Implementation of microbial whole-genome sequencing for individual patient care, local outbreak recognition and national surveillance.

Need Next-day access to micro-organism species, resistance, and relatedness would be an unprecedented advance for infection treatment and control. The existing multiplicity of disconnected pathogen-specific systems make such fast, cheap, comprehensive characterization impossible, but most such information could be deduced from whole-genome sequences. Technology We propose to translate whole-genome sequencing into routine clinical microbiology by: Optimizing a locally-implementable bench-top sequencing pathway for primary cultures with Illumina. Creating a suite of bioinformatic software to assemble, securely store, and query sequences with database support from Oracle. Developing knowledge-bases, statistical algorithms and visual analytics to predict antimicrobial resistance/virulence phenotype, identify possible transmissions, and present actionable information to service-users. Goals/Deliverables Demonstrating locally-based genome sequencing in a network of routine service laboratories (initially Oxford, Brighton, Birmingham and Leeds) as a model for national surveillance and a faster, more informative alternative to centralized reference facilities Health-economic evaluation demonstrating cost-effectiveness A clear pathway to national implementation and extension to more pathogens Impact Complete work-up' of a single sample currently takes days-to-months. We envisage providing complete pathogen information within 24h of culture, transparently linked to national surveillance and enabling faster and better targeted patient treatment, infection prevention/control and cost reductions.