Dr David Aanensen | Group Leader

Aanensen, David

David is Director of the recently established Centre for Genomic Pathogen Surveillance and holds a faculty position within the Department of Infectious Disease Epidemiology at Imperial College London.

David's group have a focus on applied public health bioinformatic research and genomic epidemiology.

David graduated with a BSc in Biochemistry (Salford) and a MSc in Neuroscience (Institute of Psychiatry, KCL). After working in the web industry for a period, David took up a position at Imperial College London within the group of Professor Brian Spratt and undertook a part-time PhD in Bioinformatics. Focusing on the molecular epidemiology of bacterial pathogens, David has been developing translational bioinformatics methods and tools for public health, for example Multilocus Sequence Typing for the identification of bacterial clones, generic mobile data gathering, spatial data visualisation and comparative genomics.

Within The Centre for Genomic Pathogen Surveillance, 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.

Toolsets include www.wgsa.net for the processing of whole genome assemblies and EpiCollect for generic metadata gathering. EpiCollect allow groups / individuals / organizations to get up and running with mobile data gathering as quickly and easily as possible. Projects people have set up range from simple surveys of wildlife and plants, through archaelogical dig sites and street art locations to the use by international organisations such as the Food and Agriculture Organisation of the United Nations, for the tracking of animal and human pathogens in Africa, for Widespread vaccination campaigns (eg Rabies in India) and for tracking EBOLA in Liberia.


  • The dynamic changes of dominant clones of Staphylococcus aureus causing bloodstream infections in the European region: results of a second structured survey.

    Grundmann H, Schouls LM, Aanensen DM, Pluister GN, Tami A et al.

    Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2014;19;49

  • EpiCollect+: linking smartphones to web applications for complex data collection projects.

    Aanensen DM, Huntley DM, Menegazzo M, Powell CI and Spratt BG

    F1000Research 2014;3;199

  • Dense genomic sampling identifies highways of pneumococcal recombination.

    Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P et al.

    Nature genetics 2014;46;3;305-309

  • Mapping the global emergence of Batrachochytrium dendrobatidis, the amphibian chytrid fungus.

    Olson DH, Aanensen DM, Ronnenberg KL, Powell CI, Walker SF et al.

    PloS one 2013;8;2;e56802

  • Geographic distribution of Staphylococcus aureus causing invasive infections in Europe: a molecular-epidemiological analysis.

    Grundmann H, Aanensen DM, van den Wijngaard CC, Spratt BG, Harmsen D et al.

    PLoS medicine 2010;7;1;e1000215

  • EpiCollect: linking smartphones to web applications for epidemiology, ecology and community data collection.

    Aanensen DM, Huntley DM, Feil EJ, al-Own F and Spratt BG

    PloS one 2009;4;9;e6968

  • Assigning strains to bacterial species via the internet.

    Bishop CJ, Aanensen DM, Jordan GE, Kilian M, Hanage WP and Spratt BG

    BMC biology 2009;7;3

  • Predicted functions and linkage specificities of the products of the Streptococcus pneumoniae capsular biosynthetic loci.

    Aanensen DM, Mavroidi A, Bentley SD, Reeves PR and Spratt BG

    Journal of bacteriology 2007;189;21;7856-76

  • The multilocus sequence typing network: mlst.net.

    Aanensen DM and Spratt BG

    Nucleic acids research 2005;33;Web Server issue;W728-33

  • 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

Aanensen, David
David's Timeline

Director of cGPS


Senior Lecturer Imperial College


Lecturer Imperial College


PhD Bioinformatics

MSc Neuroscience