Linking epidemiological and genomic data for infectious diseases

Project description

Summary: In the past few years, advances in sequencing technology and the reduction in associated costs have enabled scientists to obtain highly detailed genomic data on disease-causing pathogens on a scale never seen before. In addition to the inherent phylogenetic information contained in such data, combining genomic data with traditional epidemiological data (such as time series of case incidence) also provides an opportunity to perform microbial source attribution, i.e. determining the actual transmission pathway of the pathogen through a population.

These advances have seen a corresponding surge of activity in the modelling and statistical analysis community, so that now a number of methods and associated computer packages exist to carry out source-attribution, i.e. estimating who-infected-whom in a particular outbreak. All the methods have their own limitations; a very common issue is that the models used to perform estimation are conditional upon the observed data, which can create estimation biases and lead to misleading results. In contrast, the method developed by Worby, Kypraios and O'Neill involves a model that can explain how the data arose, overcoming such problems. This project is concerned with developing this approach to both (i) extend the idea to more complex model settings, relaxing certain technical assumptions and (ii) improve computational efficiency. A highly-detailed data set on MRSA provided by collaborators at Guy's and St Thomas' hospital trust, London, provides one opportunity for applying such methods.