Items where Author is "Gagneux, S."

2023

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.

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.

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.

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.

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.

2022

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.

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.

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.

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.

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.

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.

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.

2021

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.

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.

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.

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.

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.

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.

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.

Haraka, F. and Kakolwa, M. and Schumacher, S. G. and Nathavitharana, R. R. and Denkinger, C. M. and Gagneux, S. and Reither, K. and Ross, A.. (2021) Impact of the diagnostic test Xpert MTB/RIF on patient outcomes for tuberculosis (Review). Cochrane Database Syst Rev, 2021 (4). CD012972.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

2020

Ezewudo, M. and Borens, A. and Chiner-Oms, A. and Miotto, P. and Chindelevitch, L. and Starks, A. M. and Hanna, D. and Liwski, R. and Zignol, M. and Gilpin, C. and Niemann, S. and Kohl, T. A. and Warren, R. M. and Crook, D. and Gagneux, S. and Hoffner, S. and Rodrigues, C. and Comas, I. and Engelthaler, D. M. and Alland, D. and Rigouts, L. and Lange, C. and Dheda, K. and Hasan, R. and McNerney, R. and Cirillo, D. M. and Schito, M. and Rodwell, T. C. and Posey, J.. (2020) Author correction: Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase. Scientific Reports, 10 (1). p. 3531.

Haraka, F. and Schumacher, S. G. and Ross, A. and Mantsoki, A. and Gagneux, S. and Reither, K. and Denkinger, C. M.. (2020) Effect of history of tuberculosis on specificity of Xpert MTB/RIF. Eur Respir J, 56 (3). p. 2000343.

Loiseau, C. and Brites, D. and Reinhard, M. and Zurcher, K. and Borrell, S. and Ballif, M. and Fenner, L. and Cox, H. and Rutaihwa, L. K. and Wilkinson, R. J. and Yotebieng, M. and Carter, E. J. and Abimiku, A. and Marcy, O. and Gotuzzo, E. and Avihingsanon, A. and Zetola, N. and Doulla, B. and Bottger, E. C. and Egger, M. and Gagneux, S.. (2020) HIV coinfection is associated with low fitness rpoB variants in rifampicin-resistant Mycobacterium tuberculosis. Antimicrobial agents and chemotherapy, 64 (10). e00782-20.

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.

2019

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.

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.

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.

2018

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.

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.

2017

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.

2016

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.

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.

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.

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.

2014

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.

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.

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.

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.

Firdessa, R. and Berg, S. and Hailu, E. and Schelling, E. and Gumi, B. and Erenso, G. and Gadisa, E. and Kiros, T. and Habtamu, M. and Hussein, J. and Zinsstag, J. and Robertson, B. D. and Ameni, G. and Lohan, A. J. and Loftus, B. and Comas, I. and Gagneux, S. and Tschopp, R. and Yamuah, L. and Hewinson, G. and Gordon, S. V. and Young, D. B. and Aseffa, A.. (2013) Mycobacterial lineages causing pulmonary and extrapulmonary tuberculosis, Ethiopia. Emerging infectious diseases, Vol. 19, H. 3. pp. 460-463.

de Vos, M. and Müller, B. and Borrell, S. and Black, P. and van Helden, P. and Warren, R. and Gagneux, S. and Victor, T.. (2013) Putative compensatory mutations in the rpoC gene of rifampicin-resistant Mycobacterium tuberculosis are associated with ongoing transmission. Antimicrobial agents and chemotherapy : AAC, Vol. 57, H. 2. pp. 827-832.

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.

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.

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.

2012

Bratschi, M. W. and Njih, Tabah and Bolz, M. and Stucki, D. and Borrell, S. and Gagneux, S. and Noumen-Djeunga, B. and Junghanss, T. and Um Boock, A. and Pluschke, G.. (2012) A case of cutaneous tuberculosis in a Buruli ulcer-endemic area. PLoS neglected tropical diseases, Vol. 6, H. 8 , e1751.

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.

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.

Ballif, M. and Harino, P. and Ley, S. and Coscolla, M. and Niemann, S. and Carter, R. and Coulter, C. and Borrell, S. and Siba, P. and Phuanukoonnon, S. and Gagneux, S. and Beck, H. P.. (2012) Drug resistance-conferring mutations in Mycobacterium tuberculosis from Madang, Papua New Guinea. BMC microbiology, Vol. 12 , 191.

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.

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.

Ballif, M. and Harino, P. and Ley, S. and Carter, R. and Coulter, C. and Niemann, S. and Borrell, S. and Fenner, L. and Siba, P. and Phuanukoonnon, S. and Gagneux, S. and Beck, H. P.. (2012) Genetic diversity of Mycobacterium tuberculosis in Madang, Papua New Guinea. The international journal of tuberculosis and lung disease, Vol. 16, H. 8. pp. 1100-1107.

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.

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.

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.

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.

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.

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.

2011

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.

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.

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.

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.

2010

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.

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.

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.

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.

2001

Zhu, P. and van der Ende, A. and Falush, D. and Brieske, N. and Morelli, G. and Linz, B. and Popovic, T. and Schuurman, I. G. and Adegbola, R. A. and Zurth, K. and Gagneux, S. and Platonov, A. E. and Riou, J. Y. and Caugant, D. A. and Nicolas, P. and Achtman, M.. (2001) Fit genotypes and escape variants of subgroup III Neisseria meningitidis during three pandemics of epidemic meningitis. Proceedings of the National Academy of Sciences of the United States of America, Vol. 98, H. 9. pp. 5234-5239.

Hodgson, A. and Smith, T. and Gagneux, S. and Adjuik, M. and Pluschke, G. and Mensah, N. K. and Binka, F. and Genton, B.. (2001) Risk factors for meningococcal meningitis in northern Ghana. Transactions of the Royal Society of Tropical Medicine and Hygiene, Vol. 95, H. 5. pp. 477-480.

Hodgson, A. and Smith, T. and Gagneux, S. and Akumah, I. and Adjuik, M. and Pluschke, G. and Binka, F. and Genton, B.. (2001) Survival and sequelae of meningococcal meningitis in Ghana. International journal of epidemiology : official journal of the international epidemiological association, Vol. 30, H. 6. pp. 1440-1446.

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.