Whole-genome sequencing-based rapid diagnostics
Research type
Research Study
Full title
Rapid extraction of pathogen nucleic acid directly from clinical samples to investigate a whole genome sequencing-based diagnostic solution, including predicting antimicrobial resistance for bacterial infections
IRAS ID
228657
Contact name
Bernadette Young
Contact email
Sponsor organisation
University of Oxford
Duration of Study in the UK
4 years, 6 months, 31 days
Research summary
With new technologies, the letters in a microbe's genetic code (genetic sequence) can be read for little financial cost. Computer tools can extract information from these sequences, including the type of microbe, if bacteria what antibiotics it is resistant to (i.e. will no longer cure the infection) and how closely it is related to other microbes (i.e. where it might be transmitted from). This study will develop ways to quickly obtain microbe genetic sequences straight from patient samples (blood, sputum, cerebral spinal fluid, pus, urine, stool and samples that usually do not contain microbes). Clinical samples taken from patients for diagnostic purposes will be used in the new genetic workflow in parallel with standard routine laboratory processes.
The primary goal is to develop a sufficiently accurate (in terms of predicting the cause of infection and antibiotic resistance for bacteria) microbe whole genome sequencing workflow, which is faster in turnaround time than current routine diagnostic procedures, so it could be a model for local service provision and national surveillance. Primarily, two outcomes will be assessed: (1) turnaround time from the patient sample to prediction of the type of microbe and, it if is bacterial which antibiotics it is resistant to and (2) accuracy of the microbe and antibiotic resistance prediction.
This study is observational and will take place at Oxford University. The clinical samples and non-patient identifiable electronic data being used within the study are already routinely collected by clinical teams managing patients. The study will not collect additional samples or additional data. Results from the genomic workflow will not be returned and individual patient management will not be affected. No patient identifiable data will be available to the research team and access to anonymised data will be restricted to maintain confidentiality.
REC name
London - Queen Square Research Ethics Committee
REC reference
17/LO/1420
Date of REC Opinion
17 Aug 2017
REC opinion
Favourable Opinion