DNA test developed in Cambridge can identify secondary infections in Covid-19 patients in hours

A DNA test developed in Cambridge can quickly identify secondary infections in Covid-19 patients, who face double the risk of developing pneumonia while on ventilation compared to those with other conditions.

It is capable of detecting 52 pathogens that often cause infection in intensive care, and can pick up antibiotic resistance. It means targeted antibiotic treatments can be given within hours, rather than days.

Dr Andrew Conway Morris, from the University of Cambridge’s Department of Medicine and an intensive care consultant, said: “Early on in the pandemic we noticed that Covid-19 patients appeared to be particularly at risk of developing secondary pneumonia, and started using a rapid diagnostic test that we had developed for just such a situation.

“Using this test, we found that patients with Covid-19 were twice as likely to develop secondary pneumonia as other patients in the same intensive care unit.”

Mechanical ventilation is often the only way to keep patients with the most severe cases of Covid-19 alive while anti-inflammatory therapies are deployed to treat their inflamed lungs.

But bacteria and fungi that they may acquire in hospital leaves them particularly susceptible to so-called ‘ventilator-associated pneumonia’.

Often these infections are caused by antibiotic-resistant bacteria, making them hard to diagnose and meaning they need targeted treatment.

It is thought that Covid-19 patients are at greater risk of infection due to the amount of lung damage caused by the virus, which means they may spend more time on a ventilator than other patients. Many of these patients may also have a poorly-regulated immune system, where the immune cells damage the organs, and impaired anti-microbial functions.

Pneumonia diagnosis, however, is challenging, as a patient’s bacterial samples must be cultured and grown in the lab in a time-consuming process.

This new technique - developed at the University of Cambridge and Cambridge University Hospitals NHS Foundation Trust, with Public Health England - instead relies on detecting the DNA of pathogens to enable faster and more accurate testing.

It uses multiple polymerase chain reaction (PCR) techniques, which detects the DNA of the bacteria in around four hours, meaning there is no need to wait for them to grow.

Dr Morris said: “Often, patients have already started to receive antibiotics before the bacteria have had time to grow in the lab. This means that results from cultures are often negative, whereas PCR doesn’t need viable bacteria to detect – making this a more accurate test.”

This higher throughput DNA testing is being rolled out at Cambridge University Hospitals and offers a route to better treatments for infection more generally.

The work was led by Professor Gordon Dougan, Dr Vilas Navapurkar and Dr Conway Morris, and it was developed with Dr Martin Curran, a specialist in PCR diagnostics from Public Health England’s Cambridge laboratory.

By running multiple PCR reactions in parallel, it can simultaneously detect 52 different pathogens that often infect the lungs of patients in intensive care, while also testing for antibiotic resistance.

Mailis Maes, also from the Department of Medicine, a lead author of a paper on the test, published in the journal Critical Care, said: “We found that although patients with Covid-19 were more likely to develop secondary pneumonia, the bacteria that caused these infections were similar to those in ICU patients without Covid-19.

“This means that standard antibiotic protocols can be applied to Covid-19 patients.”

Now approved by Addenbrooke’s, it is one of the first times the technology has been used in routine clinical practice.

Similar approaches could benefit patients more broadly, the researchers predict.

This study was funded by the National Institute for Health Research Cambridge Biomedical Research Centre.

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