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.
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.
Dense genomic sampling identifies highways of pneumococcal recombination.
Nature genetics 2014;46;3;305-309
Mapping the global emergence of Batrachochytrium dendrobatidis, the amphibian chytrid fungus.
PloS one 2013;8;2;e56802
Geographic distribution of Staphylococcus aureus causing invasive infections in Europe: a molecular-epidemiological analysis.
PLoS medicine 2010;7;1;e1000215
EpiCollect: linking smartphones to web applications for epidemiology, ecology and community data collection.
PloS one 2009;4;9;e6968
Assigning strains to bacterial species via the internet.
BMC biology 2009;7;3
Predicted functions and linkage specificities of the products of the Streptococcus pneumoniae capsular biosynthetic loci.
Journal of bacteriology 2007;189;21;7856-76
The multilocus sequence typing network: mlst.net.
Nucleic acids research 2005;33;Web Server issue;W728-33
Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection.
PANINI: Pangenome Neighbour Identification for Bacterial Populations.
Microbial genomics 2018
Gene exchange drives the ecological success of a multi-host bacterial pathogen.
Nature ecology & evolution 2018
Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris.
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.
Scientific reports 2017;7;1;12711
Phandango: an interactive viewer for bacterial population genomics.
Bioinformatics (Oxford, England) 2017
Nature reviews. Microbiology 2016;14;12;730
Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection.
Scientific reports 2016;6;20954
OutbreakTools: a new platform for disease outbreak analysis using the R software.