Whole genome sequencing for the diagnosis of infections
Research type
Research Study
Full title
A proof of principle study to investigate the role of whole genome sequencing for the diagnosis of infections and detection of all organisms in residual clinical samples
IRAS ID
190174
Contact name
M Hopkins
Contact email
Sponsor organisation
Barts Health NHS Trust
Duration of Study in the UK
0 years, 11 months, 31 days
Research summary
The use of molecular diagnostics in infectious diseases is moving at a rapid rate although most of the UK laboratories continue culture based methods for the diagnosis of bacterial infections. Current diagnostic approaches used for direct detection of pathogens in routine and reference laboratories are often targeted to specific pathogens to be useful to detect unknown and difficult to culture or newly emerging bacterial and viral human pathogens. What is needed is an approach which will allow the detection of all classes of organism, including those that cannot be grown in culture in the routine diagnostic laboratory.
The Chief Investigator and Co-investigators will collaborate with the Genomics Research Unit of Public Health England to evaluate methods recently developed within the unit for new methods for the detection and interpretation of viral and bacterial pathogen-derived sequences present in different sample types at low levels. This has involved the development of methods for pathogen enrichment from sample, metagenomic nucleic acid extraction, and/or random nucleic acid amplification in concert with the latest advances in DNA and RNA deep sequencing.
We aim to determine the role of sequencing in diagnosing infections directly from samples obtained from normally sterile sites or those from non-sterile sites that are culture negative (eg. high vaginal swabs or bronchoalveolar lavage). In addition we want to determine the applicability in a routine diagnostic microbiology laboratory.
Monitoring of the spread of an infectious agent throughout a population will also be a valuable tool in reducing the spread of infection, particularly within a hospital environment. Anonymised, non-patient identifiable, residual samples left after processing in the microbiology laboratory at Royal London Hospital will be processed for whole genome sequencing (WGS) and the data will be compared against that obtained by routine culture methods. Our findings may be applied to other parts of the UK.REC name
South Central - Berkshire B Research Ethics Committee
REC reference
16/SC/0234
Date of REC Opinion
22 Apr 2016
REC opinion
Favourable Opinion