Pathogens and antimicrobial resistance gene sequencing. Sheffield
Research type
Research Study
Full title
Establishing Oxford Nanopore Technology-based metagenomic sequencing methods to detect a wide range of pathogens and antimicrobial resistance genes in clinical samples
IRAS ID
296469
Contact name
Thushan de Silva
Contact email
Sponsor organisation
Sheffield Teaching Hospitals Foundation Trust
Duration of Study in the UK
2 years, 5 months, 30 days
Research summary
This research project will evaluate the use of a novel genome sequencing technology in establishing diagnosis of infection. Genome sequencing is a technology that detects the structure of deoxyribonucleic acid (DNA). In this project we will use these technologies to detect pathogens (bacteria, viruses and fungi) that are involved in infectious diseases. Genome sequencing can also detect genes which pathogens have that allow them to develop resistance to antibiotics. Understanding which pathogens contain these genes can lead to improved antibiotic prescribing and prevent transmission.
Genome sequencing techniques are becoming an increasingly utilised investigation in medical diagnostics. They can detect pathogens which are not able to be cultured in a laboratory. Currently Sheffield Teaching Hospitals NHS Foundation Trust (STHNFT) laboratories send samples for genome sequencing to reference laboratories leading to delayed time in receiving important results. The results of this study will seek to establish ‘in house’ genome sequencing methods at STHNFT to reduce this time.
We have chosen specific scenarios to investigate. Firstly analysing stool samples of patients who have a significantly weakened immune system including patients who have undergone haematopoeitic stem cell transplants. Secondly, sputum samples of patients on critical care. These sets of patients are at high risk of developing infections, often with pathogens that would not infect those with a strong immune system. These organisms often have resistance to antibiotics. We will also examine sterile sites. These are areas of the body where one would not expect to find infections such as in the cerebrospinal (CSF) fluid that surrounds the brain and spinal cord.
The study will take place at STHNFT and University of Sheffield. The samples used for this study will be taken from already collected samples that would usually be discarded. No new samples will be requested from participants. Patient identifiers will be anonymised throughout.
REC name
London - Central Research Ethics Committee
REC reference
21/PR/0675
Date of REC Opinion
7 Jun 2021
REC opinion
Favourable Opinion