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Future Solutions In Progress

Theme 5: Infection Response Systems: Development and application of technology for prevention, diagnosis, intervention and control of infection


Theme 5 Projects:


Immediate point of care molecular diagnostics for lung inflammation/infection in critical care
Fully integrated, real-time detection, diagnosis and control of community diarrhoeal disease clusters and outbreaks
Principal Investigator:  Professor Sarah O’Brien
Organisation: University of Liverpool
Start Date 1st April 2013
End Date: 31st March 2017

View Abstract

Seventeen million people suffer a diarrhoeal disease every year. These diseases often lead to outbreaks of infections, like norovirus - now among the costliest infectious burdens on the NHS. The sooner diseases are detected, the sooner they can be brought under control - limiting their health and financial impact. It is known from outbreaks of Escherichia coli O104 in Germany and O157 at Godstone Farm in Surrey that surveillance is key to detection; but with fewer people now consulting their GP over diarrhoea, outbreaks are increasingly difficult to detect using traditional methods. This hides the true burden of disease. Professor Sarah O’Brien at the University of Liverpool and her collaborators will use data from multiple sources to scout for infection in the community, take samples and analyse them, using modern technology to detect organisms. The researchers will analyse the DNA of microbes to discover which family of organisms they belong to and how they are evolving. Since many diarrhoeal diseases can pass between humans and animals the project team will develop and integrate veterinary and medical surveillance. The ultimate goal is an integrated real-time, surveillance/diagnosis/investigation system - centred on the patient - that detects community outbreaks sooner, enables Health Protection professionals and Environmental Health Officers to intervene quickly and thus lessen short- and long-term harm.

Immediate point of care molecular diagnostics for lung inflammation/infection in critical care
Translating whole genome sequence technology into diagnostic and public health microbiology
Principal Investigator:  Professor Sharon Peacock
Organisation: University of Cambridge
Start Date 1st October 2013
End Date: 30th September 2017

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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.

Through this award to Cambridge University, Professor Sharon Peacock will 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 collaboration with the Cambridge University Hospitals NHS Trust, the Health Protection Agency and the Wellcome Trust Sanger Institute. The aim is to embed a genome sequence-driven microbiology initiative within a clinical campus, working alongside a hospital diagnostic and public health laboratory. 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 on-going practice so as to expand and enhance the current system of infectious diseases surveillance conducted.

Immediate point of care molecular diagnostics for lung inflammation/infection in critical care
Infection response through viral genomics
Principal Investigator:  Professor Andrew Hayward
Organisation: University College London
Start Date 01st October 2013
End Date: 31st December

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Viruses are a major cause of morbidity and mortality, with a high cost to the NHS. Viruses have significant genomic variation, which underpins pathogenicity, drug resistance, and transmission.

Despite enormous advances in technology, we currently lack the systems, facilities and capacity to routinely capture full-length viral gene sequences, to monitor drug resistance at the granularity to optimally guide treatment, to identify the source of viral transmissions within healthcare settings, and to track emerging epidemics.

Professor Deenan Pillay of University College London and collaborators are developing next generation sequencing technology to capture virus genomes from clinical samples. The team’s goals are to i) deploy optimal methods for preparing clinical and surveillance isolates for sequencing, ii) develop robust and reliable real time full length virus sequencing, iii) deliver data to NHS users in a form suited to inform direct clinical care, hospital control, and intervention in epidemics. It is hoped that the technology will lead to more effective treatment of HIV and HCV infections, more targeted hospital infection control regarding norovirus infections, and better dynamic assessment and targeted management of community based viral outbreaks, in particular measles and influenza.

Immediate point of care molecular diagnostics for lung inflammation/infection in critical care
Implementation of microbial whole-genome sequencing for individual patient care, local outbreak recognition and national surveillance
Principal Investigator:  Professor Derrick Crook
Organisation: University of Oxford
Start Date 01st April 2013
End Date: 31st March 2017

View Abstract

Rapid, next-day access to information regarding micro-organism species, drug resistance, and relatedness would be an unprecedented advance for infectious disease treatment and control.

The existing multiplicity of disconnected pathogen-specific systems make fast, cheap and comprehensive characterization impossible. However, such information could be deduced from whole-genome sequence analysis of the disease-causing microorganisms.

Professor Derrick Crook of Oxford University and his collaborators propose to translate whole-genome sequencing into routine clinical microbiological practice. The goals of their 3 year programme are to demonstrate locally-based genome sequencing operating in a network of routine NHS service laboratories at Oxford, Brighton, Birmingham and Leeds. This will serve as a model for a national surveillance system and a faster, more informative alternative to centralized reference facilities for infection prevention and control. Currently analysis of a single clinical sample may take days-to-months. The aim is to provide complete pathogen information within 24h of culture, linked to a national surveillance database thereby enabling more timely and better targeted patient treatment.