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


  • 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