Translating whole genome sequence technology into diagnostic and public health microbiology.

Effective mechanisms of surveillance are required to track disease trends, identify new infectious disease threats, detect serious outbreaks, monitor control measures, design effective vaccines and monitor for vaccine escape. The present public health system falls short of what is required because of a technology gap whereby it is not possible to make rapid or in some cases accurate inferences regarding pathogen outbreaks and transmission events using the currently available microbial genotyping methodology. Our goal is to seek a solution to this need through the development of a world-class system of active surveillance based on microbial whole genome sequencing (WGS), in which we will capitalize on a close existing partnership between the Cambridge University Hospitals NHS Trust (CUHFT), the Health Protection Agency (HPA) and the Wellcome Trust Sanger Institute (WTSI). We will embed a genome sequence- driven microbiology initiative within a clinical campus, working alongside a hospital diagnostic and public health laboratory (Cambridge HPA). Key objectives are to understand how to apply genomics to address the problems of infectious disease control scaled to local, regional or national levels, and how to integrate this technology into ongoing practice so as to expand and enhance the current system of infectious diseases surveillance conducted by the HPA.