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.
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
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.