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Items where Division is "09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH) > Department of Medical Parasitology and Infection Biology (MPI) > Tuberculosis Ecology and Evolution Unit (Gagneux)"

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Bouth, R. C. and Gobbo, A. R. and Barreto, J. G. and do Carmo Pinto, P. D. and Bittencourt, M. S. and Frade, M. A. C. and Nascimento, A. C. and Bandeira, S. S. and da Costa, P. F. and Conde, G. A. B. and Avanzi, C. and Ribeiro-Dos-Santos, Â and Spencer, J. S. and da Silva, M. B. and Salgado, C. G.. (2023) Specialized active leprosy search strategies in an endemic area of the Brazilian Amazon identifies a hypermutated Mycobacterium leprae strain causing primary drug resistance. Front Med (Lausanne), 10. p. 1243571.

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.

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.

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.

Hall, 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.

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.

Ndege, R. and Ngome, O. and Vanobberghen, F. and Bani, F. and Temba, Y. and Wilson, H. and Hella, J. and Gingo, W. and Sasamalo, M. and Mnzava, D. and Kimera, N. and Hiza, H. and Wigayi, J. and Mapesi, H. and Kato, I. B. and Mhimbira, F. and Reither, K. and Battegay, M. and Paris, D. H. and Weisser, M. and Rohacek, M.. (2023) Ultrasononography in managing extrapulmonary tuberculosis: a randomized, controlled, parallel, superiority, open-label trial. Clin Infect Dis, 76 (6). pp. 1013-1021.

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.

Aubry, A. and Sammarco Rosa, P. and Chauffour, A. and Lee Fletcher, M. and Cambau, E. and Avanzi, C.. (2022) Drug resistance in leprosy: an update following 70 years of chemotherapy. Infect Dis Now, 52 (5). pp. 243-251.

Cox, 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.

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.

Vaezipour, N. and Fritschi, N. and Brasier, N. and Bélard, S. and Domínguez, J. and Tebruegge, M. and Portevin, D. and Ritz, N.. (2022) Towards accurate point-of-care tests for tuberculosis in children. Pathogens, 11 (3). p. 327.

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.

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.

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.

Arbués, A. and Kammüller, M. and Portevin, D.. (2021) Generating three-dimensional human granulomas in vitro to study Mycobacterium tuberculosis-host interaction. Bio-protocol, 10 (22). e3820.

Asare, 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

López, M. G. and Chiner-Oms, A. and García de Viedma, D. and Ruiz-Rodriguez, P. and Bracho, M. A. and Cancino-Muñoz, I. and D'Auria, G. and de Marco, G. and García-González, N. and Goig, G. A. and Gómez-Navarro, I. and Jiménez-Serrano, S. and Martinez-Priego, L. and Ruiz-Hueso, P. and Ruiz-Roldán, L. and Torres-Puente, M. and Alberola, J. and Albert, E. and Aranzamendi Zaldumbide, M. and Bea-Escudero, M. P. and Boga, J. A. and Bordoy, A. E. and Canut-Blasco, A. and Carvajal, A. and Cilla Eguiluz, G. and Cordón Rodríguez, M. L. and Costa-Alcalde, J. J. and de Toro, M. and de Toro Peinado, I. and Del Pozo, J. L. and Duchêne, S. and Fernández-Pinero, J. and Fuster Escrivá, B. and Gimeno Cardona, C. and González Galán, V. and Gonzalo Jiménez, N. and Hernáez Crespo, S. and Herranz, M. and Lepe, J. A. and López-Causapé, C. and López-Hontangas, J. L. and Martín, V. and Martró, E. and Milagro Beamonte, A. and Montes Ros, M. and Moreno-Muñoz, R. and Navarro, D. and Navarro-Marí, J. M. and Not, A. and Oliver, A. and Palop-Borrás, B. and Parra Grande, M. and Pedrosa-Corral, I. and Pérez González, M. C. and Pérez-Lago, L. and Pérez-Ruiz, M. and Pineiro Vazquez, L. and Rabella, N. and Rezusta, A. and Robles Fonseca, L. and Rodríguez-Villodres, A. and Sanbonmatsu-Gámez, S. and Sicilia, J. and Soriano, A. and Tirado Balaguer, M. D. and Torres, I. and Tristancho, A. and Marimón, J. M. and SeqCovid-Spain Consortium, and Coscolla, M. and González-Candelas, F. and Comas, I.. (2021) The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant. Nat Genet, 53 (10). pp. 1405-1414.

Mariner-Llicer, C. and Goig, G. A. and Zaragoza-Infante, L. and Torres-Puente, M. and Villamayor, L. and Navarro, D. and Borras, R. and Chiner-Oms, A. and Comas, I.. (2021) Accuracy of an amplicon-sequencing nanopore approach to identify variants in tuberculosis drug-resistance-associated genes. Microb Genom, 7 (12). 00074.

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.

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.

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.

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.

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.

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.

Pfrengle, S. and Neukamm, J. and Guellil, M. and Keller, M. and Molak, M. and Avanzi, C. and Kushniarevich, A. and Montes, N. and Neumann, G. U. and Reiter, E. and Tukhbatova, R. I. and Berezina, N. Y. and Buzhilova, A. P. and Korobov, D. S. and Suppersberger Hamre, S. and Matos, V. M. J. and Ferreira, M. T. and Gonzalez-Garrido, L. and Wasterlain, S. N. and Lopes, C. and Santos, A. L. and Antunes-Ferreira, N. and Duarte, V. and Silva, A. M. and Melo, L. and Sarkic, N. and Saag, L. and Tambets, K. and Busso, P. and Cole, S. T. and Avlasovich, A. and Roberts, C. A. and Sheridan, A. and Cessford, C. and Robb, J. and Krause, J. and Scheib, C. L. and Inskip, S. A. and Schuenemann, V. J.. (2021) Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes. BMC Biol, 19. p. 220.

Röösli, M. and Hahad, O. and Dongus, S. and Loizeau, N. and Daiber, A. and Munzel, T. and Eeftens, M.. (2021) Gesundheitsrisiko Mobilfunkstrahlung? Was ändert sich mit 5G? Aktuelle Kardiologie, 10 (6). pp. 531-536.

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.

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.

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.

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.

Arbués, Ainhoa and Brees, Dominique and Chibout, Salah-Dine and Fox, Todd and Kammüller, Michael and Portevin, Damien. (2020) TNF-α antagonists differentially induce TGF-β1-dependent resuscitation of dormant-like Mycobacterium tuberculosis. PLoS Pathogens, 16 (2). e1008312.

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.

Avanzi, C. and Singh, P. and Truman, R. W. and Suffys, P. N.. (2020) Molecular epidemiology of leprosy: an update. Infect Genet Evol, 86. p. 104581.

Castro, 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Doz-Deblauwe, Émilie and Carreras, Florence and Arbues, Ainhoa and Remot, Aude and Epardaud, Mathieu and Malaga, Wladimir and Mayau, Véronique and Prandi, Jacques and Astarie-Dequeker, Catherine and Guilhot, Christophe and Demangel, Caroline and Winter, Nathalie. (2019) CR3 engaged by PGL-I triggers syk-calcineurin-NFATc to rewire the innate immune response in leprosy. Frontiers in Immunology, 10. p. 2913.

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.

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.

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.

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.

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.

Mhalu, Grace and Weiss, Mitchell G. and Hella, Jerry and Mhimbira, Francis and Mahongo, Enos and Schindler, Christian and Reither, Klaus and Fenner, Lukas and Zemp, Elisabeth and Merten, Sonja. (2019) Explaining patient delay in healthcare seeking and loss to diagnostic follow-up among patients with presumptive tuberculosis in Tanzania : a mixed-methods study. BMC health services research, 19. p. 217.

Mhimbira, 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.

Mogashoa, Tuelo and Melamu, Pinkie and Derendinger, Brigitta and Ley, Serej D. and Streicher, Elizabeth M. and Iketleng, Thato and Mupfumi, Lucy and Mokomane, Margaret and Kgwaadira, Botshelo and Rankgoane-Pono, Goabaone and Tsholofelo, Thusoyaone T. and Kasvosve, Ishmael and Moyo, Sikhulile and Warren, Robin M. and Gaseitsiwe, Simani. (2019) Detection of Second Line Drug Resistance among Drug Resistant Mycobacterium Tuberculosis Isolates in Botswana. Pathogens, 8 (4). E2018.

Mogashoa, Tuelo and Melamu, Pinkie and Ley, Serej D. and Streicher, Elizabeth M. and Iketleng, Thato and Kelentse, Nametso and Mupfumi, Lucy and Mokomane, Margaret and Kgwaadira, Botshelo and Novitsky, Vladimir and Kasvosve, Ishmael and Moyo, Sikhulile and Warren, Robin M. and Gaseitsiwe, Simani. (2019) Genetic diversity of Mycobacterium tuberculosis strains circulating in Botswana. PLoS ONE, 14 (5). e0216306.

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.

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.

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, 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.

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.

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.

Wiedemar, Natalie and Zwyer, Michaela and Zoltner, Martin and Cal, Monica and Field, Mark C. and Mäser, Pascal. (2019) Expression of a specific variant surface glycoprotein has a major impact on suramin sensitivity and endocytosis in Trypanosoma brucei. FASEB bioAdvances, 1 (10). pp. 595-608.

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.

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.

Benjak, Andrej and Avanzi, Charlotte and Singh, Pushpendra and Loiseau, Chloé and Girma, Selfu and Busso, Philippe and Fontes, Amanda N. Brum and Miyamoto, Yuji and Namisato, Masako and Bobosha, Kidist and Salgado, Claudio G. and da Silva, Moisés B. and Bouth, Raquel C. and Frade, Marco A. C. and Filho, Fred Bernardes and Barreto, Josafá G. and Nery, José A. C. and Bührer-Sékula, Samira and Lupien, Andréanne and Al-Samie, Abdul R. and Al-Qubati, Yasin and Alkubati, Abdul S. and Bretzel, Gisela and Vera-Cabrera, Lucio and Sakho, Fatoumata and Johnson, Christian R. and Kodio, Mamoudou and Fomba, Abdoulaye and Sow, Samba O. and Gado, Moussa and Konaté, Ousmane and Stefani, Mariane M. A. and Penna, Gerson O. and Suffys, Philip N. and Sarno, Euzenir Nunes and Moraes, Milton O. and Rosa, Patricia S. and Baptista, Ida M. F. Dias and Spencer, John S. and Aseffa, Abraham and Matsuoka, Masanori and Kai, Masanori and Cole, Stewart T.. (2018) Phylogenomics and antimicrobial resistance of the leprosy bacillus Mycobacterium leprae. Nature Communications, 9. p. 352.

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.

Brites, D. Loiseau and C. Menardo, F. Borrell and S. Boniotti, B. Warren and R. Dippenaar, A. Parsons and S. D. C. Beisel, C. Behr and M. A. Fyfe, J. A. Coscolla and M. Gagneux, S.. (2018) A new phylogenetic framework for the animal-adapted Mycobacterium tuberculosis complex. Frontiers in Microbiology, 9. p. 2820.

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.

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.

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.

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Hiza, Hellen and Fenner, Lukas and Hella, Jerry and Kuchaka, Davis and Sasamalo, Mohamed and Blauenfeldt, Thomas and Kibiki, Gibson and Kavishe, Reginald A. and Mhimbira, Francis and Ruhwald, Morten. (2018) Boosting effect of IL-7 in interferon gamma release assays to diagnose Mycobacterium tuberculosis infection. PLoS ONE, 13 (8). e0202525.

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.

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.

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.

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.

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.

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.

Sayasone, Somphou and Keiser, Jennifer and Meister, Isabel and Vonghachack, Youthanavanh and Xayavong, Syda and Senggnam, Kanpaseuth and Phongluxa, Khampheng and Hattendorf, Jan and Odermatt, Peter. (2018) Efficacy and safety of tribendimidine versus praziquantel against Opisthorchis viverrini in Laos : an open-label, randomised, non-inferiority, phase 2 trial. The Lancet infectious diseases, 18 (2). pp. 155-161.

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.

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.

Wittwer, Matthias and Altpeter, Ekkehard and Pilo, Paola and Gygli, Sebastian M. and Beuret, Christian and Foucault, Frederic and Ackermann-Gäumann, Rahel and Karrer, Urs and Jacob, Daniela and Grunow, Roland and Schürch, Nadia. (2018) Population genomics of Francisella tularensis subsp. holarctica and its implication on the eco-epidemiology of tularemia in Switzerland. Frontiers in Cellular and Infection Microbiology, 8. p. 89.

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.

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Andre, 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.

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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.

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.

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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.

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Sánchez-Busó, Leonor and Coscollá, Mireia and Pinto-Carbó, Marta and Catalán, Vicente and González-Candelas, Fernando. (2013) Genetic characterization of Legionella pneumophila isolated from a common watershed in comunidad Valenciana, Spain. PLoS ONE, Vol. 8, H. 4 , e61564.

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. Teresa and Tomko, Jaime and Paripati, Praveen and Orandle, Marlene and Kastenmayer, Robin J. and Tartakovsky, Michael and Rosenthal, Alexander and Portevin, Damien and Eum, Seok Yong and Lahouar, Saher and Gagneux, Sebastien and Young, Douglas B. and Flynn, Joanne L. and Barry, Clifton E.. (2013) Differential virulence and disease progression following Mycobacterium tuberculosis complex infection of the common marmoset (Callithrix jacchus). Infection and immunity, Vol. 81, H. 8. pp. 2909-2919.

Wampande, Eddie M. and Mupere, Ezekiel and Debanne, Sara M. and Asiimwe, Benon B. and Nsereko, Mary and Mayanja, Harriet and Eisenach, Kathleen and Kaplan, Gilla and Boom, Henry W. and Sebastien, Gagneux and Joloba, Moses L.. (2013) Long-term dominance of Mycobacterium tuberculosis Uganda family in peri-urban Kampala-Uganda is not associated with cavitary disease. BMC infectious diseases, Vol. 13 , 484.

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.

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.

Beyene, N. and Mahoney, A. and Cox, C. and Weetjens, B. and Makingi, G. and Mgode, G. and Durgin, A. and Kuipers, D. and Jubitana, M. and Egwaga, S. and Kamara, D. and Lwilla, F. and Mfinanga, S. G. and Kahwa, A. and Machang'u, R. and Kazwala, R. and Reither, K. and Kaufmann, S. H. E. and Poling, A.. (2012) APOPO's tuberculosis research agenda : achievements, challenges and prospects. Tanzania journal of health research, Vol. 14, H. 2. pp. 1-13.

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.

Comas, Iñaki and Borrell, Sonia and Roetzer, Andreas and Rose, Graham and Malla, Bijaya and Kato-Maeda, Midori and Galagan, James and Niemann, Stefan and Gagneux, Sebastien. (2012) Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nature genetics, Vol. 44, H. 1. pp. 106-110.

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.

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.

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.

Haraka, F. and Rutaihwa, L. K. and Battegay, M. and Reither, K.. (2012) Mycobacterium intracellulare infection in non-HIV infected patient in a region with a high burden of tuberculosis. BMJ case reports, 8 May 2012. p. 3.

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.

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.

Mahoney, Amanda and Weetjens, Bart J. and Cox, Christophe and Beyene, Negussie and Reither, Klaus and Makingi, George and Jubitana, Maureen and Kazwala, Rudovick and Mfinanga, Godfrey S. and Kahwa, Amos and Durgin, Amy and Poling, Alan. (2012) Pouched rats' detection of tuberculosis in human sputum : comparison to culturing and polymerase chain reaction. Tuberculosis research and treatment, Vol. 2012 , 716989.

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.

Ntinginya, E. N. and Squire, S. B. and Millington, K. A. and Mtafya, B. and Saathoff, E. and Heinrich, N. and Rojas-Ponce, G. and Kowuor, D. and Maboko, L. and Reither, K. and Clowes, P. and Hoelscher, M. and Rachow, A.. (2012) Performance of the Xpert® MTB/RIF assay in an active case-finding strategy : a pilot study from Tanzania. The international journal of tuberculosis and lung disease : the official journal of the International Union Against Tuberculosis and Lung Disease, Vol. 16, H. 11. pp. 1468-1470.

Rachow, A. and Clowes, P. and Saathoff, E. and Mtafya, B. and Michael, E. and Ntinginya, E. N. and Kowour, D. and Rojas-Ponce, G. and Kroidl, A. and Maboko, L. and Heinrich, N. and Reither, K. and Hoelscher, M.. (2012) Increased and expedited case detection by Xpert MTB/RIF assay in childhood tuberculosis : a prospective cohort study. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, Vol. 54, H. 10. pp. 1388-1396.

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.

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.

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.

Borrell, 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.

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.

Coscolla, M. and Comas, I. and Gonzalez-Candelas, F.. (2011) Quantifying nonvertical inheritance in the evolution of Legionella pneumophila. Molecular biology and evolution, 28 (2). pp. 985-1001.

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.

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.

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.

Rachow, A. and Zumla, A. and Heinrich, N. and Rojas-Ponce G., and Mtafya, B. and Reither, K. and Ntinginya, E. N. and O'Grady J., and Huggett, J. and Dheda, K. and Boehme, C. and Perkins, M. and Saathoff, E. and Hoelscher, M.. (2011) Rapid and accurate detection of Mycobacterium tuberculosis in sputum samples by Cepheid Xpert MTB/RIF assay : a clinical validation study. PLoS ONE, Vol. 6, H. 6 , e20458.

Rey-Jurado, Emma and Tudó, Griselda and Borrell, Sònia and Alcaide, Fernando and Coll, Pere and Español, Montserrat and Martín-Casabona, Núria and Mick, Virginie and Montemayor, Michel and Moure, Raquel and Salvadó, Margarita and Vicente, Eva and González-Martín, Julià. (2011) Impaired fitness of Mycobacterium tuberculosis resistant isolates in a cell culture model of murine macrophages. The journal of antimicrobial chemotherapy, 66 (10). pp. 2277-2280.

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.

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.

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.

Coscolla, M. and Gagneux, S.. (2010) Does M. tuberculosis genomic diversity explain disease diversity? Drug discovery today. Disease mechanisms, Vol. 7, H. 1 , e43-e59.

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.

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.

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.

Borrell, 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.

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.

Leimkugel, 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.

Forgor, 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.

Gagneux, 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.

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.

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.

Gagneux, 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.

No

Asante-Poku, Adwoa. Genotypic and epidemiological characterization of Mycobacterium tuberculosis complex in Ghana. 2015, Doctoral Thesis, University of Basel, Faculty of Science.

Stucki, David. Transmission and evolution of "Mycobacterium tuberculosis" studied by whole genome sequencing and single nucleotide polymorphism-typing. 2015, Doctoral Thesis, University of Basel, Faculty of Science.

Malla, Bijaya. Molecular epidemiology of "mycobacterium tuberculosis" in Nepal. 2013, Doctoral Thesis, University of Basel, Faculty of Science.

This list was generated on Fri Mar 29 03:47:19 2024 CET.