Sébastien Gagneux, Professor, PhD

Function(s)
Head of Department

Organisational Entity

Sébastien Gagneux is Professor of Infection Biology and Head of the Department of Medical Parasitology and Infection Biology at the Swiss Tropical and Public Health Institute (Swiss TPH)/University of Basel. After receiving his PhD from the University of Basel, he worked as a postdoctoral fellow at Stanford University and at the Institute for Systems Biology in Seattle, USA. He then spent three years as a Program Leader at the MRC National Institute for Medical Research in London, UK before joining Swiss TPH. His research focuses on the ecology and evolution of Mycobacterium tuberculosis with a particular focus on antimicrobial resistance.

 

Profile

Research activities at Swiss TPH

  • Population genomics of Mycobacterium tuberculosis
  • Ecology and evolution of antibiotic resistance in Mycobacterium tuberculosis
  • Genomic epidemiology of tuberculosis

Higher education

  • MSc, 1997: Biology & Medical Parasitology, Swiss Tropical Institute/University of Basel, Switzerland
  • PhD, 2001: Epidemiology, Swiss Tropical Institute/University of Basel, Switzerland
  • 2001-2005: Postdoc, Division of Infectious Diseases & Geographic Medicine, Stanford University, USA
  • 2005-2006: Postdoc, Institute for Systems Biology, Seattle, USA

Work experience

  • 2022- : Professor of Infection Biology, Swiss TPH/University of Basel, Basel, Switzerland
  • 2016- : Head of Department, Department of Medical Parasitology & Infection Biology, Swiss TPH, Basel, Switzerland
  • 2016- 2021: Associate Professor of Infection Biology, Swiss TPH/University of Basel, Basel, Switzerland
  • 2014-2016: Deputy Head of Department, Department of Medical Parasitology & Infection Biology, Swiss TPH, Basel, Switzerland
  • 2010-2016: SNF-Professor, Swiss TPH/University of Basel, Basel, Switzerland
  • 2007-2010: Programme Leader, Medical Research Council, National Institute for Medical Research, London, UK
  • 2006-2007: Senior Scientist, Institute for Systems Biology, Seattle, USA

Latest Publications

All Publications

Cox H et al. Whole genome sequencing has the potential to improve treatment for rifampicin-resistant tuberculosis in high burden settings: a retrospective cohort study. J Clin Microbiol. 2022(in press). DOI: 10.1128/jcm.02362-21

Maghradze N et al. Developing customized stepwise MIRU-VNTR typing for tuberculosis surveillance in Georgia. PLoS One. 2022;17(3):e0264472. DOI: 10.1371/journal.pone.0264472

Vera-Cabrera L et al. Mycobacterium leprae Infection in a Wild Nine-Banded Armadillo, Nuevo Leon, Mexico. Emerg Infect Dis. 2022;28(3):747-749. DOI: 10.3201/eid2803.211295

Xu Z.M et al. Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations. PLoS Comput Biol. 2022;18(1):e1009628. DOI: 10.1371/journal.pcbi.1009628

Alagna R et al. Is the new WHO definition of extensively drug-resistant tuberculosis easy to apply in practice?. Eur Respir J. 2021;58:2100959. DOI: 10.1183/13993003.00959-2021

Asare P et al. 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. 2021;106:13-22. DOI: 10.1016/j.ijid.2021.02.110

Castro R.A.D, Borrell S, Gagneux S. The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis. FEMS Microbiol Rev. 2021;45(4):fuaa071. DOI: 10.1093/femsre/fuaa071

Coscolla M et al. Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history. Microb Genom. 2021;7(2):000477. DOI: 10.1099/mgen.0.000477

Cox H et al. 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. 2021;2(11):e584-e593. DOI: 10.1016/S2666-5247(21)00144-0

Guimarães A.E.D.S et al. Evaluation of drug susceptibility profile of Mycobacterium tuberculosis lineage 1 from Brazil based on whole genome sequencing and phenotypic methods. Mem Inst Oswaldo Cruz. 2021;115:e200520. DOI: 10.1590/0074-02760200520