Oxford Nanopore and Guy’s and St Thomas’ NHS Foundation Trust showcase a world-first collaboration in infectious disease

Successful pilot programme results in government funding to embed rapid pathogen genomic sequencing capability into clinical research settings to improve patient outcomes and biosecurity.

Oxford Nanopore Technologies today announced the completion and expansion of a successful pilot programme lead by a collaboration from across the genomics sector to deliver a respiratory metagenomics service with an integrated respiratory infection and biosecurity application. With a visit to the programme at Guy’s and St Thomas’ NHS Foundation Trust (GSTT) by the Deputy Prime Minister Oliver Dowden, the government announced the funding to expand sequencing capabilities across a consortium of NHS hospital sites. This world-first programme combines effective infectious disease management with rapid emerging pathogen detection and notification.

A three-year pilot, led by GSTT in partnership with Oxford Nanopore Technologies, and a cross-sector taskforce, to inform future implementation of rapid identification and analysis of pathogens in an NHS Intensive Care Unit environment using nanopore sequencing technology has been successfully completed. The pilot developed workflows to enable the rapid characterisation of all pathogens and their antimicrobial resistance in respiratory samples, leading to not only improved patient outcomes, but also providing an early detection mechanism for emerging pathogens. Nanopore sequencing was shown to be ideal for this rapid, accurate, targeted service in a research laboratory close to the clinical setting.

In a paper published recently in the American Journal of Respiratory and Critical Care Medicinei the study team found integrating sequencing technology into critical care led to rapid, targeted treatment decisions based on comprehensive insights of the pathogen(s) and drug resistance. Based on this almost half of patients had their antibiotics altered on the first day, the study authors reported a median turnaround time from sample to result of just 6.7 hours. Not only does this deliver a significant impact for clinical management, it is also anticipated to show important health system benefits in a forthcoming health economic assessment.

Metagenomic sequencing of the respiratory samples also revealed a hidden burden of infections in routinely admitted, seriously unwell sepsis patients, undetected by traditional microbiology, which can fundamentally improve management of patients with prolonged intensive care unit stays. Each year, sepsis claims around 31,000 lives and costs the NHS in England about £2 billionii.

A final crucial finding was that roughly 3% of pathogens identified by sequencing in critical care resulted in notification to infection control and public health bodies, such as UKHSA, driving a novel surveillance function for emerging infections.

Dr Emma Stanton, SVP Clinical, Oxford Nanopore Technologies, commented:

“We are delighted that this pilot collaboration has been so successful. Building sequencing capabilities across intensive care units in the UK lays the groundwork for the world’s first integrated, national respiratory metagenomics and public health detection system and could have profound implications for the navigation of future infectious diseases.”

There is a pressing public health need for greater pandemic preparedness, especially due to a 5-25% chance of another pandemic within the next 10 yearsiii. There is currently low visibility of antimicrobial resistance in pathogens and of new viral pathogens, which is made more challenging by imprecise, slow methods of characterising infections in critical care.

The full Department of Science, Innovation and Technology announcement can be found here.

Editorial to the recent AJRCCM paper


i Routine Metagenomics Service for Intensive Care Unit Patients with Respiratory Infection

ii New action to reduce sepsis

iii HM Government National Risk Register 2023