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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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Number of items at this level: 278.

2024

Bright, Frederick Kodzo. Bacterial reasons for treatment failure in Mycobacterium abscessus. 2024, Doctoral Thesis, University of Basel, Associated Institution, Faculty of Science.

Hiza, Hellen Charles. Dissecting patient macrophage responses to Mycobacterium tuberculosis Complex strains from Tanzania and assessing T cell biomarkers for TB diagnosis and treatment monitoring. 2024, Doctoral Thesis, University of Basel, Associated Institution, Faculty of Science.

Maghradze, Nino. Molecular epidemiology of "mycobacterium tuberculosis" in the country of Georgia. 2024, Doctoral Thesis, University of Basel, Associated Institution, Faculty of Science.

Zwyer, Michaela. Exploring the tuberculosis epidemic in Tanzania by combining human and bacterial genomics. 2024, Doctoral Thesis, University of Basel, Associated Institution, Faculty of Science.

2023

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.

2022

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.

Hella, Jerry. Understanding the epidemiology and transmission of tuberculosis among adults in rural and urban Tanzania. 2022, Doctoral Thesis, University of Basel, Associated Institution, Faculty of Science.

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.

2021

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.

Ticlla Ccenhua, Monica Roxana. Towards an understanding of the host’s airway microbiome and the pathogen’s compensatory evolution for drug resistance in human tuberculosis. 2021, Doctoral Thesis, University of Basel, Associated Institution, Faculty of Science.

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.

2020

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.

Haraka, Frederick. Xpert MTB/RIF for diagnosis of tuberculosis : performance variability and impact on patient-important outcomes. 2020, Doctoral Thesis, University of Basel, Faculty of Science.

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. Evolutionary Epidemiology of the Mycobacterium tuberculosis Complex. 2020, Doctoral Thesis, University of Basel, Associated Institution, Faculty of Science.

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.

2019

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.

Castro, Rhastin Allan Del Rio. The evolution of fluoroquinolone-resistance in In Vitro and in natural populations of mycobacterium tuberculosis. 2019, Doctoral Thesis, University of Basel, Faculty of Science.

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.

2018

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.

Gagneux, Sebastien. (2018) Ecology and evolution of Mycobacterium tuberculosis. Nature Reviews Microbiology, 16 (4). pp. 202-213.

Gygli, Sebastian Mark. Evolution of antimicrobial resistance in Mycobacterium tuberculosis studied in the field and the laboratory. 2018, Doctoral Thesis, University of Basel, Faculty of Science.

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.

Rutaihwa, Liliana Kokusanilwa. Evolutionary history and molecular epidemiology of "Mycobacterium tuberculosis" in Tanzania and across Africa. 2018, Doctoral Thesis, University of Basel, Faculty of Science.

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.

2017

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.

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.

Armitage, Sophie A. O. and Kurtz, Joachim and Brites, Daniela and Dong, Yuemei and Du Pasquier, Louis and Wang, Han-Ching. (2017) Dscam1 in pancrustacean immunity: current status and a look to the future. Frontiers in immunology, 8. p. 662.

Blondiaux, Nicolas and Moune, Martin and Desroses, Matthieu and Frita, Rosangela and Flipo, Marion and Mathys, Vanessa and Soetaert, Karine and Kiass, Mehdi and Delorme, Vincent and Djaout, Kamel and Trebosc, Vincent and Kemmer, Christian and Wintjens, René and Wohlkönig, Alexandre and Antoine, Rudy and Huot, Ludovic and Hot, David and Coscolla, Mireia and Feldmann, Julia and Gagneux, Sebastien and Locht, Camille and Brodin, Priscille and Gitzinger, Marc and Déprez, Benoit and Willand, Nicolas and Baulard, Alain R.. (2017) Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420. Science, 355 (6330). pp. 1206-1211.

Borrell, Sonia and Trauner, Andrej. (2017) Strain diversity and the evolution of antibiotic resistance. Advances in experimental medicine and biology, 1019. pp. 263-279.

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.

Coscolla, Mireia. (2017) Biological and epidemiological consequences of MTBC diversity. Advances in experimental medicine and biology, 1019. pp. 95-116.

Fenner, Lukas and Atkinson, Andrew and Boulle, Andrew and Fox, Matthew P. and Prozesky, Hans and Zürcher, Kathrin and Ballif, Marie and Furrer, Hansjakob and Zwahlen, Marcel and Davies, Mary-Ann and Egger, Matthias and International Epidemiology Database to Evaluate Aids in Southern, . (2017) HIV viral load as an independent risk factor for tuberculosis in South Africa: collaborative analysis of cohort studies. Journal of the International AIDS Society, 20. p. 21327.

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.

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.

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.

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.

Mhimbira, Francis Apolinary. Epidemiology of co-infections in tuberculosis patients in Tanzania : HIV, helminth infection and respiratory pathogens. 2017, Doctoral Thesis, University of Basel, Faculty of Science.

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.

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.

Reither, Klaus. Improving the diagnosis of tuberculosis - clinical evaluation of four new diagnostics. 2017, Doctoral Thesis, University of Basel, Faculty of Science.

Said, Khadija and Hella, Jerry and Mhalu, Grace and Chiryankubi, Mary and Masika, Edward and Maroa, Thomas and Mhimbira, Francis and Kapalata, Neema and Fenner, Lukas. (2017) Diagnostic delay and associated factors among patients with pulmonary tuberculosis in Dar es Salaam, Tanzania. Infectious Diseases of Poverty, 6. p. 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.

4 January 2016

Swiss Institute of Bioinformatics Members, SIB. (2016) The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic acids research, 44 (D1). D27-D37.

2016

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.

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.

Charles, M. Katherine and Lindegren, Mary Lou and Wester, C. William and Blevins, Meridith and Sterling, Timothy R. and Dung, Nguyen Thi and Dusingize, Jean Claude and Avit-Edi, Divine and Durier, Nicolas and Castelnuovo, Barbara and Nakigozi, Gertrude and Cortes, Claudia P. and Ballif, Marie and Fenner, Lukas. (2016) Implementation of tuberculosis intensive case finding, isoniazid preventive therapy, and infection control ("Three I's") and HIV-tuberculosis service integration in lower income countries. PLoS ONE, 11 (4). e0153243.

Demers, Anne-Marie and Venter, Amour and Friedrich, Sven O. and Rojas-Ponce, Gabriel and Mapamba, Daniel and Jugheli, Levan and Sasamalo, Mohammed and Almeida, Deepak and Dorasamy, Afton and Jentsch, Ute and Gibson, Mara and Everitt, Daniel and Eisenach, Kathleen D. and Diacon, Andreas H.. (2016) Direct susceptibility testing of Mycobacterium tuberculosis for pyrazinamide by use of the bactec MGIT 960 system. Journal of clinical microbiology, 54 (5). pp. 1276-1281.

Domínguez, 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.

Mhimbira, Francis and Hella, Jerry and Maroa, Thomas and Kisandu, Shadrack and Chiryamkubi, Magreth and Said, Khadija and Mhalu, Grace and Mkopi, Abdallah and Mutayoba, Beatrice and Reither, Klaus and Gagneux, Sébastien and Fenner, Lukas. (2016) Home-based and facility-based directly observed therapy of tuberculosis treatment under programmatic conditions in urban Tanzania. 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.

Petrone, L. and Cannas, A. and Vanini, V. and Cuzzi, G. and Aloi, F. and Nsubuga, M. and Sserunkuma, J. and Nazziwa, R. A. and Jugheli, L. and Lukindo, T. and Giradi, E. and Antinori, A. and Pucci, L. and Reither, K. and Goletti, D.. (2016) Blood and urine inducible protein 10 as potential markers of disease activity. The international journal of tuberculosis and lung disease, 20 (11). pp. 1554-1561.

Pohl, Christian and Rutaihwa, Liliana K. and Haraka, Frederick and Nsubuga, Martin and Aloi, Francesco and Ntinginya, Nyanda E. and Mapamba, Daniel and Heinrich, Norbert and Hoelscher, Michael and Marais, Ben J. and Jugheli, Levan and Reither, Klaus. (2016) Limited value of whole blood Xpert(®) MTB/RIF for diagnosing tuberculosis in children. The journal of infection, 73 (4). pp. 326-335.

Sikalengo, George and Ramirez, Adria and Faini, Diana and Mwamelo, Kim and Battegay, Manuel and Jugheli, Levan and Hatz, Christoph and Reither, Klaus and Letang, Emilio. (2016) Tuberculous spondylitis diagnosed through Xpert MTB/RIF assay in urine: a case report. BMC Infectious Diseases, 16 (1). p. 514.

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.

Stucki, David and Brites, Daniela and Jeljeli, Leïla and Coscolla, Mireia and Liu, Qingyun and Trauner, Andrej and Fenner, Lukas and Rutaihwa, Liliana and Borrell, Sonia and Luo, Tao and Gao, Qian and Kato-Maeda, Midori and Ballif, Marie and Egger, Matthias and Macedo, Rita and Mardassi, Helmi and Moreno, Milagros and Vilanova, Griselda Tudo and Fyfe, Janet and Globan, Maria and Thomas, Jackson and Jamieson, Frances and Guthrie, Jennifer L. and Asante-Poku, Adwoa and Yeboah-Manu, Dorothy and Wampande, Eddie and Ssengooba, Willy and Joloba, Moses and Boom, W. Henry and Basu, Indira and Bower, James and Saraiva, Margarida and Vasconcellos, Sidra E. G. and Suffys, Philip and Koch, Anastasia and Wilkinson, Robert and Gail-Bekker, Linda and Malla, Bijaya and Ley, Serej D. and Beck, Hans-Peter and de Jong, Bouke C. and Toit, Kadri and Sanchez-Padilla, Elisabeth and Bonnet, Maryline and Gil-Brusola, Ana and Frank, Matthias and Penlap Beng, Veronique N. and Eisenach, Kathleen and Alani, Issam and Ndung'u, Perpetual Wangui and Revathi, Gunturu and Gehre, Florian and Akter, Suriya and Ntoumi, Francine and Stewart-Isherwood, Lynsey and Ntinginya, Nyanda E. and Rachow, Andrea and Hoelscher, Michael and Cirillo, Daniela Maria and Skenders, Girts and Hoffner, Sven and Bakonyte, Daiva and Stakenas, Petras and Diel, Roland and Crudu, Valeriu and Moldovan, Olga and Al-Hajoj, Sahal and Otero, Larissa and Barletta, Francesca and Carter, E. Jane and Diero, Lameck and Supply, Philip and Comas, Iñaki and Niemann, Stefan and Gagneux, Sebastien. (2016) Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nature genetics, 48 (12). pp. 1535-1543.

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. (2016) Spatio-temporal distribution of Mycobacterium tuberculosis complex strains in Ghana. PLoS ONE, 11 (8). e0161892.

Zumla, Alimuddin and Rao, Martin and Wallis, Robert S. and Kaufmann, Stefan H. E. and Rustomjee, Roxana and Mwaba, Peter and Vilaplana, Cris and Yeboah-Manu, Dorothy and Chakaya, Jeremiah and Ippolito, Giuseppe and Azhar, Esam and Hoelscher, Michael and Maeurer, Markus and Host-Directed Therapies Network consortium, . (2016) Host-directed therapies for infectious diseases : current status, recent progress, and future prospects. The Lancet infectious diseases, 16 (4). e47-e63.

Zürcher, Kathrin and Ballif, Marie and Zwahlen, Marcel and Rieder, Hans L. and Egger, Matthias and Fenner, Lukas. (2016) Tuberculosis mortality and living conditions in Bern, Switzerland, 1856-1950. PLoS ONE, 11 (2). e0149195.

2015

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.

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

Asante-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.

Ballif, Marie and Renner, Lorna and Claude Dusingize, Jean and Leroy, Valeriane and Ayaya, Samuel and Wools-Kaloustian, Kara and Cortes, Claudia P. and McGowan, Catherine C. and Graber, Claire and Mandalakas, Anna M. and Mofenson, Lynne M. and Egger, Matthias and Kumara Wati, Ketut Dewi and Nallusamy, Revathy and Reubenson, Gary and Davies, Mary-Ann and Fenner, Lukas and International Epidemiologic Databases to Evaluate Aids, and International Epidemiologic Databases to Evaluate Aids IeDEA, . (2015) Tuberculosis in pediatric antiretroviral therapy programs in low- and middle-income countries : diagnosis and screening practices. Journal of the Pediatric Infectious Diseases Society, Vol. 4, H. 1. pp. 30-38.

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.

Brites, Daniela and Du Pasquier, Louis. (2015) Somatic and germline diversification of a putative immunoreceptor within one Phylum: dscam in arthropods. Results and Problems in Cell Differentiation, 57. pp. 131-158.

Brites, Daniela and Gagneux, Sebastien. (2015) Co-evolution of Mycobacterium tuberculosis and Homo sapiens. Immunological reviews, Vol. 264, H. 1. pp. 6-24.

Cabibbe, Andrea M. and Miotto, Paolo and Moure, Raquel and Alcaide, Fernando and Feuerriegel, Silke and Pozzi, Gianni and Nikolayevskyy, Vladislav and Drobniewski, Francis and Niemann, Stefan and Reither, Klaus and Cirillo, Daniela M.. (2015) Lab-on-chip-based platform for fast molecular diagnosis of multidrug-resistant tuberculosis. Journal of clinical microbiology, 53 (12). pp. 3876-3880.

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 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.

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.

Dawson, Rodney and Diacon, Andreas H. and Everitt, Daniel and van Niekerk, Christo and Donald, Peter R. and Burger, Divan A. and Schall, Robert and Spigelman, Melvin and Conradie, Almari and Eisenach, Kathleen and Venter, Amour and Ive, Prudence and Page-Shipp, Liesl and Variava, Ebrahim and Reither, Klaus and Ntinginya, Nyanda E. and Pym, Alexander and von Groote-Bidlingmaier, Florian and Mendel, Carl M.. (2015) Efficiency and safety of the combination of moxifloxacin, pretomanid (PA-824), and pyrazinamide during the first 8 weeks of antituberculosis treatment : a phase 2b, open-label, partly randomised trial in patients with drug-susceptible or drug-resistant pulmonary tuberculosis. Lancet, Vol. 385, no. 9979. pp. 1738-1747.

Elkon, Ran and Milon, Beatrice and Morrison, Laura and Shah, Manan and Vijayakumar, Sarath and Racherla, Manoj and Leitch, Carmen C. and Silipino, Lorna and Hadi, Shadan and Weiss-Gayet, Michèle and Barras, Emmanuèle and Schmid, Christoph D. and Ait-Lounis, Aouatef and Barnes, Ashley and Song, Yang and Eisenman, David J. and Eliyahu, Efrat and Frolenkov, Gregory I. and Strome, Scott E. and Durand, Bénédicte and Zaghloul, Norann A. and Jones, Sherri M. and Reith, Walter and Hertzano, Ronna. (2015) RFX transcription factors are essential for hearing in mice. Nature communications, 6. p. 8549.

Heinrich, Norbert and Dawson, Rodney and du Bois, Jeannine and Narunsky, Kim and Horwith, Gary and Phipps, Andrew J. and Nacy, Carol A. and Aarnoutse, Rob E. and Boeree, Martin J. and Gillespie, Stephen H. and Venter, Amour and Henne, Sonja and Rachow, Andrea and Phillips, Patrick P. J. and Hoelscher, Michael and Diacon, Andreas H. and Pan African Consortium for the Evaluation of Antituberculosis An, and Pan African Consortium for the Evaluation of Antituberculosis An, . (2015) Early phase evaluation of SQ109 alone and in combination with rifampicin in pulmonary TB patients. The journal of antimicrobial chemotherapy, 70 (5). pp. 1558-1566.

Kroidl, Inge and Clowes, Petra and Reither, Klaus and Mtafya, Bariki and Rojas-Ponce, Gabriel and Ntinginya, Elias N. and Kalomo, Mariam and Minja, Lilian T. and Kowuor, Dickens and Saathoff, Elmar and Kroidl, Arne and Heinrich, Norbert and Maboko, Leonard and Bates, Matthew and O'Grady, Justin and Zumla, Alimuddin and Hoelscher, Michael and Rachow, Andrea. (2015) Performance of urine lipoarabinomannan assays for paediatric tuberculosis in Tanzania. The European respiratory journal, 46 (3). pp. 761-770.

Luisoni, Stefania and Suomalainen, Maarit and Boucke, Karin and Tanner, Lukas B. and Wenk, Markus R. and Guan, Xue Li and Grzybek, Michał and Coskun, Ünal and Greber, Urs F.. (2015) Co-option of membrane wounding enables virus penetration into cells. Cell host & microbe, Vol. 18, H. 1. pp. 75-85.

Luo, Tao and Comas, Iñaki and Luo, Dan and Lu, Bing and Wu, Jie and Wei, Lanhai and Yang, Chongguang and Liu, Qingyun and Gan, Mingyu and Sun, Gang and Shen, Xin and Liu, Feiying and Gagneux, Sebastien and Mei, Jian and Lan, Rushu and Wan, Kanglin and Gao, Qian. (2015) Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese. Proceedings of the National Academy of Sciences of the United States of America, Vol. 112, no. 26. pp. 8136-8141.

Melendez, Jaime and van Ginneken, Bram and Maduskar, Pragnya and Philipsen, Rick H. H. M. and Reither, Klaus and Breuninger, Marianne and Adetifa, Ifedayo M. O. and Maane, Rahmatulai and Ayles, Helen and Sanchez, Clara I.. (2015) A novel multiple-instance learning-based approach to computer-aided detection of tuberculosis on chest x-rays. IEEE transactions on medical imaging, Vol. 34, H. 1. pp. 179-192.

Merker, Matthias and Blin, Camille and Mona, Stefano and Duforet-Frebourg, Nicolas and Lecher, Sophie and Willery, Eve and Blum, Michael G. B. and Rüsch-Gerdes, Sabine and Mokrousov, Igor and Aleksic, Eman and Allix-Béguec, Caroline and Antierens, Annick and Augustynowicz-Kopeć, Ewa and Ballif, Marie and Barletta, Francesca and Beck, Hans Peter and Barry, Clifton E. and Bonnet, Maryline and Borroni, Emanuele and Campos-Herrero, Isolina and Cirillo, Daniela and Cox, Helen and Crowe, Suzanne and Crudu, Valeriu and Diel, Roland and Drobniewski, Francis and Fauville-Dufaux, Maryse and Gagneux, Sébastien and Ghebremichael, Solomon and Hanekom, Madeleine and Hoffner, Sven and Jiao, Wei-Wei and Kalon, Stobdan and Kohl, Thomas A. and Kontsevaya, Irina and Lillebæk, Troels and Maeda, Shinji and Nikolayevskyy, Vladyslav and Rasmussen, Michael and Rastogi, Nalin and Samper, Sofia and Sanchez-Padilla, Elisabeth and Savic, Branislava and Shamputa, Isdore Chola and Shen, Adong and Sng, Li-Hwei and Stakenas, Petras and Toit, Kadri and Varaine, Francis and Vukovic, Dragana and Wahl, Céline and Warren, Robin and Supply, Philip and Niemann, Stefan and Wirth, Thierry. (2015) Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nature genetics, Vol. 47, H. 3. pp. 242-249.

Mhalu, Grace and Hella, Jerry and Doulla, Basra and Mhimbira, Francis and Mtutu, Hawa and Hiza, Helen and Sasamalo, Mohamed and Rutaihwa, Liliana and Rieder, Hans L. and Seimon, Tamsyn and Mutayoba, Beatrice and Weiss, Mitchell G. and Fenner, Lukas. (2015) Do instructional videos on sputum submission result in increased tuberculosis case detection? : a randomized controlled trial. PLoS ONE, Vol. 10, H. 9 , e0138413.

Molefi, Mooketsi and Chofle, Awilly A. and Molloy, Síle F. and Kalluvya, Samuel and Changalucha, John M. and Cainelli, Francesca and Leeme, Tshepo and Lekwape, Nametso and Goldberg, Drew W. and Haverkamp, Miriam and Bisson, Gregory P. and Perfect, John R. and Letang, Emili and Fenner, Lukas and Meintjes, Graeme and Burton, Rosie and Makadzange, Tariro and Ndhlovu, Chiratidzo E. and Hope, William and Harrison, Thomas S. and Jarvis, Joseph N.. (2015) AMBITION-cm : intermittent high dose AmBisome on a high dose fluconazole backbone for cryptococcal meningitis induction therapy in sub-Saharan Africa : study protocol for a randomized controlled trial. Trials, Vol. 16. p. 276.

Nicol, Mark Patrick and Gnanashanmugam, Devasena and Browning, Renee and Click, Eleanor S. and Cuevas, Luis E. and Detjen, Anne and Graham, Steve M. and Levin, Michael and Makhene, Mamodikoe and Nahid, Payam and Perez-Velez, Carlos M. and Reither, Klaus and Song, Rinn and Spiegel, Hans M. L. and Worrell, Carol and Zar, Heather J. and Walzl, Gerhard. (2015) A blueprint to address research gaps in the development of biomarkers for pediatric tuberculosis. Clinical infectious diseases, Vol. 61, H. Suppl. 3 , S164-S172.

Olaru, I. D. and Rachow, A. and Lange, C. and Ntinginya, N. E. and Reither, K. and Hoelscher, M. and Vollrath, O. and Niemann, S.. (2015) Ascertaining in vivo virulence of Mycobacterium tuberculosis lineages in patients in Mbeya, Tanzania. The international journal of tuberculosis and lung disease, Vol. 19, H. 1. pp. 70-73.

Petrone, Linda and Cannas, Angela and Aloi, Francesco and Nsubuga, Martin and Sserumkuma, Joseph and Nazziwa, Ritah Angella and Jugheli, Levan and Lukindo, Tedson and Girardi, Enrico and Reither, Klaus and Goletti, Delia. (2015) Blood or urine IP-10 cannot discriminate between active tuberculosis and respiratory diseases different from tuberculosis in children. BioMed research international, 2015. ID589471.

Reither, Klaus and Jugheli, Levan and Glass, Tracy R. and Sasamalo, Mohamed and Mhimbira, Francis A. and Weetjens, Bart J. and Cox, Christophe and Edwards, Timothy L. and Mulder, Christiaan and Beyene, Negussie W. and Mahoney, Amanda. (2015) Evaluation of giant african pouched rats for detection of pulmonary tuberculosis in patients from a high-endemic setting. PLoS ONE, Vol. 10, H. 10 , e0135877.

Reither, Klaus and Manyama, Christina and Clowes, Petra and Rachow, Andrea and Mapamba, Daniel and Steiner, Andreas and Ross, Amanda and Mfinanga, Elirehema and Sasamalo, Mohamed and Nsubuga, Martin and Aloi, Francesco and Cirillo, Daniela and Jugheli, Levan and Lwilla, Fred. (2015) Xpert MTB/RIF assay for diagnosis of pulmonary tuberculosis in children : a prospective, multi-centre evaluation. The journal of infection, Vol. 70, H. 4. pp. 392-399.

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.

Steiner, A. and Mangu, C. and van den Hombergh, J. and van Deutekom, H. and van Ginneken, B. and Clowes, P. and Mhimbira, F. and Mfinanga, S. and Rachow, A. and Reither, K. and Hoelscher, M.. (2015) Screening for pulmonary tuberculosis in a Tanzanian prison and computer-aided interpretation of chest X-rays. Public health action, 5 (4). pp. 249-254.

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.

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.

Sánchez-Busó, Leonor and Coscollà, Mireia and Palero, Ferran and Camaró, María Luisa and Gimeno, Ana and Moreno, Pilar and Escribano, Isabel and López Perezagua, María Mar and Colomina, Javier and Vanaclocha, Herme and González-Candelas, Fernando. (2015) Geographical and temporal structures of Legionella pneumophila sequence types in comunitat Valenciana (Spain), 1998 to 2013. Applied and Environmental Microbiology, 81 (20). pp. 7106-7113.

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. Henry and Gagneux, Sebastien and Joloba, Moses L. and Tuberculosis Research Unit, . (2015) A single-nucleotide-polymorphism real-time PCR assay for genotyping of mycobacterium tuberculosis complex in peri-urban Kampala. BMC infectious diseases, Vol. 15 , 396.

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.

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.

Zumla, A. and Chakaya, J. and Hoelscher, M. and Ntoumi, F. and Rustomjee, R. and Vilaplana, C. and Yeboah-Manu, D. and Rasolof, V. and Munderi, P. and Singh, N. and Aklillu, E. and Padayatchi, N. and Macete, E. and Kapata, N. and Mulenga, M. and Kibiki, G. and Mfinanga, S. and Nyirenda, T. and Maboko, L. and Garcia-Basteiro, A. and Rakotosamimanana, N. and Bates, M. and Mwaba, P. and Reither, K. and Gagneux, S. and Edwards, S. and Mfinanga, E. and Abdulla, S. and Cardona, P. J. and Russell, J. B. and Gant, V. and Noursadeghi, M. and Elkington, P. and Bonnet, M. and Menendez, C. and Dieye, T. N. and Diarra, B. and Maiga, A. and Aseffa, A. and Parida, S. and Wejse, C. and Petersen, E. and Kaleebu, P. and Oliver, M. and Craig, G. and Corrah, T. and Tientcheu, L. and Antonio, M. and Rao, M. and McHugh, T. D. and Sheikh, A. and Ippolito, G. and Ramjee, G. and Kaufmann, S. H. and Churchyard, G. and Steyn, A. and Grobusch, M. and Sanne, I. and Martinson, N. and Madansein, R. and Wilkinson, R. J. and Mayosi, B. and Schito, M. and Wallis, R. S. and Maeurer, M.. (2015) Towards host-directed therapies for tuberculosis. Nature reviews. Drug discovery, 14 (8). pp. 511-512.

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.

2014

Asante-Poku, Adwoa and Nyaho, Michael Selasi and Borrell, Sonia and Comas, Iñaki and Gagneux, Sebastien and Yeboah-Manu, Dorothy. (2014) Evaluation of customised lineage-specific sets of MIRU-VNTR loci for genotyping Mycobacterium tuberculosis complex isolates in Ghana. PLoS ONE, Vol. 9, H. 3 , e92675.

Ballif, M. and Nhandu, V. and Wood, R. and Dusingize, J. C. and Carter, E. J. and Cortes, C. P. and McGowan, C. C. and Diero, L. and Graber, C. and Renner, L. and Hawerlander, D. and Kiertiburanakul, S. and Du, Q. T. and Sterling, T. R. and Egger, M. and Fenner, L. and International epidemiological Databases to Evaluate Aids, . (2014) Detection and management of drug-resistant tuberculosis in HIV-infected patients in lower-income countries. The international journal of tuberculosis and lung disease, Vol. 18, H. 11. pp. 1327-1336.

Bos, K. I. and Harkins, K. M. and Herbig, A. and Coscolla, M. and Weber, N. and Comas, I. and Forrest, S. A. and Bryant, J. M. and Harris, S. R. and Schuenemann, V. J. and Campbell, T. J. and Majander, K. and Wilbur, A. K. and Guichon, R. A. and Wolfe Steadman, D. L. and Cook, D. C. and Niemann, S. and Behr, M. A. and Zumarraga, M. and Bastida, R. and Huson, D. and Nieselt, K. and Young, D. and Parkhill, J. and Buikstra, J. E. and Gagneux, S. and Stone, A. C. and Krause, J.. (2014) Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature, Vol. 514, H. 7523. pp. 494-497.

Chipman, Ariel D. and Ferrier, David E. K. and Brena, Carlo and Qu, Jiaxin and Hughes, Daniel S. T. and Schröder, Reinhard and Torres-Oliva, Montserrat and Znassi, Nadia and Jiang, Huaiyang and Almeida, Francisca C. and Alonso, Claudio R. and Apostolou, Zivkos and Aqrawi, Peshtewani and Arthur, Wallace and Barna, Jennifer C. J. and Blankenburg, Kerstin P. and Brites, Daniela and Capella-Gutiérrez, Salvador and Coyle, Marcus and Dearden, Peter K. and Du Pasquier, Louis and Duncan, Elizabeth J. and Ebert, Dieter and Eibner, Cornelius and Erikson, Galina and Evans, Peter D. and Extavour, Cassandra G. and Francisco, Liezl and Gabaldón, Toni and Gillis, William J. and Goodwin-Horn, Elizabeth A. and Green, Jack E. and Griffiths-Jones, Sam and Grimmelikhuijzen, Cornelis J. P. and Gubbala, Sai and Guigó, Roderic and Han, Yi and Hauser, Frank and Havlak, Paul and Hayden, Luke and Helbing, Sophie and Holder, Michael and Hui, Jerome H. L. and Hunn, Julia P. and Hunnekuhl, Vera S. and Jackson, LaRonda and Javaid, Mehwish and Jhangiani, Shalini N. and Jiggins, Francis M. and Jones, Tamsin E. and Kaiser, Tobias S. and Kalra, Divya and Kenny, Nathan J. and Korchina, Viktoriya and Kovar, Christie L. and Kraus, F. Bernhard and Lapraz, François and Lee, Sandra L. and Lv, Jie and Mandapat, Christigale and Manning, Gerard and Mariotti, Marco and Mata, Robert and Mathew, Tittu and Neumann, Tobias and Newsham, Irene and Ngo, Dinh N. and Ninova, Maria and Okwuonu, Geoffrey and Ongeri, Fiona and Palmer, William J. and Patil, Shobha and Patraquim, Pedro and Pham, Christopher and Pu, Ling-Ling and Putman, Nicholas H. and Rabouille, Catherine and Ramos, Olivia Mendivil and Rhodes, Adelaide C. and Robertson, Helen E. and Robertson, Hugh M. and Ronshaugen, Matthew and Rozas, Julio and Saada, Nehad and Sánchez-Gracia, Alejandro and Scherer, Steven E. and Schurko, Andrew M. and Siggens, Kenneth W. and Simmons, DeNard and Stief, Anna and Stolle, Eckart and Telford, Maximilian J. and Tessmar-Raible, Kristin and Thornton, Rebecca and van der Zee, Maurijn and von Haeseler, Arndt and Williams, James M. and Willis, Judith H. and Wu, Yuanqing and Zou, Xiaoyan and Lawson, Daniel and Muzny, Donna M. and Worley, Kim C. and Gibbs, Richard A. and Akam, Michael and Richards, Stephen. (2014) The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede strigamia maritima. PLoS biology, 12 (11). e1002005.

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.

Copin, Richard and Coscollá, Mireia and Seiffert, Salome N. and Bothamley, Graham and Sutherland, Jayne and Mbayo, Georgetta and Gagneux, Sebastien and Ernst, Joel D.. (2014) Sequence diversity in the pe_pgrs genes of Mycobacterium tuberculosis is independent of human T cell recognition. mBio, Vol. 5, H. 1 , e00960-13.

Coscolla, Mireia and Gagneux, Sebastien. (2014) Consequences of genomic diversity in Mycobacterium tuberculosis. Seminars in immunology, Vol. 26, H. 6. pp. 431-444.

Coscollá, Mireia and Fernández, Carmen and Colomina, Javier and Sánchez-Busó, Leonor and González-Candelas, Fernando. (2014) Mixed infection by Legionella pneumophila in outbreak patients. Zentralblatt für Bakteriologie = International journal of medical microbiology, Vol. 304, H. 3/4. pp. 307-313.

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.

Kroidl, Inge and Clowes, Petra and Mwakyelu, Joshua and Maboko, Leonard and Kiangi, Abubakary and Rachow, Andrea and Reither, Klaus and Jung, Jutta and Nsojo, Anthony and Saathoff, Elmar and Hoelscher, Michael. (2014) Reasons for false-positive lipoarabinomannan ELISA results in a Tanzanian population. Scandinavian journal of infectious diseases, Vol. 46, H. 2. pp. 144-148.

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.

Ley, Serej D. and Harino, Paul and Vanuga, Kilagi and Kamus, Ruben and Carter, Robyn and Coulter, Christopher and Pandey, Sushil and Feldmann, Julia and Ballif, Marie and Siba, Peter M. and Phuanukoonnon, Suparat and Gagneux, Sebastien and Beck, Hans-Peter. (2014) Diversity of Mycobacterium tuberculosis and drug resistance in different provinces of Papua New Guinea. BMC microbiology, Vol. 14 , 307.

Narayanaswamy, Pradeep and Shinde, Sudhirkumar and Sulc, Robert and Kraut, Rachel and Staples, Gregory and Thiam, Chung Hwee and Grimm, Rudolf and Sellergren, Börje and Torta, Federico and Wenk, Markus R.. (2014) Lipidomic "deep profiling" : an enhanced workflow to reveal new molecular species of signaling lipids. Analytical chemistry, Vol. 86, H. 6. pp. 3043-3047.

Portevin, Damien and Sukumar, Sudarkodi and Coscolla, Mireia and Shui, Guanghou and Li, Bowen and Guan, Xue Li and Bendt, Anne K. and Young, Douglas and Gagneux, Sebastien and Wenk, Markus R.. (2014) Lipidomics and genomics of Mycobacterium tuberculosis reveal lineage-specific trends in mycolic acid biosynthesis. MicrobiologyOpen, Vol. 3, H. 6. pp. 823-835.

Reither, Klaus and Katsoulis, Lynn and Beattie, Trevor and Gardiner, Nicolene and Lenz, Nicole and Said, Khadija and Mfinanga, Elirehema and Pohl, Christian and Fielding, Katherine L. and Jeffery, Hannah and Kagina, Benjamin M. and Hughes, Elisabeth J. and Scriba, Thomas J. and Hanekom, Willem A. and Hoff, Søren T. and Bang, Peter and Kromann, Ingrid and Daubenberger, Claudia and Andersen, Peter and Churchyard, Gavin J.. (2014) Safety and immunogenicity of H1/IC31®, an adjuvanted TB subunit vaccine, in HIV-infected adults with CD4+ lymphocyte counts greater than 350 cells/mm3 : a phase II, multi-centre, double-blind, randomized, placebo-controlled trial. PLoS ONE, Vol. 9, H. 12 , e114602.

Seguín-Estévez, Queralt and Dunand-Sauthier, Isabelle and Lemeille, Sylvain and Iseli, Christian and Ibberson, Mark and Ioannidis, Vassilios and Schmid, Christoph D. and Rousseau, Philippe and Barras, Emmanuèle and Geinoz, Antoine and Xenarios, Ioannis and Acha-Orbea, Hans and Reith, Walter. (2014) Extensive remodeling of DC function by rapid maturation-induced transcriptional silencing. Nucleic acids symposium series, Vol. 42, H. 15. pp. 9641-9655.

Steiner, Andreas and Stucki, David and Coscolla, Mireia and Borrell, Sonia and Gagneux, Sebastien. (2014) KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes. BMC genomics, Vol. 15 , 881.

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.

2013

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.

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.

Brites, D. and Brena, C. and Ebert, Dieter and Du Pasquier, L.. (2013) More than one way to produce protein diversity: duplication and limited alternative splicing of an adhesion molecule gene in basal arthropods. Evolution, 67 (10). pp. 2999-3011.

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.

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.

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.

Fenner, Lukas and Ballif, Marie and Graber, Claire and Nhandu, Venerandah and Dusingize, Jean Claude and Cortes, Claudia P. and Carriquiry, Gabriela and Anastos, Kathryn and Garone, Daniela and Jong, Eefje and Gnokoro, Joachim Charles and Sued, Omar and Ajayi, Samuel and Diero, Lameck and Wools-Kaloustian, Kara and Kiertiburanakul, Sasisopin and Castelnuovo, Barbara and Lewden, Charlotte and Durier, Nicolas and Sterling, Timothy R. and Egger, Matthias and International epidemiological Databases to Evaluate Aids, . (2013) Tuberculosis in antiretroviral treatment programs in lower income countries: availability and use of diagnostics and screening. PLoS ONE, Vol. 8, H. 10 , e77697.

Fenner, 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.

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.

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.

Gagneux, Sebastien. (2013) Genetic diversity in Mycobacterium tuberculosis. Current topics in microbiology and immunology, Vol. 374. pp. 1-25.

Garcia-Garcerà, Marc and Garcia-Etxebarria, Koldo and Coscollà, Mireia and Latorre, Amparo and Calafell, Francesca. (2013) A new method for extracting skin microbes allows metagenomic analysis of whole-deep skin. PLoS ONE, Vol. 8, H. 9 , e74914.

Hella, J. J. and Hiza, H. C. and Mfinanga, E. and Reither, K.. (2013) Paraspinal abscess secondary to tuberculous spondylitis diagnosed by Xpert MTB/RIF assay in rural Tanzania. BMJ case reports, 2013, Apr 10. pp. 1-3.

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.

Klopper, M. and Warren, R. M. and Hayes, C. and van Pittius, N. C. G. and Streicher, E. M. and Müller, B. and Sirgel, F. A. and Chabula-Nxiweni, M. and Hoosain, E. and Coetzee, G. and van Helden, P. D. and Victor, T. C. and Trollip, A. P.. (2013) Emergence and spread of extensively and totally drug-resistant tuberculosis, South Africa. Emerging infectious diseases, Vol. 19, H. 3. pp. 449-455.

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

Miotto, Paolo and Mwangoka, Grace and Valente, Ilaria C. and Norbis, Luca and Sotgiu, Giovanni and Bosu, Roberta and Ambrosi, Alessandro and Codecasa, Luigi R. and Goletti, Delia and Matteelli, Alberto and Ntinginya, Elias N. and Aloi, Francesco and Heinrich, Norbert and Reither, Klaus and Cirillo, Daniela M.. (2013) miRNA signatures in Sera of patients with active pulmonary tuberculosis. PLoS ONE, Vol. 8, H. 11 , e80149.

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.

Müller, Borna and Chihota, Violet N. and Pillay, Manormoney and Klopper, Marisa and Streicher, Elizabeth M. and Coetzee, Gerrit and Trollip, Andre and Hayes, Cindy and Bosman, Marlein E. and Gey van Pittius, Nicolaas C. and Victor, Thomas C. and Gagneux, Sebastien and van Helden, Paul D. and Warren, Robin M.. (2013) Programmatically selected multidrug-resistant strains drive the emergence of extensively drug-resistant tuberculosis in South Africa. PLoS ONE, Vol. 8, H. 8 , e70919.

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.

Pohl, Christian and Jugheli, Levan and Haraka, Fredrick and Mfinanga, Elirehema and Said, Khadija and Reither, Klaus. (2013) Pulmonary aspergilloma : a treatment challenge in sub-Saharan Africa. PLoS neglected tropical diseases, Vol. 7, H. 10 , e2352.

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.

Said, Khadija and Mkopi, Abdallah and Verver, Suzanne and Lwilla, Fred and Churchyard, Gavin and Shekalaghe, Seif and Battegay, Manuel and Reither, Klaus. (2013) Improved services to enrollees into an HIV rural care and treatment center in Tanzania. Pan African medical journal, Vol. 16 , 34.

Schomaker, Michael and Egger, Matthias and Maskew, Mhairi and Garone, Daniela and Prozesky, Hans and Hoffmann, Christopher J. and Boulle, Andrew and Fenner, Lukas. (2013) Immune recovery after starting ART in HIV-infected patients presenting and not presenting with Tuberculosis in south Africa. JAIDS : journal of acquired immune deficiency syndromes : official publication of the International Retrovirology Association, Vol. 63, H. 1. pp. 142-145.

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.

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.

2012

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.

2011

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.

2010

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.

2009

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.

2007

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.

2005

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.

2002

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.

2001

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.

2000

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.

This list was generated on Thu Oct 3 03:58:19 2024 CEST.