Title: MODERNISING MEDICAL MICROBIOLOGY: ESTABLISHING HOW NEW TECHNOLOGIES CAN BE OPTIMALLY INTEGRATED INTO MICROBIOLOGY
Funder: Medical Research Council

Abstract: Three areas continue to challenge medical microbiology: detecting and managing outbreaks, identifying microbial pathogenic factors causing specific disease manifestations, and understanding the contribution of human host susceptibility. Ongoing advances in sequencing, bioinformatics and web-based technologies have now reached a stage where their potential for revolutionising the way we characterise microbes and investigate human disease can be envisaged. The real challenge is to harness and translate this potential into clinical practice and public health. The goal of this Consortium is therefore to transfer new and established sequencing technologies into effective everyday public health and clinical microbiology practice. Specific primary objectives are (i) at a national level, to rapidly detect and track the spread of new epidemic strains (ii) at a local level, to identify hitherto unrecognised outbreaks within an endemic setting, by coupling more discriminatory sequence typing with carefully defined sampling frames (iii) at an individual patient level, to recognise and follow outbreaks early enough to intervene effectively (iv) to develop attractive, easy-to-use web-accessible bioinformatics tools enabling local practitioners to direct routine infection control practices efficiently. Our secondary objective is to enable future population-based studies of microbial pathogenic factors and host genetically-determined susceptibility by assembling isolate collections and matched human DNA. Our strategy focuses on four major pathogens providing diverse challenges and varying potential for successful application. We will use ultra-fast whole genomic sequencing to identify regions of informative diversity to augment established and lower resolution typing schemes, and to achieve sufficient power to detect transmission even of highly prevalent pathogenic strains. Rigorous population-based sampling frames appropriate for each organism will be defined, relevant clinical/epidemiological data collected, and infecting organisms and host DNA archived. Improved typing schemes will be implemented using established sequencing platforms, and outputs integrated in a single web-based environment for reporting and analysis. This should deliver near-real-time data-driven national surveillance and local clinical decision making, and could be integrated into the HPA Regional Microbiology Network (RMN). To realise our scientific goal we will draw together the breadth of the HPA RMN, research strengths of the University of Oxford, and the sequencing/informatic resources of the Wellcome Trust Sanger Institute, enhancing training opportunities and leadership development in cutting-edge technologies for a large pool of microbiologists. UK capacity will be strengthened by creating a novel partnership with national reach, nurturing research trainees, developing practical software and analytical tools and assembling large well-defined sample archives.


Research activity codes: 2.4 SURVEILLANCE AND DISTRIBUTION;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;7.3 MANAGEMENT AND DECISION MAKING;4.4 POPULATION SCREENING
Health categories: INFECTION