Aanensen Group | Genomic Epidemiology of Infectious Diseases

Aanensen Group | Genomic Epidemiology of Infectious Diseases

Aanensen Group

aanensen-group-2.jpgSanger Institute, Genome Research Limited

Our Research and Approach

Our group consistis of a mix of genomic epidemiologists, computational biologists and web software engineers within The Centre for Genomic Pathogen Surveillance (CGPS) a collaboration with Imperial College London.

Within CGPS, broad aims are to provide data and tools for local, national and international utility focused on antimicrobial resistance and genomic surveillance. We are addressing the utility of large-scale structured pathogen surveys to provide contextual WGS datasets and population structure. Key aims are to enable the identification of high risk clones of public health importance, their risk assessment (eg resistance, virulence and transmissibility) and ultimately management.

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Dr David Aanensen
Group Leader

David holds a joint faculty position at Imperial College London

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Key Projects, Collaborations, Tools & Data

We work with international agencies, surveillance networks and the broader molecular epidemiology and public health community to enable the utility of whole genome sequencing for global public health.

Research Programmes and Faciltites

Partners and Funders

Internal Partners


  • PANINI: Pangenome Neighbour Identification for Bacterial Populations.

    Abudahab K, Prada JM, Yang Z, Bentley SD, Croucher NJ et al.

    Microbial genomics 2018

  • Gene exchange drives the ecological success of a multi-host bacterial pathogen.

    Richardson EJ, Bacigalupe R, Harrison EM, Weinert LA, Lycett S et al.

    Nature ecology & evolution 2018

  • Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris.

    Rhodes J, Abdolrasouli A, Farrer RA, Cuomo CA, Aanensen DM et al.

    Emerging microbes & infections 2018;7;1;43

  • Emergence and clonal spread of colistin resistance due to multiple mutational mechanisms in carbapenemase-producing Klebsiella pneumoniae in London.

    Otter JA, Doumith M, Davies F, Mookerjee S, Dyakova E et al.

    Scientific reports 2017;7;1;12711

  • Phandango: an interactive viewer for bacterial population genomics.

    Hadfield J, Croucher NJ, Goater RJ, Abudahab K, Aanensen DM and Harris SR

    Bioinformatics (Oxford, England) 2017

  • Species Mash-up.

    Argimón S and Aanensen DM

    Nature reviews. Microbiology 2016;14;12;730

  • Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection.

    Crellen T, Allan F, David S, Durrant C, Huckvale T et al.

    Scientific reports 2016;6;20954

  • OutbreakTools: a new platform for disease outbreak analysis using the R software.

    Jombart T, Aanensen DM, Baguelin M, Birrell P, Cauchemez S et al.

    Epidemics 2014;7;28-34