Aanensen Group | Genomic Epidemiology of Infectious Diseases

Aanensen Group | Genomic Epidemiology of Infectious Diseases

Aanensen Group

Our Research and Approach

Our mission is to inform control strategies and interventions on a local, national and international scale.

Through our global research partnerships with the US CDC, the European CDC, the World Health Organisation and Food and Agriculture Organisation, National Institutes of Health and Public Health England we are helping lead the fight against antimicrobial resistance (AMR) – one of the biggest threats to global health security.

We achieve our mission through a combination of structured population surveys and whole genome sequencing to generate high quality openly available surveillance data and identify high risk clones; by developing software tools and technologies that make data visualisation and interpretation accessible to all; and by investing in capacity building across low- and middle-income countries (LMICs), helping to train future leaders of new national and emerging surveillance programmes. 

Our international and diverse team brings together expertise in data modelling, software development, epidemiology, bioinformatics and machine learning, genomic technology, Good Financial Grant Practice (GFGP), training and capacity building.  

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Professor David Aanensen
Group Leader

David holds a joint faculty position at The Big Data Institute, University of Oxford

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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.

Programmes, Associate Research Programmes and Facilities

Partners and Funders

Internal Partners


  • Novel Subclone of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 with Enhanced Virulence and Transmissibility, China.

    Zhou K, Xiao T, David S, Wang Q, Zhou Y et al.

    Emerging infectious diseases 2020;26;2;289-297

  • 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

  • Phandango: an interactive viewer for bacterial population genomics.

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

    Bioinformatics (Oxford, England) 2018;34;2;292-293

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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