NHS England and the Department for Science, Innovation, and Technology, are funding a national pilot project across ten hospital trusts with the intention of testing advanced DNA sequencing technology. Led by Guy’s and St Thomas NHS Foundation Trust, the team hope this research will lead to improved technology to support critically ill patients and increase surveillance of existing and emerging pathogens that pose a wider threat to public health.
We connected with Simon Rock, Principal Scientist at North East Innovation Lab, The Newcastle upon Tyne Hospitals NHS Foundation Trust, to learn more about this national pilot.
Credit: North East Innovation Lab
What are the aims of this research?
The aims of the national pilot are to establish whether a rapid pathogen detection service can be established in clinical microbiology labs across England for the benefit of patients in intensive care, and patients suspected of having an infection. We will also test the feasibility of using this data for national biosurveillance. The work at The Newcastle upon Tyne Hospitals NHS Foundation Trust will look at the technical accuracy of the test in Newcastle, and also how the logistics of collecting samples and returning a result the same day could be delivered in practice.
Can you tell us more about the metagenomics technology you’re piloting?
Metagenomics enables fast and accurate testing to identify any pathogens in a patient sample with a single test. In the national pilot program, researchers are using long-read nanopore sequencing to detect all bacteria, viruses, and fungi in patients suspected of infection.
To focus on pathogens, human DNA is removed from the sample, leaving only non-human genetic material (DNA/RNA). This material is then run through a nanopore, where each genetic base causes a specific electrical change as it passes through. By reading these electrical signals, the sequence of the genetic material is revealed. The data is then analyzed to identify the organisms present and even detect genes that might make them resistant to antibiotics. This technology offers high accuracy and can identify multiple pathogens at once.
What are the potential applications of this technique?
Potential applications of this approach include rapid identification of infection-causing pathogens in patient samples without requiring multiple tests. This would ensure appropriate treatments reached patients at a faster rate.
Additionally, this metagenomic technology opens avenues in pathogen surveillance, allowing clinicians to monitor the spread of existing pathogens that could pose wider public health risks, track changes in antibiotic resistance, and identify new, emerging pathogens.
With wider rollout, this test could provide more targeted and timely delivery of diagnosis and treatment to critically ill patients.
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