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New test slashes wait for secondary infection detection in COVID-19 patients

A same-day test has cut the time taken to identify secondary infections in intensive care COVID-19 patients from four days to within 24 hours.

This research, from the NIHR Guy’s and St Thomas’ Biomedical Research Center (BRC), showed how the rapid new test will ensure patients get the right antibiotic faster, minimising unnecessary prescriptions and reducing the risk of antimicrobial resistance. It will now be rolled out into clinical practice this winter for patients with COVID-19 or influenza in intensive care units (ICUs).

Invasive ventilation, very common in patients with COVID-19 admitted to ICU, can often introduce pathogens into the lungs, causing pneumonia. This carries a high mortality risk and drives up to 70% of antimicrobial prescribing. Consequently, this research is particularly important for COVID-19 patients.

Current practice involves samples taken from patients' lungs being sent to labs where bacterial and fungal cultures are grown and other complex tests undertaken. It can take two to four days to receive results using this approach. During this time patients generally remain on standard antibiotic treatments which are often either unnecessary, due to an absence of bacterial infection, or ineffective if the bacteria are resistant. The new test has been shown to identify both bacterial and fungal infections within 24 hours.

The team - in collaboration with researchers from King’s College London, the Quadram Institute, Viapath and Oxford Nanopore Technologies - developed a DNA sequencing test at St Thomas’ Hospital. The researchers investigated the test in 34 ICU patients, publishing their results in Genome Medicine.

The advanced sequencing technology used by the test allows all bacterial and fungal samples to be identified, as well as any resistance genes, meaning the right treatment can be started sooner. The following day, this same test can compare genomes of pathogens to identify if any patients have the same strain, halting outbreaks at their very beginning. This is the first time this combined benefit of a single test has been demonstrated.

Professor Jonathan Edgeworth, Director of the Centre for Clinical Infection and Diagnostics Research (CIDR), who led the research, said, “As soon as the pandemic started, our scientists realised there would be a benefit to sequencing genomes of all bacteria and fungi causing infection in COVID-19 patients while on ICU. We showed it can diagnose secondary infection, target antibiotic treatment and detect outbreaks much earlier than current technologies – all from a single sample. This will revolutionise our approach to prevention and treatment of serious infection on ICU and we now plan to offer it as a clinical service for COVID-19 and influenza patients this coming winter.”

Dr Andrew Page of the Quadram Institute said: “We have been working on metagenomics technology for the last seven years. It is great to see it applied to patient care during the COVID-19 pandemic, demonstrating how one test can help answer several clinical questions. We are really excited this technology is now in the process of being implemented in one of the best hospitals in the world, to improve patient management and reduce antimicrobial resistance.”

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