Same Day DNA Sequencing-Based Test Identifies Secondary Infections in COVID-19 Patients

The DNA sequencing-based test developed by researchers at Guy’s and St Thomas’ (London, UK) was evaluated by doctors in the ICU at St Thomas’ Hospital with 34 ICU patients during the first COVID-19 pandemic wave. The study showed how this rapid test will ensure patients get the right antibiotic faster, while also minimizing unnecessary antibiotic prescriptions to reduce the risk of antimicrobial resistance. The tests were evaluated for COVID-19 patients and shown to identify both bacterial and fungal infections and identify outbreaks with resistant bacteria within 24 hours. This is particularly important for COVID-19 patients who are highly susceptible to secondary infection and outbreaks.

When critically ill patients are cared for in the ICU, doctors take deep samples from their lungs. Currently, these samples are often sent to multiple labs where different bacterial and fungal cultures are set up alongside other complex molecular tests. Initial results take two to four days to return. During this time the patient often remains on standard antibiotic treatment, some of which may be unnecessary. In other patients, the treatment may be ineffective, as the bacteria has resistance genes to the standard antibiotics. The new same-day service uses cutting edge Nanopore sequencing technology to identify all bacterial and fungal pathogens present in patients’ samples, as well as any resistance genes present. The advance means that unnecessary treatment can be reduced, and patients can benefit from starting the right treatment sooner. The following day, the same test provides enough genetic sequence to compare pathogen genomes with a database that accurately identifies patients carrying the same strain so outbreaks can be detected at the very start. This is the first time this combined benefit of a single test has been demonstrated.

“As soon as the pandemic started, our scientists realized there would be a benefit to sequencing genomes of all bacteria and fungi causing infection in COVID-19 patients while on ICU,” said Professor Jonathan Edgeworth, Director of the Centre for Clinical Infection and Diagnostics Research (CIDR) and Medical Director of Viapath, who led the research. “Within a few weeks 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 revolutionize 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.”

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