Publications

Ngabonziza, J. C. S., Loiseau, C., Marceau, M., Jouet, A., Menardo, F., Tzfadia, O., Antoine, R., Niyigena, E. B., Mulders, W., Fissette, K., Diels, M., Gaudin, C., Duthoy, S., Ssengooba, W., André, E., Kaswa, M. K., Habimana, Y. M., Brites, D., Affolabi, D., Mazarati, J. B., de Jong, B. C., Rigouts, L., Gagneux, S., Meehan, C. J. and Supply, P. (2020) “A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region”, Nature Communications. Nature Publishing Group, 11, p. 2917. doi: 10.1038/s41467-020-16626-6.   edoc | Open Access
Asare, P., Otchere, I. D., Bedeley, E., Brites, D., Loiseau, C., Baddoo, N. A., Asante-Poku, A., Osei-Wusu, S., Prah, D. A., Borrell, S., Reinhard, M., Forson, A., Koram, K. A., Gagneux, S. and Yeboah-Manu, D. (2020) “Whole genome sequencing and spatial analysis identifies recent tuberculosis transmission hotspots in Ghana”, Frontiers in medicine. Frontiers Media, 7, p. 161. doi: 10.3389/fmed.2020.00161.   edoc | Open Access
McHenry, M. L., Bartlett, J., Igo, R. P., Wampande, E. M., Benchek, P., Mayanja-Kizza, H., Fluegge, K., Hall, N. B., Gagneux, S., Tishkoff, S. A., Wejse, C., Sirugo, G., Boom, W. H., Joloba, M., Williams, S. M. and Stein, C. M. (2020) “Interaction between host genes and Mycobacterium tuberculosis lineage can affect tuberculosis severity: evidence for coevolution?”, PLoS genetics. Public Library of Science, 16(4), p. e1008728. doi: 10.1371/journal.pgen.1008728.   edoc
Sousa, J., Cá, B., Maceiras, A. R., Simões-Costa, L., Fonseca, K. L., Fernandes, A. I., Ramos, A., Carvalho, T., Barros, L., Magalhães, C., Chiner-Oms, Álvaro, Machado, H., Veiga, M. I., Singh, A., Pereira, R., Amorim, A., Vieira, J., Vieira, C. P., Bhatt, A., Rodrigues, F., Rodrigues, P. N. S., Gagneux, S., Castro, A. G., Guimarães, J. T., Bastos, H. N., Osório, N. S., Comas, I. and Saraiva, M. (2020) “Mycobacterium tuberculosis associated with severe tuberculosis evades cytosolic surveillance systems and modulates IL-1β production”, Nature Communications. Nature Publishing Group, 11, p. 1949. doi: 10.1038/s41467-020-15832-6.   edoc | Open Access
Øyås, O., Borrell, S., Trauner, A., Zimmermann, M., Feldmann, J., Liphardt, T., Gagneux, S., Stelling, J., Sauer, U. and Zampieri, M. (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. National Academy of Sciences, 117(15), pp. 8494–8502. doi: 10.1073/pnas.1915551117.   edoc
Loiseau, C., Menardo, F., Aseffa, A., Hailu, E., Gumi, B., Ameni, G., Berg, S., Rigouts, L., Robbe-Austerman, S., Zinsstag, J., Gagneux, S. and Brites, D. (2020) “An African origin for Mycobacterium bovis”, Evolution, medicine, and public health. Oxford Univ. Press , 2020, pp. 49–59. doi: 10.1093/emph/eoaa005.   edoc | Open Access
Ezewudo, M., Borens, A., Chiner-Oms, A., Miotto, P., Chindelevitch, L., Starks, A. M., Hanna, D., Liwski, R., Zignol, M., Gilpin, C., Niemann, S., Kohl, T. A., Warren, R. M., Crook, D., Gagneux, S., Hoffner, S., Rodrigues, C., Comas, I., Engelthaler, D. M., Alland, D., Rigouts, L., Lange, C., Dheda, K., Hasan, R., McNerney, R., Cirillo, D. M., Schito, M., 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. Nature Publishing Group, 10(1), p. 3531. doi: 10.1038/s41598-020-58955-y.   edoc | Open Access
Castro, R. A. D., Ross, A., Kamwela, L., Reinhard, M., Loiseau, C., Feldmann, J., Borrell, S., Trauner, A. and Gagneux, S. (2020) “The genetic background modulates the evolution of fluoroquinolone-resistance in Mycobacterium tuberculosis”, Molecular biology and evolution. Oxford University Press, 37(1), pp. 195–207. doi: 10.1093/molbev/msz214.   edoc | Open Access
Mulholland, C. V., Shockey, A. C., Aung, H. L., Cursons, R. T., O’Toole , R. F., Gautam, S. S., Brites, D., Gagneux, S., Roberts, A. R., Karalus, N., Cook, G. M., Pepperell, C. S. and Arcus, V. L. (2019) “Dispersal of Mycobacterium tuberculosis driven by historical European trade in the South Pacific”, Frontiers in Microbiology. Frontiers Media, 10(4), p. 2778. doi: 10.3389/fmicb.2019.02778.   edoc
Maghradze, N., Jugheli, L., Borrell, S., Tukvadze, N., Aspindzelashvili, R., Avaliani, Z., Reither, K. and Gagneux, S. (2019) “Classifying recurrent Mycobacterium tuberculosis cases in Georgia using MIRU-VNTR typing”, PLoS ONE. Public Library of Science, 14(10), p. e0223610. doi: 10.1371/journal.pone.0223610.   edoc | Open Access
Wampande, E. M., Naniima, P., Mupere, E., Kateete, D. P., Malone, L. L., Stein, C. M., Mayanja-Kizza, H., Gagneux, S., Boom, W. H. and Joloba, M. L. (2019) “Genetic variability and consequence of Mycobacterium tuberculosis lineage 3 in Kampala-Uganda”, PLoS ONE. Public Library of Science, 14(9), p. e0221644. doi: 10.1371/journal.pone.0221644.   edoc | Open Access
Menardo, F., Duchêne, S., Brites, D. and Gagneux, S. (2019) “The molecular clock of Mycobacterium tuberculosis”, PLoS Pathogens. Public Library of Science, 15(9), p. e1008067. doi: 10.1371/journal.ppat.1008067.   edoc
Meehan, C. J., Goig, G. A., Kohl, T. A., Verboven, L., Dippenaar, A., Ezewudo, M., Farhat, M. R., Guthrie, J. L., Laukens, K., Miotto, P., Ofori-Anyinam, B., Dreyer, V., Supply, P., Suresh, A., Utpatel, C., van Soolingen, D., Zhou, Y., Ashton, P. M., Brites, D., Cabibbe, A. M., de Jong, B. C., de Vos, M., Menardo, F., Gagneux, S., Gao, Q., Heupink, T. H., Liu, Q., Loiseau, C., Rigouts, L., Rodwell, T. C., Tagliani, E., Walker, T. M., Warren, R. M., Zhao, Y., Zignol, M., Schito, M., Gardy, J., Cirillo, D. M., Niemann, S., Comas, I. and Van Rie, A. (2019) “Whole genome sequencing of Mycobacterium tuberculosis : current standards and open issues”, Nature Reviews Microbiology. Nature Publishing Group, 17(9), pp. 533–545. doi: 10.1038/s41579-019-0214-5.   edoc
Chiner-Oms, Álvaro, Berney, M., Boinett, C., González-Candelas, F., Young, D. B., Gagneux, S., Jacobs, W. R., Parkhill, J., Cortes, T. and Comas, I. (2019) “Genome-wide mutational biases fuel transcriptional diversity in the Mycobacterium tuberculosis complex”, Nature Communications. Nature Publishing Group, 10, p. 3994. doi: 10.1038/s41467-019-11948-6.   edoc | Open Access
Chiner-Oms, A., Sánchez-Busó, L., Corander, J., Gagneux, S., Harris, S. R., Young, D., González-Candelas, F. and Comas, I. (2019) “Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex”, Science Advances, 5(6), p. eaaw3307. doi: 10.1126/sciadv.aaw3307.   edoc | Open Access
Conceição, E. C., Refregier, G., Gomes, H. M., Olessa-Daragon, X., Coll, F., Ratovonirina, N. H., Rasolofo-Razanamparany, V., Lopes, M. L., van Soolingen, D., Rutaihwa, L., Gagneux, S., Bollela, V. R., Suffys, P. N., Duarte, R. S., Lima, K. V. B. and Sola, C. N. (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. doi: 10.1016/j.meegid.2019.06.001.   edoc
Loiseau, C., Brites, D., Moser, I., Coll, F., Pourcel, C., Robbe-Austerman, S., Escuyer, V., Musser, K. A., Peacock, S. J., Feuerriegel, S., Kohl, T. A., Niemann, S., Gagneux, S. and Köser, C. 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. American Society for Microbiology, 63(6), pp. e00159–19. doi: 10.1128/AAC.00159-19.   edoc
Rutaihwa L, M. F., Stucki D, G. S. M., Ley SD, M. B., Feldmann J, B. S., Beisel C, M. K., Carter JE, D. L., Ballif M, J. L., Reither K, F. L. and Brites D, G. S. (2019) “Multiple introductions of Mycobacterium tuberculosis lineage 2-Beijing into Africa over centuries”, Frontiers in Ecology and Evolution. Frontiers Media , 7, p. 112. doi: 10.3389/fevo.2019.00112.   edoc | Open Access
Payne, J. L., Menardo, F., Trauner, A., Borrell, S., Gygli, S. M., Loiseau, C., Gagneux, S. and Hall, A. R. (2019) “Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis”, PLoS Biology. Public Library of Science, 17(5), p. e3000265. doi: 10.1371/journal.pbio.3000265.   edoc
Mhalu, G., Hella, J., Mhimbira, F., Said, K., Mosabi, T., Mlacha, Y. P., Schindler, C., Gagneux, S., Reither, K., de Hoogh, K., Weiss, M. G., Zemp, E. and Fenner, L. (2019) “Pathways and associated costs of care in patients with confirmed and presumptive tuberculosis in Tanzania : a cross-sectional study”, BMJ Open. BMJ Publishing Group, 9(4), p. e025079. doi: 10.1136/bmjopen-2018-025079.   edoc | Open Access
Rutaihwa, L. K., Sasamalo, M., Jaleco, A., Hella, J., Kingazi, A., Kamwela, L., Kingalu, A., Malewo, B., Shirima, R., Doetsch, A., Feldmann, J., Reinhard, M., Borrell, S., Brites, D., Reither, K., Doulla, B., Fenner, L. and Gagneux, S. (2019) “Insights into the genetic diversity of Mycobacterium tuberculosis in Tanzania”, PLoS ONE. Public Library of Science, 14(4), p. e0206334. doi: 10.1371/journal.pone.0206334.   edoc | Open Access
Gygli, S. M., Keller, P. M., Ballif, M., Blöchliger, N., Hömke, R., Reinhard, M., Loiseau, C., Ritter, C., Sander, P., Borrell, S., Collantes Loo, J., Avihingsanon, A., Gnokoro, J., Yotebieng, M., Egger, M., Gagneux, S. and Böttger, E. C. (2019) “Whole-genome sequencing for drug resistance profile prediction in Mycobacterium tuberculosis”, Antimicrobial agents and chemotherapy. American Society for Microbiology, 63(4), pp. e02175–18. doi: 10.1128/AAC.02175-18.   edoc | Open Access
Borrell, S., Trauner, A., Brites, D., Rigouts, L., Loiseau, C., Coscolla, M., Niemann, S., De Jong, B., Yeboah-Manu, D., Kato-Maeda, M., Feldmann, J., Reinhard, M., Beisel, C. and Gagneux, S. (2019) “Reference set of Mycobacterium tuberculosis clinical strains: a tool for research and product development”, PLoS ONE. Public Library of Science, 14(3), p. e0214088. doi: 10.1371/journal.pone.0214088.   edoc | Open Access
Otchere, I. D., van Tonder, A. J., Asante-Poku, A., Sánchez-Busó, L., Coscollá, M., Osei-Wusu, S., Asare, P., Aboagye, S. Y., Ekuban, S. A., Yahayah, A. I., Forson, A., Baddoo, A., Laryea, C., Parkhill, J., Harris, S. R., Gagneux, S. and Yeboah-Manu, D. (2019) “Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana”, PLoS ONE. Public Library of Science, 14(3), p. e0209395. doi: 10.1371/journal.pone.0209395.   edoc | Open Access
Zürcher, K., Ballif, M., Fenner, L., Borrell, S., Keller, P. M., Gnokoro, J., Marcy, O., Yotebieng, M., Diero, L., Carter, E. J., Rockwood, N., Wilkinson, R. J., Cox, H., Ezati, N., Abimiku, A. G., Collantes, J., Avihingsanon, A., Kawkitinarong, K., Reinhard, M., Hömke, R., Huebner, R., Gagneux, S., Böttger, E. C., Egger, M. 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. Elsevier, 19(3), pp. 298–307. doi: 10.1016/S1473-3099(18)30673-X.   edoc
Asante-Poku, A., Asare, P., Baddoo, N. A., Forson, A., Klevor, P., Otchere, I. D., Aboagye, S. Y., Osei-Wusu, S., Danso, E. K., Koram, K., Gagneux, S. and Yeboah-Manu, D. (2019) “TB-diabetes co-morbidity in Ghana : the importance of Mycobacterium africanum infection”, PLoS ONE. Public Library of Science, 14(2), p. e0211822. doi: 10.1371/journal.pone.0211822.   edoc | Open Access
Mhimbira, F., Hiza, H., Mbuba, E., Hella, J., Kamwela, L., Sasamalo, M., Ticlla, M., Said, K., Mhalu, G., Chiryamkubi, M., Schindler, C., Reither, K., 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), pp. 107.e1–107.e7. doi: 10.1016/j.cmi.2018.03.019.   edoc
Menardo, F., Loiseau, C., Brites, D., Coscolla, M., Gygli, S. M., Rutaihwa, L. K., Trauner, A., Beisel, C., Borrell, S. and Gagneux, S. (2018) “Treemmer : a tool to reduce large phylogenetic datasets with minimal loss of diversity”, BMC bioinformatics. BioMed Central, 19(1), p. 164. doi: 10.1186/s12859-018-2164-8.   edoc | Open Access
Seth-Smith, H. M. B., Imkamp, F., Tagini, F., Cuénod, A., Hömke, R., Jahn, K., Tschacher, A., Grendelmeier, P., Bättig, V., Erb, S., Reinhard, M., Rütimann, G., Borrell, S., Gagneux, S., Casanova, C., Droz, S., Osthoff, M., Tamm, M., Nübel, U., Greub, G., Keller, P. M. and Egli, A. (2018) “Discovery and characterization of Mycobacterium basiliense sp. nov., a nontuberculous mycobacterium isolated from human lungs”, Frontiers in Microbiology. Frontiers Media, 9, p. 3184. doi: 10.3389/fmicb.2018.03184.   edoc | Open Access
Liu, Q., Ma, A., Wei, L., Pang, Y., Wu, B., Luo, T., Zhou, Y., Zheng, H.-X., Jiang, Q., Gan, M., Zuo, T., Liu, M., Yang, C., Jin, L., Comas, I., Gagneux, S., Zhao, Y., Pepperell, C. S. and Gao, Q. (2018) “China’s tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis”, Nature ecology & evolution. Nature Publishing Group, 2(12), pp. 1982–1992. doi: 10.1038/s41559-018-0680-6.   edoc
Sanoussi, C. N., de Jong, B. C., Odoun, M., Arekpa, K., Ali Ligali, M., Bodi, O., Harris, S., Ofori-Anyinam, B., Yeboah-Manu, D., Otchere, I. D., Asante-Poku, A., Anagonou, S., Gagneux, S., Coscolla, M., Rigouts, L. and Affolabi, D. (2018) “Low sensitivity of the MPT64 identification test to detect lineage 5 of the Mycobacterium tuberculosis complex”, Journal of medical microbiology. Lippincott Williams & Wilkins, 67(12), pp. 1718–1727. doi: 10.1099/jmm.0.000846.   edoc | Open Access
Kühnert, D., Coscolla, M., Brites, D., Stucki, D., Metcalfe, J., Fenner, L., Gagneux, S. and Stadler, T. (2018) “Tuberculosis outbreak investigation using phylodynamic analysis”, Epidemics. Elsevier, 25, pp. 47–53. doi: 10.1016/j.epidem.2018.05.004.   edoc | Open Access
Merker, M., Barbier, M., Cox, H., Rasigade, J.-P., Feuerriegel, S., Kohl, T. A., Diel, R., Borrell, S., Gagneux, S., Nikolayevskyy, V., Andres, S., Nübel, U., Supply, P., Wirth, T. and Niemann, S. (2018) “Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia”, eLife. eLife Sciences Publications , 7, p. e38200. doi: 10.7554/eLife.38200.   edoc | Open Access
Conceição, E. C., Guimarães, A. E. D. S., Lopes, M. L., Furlaneto, I. P., Rodrigues, Y. C., da Conceição, M. L., Barros, W. A., Cardoso, N. C., Sharma, A., Lima, L. N. G. C., Gomes, H. M., Duarte, R. S., Frota, C., Rutaihwa, L. K., Gagneux, S., Suffys, P. N. and Lima, K. V. B. (2018) “Analysis of potential household transmission events of tuberculosis in the city of Belem, Brazil”, Tuberculosis. Elsevier, 113, pp. 125–129. doi: 10.1016/j.tube.2018.09.011.   edoc
Ezewudo, M., Borens, A., Chiner-Oms, Álvaro, Miotto, P., Chindelevitch, L., Starks, A. M., Hanna, D., Liwski, R., Zignol, M., Gilpin, C., Niemann, S., Kohl, T. A., Warren, R. M., Crook, D., Gagneux, S., Hoffner, S., Rodrigues, C., Comas, I., Engelthaler, D. M., Alland, D., Rigouts, L., Lange, C., Dheda, K., Hasan, R., McNerney, R., Cirillo, D. M., Schito, M., Rodwell, T. C. and Posey, J. (2018) “Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase”, Scientific Reports. Springer Nature, 8(1), p. 15382. doi: 10.1038/s41598-018-33731-1.   edoc | Open Access
Asare, P., Asante-Poku, A., Prah, D. A., Borrell, S., Osei-Wusu, S., Otchere, I. D., Forson, A., Adjapong, G., Koram, K. A., Gagneux, S. and Yeboah-Manu, D. (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. Elsevier, 73, pp. 30–42. doi: 10.1016/j.ijid.2018.05.014.   edoc | Open Access
Otchere, I. D., Coscollá, M., Sánchez-Busó, L., Asante-Poku, A., Brites, D., Loiseau, C., Meehan, C., Osei-Wusu, S., Forson, A., Laryea, C., Yahayah, A. I., Baddoo, A., Ansa, G. A., Aboagye, S. Y., Asare, P., Borrell, S., Gehre, F., Beckert, P., Kohl, T. A., N’dira, S., Beisel, C., Antonio, M., Niemann, S., de Jong, B. C., Parkhill, J., Harris, S. R., Gagneux, S. and Yeboah-Manu, D. (2018) “Comparative genomics of Mycobacterium africanum lineage 5 and lineage 6 from Ghana suggests distinct ecological niches”, Scientific reports. Springer Nature, 8, p. 11269. doi: 10.1038/s41598-018-29620-2.   edoc | Open Access
Gagneux, S. (2018) “Ecology and evolution of Mycobacterium tuberculosis”, Nature Reviews Microbiology. Nature Publishing Group, 16(4), pp. 202–213. doi: 10.1038/nrmicro.2018.8.   edoc
Boillat-Blanco, N., Tumbo, A.-M. N., Perreau, M., Amelio, P., Ramaiya, K. L., Mganga, M., Schindler, C., Gagneux, S., Reither, K., Probst-Hensch, N., Pantaleo, G., Daubenberger, C. and Portevin, D. (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. doi: 10.1002/iid3.222.   edoc | Open Access
Nahid, P., Jarlsberg, L. G., Kato-Maeda, M., Segal, M. R., Osmond, D. H., Gagneux, S., Dobos, K., Gold, M., Hopewell, P. C. and Lewinsohn, D. M. (2018) “Interplay of strain and race/ethnicity in the innate immune response to M. tuberculosis”, PLoS ONE. Public Library of Science, 13(5), p. e0195392. doi: 10.1371/journal.pone.0195392.   edoc | Open Access
Sikalengo, G., Hella, J., Mhimbira, F., Rutaihwa, L. K., Bani, F., Ndege, R., Sasamalo, M., Kamwela, L., Said, K., Mhalu, G., Mlacha, Y., Hatz, C., Knopp, S., Gagneux, S., Reither, K., Utzinger, J., Tanner, M., Letang, E., Weisser, M. and Fenner, L. (2018) “Distinct clinical characteristics and helminth co-infections in adult tuberculosis patients from urban compared to rural Tanzania”, Infectious Diseases of Poverty. Biomed Central, 7, p. 24. doi: 10.1186/s40249-018-0404-9.   edoc | Open Access
Zampieri, M., Szappanos, B., Buchieri, M. V., Trauner, A., Piazza, I., Picotti, P., Gagneux, S., Borrell, S., Gicquel, B., Lelievre, J., Papp, B. and Sauer, U. (2018) “High-throughput metabolomic analysis predicts mode of action of uncharacterized antimicrobial compounds”, Science Translational Medicine. American Association for the Advancement of Science, 10(429), p. eaal3973. doi: 10.1126/scitranslmed.aal3973.   edoc
Carey, A. F., Rock, J. M., Krieger, I. V., Chase, M. R., Fernandez-Suarez, M., Gagneux, S., Sacchettini, J. C., Ioerger, T. R. and Fortune, S. M. (2018) “TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities”, PLoS Pathogens. Public Library of Science, 14(3), p. e1006939. doi: 10.1371/journal.ppat.1006939.   edoc | Open Access
Bastos, H. N., Osório, N. S., Gagneux, S., Comas, I. and Saraiva, M. (2018) “The troika host-pathogen-extrinsic factors in Tuberculosis: modulating inflammation and clinical outcomes”, Frontiers in Immunology. Frontiers Media, 8, p. 1948. doi: 10.3389/fimmu.2017.01948.   edoc | Open Access
Hella, J., Cercamondi, C. I., Mhimbira, F., Sasamalo, M., Stoffel, N., Zwahlen, M., Bodmer, T., Gagneux, S., Reither, K., Zimmermann, M. B., Risch, L. and Fenner, L. (2018) “Anemia in tuberculosis cases and household controls from Tanzania: contribution of disease, coinfections, and the role of hepcidin”, PLoS ONE. Public Library of Science, 13(4), p. e0195985. doi: 10.1371/journal.pone.0195985.   edoc | Open Access
Rasoahanitralisoa, R., Rakotosamimanana, N., Stucki, D., Sola, C., Gagneux, S. and Rasolofo Razanamparany, V. (2017) “Evaluation of spoligotyping, SNPs and customised MIRU-VNTR combination for genotyping Mycobacterium tuberculosis clinical isolates in Madagascar”, PLoS ONE. Public Library of Science, 12(10), p. e0186088. doi: 10.1371/journal.pone.0186088.   edoc
Gagneux, S. (ed.) (2017) Strain variation in the Mycobacterium tuberculosis complex: its role in biology, epidemiology and control. Cham: Springer (Advances in Experimental Medicine and Biology). doi: 10.1007/978-3-319-64371-7.   edoc
Miotto, P., Tessema, B., Tagliani, E., Chindelevitch, L., Starks, A. M., Emerson, C., Hanna, D., Kim, P. S., Liwski, R., Zignol, M., Gilpin, C., Niemann, S., Denkinger, C. M., Fleming, J., Warren, R. M., Crook, D., Posey, J., Gagneux, S., Hoffner, S., Rodrigues, C., Comas, I., Engelthaler, D. M., Murray, M., Alland, D., Rigouts, L., Lange, C., Dheda, K., Hasan, R., Ranganathan, U. D. K., McNerney, R., Ezewudo, M., Cirillo, D. M., Schito, M., Köser, C. U. and Rodwell, T. C. (2017) “A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis”, The European respiratory journal. Munksgaard, 50(6), p. 1701354. doi: 10.1183/13993003.01354-2017.   edoc
Brites, D. and Gagneux, S. (2017) “The nature and evolution of genomic diversity in the Mycobacterium tuberculosis complex”, Advances in experimental medicine and biology. Springer, 1019, pp. 1–26. doi: 10.1007/978-3-319-64371-7_1.   edoc
Ghielmetti, G., Coscolla, M., Ruetten, M., Friedel, U., Loiseau, C., Feldmann, J., Steinmetz, H. W., Stucki, D. and Gagneux, S. (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. Nature Publishing Group, 7(1), p. 14647. doi: 10.1038/s41598-017-15278-9.   edoc | Open Access
Hiza, H., Doulla, B., Sasamalo, M., Hella, J., Kamwela, L., Mhimbira, F., Reither, K., Gagneux, S., Jugheli, L. and Fenner, L. (2017) “Preservation of sputum samples with cetylpyridinium chloride (CPC) for tuberculosis cultures and Xpert MTB/RIF in a low-income country”, BMC Infectious Diseases. BioMed Central, 17, p. 542. doi: 10.1186/s12879-017-2642-z.   edoc | Open Access
Hella, J., Morrow, C., Mhimbira, F., Ginsberg, S., Chitnis, N., Gagneux, S., Mutayoba, B., Wood, R. and Fenner, L. (2017) “Tuberculosis transmission in public locations in Tanzania: A novel approach to studying airborne disease transmission”, Journal of Infection. Elsevier, 75(3), pp. 191–197. doi: 10.1016/j.jinf.2017.06.009.   edoc
Yahyaoui-Azami, H., Aboukhassib, H., Bouslikhane, M., Berrada, J., Rami, S., Reinhard, M., Gagneux, S., Feldmann, J., Borrell, S. and Zinsstag, J. (2017) “Molecular characterization of bovine tuberculosis strains in two slaughterhouses in Morocco”, BMC Veterinary Research. BioMed Central, 13, p. 272. doi: 10.1186/s12917-017-1165-6.   edoc
Koch, A. S., Brites, D., Stucki, D., Evans, J. C., Seldon, R., Heekes, A., Mulder, N., Nicol, M., Oni, T., Mizrahi, V., Warner, D. F., Parkhill, J., Gagneux, S., Martin, D. P. and Wilkinson, R. J. (2017) “The influence of HIV on the evolution of Mycobacterium tuberculosis”, Molecular biology and evolution. Oxford University Press, 34(7), pp. 1654–1668. doi: 10.1093/molbev/msx107.   edoc | Open Access
Gygli, S. M., Borrell, S., Trauner, A. and Gagneux, S. (2017) “Antimicrobial resistance in Mycobacterium tuberculosis : mechanistic and evolutionary perspectives”, FEMS Microbiology Reviews. Blackwell, 41(3), pp. 354–373. doi: 10.1093/femsre/fux011.   edoc | Open Access
Trauner, A., Liu, Q., Via, L. E., Liu, X., Ruan, X., Liang, L., Shi, H., Chen, Y., Wang, Z., Liang, R., Zhang, W., Wei, W., Gao, J., Sun, G., Brites, D., England, K., Zhang, G., Gagneux, S., Barry, C. E. and Gao, Q. (2017) “The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy”, Genome biology. BioMed Central, 18, p. 71. doi: 10.1186/s13059-017-1196-0.   edoc | Open Access
Ofori-Anyinam, B., Dolganov, G., Van, T., Davis, J. L., Walter, N. D., Garcia, B. J., Voskuil, M., Fissette, K., Diels, M., Driesen, M., Meehan, C. J., Yeboah-Manu, D., Coscolla, M., Gagneuyx, S., Antonio, M., Schoolnik, G. K., Gehre, F. and de Jong, B. C. (2017) “Significant under expression of the DosR regulon in M. tuberculosis complex lineage 6 in sputum”, Tuberculosis. Elsevier, 104, pp. 58–64. doi: 10.1016/j.tube.2017.03.001.   edoc
Mhimbira, F., Hella, J., Said, K., Kamwela, L., Sasamalo, M., Maroa, T., Chiryamkubi, M., Mhalu, G., Schindler, C., Reither, K., Knopp, S., Utzinger, J., Gagneux, S. and Fenner, L. (2017) “Prevalence and clinical relevance of helminth co-infections among tuberculosis patients in urban Tanzania”, PLoS Neglected Tropical Diseases. Public Library of Science, 11(2), p. e0005342. doi: 10.1371/journal.pntd.0005342.   edoc | Open Access
Andre, E., Goeminne, L., Cabibbe, A., Beckert, P., Kabamba Mukadi, B., Mathys, V., Gagneux, S., Niemann, S., 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. doi: 10.1016/j.cmi.2016.09.006.   edoc
Stucki, D., Brites, D., Jeljeli, L., Coscolla, M., Liu, Q., Trauner, A., Fenner, L., Rutaihwa, L., Borrell, S., Luo, T., Gao, Q., Kato-Maeda, M., Ballif, M., Egger, M., Macedo, R., Mardassi, H., Moreno, M., Vilanova, G. T., Fyfe, J., Globan, M., Thomas, J., Jamieson, F., Guthrie, J. L., Asante-Poku, A., Yeboah-Manu, D., Wampande, E., Ssengooba, W., Joloba, M., Boom, W. H., Basu, I., Bower, J., Saraiva, M., Vasconcellos, S. E. G., Suffys, P., Koch, A., Wilkinson, R., Gail-Bekker, L., Malla, B., Ley, S. D., Beck, H.-P., de Jong, B. C., Toit, K., Sanchez-Padilla, E., Bonnet, M., Gil-Brusola, A., Frank, M., Penlap Beng, V. N., Eisenach, K., Alani, I., Ndung’u, P. W., Revathi, G., Gehre, F., Akter, S., Ntoumi, F., Stewart-Isherwood, L., Ntinginya, N. E., Rachow, A., Hoelscher, M., Cirillo, D. M., Skenders, G., Hoffner, S., Bakonyte, D., Stakenas, P., Diel, R., Crudu, V., Moldovan, O., Al-Hajoj, S., Otero, L., Barletta, F., Carter, E. J., Diero, L., Supply, P., Comas, I., Niemann, S. and Gagneux, S. (2016) “Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages”, Nature genetics. Nature Publ, 48(12), pp. 1535–1543. doi: 10.1038/ng.3704.   edoc
Copin, R., Wang, X., Louie, E., Escuyer, V., Coscolla, M., Gagneux, S., Palmer, G. H. and Ernst, J. D. (2016) “Within host evolution selects for a dominant genotype of Mycobacterium tuberculosis while T cells increase pathogen genetic diversity”, PLoS Pathogens. Public Library of Science, 12(12), p. e1006111. doi: 10.1371/journal.ppat.1006111.   edoc | Open Access
Otchere, I. D., Asante-Poku, A., Osei-Wusu, S., Baddoo, A., Sarpong, E., Ganiyu, A. H., Aboagye, S. Y., Forson, A., Bonsu, F., Yahayah, A. I., Koram, K., 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. Elsevier, 99, pp. 147–154. doi: 10.1016/j.tube.2016.05.014.   edoc
Zumla, A., Rao, M., Wallis, R. S., Kaufmann, S. H. E., Rustomjee, R., Mwaba, P., Vilaplana, C., Yeboah-Manu, D., Chakaya, J., Ippolito, G., Azhar, E., Hoelscher, M., Maeurer, M. and Host-Directed Therapies Network consortium (2016) “Host-directed therapies for infectious diseases : current status, recent progress, and future prospects”, The Lancet infectious diseases. Elsevier, 16(4), pp. e47-e63. doi: 10.1016/S1473-3099(16)00078-5.   edoc
Boillat-Blanco, N., Bovet, P., Ramaiya, K. L., Mganga, M., Minja, L. T., Saleh, L., Imboden, M., Schindler, C., Gagneux, S., Daubenberger, C., Reither, K. and Probst-Hensch, N. (2016) “Association between tuberculosis, diabetes and 25 hydroxyvitamin D in Tanzania: a longitudinal case control study”, BMC Infectious Diseases. BioMed Central, 16(1), p. 626. doi: 10.1186/s12879-016-1960-x.   edoc | Open Access
Mhimbira, F., Hella, J., Maroa, T., Kisandu, S., Chiryamkubi, M., Said, K., Mhalu, G., Mkopi, A., Mutayoba, B., Reither, K., Gagneux, S. and Fenner, L. (2016) “Home-based and facility-based directly observed therapy of tuberculosis treatment under programmatic conditions in urban Tanzania”, PLoS ONE. Public Library of Science, 11(8), p. e0161171. doi: 10.1371/journal.pone.0161171.   edoc | Open Access
Yeboah-Manu, D., Asare, P., Asante-Poku, A., Otchere, I. D., Osei-Wusu, S., Danso, E., Forson, A., Koram, K. A. and Gagneux, S. (2016) “Spatio-temporal distribution of Mycobacterium tuberculosis complex strains in Ghana”, PLoS ONE. Public Library of Science, 11(8), p. e0161892. doi: 10.1371/journal.pone.0161892.   edoc | Open Access
Asante-Poku, A., Otchere, I. D., Osei-Wusu, S., Sarpong, E., Baddoo, A., Forson, A., Laryea, C., Borrell, S., Bonsu, F., Hattendorf, J., Ahorlu, C., Koram, K. A., Gagneux, S. and Yeboah-Manu, D. (2016) “Molecular epidemiology of Mycobacterium africanum in Ghana”, BMC Infectious Diseases. BioMed Central, 16, p. 385. doi: 10.1186/s12879-016-1725-6.   edoc | Open Access
Boillat-Blanco, N., Ramaiya, K. L., Mganga, M., Minja, L. T., Bovet, P., Schindler, C., Von Eckardstein, A., Gagneux, S., Daubenberger, C., Reither, K. and Probst-Hensch, N. (2016) “Transient hyperglycemia in patients with tuberculosis in Tanzania : implications for diabetes screening algorithms”, Journal of Infectious Diseases. Oxford University Press, 213(7), pp. 1163–1172. doi: 10.1093/infdis/jiv568.   edoc | Open Access
Stucki, D., Ballif, M., Egger, M., Furrer, H., Altpeter, E., Battegay, M., Droz, S., Bruderer, T., Coscolla, M., Borrell, S., Zürcher, K., Janssens, J.-P., Calmy, A., Mazza Stalder, J., Jaton, K., Rieder, H. L., Pfyffer, G. E., Siegrist, H. H., Hoffmann, M., Fehr, J., Dolina, M., Frei, R., Schrenzel, J., Böttger, E. C., Gagneux, S. and Fenner, L. (2016) “Standard genotyping overestimates transmission of Mycobacterium tuberculosis among immigrants in a low-incidence country”, Journal of clinical microbiology, 54(7), pp. 1862–1870. doi: 10.1128/JCM.00126-16.   edoc
Domínguez, J., Boettger, E. C., Cirillo, D., Cobelens, F., Eisenach, K. D., Gagneux, S., Hillemann, D., Horsburgh, R., Molina-Moya, B., Niemann, S., Tortoli, E., Whitelaw, A., Lange, C., 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. IUATLD, 20(1), pp. 24–42. doi: 10.5588/ijtld.15.0221.   edoc
Zumla, A., Chakaya, J., Hoelscher, M., Ntoumi, F., Rustomjee, R., Vilaplana, C., Yeboah-Manu, D., Rasolof, V., Munderi, P., Singh, N., Aklillu, E., Padayatchi, N., Macete, E., Kapata, N., Mulenga, M., Kibiki, G., Mfinanga, S., Nyirenda, T., Maboko, L., Garcia-Basteiro, A., Rakotosamimanana, N., Bates, M., Mwaba, P., Reither, K., Gagneux, S., Edwards, S., Mfinanga, E., Abdulla, S., Cardona, P. J., Russell, J. B., Gant, V., Noursadeghi, M., Elkington, P., Bonnet, M., Menendez, C., Dieye, T. N., Diarra, B., Maiga, A., Aseffa, A., Parida, S., Wejse, C., Petersen, E., Kaleebu, P., Oliver, M., Craig, G., Corrah, T., Tientcheu, L., Antonio, M., Rao, M., McHugh, T. D., Sheikh, A., Ippolito, G., Ramjee, G., Kaufmann, S. H., Churchyard, G., Steyn, A., Grobusch, M., Sanne, I., Martinson, N., Madansein, R., Wilkinson, R. J., Mayosi, B., Schito, M., Wallis, R. S. and Maeurer, M. (2015) “Towards host-directed therapies for tuberculosis”, Nature reviews. Drug discovery. Nature Publishing Group, 14(8), pp. 511–512. doi: 10.1038/nrd4696.   edoc
Zumla, A., Maeurer, M. 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. Oxford University Press, 61(9), pp. 1432–1438. doi: 10.1093/cid/civ631.   edoc
Comas, I., Hailu, E., Kiros, T., Bekele, S., Mekonnen, W., Gumi, B., Tschopp, R., Ameni, G., Hewinson, R. G., Robertson, B. D., Goig, G. A., Stucki, D., Gagneux, S., Aseffa, A., Young, D. and Berg, S. (2015) “Population genomics of Mycobacterium tuberculosis in Ethiopia contradicts the virgin soil hypothesis for human tuberculosis in sub-saharan Africa”, Current biology. Cell Press, 25(24), pp. 3260–3206. doi: 10.1016/j.cub.2015.10.061.   edoc
Coscolla, M., Copin, R., Sutherland, J., Gehre, F., de Jong, B., Owolabi, O., Mbayo, G., Giardina, F., Ernst, J. D. and Gagneux, S. (2015) “M. tuberculosis T cell epitope analysis reveals paucity of antigenic variation and identifies rare variable TB antigens”, Cell host & microbe. Cell Press, 18(5), pp. 538–548. doi: 10.1016/j.chom.2015.10.008.   edoc
Bloemberg, G. V., Keller, P. M., Stucki, D., Stuckia, D., Trauner, A., Borrell, S., Latshang, T., Coscolla, M., Rothe, T., Hömke, R., Ritter, C., Feldmann, J., Schulthess, B., Gagneux, S. and Böttger, E. C. (2015) “Acquired resistance to bedaquiline and delamanid in therapy for tuberculosis”, The New England journal of medicine. Massachusetts Medical Society, pp. 1986–1988. doi: 10.1056/NEJMc1505196.   edoc
Luo, T., Comas, I., Luo, D., Lu, B., Wu, J., Wei, L., Yang, C., Liu, Q., Gan, M., Sun, G., Shen, X., Liu, F., Gagneux, S., Mei, J., Lan, R., Wan, K. and Gao, Q. (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. National Academy of Sciences, Vol. 112, no. 26, pp. 8136–8141. doi: 10.1073/pnas.1424063112.   edoc
Wampande, E. M., Mupere, E., Jaganath, D., Nsereko, M., Mayanja, H. K., Eisenach, K., Boom, W. H., Gagneux, S., Joloba, M. L. and Tuberculosis Research Unit (2015) “Distribution and transmission of mycobacterium tuberculosis complex lineages among children in peri-urban Kampala, Uganda”, BMC pediatrics. BioMed Central, Vol. 15 , 140. doi: 10.1186/s12887-015-0455-z.   edoc | Open Access
Wampande, E. M., Hatzios, S. K., Achan, B., Mupere, E., Nsereko, M., Mayanja, H. K., Eisenach, K., Boom, W. H., Gagneux, S., Joloba, M. 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. BioMed Central, Vol. 15 , 396. doi: 10.1186/s12879-015-1121-7.   edoc | Open Access
Coscolla, M., Barry, P. M., Oeltmann, J. E., Koshinsky, H., Shaw, T., Cilnis, M., Posey, J., Rose, J., Weber, T., Fofanov, V. Y., Gagneux, S., Kato-Maeda, M. and Metcalfe, J. Z. (2015) “Genomic epidemiology of multidrug-resistant Mycobacterium tuberculosis during transcontinental spread”, Journal of infectious diseases. Oxford University Press, Vol. 212, H. 2, pp. 302–310. doi: 10.1093/infdis/jiv025.   edoc
Asante-Poku, A., Otchere, I. D., Danso, E., Mensah, D. D., Bonsu, F., 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. IUATLD, Vol. 19, H. 8, pp. 954–959. doi: 10.5588/ijtld.14.0864.   edoc
Rock, J. M., Lang, U. F., Chase, M. R., Ford, C. B., Gerrick, E. R., Gawande, R., Coscolla, M., Gagneux, S., Fortune, S. M. and Lamers, M. H. (2015) “DNA replication fidelity in Mycobacterium tuberculosis is mediated by an ancestral prokaryotic proofreader”, Nature genetics. Nature Publ, Vol. 47, H. 6, pp. 677–681. doi: 10.1038/ng.3269.   edoc
Stucki, D., Ballif, M., Bodmer, T., Coscolla, M., Maurer, A.-M., Droz, S., Butz, C., Borrell, S., Längle, C., Feldmann, J., Furrer, H., Mordasini, C., Helbling, P., Rieder, H. L., Egger, M., Gagneux, S. and Fenner, L. (2015) “Tracking a tuberculosis outbreak over 21 years : strain-specific single-nucleotide polymorphism typing combined with targeted whole-genome sequencing”, Journal of infectious diseases. Oxford University Press, Vol. 211, H. 8, pp. 1306–1316. doi: 10.1093/infdis/jiu601.   edoc
Young, D. C., Layre, E., Pan, S.-J., Tapley, A., Adamson, J., Seshadri, C., Wu, Z., Buter, J., Minnaard, A. J., Coscolla, M., Gagneux, S., Copin, R., Ernst, J. D., Bishai, W. R., Snider, B. B. and Moody, D. B. (2015) “In vivo biosynthesis of terpene nucleosides provides unique chemical markers of Mycobacterium tuberculosis infection”, Chemistry & biology. Elsevier Science, Vol. 22, H. 4, pp. 516–526. doi: 10.1016/j.chembiol.2015.03.015.   edoc
Merker, M., Blin, C., Mona, S., Duforet-Frebourg, N., Lecher, S., Willery, E., Blum, M. G. B., Rüsch-Gerdes, S., Mokrousov, I., Aleksic, E., Allix-Béguec, C., Antierens, A., Augustynowicz-Kopeć, E., Ballif, M., Barletta, F., Beck, H. P., Barry, C. E., Bonnet, M., Borroni, E., Campos-Herrero, I., Cirillo, D., Cox, H., Crowe, S., Crudu, V., Diel, R., Drobniewski, F., Fauville-Dufaux, M., Gagneux, S., Ghebremichael, S., Hanekom, M., Hoffner, S., Jiao, W.-W., Kalon, S., Kohl, T. A., Kontsevaya, I., Lillebæk, T., Maeda, S., Nikolayevskyy, V., Rasmussen, M., Rastogi, N., Samper, S., Sanchez-Padilla, E., Savic, B., Shamputa, I. C., Shen, A., Sng, L.-H., Stakenas, P., Toit, K., Varaine, F., Vukovic, D., Wahl, C., Warren, R., Supply, P., Niemann, S. and Wirth, T. (2015) “Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage”, Nature genetics. Nature Publ, Vol. 47, H. 3, pp. 242–249. doi: 10.1038/ng.3195.   edoc
Brites, D. and Gagneux, S. (2015) “Co-evolution of Mycobacterium tuberculosis and Homo sapiens”, Immunological reviews. Munksgaard, Vol. 264, H. 1, pp. 6–24. doi: 10.1111/imr.12264.   edoc
Asante-Poku, A., Yeboah-Manu, D., Otchere, I. D., Aboagye, S. Y., Stucki, D., Hattendorf, J., Borrell, S., Feldmann, J., Danso, E. and Gagneux, S. (2015) “Mycobacterium africanum is associated with patient ethnicity in Ghana”, PLoS neglected tropical diseases. Public Library of Science, Vol. 9, H. 1, e3370. doi: 10.1371/journal.pntd.0003370.   edoc | Open Access
Ley, S. D., Harino, P., Vanuga, K., Kamus, R., Carter, R., Coulter, C., Pandey, S., Feldmann, J., Ballif, M., Siba, P. M., Phuanukoonnon, S., Gagneux, S. and Beck, H.-P. (2014) “Diversity of Mycobacterium tuberculosis and drug resistance in different provinces of Papua New Guinea”, BMC microbiology. BioMed Central, Vol. 14 , 307. doi: 10.1186/s12866-014-0307-2.   edoc | Open Access
Portevin, D., Sukumar, S., Coscolla, M., Shui, G., Li, B., Guan, X. L., Bendt, A. K., Young, D., Gagneux, S. and Wenk, M. R. (2014) “Lipidomics and genomics of Mycobacterium tuberculosis reveal lineage-specific trends in mycolic acid biosynthesis”, MicrobiologyOpen. Wiley], Vol. 3, H. 6, pp. 823–835. doi: 10.1002/mbo3.193.   edoc
Coscolla, M. and Gagneux, S. (2014) “Consequences of genomic diversity in Mycobacterium tuberculosis”, Seminars in immunology. Elsevier, pp. 431–444. doi: 10.1016/j.smim.2014.09.012.   edoc
Bos, K. I., Harkins, K. M., Herbig, A., Coscolla, M., Weber, N., Comas, I., Forrest, S. A., Bryant, J. M., Harris, S. R., Schuenemann, V. J., Campbell, T. J., Majander, K., Wilbur, A. K., Guichon, R. A., Wolfe Steadman, D. L., Cook, D. C., Niemann, S., Behr, M. A., Zumarraga, M., Bastida, R., Huson, D., Nieselt, K., Young, D., Parkhill, J., Buikstra, J. E., Gagneux, S., Stone, A. C. and Krause, J. (2014) “Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis”, Nature. Macmillan, pp. 494–497. doi: 10.1038/nature13591.   edoc
Steiner, A., Stucki, D., Coscolla, M., Borrell, S. and Gagneux, S. (2014) “KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes”, BMC genomics. BioMed Central, Vol. 15 , 881. doi: 10.1186/1471-2164-15-881.   edoc | Open Access
Copin, R., Coscollá, M., Efstathiadis, E., Gagneux, S. and Ernst, J. D. (2014) “Impact of in vitro evolution on antigenic diversity of Mycobacterium bovis bacillus Calmette-Guerin (BCG)”, Vaccine : the official journal of the International Society for Vaccines. Elsevier ; [Online:] Amsterdam, 32(45), pp. 5998–6004. doi: 10.1016/j.vaccine.2014.07.113.   edoc
Köser, C. U., Bryant, J. M., Comas, I., Feuerriegel, S., Niemann, S., Gagneux, S., Parkhill, J. and Peacock, S. J. (2014) “Genetic diversity within Mycobacterium tuberculosis complex impacts on the accuracy of genotypic pyrazinamide drug-susceptibility assay”, Tuberculosis. Elsevier, pp. 451–453. doi: 10.1016/j.tube.2014.04.002.   edoc
Köser, C. U., Bryant, J. M., Comas, I., Feuerriegel, S., Niemann, S., Gagneux, S., 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. Academic Press, Vol. 69, H. 8, pp. 2298–2299. doi: 10.1093/jac/dku101.   edoc
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: Oxford Fajar Sdn Bhd, pp. 337–349.   edoc
Trauner, A., Borrell, S., Reither, K. and Gagneux, S. (2014) “Evolution of drug resistance in tuberculosis : recent progress and implications for diagnosis and therapy”, Drugs. Adis Press, Vol. 74, H. 10, pp. 1063–1072. doi: 10.1007/s40265-014-0248-y.   edoc
Coll, F., Preston, M., Guerra-Assunção, J. A., Hill-Cawthorn, G., Harris, D., Perdigão, J., Viveiros, M., Portugal, I., Drobniewski, F., Gagneux, S., Glynn, J. R., Pain, A., Parkhill, J., McNerney, R., Martin, N. and Clark, T. G. (2014) “PolyTB : a genomic variation map for Mycobacterium tuberculosis”, Tuberculosis. Elsevier, Vol. 94, H. 3, pp. 346–354.   edoc
Copin, R., Coscollá, M., Seiffert, S. N., Bothamley, G., Sutherland, J., Mbayo, G., Gagneux, S. and Ernst, J. D. (2014) “Sequence diversity in the pe_pgrs genes of Mycobacterium tuberculosis is independent of human T cell recognition”, mBio. American Society for Microbiology, Vol. 5, H. 1 , e00960-13. doi: 10.1128/mBio.00960-13.   edoc
Asante-Poku, A., Nyaho, M. S., Borrell, S., Comas, I., Gagneux, S. and Yeboah-Manu, D. (2014) “Evaluation of customised lineage-specific sets of MIRU-VNTR loci for genotyping Mycobacterium tuberculosis complex isolates in Ghana”, PLoS ONE. Public Library of Science, Vol. 9, H. 3 , e92675. doi: 10.1371/journal.pone.0092675.   edoc | Open Access
Müller, B., Chihota, V. N., Pillay, M., Klopper, M., Streicher, E. M., Coetzee, G., Trollip, A., Hayes, C., Bosman, M. E., Gey van Pittius, N. C., Victor, T. C., Gagneux, S., van Helden, P. D. and Warren, R. M. (2013) “Programmatically selected multidrug-resistant strains drive the emergence of extensively drug-resistant tuberculosis in South Africa”, PLoS ONE. Public Library of Science, Vol. 8, H. 8 , e70919. doi: 10.1371/journal.pone.0070919.   edoc | Open Access
Gagneux, S. (2013) “Genetic diversity in Mycobacterium tuberculosis”, Current topics in microbiology and immunology. Springer, Vol. 374, pp. 1–25. doi: 10.1007/82_2013_329.   edoc
Via, L. E., Weiner, D. M., Schimel, D., Lin, P. L., Dayao, E., Tankersley, S. L., Cai, Y., Coleman, M. T., Tomko, J., Paripati, P., Orandle, M., Kastenmayer, R. J., Tartakovsky, M., Rosenthal, A., Portevin, D., Eum, S. Y., Lahouar, S., Gagneux, S., Young, D. B., Flynn, J. L. and Barry, C. E. (2013) “Differential virulence and disease progression following Mycobacterium tuberculosis complex infection of the common marmoset (Callithrix jacchus)”, Infection and immunity. American Society for Microbiology, Vol. 81, H. 8, pp. 2909–2919.   edoc
Wampande, E. M., Mupere, E., Debanne, S. M., Asiimwe, B. B., Nsereko, M., Mayanja, H., Eisenach, K., Kaplan, G., Boom, H. W., Sebastien, G. and Joloba, M. L. (2013) “Long-term dominance of Mycobacterium tuberculosis Uganda family in peri-urban Kampala-Uganda is not associated with cavitary disease”, BMC infectious diseases. BioMed Central, Vol. 13 , 484. doi: 10.1186/1471-2334-13-484.   edoc | Open Access
Borrell, S., Teo, Y., Giardina, F., Streicher, E. M., Klopper, M., Feldmann, J., Müller, B., Victor, T. C. and Gagneux, S. (2013) “Epistasis between antibiotic resistance mutations drives the evolution of extensively drug-resistant tuberculosis”, Evolution, medicine, and public health. Oxford Univ. Press, H. 1, pp. 65–74.   edoc
Ford, C. B., Shah, R. R., Maeda, M. K., Gagneux, S., Murray, M. B., Cohen, T., Johnston, J. C., Gardy, J., Lipsitch, M. and Fortune, S. M. (2013) “Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis”, Nature genetics. Nature Publ, Vol. 45, H. 7, pp. 784–790.   edoc
Comas, I., Coscolla, M., Luo, T., Borrell, S., Holt, K. E., Kato-Maeda, M., Parkhill, J., Malla, B., Berg, S., Thwaites, G., Yeboah-Manu, D., Bothamley, G., Mei, J., Wei, L., Bentley, S., Harris, S. R., Niemann, S., Diel, R., Aseffa, A., Gao, Q., Young, D. and Gagneux, S. (2013) “Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans”, Nature genetics. Nature Publ, Vol. 45, H. 10, pp. 1176–1182. doi: 10.1038/ng.2744.   edoc
Farhat, M. R., Shapiro, B. J., Kieser, K. J., Sultana, R., Jacobson, K. R., Victor, T. C., Warren, R. M., Streicher, E. M., Calver, A., Sloutsky, A., Kaur, D., Posey, J. E., Plikaytis, B., Oggioni, M. R., Gardy, J. L., Johnston, J. C., Rodrigues, M., Tang, P. K. C., Kato-Maeda, M., Borowsky, M. L., Muddukrishna, B., Kreiswirth, B. N., Kurepina, N., Galagan, J., Gagneux, S., Birren, B., Rubin, E. J., Lander, E. S., Sabeti, P. C. and Murray, M. (2013) “Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis”, Nature genetics. Nature Publ, Vol. 45, H. 10, pp. 1183–1189. doi: 10.1038/ng.2747.   edoc
Osório, N. S., Rodrigues, F., Gagneux, S., Pedrosa, J., Pinto-Carbó, M., Castro, A. G., Young, D., Comas, I. and Saraiva, M. (2013) “Evidence for diversifying selection in a set of Mycobacterium tuberculosis genes in response to antibiotic- and nonantibiotic-related pressure”, Molecular biology and evolution. Oxford University Press, Vol. 30, no. 6, pp. 1326–1336. doi: 10.1093/molbev/mst038.   edoc
Rose, G., Cortes, T., Comas, I., Coscolla, M., Gagneux, S. and Young, D. B. (2013) “Mapping of genotype-phenotype diversity among clinical isolates of Mycobacterium tuberculosis by sequence-based transcriptional profiling”, Genome biology and evolution. Oxford University Press, Vol. 5, H. 10, pp. 1849–1862. doi: 10.1093/gbe/evt138.   edoc
Stucki, D. and Gagneux, S. (2013) “Single nucleotide polymorphisms in Mycobacterium tuberculosis and the need for a curated database”, Tuberculosis. Elsevier, Vol. 93, H. 1, pp. 30–39. doi: 10.1016/j.tube.2012.11.002.   edoc
Müller, B., Borrell, S., Rose, G. and Gagneux, S. (2013) “The heterogeneous evolution of multidrug-resistant Mycobacterium tuberculosis”, Trends in genetics : DNA, differentiation and development. Elsevier, Vol. 29, H. 3, pp. 160–169. doi: 10.1016/j.tig.2012.11.005.   edoc
Kato-Maeda, M., Ho, C., Passarelli, B., Banaei, N., Grinsdale, J., Flores, L., Anderson, J., Murray, M., Rose, G., Kawamura, L. M., Pourmand, N., Tariq, M. A., Gagneux, S. and Hopewell, P. C. (2013) “Use of whole genome sequencing to determine the microevolution of Mycobacterium tuberculosis during an outbreak”, PLoS ONE. Public Library of Science, Vol. 8, H. 3 , e58235. doi: 10.1371/journal.pone.0058235.   edoc
de Vos, M., Müller, B., Borrell, S., Black, P., van Helden, P., Warren, R., 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. American Society for Microbiology, Vol. 57, H. 2, pp. 827–832. doi: 10.1128/AAC.01541-12.   edoc
Firdessa, R., Berg, S., Hailu, E., Schelling, E., Gumi, B., Erenso, G., Gadisa, E., Kiros, T., Habtamu, M., Hussein, J., Zinsstag, J., Robertson, B. D., Ameni, G., Lohan, A. J., Loftus, B., Comas, I., Gagneux, S., Tschopp, R., Yamuah, L., Hewinson, G., Gordon, S. V., Young, D. B. and Aseffa, A. (2013) “Mycobacterial lineages causing pulmonary and extrapulmonary tuberculosis, Ethiopia”, Emerging infectious diseases. National Center for Infectious Diseases, Vol. 19, H. 3, pp. 460–463. doi: 10.3201/eid1903.120256.   edoc
Aseffa, A., Mihret, A., Habte, A., Abebe, M., Wassie, L., Tschopp, R., Beyene, D., Ameni, G., Berg, S., Doherty, T. M., Gagneux, S., Young, D. and Howe, R. (2013) “Advances in tuberculosis”, African journal of microbiology research. Academic Journals, Vol. 7, H. 2, pp. 73–81.   edoc
Coscolla, M., Lewin, A., Metzger, S., Maetz-Rennsing, K., Calvignac-Spencer, S., Nitsche, A., Dabrowski, P. W., Radonic, A., Niemann, S., Parkhill, J., Couacy-Hymann, E., Feldman, J., Comas, I., Boesch, C., Gagneux, S. and Leendertz, F. H. (2013) “Novel Mycobacterium tuberculosis complex isolate from a wild chimpanzee”, Emerging infectious diseases. National Center for Infectious Diseases, Vol. 19, H. 6, pp. 969–976. doi: 10.3201/eid1906.121012.   edoc
Fenner, L., Egger, M., Bodmer, T., Furrer, H., Ballif, M., Battegay, M., Helbling, P., Fehr, J., Gsponer, T., Rieder, H. L., Zwahlen, M., Hoffmann, M., Bernasconi, E., Cavassini, M., Calmy, A., Dolina, M., Frei, R., Janssens, J.-P., Borrell, S., Stucki, D., Schrenzel, J., Böttger, E. C., Gagneux, S., Swiss HIV Cohort and Molecular Epidemiology of Tuberculosis Study Groups (2013) “HIV infection disrupts the sympatric host-pathogen relationship in human tuberculosis”, PLoS genetics. Public Library of Science, Vol. 9, H. 3 , e1003318. doi: 10.1371/journal.pgen.1003318.   edoc
Bratschi, M. W., Njih, T., Bolz, M., Stucki, D., Borrell, S., Gagneux, S., Noumen-Djeunga, B., Junghanss, T., Um Boock, A. and Pluschke, G. (2012) “A case of cutaneous tuberculosis in a Buruli ulcer-endemic area”, PLoS neglected tropical diseases. Public Library of Science, Vol. 6, H. 8 , e1751. doi: 10.1371/journal.pntd.0001751.   edoc | Open Access
Fenner, L., Gagneux, S., Helbling, P., Battegay, M., Rieder, H. L., Pfyffer, G. E., Zwahlen, M., Furrer, H., Siegrist, H. H., Fehr, J., Dolina, M., Calmy, A., Stucki, D., Jaton, K., Janssens, J. P., Stalder, J. M., Bodmer, T., Ninet, B., 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. doi: 10.1128/JCM.05392-11.   edoc
Luo, T., Yang, C., Gagneux, S., Gicquel, B., Jian, M. and Gao, Q. (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. doi: 10.1128/JCM.05539-11.   edoc
Stucki, D., Malla, B., Hostettler, S., Huna, T., Feldmann, J., Yeboah-Manu, D., Borrell, S., Fenner, L., Comas, I., Coscolla, M. and Gagneux, S. (2012) “Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages”, PLoS ONE. Public Library of Science, Vol. 7, H. 7 , e41253. doi: 10.1371/journal.pone.0041253.   edoc | Open Access
Brites, D. and Gagneux, S. (2012) “Old and new selective pressures on Mycobacterium tuberculosis”, Infection, genetics and evolution. Elsevier Science, Vol. 12, H. 4, pp. 678–685. doi: 10.1016/j.meegid.2011.08.010.   edoc
Fenner, L., Egger, M., Bodmer, T., Altpeter, E., Zwahlen, M., Jaton, K., Pfyffer, G. E., Borrell, S., Dubuis, O., Bruderer, T., Siegrist, H. H., Furrer, H., Calmy, A., Fehr, J., Stalder, J. M., Ninet, B., Bottger, E. C. and Gagneux, S. (2012) “Effect of mutation and genetic background on drug resistance in Mycobacterium tuberculosis”, Antimicrobial agents and chemotherapy. American Society for Microbiology, Vol. 56, H. 6, pp. 3047–3053. doi: 10.1128/AAC.06460-11.   edoc
Fenner, L., Gagneux, S., Janssens, J. P., Fehr, J., Cavassini, M., Hoffmann, M., Bernasconi, E., Schrenzel, J., Bodmer, T., Bottger, E. C., 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. Public Library of Science, Vol. 7, H. 3 , e34186. doi: 10.1371/journal.pone.0034186.   edoc | Open Access
Gagneux, S. (2012) “Host-pathogen coevolution in human tuberculosis”, Philosophical transactions / The Royal Society of London. Biological sciences. Royal Society of London, Vol. 367, H. 1590, pp. 850–859. doi: 10.1098/rstb.2011.0316.   edoc
Kato-Maeda, M., Shanley, C. A., Ackart, D., Jarlsberg, L. G., Shang, S., Obregon-Henao, A., Harton, M., Basaraba, R. J., Henao-Tamayo, M., Barrozo, J. C., Rose, J., Kawamura, L. M., Coscolla, M., Fofanov, V. Y., Koshinsky, H., Gagneux, S., Hopewell, P. C., Ordway, D. J. and Orme, I. M. (2012) “Beijing sublineages of Mycobacterium tuberculosis differ in pathogenicity in the Guinea pig”, Clinical and vaccine immunology. American Society for Microbiology, Vol. 19, H. 8, pp. 1227–1237. doi: 10.1128/CVI.00250-12.   edoc
McEvoy, C. R., Cloete, R., Müller, B., Schurch, A. C., van Helden, P. D., Gagneux, S., 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. Public Library of Science, Vol. 7, H. 4 , e30593. doi: 10.1371/journal.pone.0030593.   edoc | Open Access
Bentley, S. D., Comas, I., Bryant, J. M., Walker, D., Smith, N. H., Harris, S. R., Thurston, S., Gagneux, S., Wood, J., Antonio, M., Quail, M. A., Gehre, F., Adegbola, R. A., 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. Public Library of Science, Vol. 6, H. 2 , e1552. doi: 10.1371/journal.pntd.0001552.   edoc | Open Access
Malla, B., Stucki, D., Borrell, S., Feldmann, J., Maharjan, B., Shrestha, B., Fenner, L. and Gagneux, S. (2012) “First insights into the phylogenetic diversity of Mycobacterium tuberculosis in Nepal”, PLoS ONE. Public Library of Science, Vol. 7, H. 12 , e52297. doi: 10.1371/journal.pone.0052297.   edoc | Open Access
Weiner, B., Gomez, J., Victor, T. C., Warren, R. M., Sloutsky, A., Plikaytis, B. B., Posey, J. E., van Helden, P. D., Gey van Pittius, N. C., Koehrsen, M., Sisk, P., Stolte, C., White, J., Gagneux, S., Birren, B., Hung, D., Murray, M. and Galagan, J. (2012) “Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region”, PLoS ONE. Public Library of Science, Vol. 7, H. 2 , e26038. doi: 10.1371/journal.pone.0026038.   edoc | Open Access
Ballif, M., Harino, P., Ley, S., Coscolla, M., Niemann, S., Carter, R., Coulter, C., Borrell, S., Siba, P., Phuanukoonnon, S., Gagneux, S. and Beck, H. P. (2012) “Drug resistance-conferring mutations in Mycobacterium tuberculosis from Madang, Papua New Guinea”, BMC microbiology. BioMed Central, Vol. 12 , 191. doi: 10.1186/1471-2180-12-191.   edoc | Open Access
Ballif, M., Harino, P., Ley, S., Carter, R., Coulter, C., Niemann, S., Borrell, S., Fenner, L., Siba, P., Phuanukoonnon, S., 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. IUATLD, Vol. 16, H. 8, pp. 1100–1107. doi: 10.5588/ijtld.11.0779.   edoc
Comas, I., Borrell, S., Roetzer, A., Rose, G., Malla, B., Kato-Maeda, M., Galagan, J., Niemann, S. and Gagneux, S. (2012) “Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes”, Nature genetics. Nature Publ, Vol. 44, H. 1, pp. 106–110. doi: 10.1038/ng.1038.   edoc
Behr, M. A. and Gagneux, S. (2011) “The rise and fall of Mycobacterium tuberculosis complex”, in Tibayrenc, M. (ed.) Genomics and evolution of infectious diseases. Amsterdam: Elsevier, pp. 651–667. doi: 10.1016/B978-0-12-384890-1.00024-8.   edoc
Sherman, D. R. and Gagneux, S. (2011) “Estimating the mutation rate of Mycobacterium tuberculosis during infection”, Nature genetics. Nature Publ, Vol. 43, H. 5, pp. 400–401.   edoc
Yeboah-Manu D., Asante-Poku A., Bodmer, T., Stucki, D., Koram, K., Bonsu, F., Pluschke, G. and Gagneux, S. (2011) “Genotypic diversity and drug susceptibility patterns among M. tuberculosis complex isolates from South-Western Ghana”, PLoS ONE. Public Library of Science, Vol. 6, H. 7 , e21906. doi: 10.1371/journal.pone.0021906.   edoc
Fenner, L., Malla, B., Ninet, B., Dubuis, O., Stucki, D., Borrell, S., Huna, T., Bodmer, T., Egger, M. and Gagneux, S. (2011) “‘Pseudo-Beijing’ : evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis”, PLoS ONE. Public Library of Science, Vol. 6, H. 9 , e24737. doi: 10.1371/journal.pone.0024737.   edoc
Comas, I. and Gagneux, S. (2011) “A role for systems epidemiology in tuberculosis research”, Trends in microbiology : virulence, infection and pathogenesis. Elsevier, Vol. 19, H. 10, pp. 492–500. doi: 10.1016/j.tim.2011.07.002.   edoc
Portevin, D., Gagneux, S., Comas, I. and Young, D. (2011) “Human macrophage responses to clinical isolates from the Mycobacterium tuberculosis complex discriminate between ancient and modern lineages”, PLoS Pathogens. Public Library of Science, Vol. 7, H. 3 , e1001307. doi: 10.1371/journal.ppat.1001307.   edoc
Kato-Maeda M., Gagneux, S., Flores, L. L., Kim, E. Y., Small, P. M., 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. IUATLD, Vol. 15, H. 1, pp. 131–133.   edoc
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. Blackwell, Vol. 17, H. 6, pp. 815–820. doi: 10.1111/j.1469-0691.2011.03556.x.   edoc
Comas, I., Chakravartti, J., Small, P. M., Galagan, J., Niemann, S., Kremer, K., Ernst, J. D. and Gagneux, S. (2010) “Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved”, Nature genetics. Nature Publ, 42(6), pp. 498–503.   edoc
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: Oxford Fajar, pp. 130–147.   edoc
Nahid, P., Bliven, E. E., Kim, E. Y., Mac Kenzie W. R., Stout, J. E., Diem, L., Johnson, J. L., Gagneux, S., Hopewell, P. C. and Kato-Maeda M. (2010) “Influence of M. tuberculosis lineage variability within a clinical trial for pulmonary tuberculosis”, PLoS ONE. Public Library of Science, Vol. 5, H. 5 , e10753.   edoc
de Jong B. C., Antonio, M. and Gagneux, S. (2010) “Mycobacterium africanum : review of an important cause of human tuberculosis in West Africa”, PLoS neglected tropical diseases. Library of Science, Vol. 4, H. 9 , e744.   edoc
Coscolla, M. and Gagneux, S. (2010) “Does M. tuberculosis genomic diversity explain disease diversity?”, Drug discovery today. Disease mechanisms. Elsevier, Vol. 7, H. 1 , e43-e59.   edoc
Borrell, S. and Gagneux, S. (2009) “Infectiousness, reproductive fitness and evolution of drug-resistant Mycobacterium tuberculosis”, The international journal of tuberculosis and lung disease. IUATLD, 13(12), pp. 1456–1466.   edoc
Leimkugel, J., Forgor, A. A., Dangy, J.-P., Pflüger, V., Gagneux, S., Hodgson, A. and Pluschke, G. (2007) “Genetic diversification of Neisseria meningitidis during waves of colonization and disease in the meningitis belt of sub-Saharan Africa”, Vaccine : the official journal of the International Society for Vaccines. Elsevier, 25(1), pp. A18-A23. doi: 10.1016/j.vaccine.2007.04.035.   edoc
Leimkugel, J., Hodgson, A., Forgor, A. A., Pflüger, V., Dangy, J.-P., Smith, T., Achtman, M., Gagneux, S. and Pluschke, G. (2007) “Clonal waves of Neisseria colonisation and disease in the African meningitis belt : eight- year longitudinal study in northern Ghana”, PLoS medicine. PLoS, Vol. 4, H. 3 , e101.   edoc
Leimkugel, J., Adams Forgor, A., Gagneux, S., Pflüger, V., Flierl, C., Awine, E., Naegeli, M., Dangy, J.-P., Smith, T., Hodgson, A. and Pluschke, G. (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. Oxford University Press, Vol. 192, H. 2, pp. 192–199.   edoc
Forgor, A. A., Leimkugel, J., Hodgson, A., Bugri, A., Dangy, J.-P., Gagneux, S., Smith, T. and Pluschke, G. (2005) “Emergence of W135 meningococcal meningitis in Ghana”, Tropical medicine and international health : TM & IH : a European journal. Blackwell Science, 10(12), pp. 1229–1234. doi: 10.1111/j.1365-3156.2005.01520.x.   edoc
Gagneux, S. P., Hodgson, A., Smith, T. A., Wirth, T., Ehrhard, I., Morelli, G., Genton, B., Binka, F. N., Achtman, M. and Pluschke, G. (2002) “Prospective study of a serogroup X Neisseria meningitidis outbreak in northern Ghana”, Journal of infectious diseases. Oxford University Press, Vol. 185, H. 5, pp. 618–626.   edoc
Gagneux, S., Wirth, T., Hodgson, A., Ehrhard, I., Morelli, G., Kriz, P., Genton, B., Smith, T., Binka, F., Pluschke, G. and Achtman, M. (2002) “Clonal groupings in serogroup X Neisseria meningitidis”, Emerging Infectious Diseases. National Center for Infectious Diseases, Vol. 8, H. 5, pp. 462–466.   edoc
Hodgson, A., Smith, T., Gagneux, S., Akumah, I., Adjuik, M., Pluschke, G., 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. Oxford University Press, Vol. 30, H. 6, pp. 1440–1446.   edoc
Hodgson, A., Smith, T., Gagneux, S., Adjuik, M., Pluschke, G., Mensah, N. K., Binka, F. and Genton, B. (2001) “Risk factors for meningococcal meningitis in northern Ghana”, Transactions of the Royal Society of Tropical Medicine and Hygiene. Transactions of the Royal Society of Tropical Medicine and Hygiene, Vol. 95, H. 5, pp. 477–480.   edoc
Zhu, P., van der Ende, A., Falush, D., Brieske, N., Morelli, G., Linz, B., Popovic, T., Schuurman, I. G., Adegbola, R. A., Zurth, K., Gagneux, S., Platonov, A. E., Riou, J. Y., Caugant, D. A., 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. National Academy of Sciences, Vol. 98, H. 9, pp. 5234–5239.   edoc
Gagneux, S. (2001) Molecular epidemiology of meningococcal disease in Northern Ghana. doi: 10.5451/unibas-002399498.   edoc | Open Access
Gagneux, S., Hodgson, A., Ehrhard, I., Morelli, G., Genton, B., Smith, T., Tanner, M., Binka, F., 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. Blackwell Science, 5(4), pp. 280–287. doi: 10.1046/j.1365-3156.2000.00550.x.   edoc