Professor David Aanensen | Director of the Centre for Genomic Pathogen Surveillance and Group Leader

Aanensen, David

David is the Director of the Centre for Genomic Pathogen Surveillance (CGPS) which is based at The Wellcome Sanger Institute brings together expertise in data modeling, software development, epidemiology, bioinformatics and machine learning, genomic technology, Good Financial Grant Practice (GFGP), training and capacity building. David is also a Senior Group Leader in Genomic Surveillance at the Big Data Institute, University of Oxford.

For endemic pathogens (and outbreak scenarios), epidemiological data combined with genomics can inform control strategies and interventions on a local, national and international scale. Data generation, integration, analytical flow and interpretation in real-time is challenging, but crucial for decision making and action.

Within the CGPS, David and his team focus on data flow and the use of genome sequencing for surveillance of microbial pathogens through a combination of web application and software engineering, methods development and large-scale structured pathogen surveys and sequencing of microbes with delivery of information for decision making.

Working with major public health agencies such as the US CDC, the European CDC, Public Health England and the WHO, systems are utilised to interpret and aid decision making for infection control.

David is also Director of the NIHR funded Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance (AMR) working with partners leading National AMR strategies in The Phillipines, Colombia, Nigeria and India to implement genomic surveillance and linking to routine phenotypic and epidemiological data for priority pathogens.

Major Applications include:


Mobile data gathering platform used globally and by major health agencies, citizen scientists, ecologists, epidemiologists, business analytics, schools and colleges over 14,000 projects and > 28Million data points.


Open data visualisation and sharing for genomic epidemiology. Used by major agencies such as CDC, eCDC and PHE for routine investigation of public health incidents.


A global platform for genomic surveillance of microbial pathogens (including all major WHO Priority bacterial pathogens) Rapid prediction of resistant genotypes, and clustering giving epidemiological context.


  • 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:

    Aanensen DM and Spratt BG

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

  • Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread.

    David S, Reuter S, Harris SR, Glasner C, Feltwell T et al.

    Nature microbiology 2019;4;11;1919-1929

  • Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection.

    McNally A, Kallonen T, Connor C, Abudahab K, Aanensen DM et al.

    mBio 2019;10;2

  • PANINI: Pangenome Neighbour Identification for Bacterial Populations.

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

    Microbial genomics 2019;5;4

  • 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;2;9;1468-1478

  • 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