected patients in a low-incidence country : clinical characteristics and treatment outcomes. PLoS ONE, Vol. 7, H. 3 , e34186. Gagneux, S.. (2012) Host-pathogen coevolution in human tuberculosis. Philosophical transactions / The Royal Society of London. Biological sciences, Vol. 367, H. 1590. pp. 850-859. Brites, Daniela and Gagneux, Sebastien. (2012) Old and new selective pressures on Mycobacterium tuberculosis. Infection, genetics and evolution, Vol. 12, H. 4. pp. 678-685. Fenner, L. and Egger, M. and Bodmer, T. and Altpeter, E. and Zwahlen, M. and Jaton, K. and Pfyffer, G. E. and Borrell, S. and Dubuis, O. and Bruderer, T. and Siegrist, H. H. and Furrer, H. and Calmy, A. and Fehr, J. and Stalder, J. M. and Ninet, B. and Bottger, E. C. and Gagneux, S.. (2012) Effect of mutation and genetic background on drug resistance in Mycobacterium tuberculosis. Antimicrobial agents and chemotherapy, Vol. 56, H. 6. pp. 3047-3053. Stucki, D. and Malla, B. and Hostettler, S. and Huna, T. and Feldmann, J. and Yeboah-Manu, D. and Borrell, S. and Fenner, L. and Comas, I. and Coscolla, M. and Gagneux, S.. (2012) Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages. PLoS ONE, Vol. 7, H. 7 , e41253. Luo, Tao and Yang, Chongguang and Gagneux, Sebastien and Gicquel, Brigitte and Jian, Mei and Gao, Qian. (2012) Combination of single nucleotide polymorphism and variable-number tandem repeats for genotyping a homogenous population of Mycobacterium tuberculosis Beijing strains in China. Journal of clinical microbiology, Vol. 50, H. 3. pp. 633-639. Fenner, L. and Gagneux, S. and Helbling, P. and Battegay, M. and Rieder, H. L. and Pfyffer, G. E. and Zwahlen, M. and Furrer, H. and Siegrist, H. H. and Fehr, J. and Dolina, M. and Calmy, A. and Stucki, D. and Jaton, K. and Janssens, J. P. and Stalder, J. M. and Bodmer, T. and Ninet, B. and Böttger, E. C. and Egger, M.. (2012) Mycobacterium tuberculosis transmission in a country with low tuberculosis incidence : role of immigration and HIV infection. Journal of clinical microbiology, Vol. 50, H. 2. pp. 388-395. Bratschi, M. W. and Njih, Tabah and Bolz, M. and Stucki, D. and Borrell, S. and Gagneux, S. and Noumen-Djeunga, B. and Junghanss, T. and Um Boock, A. and Pluschke, G.. (2012) A case of cutaneous tuberculosis in a Buruli ulcer-endemic area. PLoS neglected tropical diseases, Vol. 6, H. 8 , e1751. 2011Borrell, S. and Gagneux, S.. (2011) Strain diversity, epistasis and the evolution of drug resistance in Mycobacterium tuberculosis. Clinical microbiology and infection : CMI : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, Vol. 17, H. 6. pp. 815-820. Kato-Maeda M., and Gagneux, S. and Flores, L. L. and Kim, E. Y. and Small, P. M. and Desmond, E. P. and Hopewell, P. C.. (2011) Strain classification of Mycobacterium tuberculosis : congruence between large sequence polymorphisms and spoligotypes. The international journal of tuberculosis and lung disease : the official journal of the International Union Against Tuberculosis and Lung Disease, Vol. 15, H. 1. pp. 131-133. Comas, I. and Gagneux, S.. (2011) A role for systems epidemiology in tuberculosis research. Trends in microbiology : virulence, infection and pathogenesis, Vol. 19, H. 10. pp. 492-500. Portevin, Damien and Gagneux, Sébastien and Comas, Iñaki and Young, Douglas. (2011) Human macrophage responses to clinical isolates from the Mycobacterium tuberculosis complex discriminate between ancient and modern lineages. PLoS Pathogens, Vol. 7, H. 3 , e1001307. Fenner, Lukas and Malla, Bijaya and Ninet, Béatrice and Dubuis, Olivier and Stucki, David and Borrell, Sonia and Huna, Thembela and Bodmer, Thomas and Egger, Matthias and Gagneux, Sebastien. (2011) "Pseudo-Beijing" : evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis. PLoS ONE, Vol. 6, H. 9 , e24737. Yeboah-Manu D., and Asante-Poku A., and Bodmer, T. and Stucki, D. and Koram, K. and Bonsu, F. and Pluschke, G. and Gagneux, S.. (2011) Genotypic diversity and drug susceptibility patterns among M. tuberculosis complex isolates from South-Western Ghana. PLoS ONE, Vol. 6, H. 7 , e21906. Sherman, David R. and Gagneux, Sebastien. (2011) Estimating the mutation rate of Mycobacterium tuberculosis during infection. Nature genetics, Vol. 43, H. 5. pp. 400-401. Behr, Marcel A. and Gagneux, Sébastien. (2011) The rise and fall of Mycobacterium tuberculosis complex. In: Genomics and evolution of infectious diseases. Amsterdam, pp. 651-667. 2010Coscolla, M. and Gagneux, S.. (2010) Does M. tuberculosis genomic diversity explain disease diversity? Drug discovery today. Disease mechanisms, Vol. 7, H. 1 , e43-e59. de Jong B. C., and Antonio, M. and Gagneux, S.. (2010) Mycobacterium africanum : review of an important cause of human tuberculosis in West Africa. PLoS neglected tropical diseases, Vol. 4, H. 9 , e744. Nahid, P. and Bliven, E. E. and Kim, E. Y. and Mac Kenzie W. R., and Stout, J. E. and Diem, L. and Johnson, J. L. and Gagneux, S. and Hopewell, P. C. and Kato-Maeda M., . (2010) Influence of M. tuberculosis lineage variability within a clinical trial for pulmonary tuberculosis. PLoS ONE, Vol. 5, H. 5 , e10753. Gagneux, S. and Brennan, M.. (2010) Strain and antigen variation in Mycobacterium tuberculosis : implications for the development of new tools for tuberculosis. In: >>The<< art and science of tuberculosis vaccine development. Shah Alam, pp. 130-147. Comas, Iñaki and Chakravartti, Jaidip and Small, Peter M. and Galagan, James and Niemann, Stefan and Kremer, Kristin and Ernst, Joel D. and Gagneux, Sébastien. (2010) Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nature genetics, 42 (6). pp. 498-503. 2009Borrell, S. and Gagneux, S.. (2009) Infectiousness, reproductive fitness and evolution of drug-resistant Mycobacterium tuberculosis. The international journal of tuberculosis and lung disease, 13 (12). pp. 1456-1466. 2007Leimkugel, Julia and Hodgson, Abraham and Forgor, Abudulai Adams and Pflüger, Valentin and Dangy, Jean-Pierre and Smith, Tom and Achtman, Mark and Gagneux, Sébastien and Pluschke, Gerd. (2007) Clonal waves of Neisseria colonisation and disease in the African meningitis belt : eight- year longitudinal study in northern Ghana. PLoS medicine, Vol. 4, H. 3 , e101. Leimkugel, Julia and Forgor, Abudulai Adams and Dangy, Jean-Pierre and Pflüger, Valentin and Gagneux, Sebastien and Hodgson, Abraham and Pluschke, Gerd. (2007) Genetic diversification of Neisseria meningitidis during waves of colonization and disease in the meningitis belt of sub-Saharan Africa. Vaccine : the official journal of the International Society for Vaccines, 25 (1). A18-A23. 2005Forgor, Abdulai Adams and Leimkugel, Julia and Hodgson, Abraham and Bugri, Akalifa and Dangy, Jean-Pierre and Gagneux, Sébastien and Smith, Tom and Pluschke, Gerd. (2005) Emergence of W135 meningococcal meningitis in Ghana. Tropical medicine and international health : TM & IH : a European journal, 10 (12). pp. 1229-1234. Leimkugel, Julia and Adams Forgor, Abudulai and Gagneux, Sébastien and Pflüger, Valentin and Flierl, Christian and Awine, Elizabeth and Naegeli, Martin and Dangy, Jean-Pierre and Smith, Tom and Hodgson, Abraham and Pluschke, Gerd. (2005) An outbreak of serotype 1 Streptococcus pneumoniae meningitis in northern Ghana with features that are characteristic of Neisseria meningitidis meningitis epidemics. Journal of infectious diseases, Vol. 192, H. 2. pp. 192-199. 2002Gagneux, Sébastien and Wirth, Thierry and Hodgson, Abraham and Ehrhard, Ingrid and Morelli, Giovanna and Kriz, Paula and Genton, Blaise and Smith, Tom and Binka, Fred and Pluschke, Gerd and Achtman, Mark. (2002) Clonal groupings in serogroup X Neisseria meningitidis. Emerging Infectious Diseases, Vol. 8, H. 5. pp. 462-466. Gagneux, Sébastien P. and Hodgson, Abraham and Smith, Tom A. and Wirth, Thierry and Ehrhard, Ingrid and Morelli, Giovanna and Genton, Blaise and Binka, Fred N. and Achtman, Mark and Pluschke, Gerd. (2002) Prospective study of a serogroup X Neisseria meningitidis outbreak in northern Ghana. Journal of infectious diseases, Vol. 185, H. 5. pp. 618-626. 2001Gagneux, Sébastien. Molecular epidemiology of meningococcal disease in Northern Ghana. 2001, Doctoral Thesis, University of Basel, Faculty of Science. Zhu, P. and van der Ende, A. and Falush, D. and Brieske, N. and Morelli, G. and Linz, B. and Popovic, T. and Schuurman, I. G. and Adegbola, R. A. and Zurth, K. and Gagneux, S. and Platonov, A. E. and Riou, J. Y. and Caugant, D. A. and Nicolas, P. and Achtman, M.. (2001) Fit genotypes and escape variants of subgroup III Neisseria meningitidis during three pandemics of epidemic meningitis. Proceedings of the National Academy of Sciences of the United States of America, Vol. 98, H. 9. pp. 5234-5239. Hodgson, A. and Smith, T. and Gagneux, S. and Adjuik, M. and Pluschke, G. and Mensah, N. K. and Binka, F. and Genton, B.. (2001) Risk factors for meningococcal meningitis in northern Ghana. Transactions of the Royal Society of Tropical Medicine and Hygiene, Vol. 95, H. 5. pp. 477-480. Hodgson, A. and Smith, T. and Gagneux, S. and Akumah, I. and Adjuik, M. and Pluschke, G. and Binka, F. and Genton, B.. (2001) Survival and sequelae of meningococcal meningitis in Ghana. International journal of epidemiology : official journal of the international epidemiological association, Vol. 30, H. 6. pp. 1440-1446. 2000Gagneux, S. and Hodgson, A. and Ehrhard, I. and Morelli, G. and Genton, B. and Smith, T. and Tanner, M. and Binka, F. and Achtman, M. and Pluschke, G.. (2000) Microheterogeneity of serogroup A (subgroup III) Neisseria meningitidis during an outbreak in northern Ghana. Tropical medicine and international health : TM & IH : a European journal, 5 (4). pp. 280-287. |
