Rapid PCR-Based Test Developed to Detect Pneumonia in Patients with Severe COVID-19

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Researchers have developed a PCR-based test to quickly identify secondary infections in COVID-19 patients, who have double the risk of developing pneumonia while on ventilation than non-COVID-19 patients.

Normally, confirming a pneumonia diagnosis requires growing bacterial samples from patients in a lab, which is time-consuming. The new test uses multiple polymerase chain reactions (PCR) run in parallel, it can identify 52 different pathogens, and can be done in around four hours, without needing to grow the bacteria. It can also test for antibiotic resistance.

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

The test was developed with Martin Curran, a specialist in PCR diagnostics from Public Health England’s Cambridge laboratory. The team included scientists and doctors at the University of Cambridge and Cambridge University Hospitals NHS Foundation Trust. The lead author on the paper is Mailis Mae, and it is featured in a recent issue of Critical Care. https://ccforum.biomedcentral.com/articles/10.1186/s13054-021-03460-5

For patients with the most severe forms of COVID-19, mechanical ventilation is often the only way to keep them alive. However, these patients are susceptible to further infections from bacteria and fungi that they may acquire while in hospital – so called ‘ventilator-associated pneumonia’. These infections are often caused by antibiotic-resistant bacteria, and are hard to diagnose and need targeted treatment.

The new test gives doctors the information they need to start treatment within hours rather than days, fine-tuning treatment as required and reducing the inappropriate use of antibiotics. The test is being rolled out at Cambridge University Hospitals and offers a route towards better treatments for infection more generally.

The UK is experiencing a surge in COVID-19 cases.  About 55,700 people are testing positive on a daily basis, that’s about 555 people per 100,000 residents.  Of these people, about 4,200 are being admitted per day. While the vaccine rollout is ongoing, and more than 3 million people have been vaccinated, the daily infection rate has continued to grow.

“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,” said Morris from Cambridge’s Department of Medicine and an intensive care consultant. “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.”

COVID-19 patients are thought to be at increased risk of infection for several reasons. Due to the amount of lung damage, these severe COVID-19 cases tend to spend more time on a ventilator than patients without COVID-19. In addition, many of these patients also have a poorly-regulated immune system, where the immune cells damage the organs, but also have impaired anti-microbial functions, increasing the risk of infection.

“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,” said Maes, also from the Department of Medicine. “This means that standard antibiotic protocols can be applied to COVID-19 patients.”

This is one of the first times that this technology has been used in routine clinical practice and has now been approved by the hospital. The researchers anticipate that similar approaches would benefit patients if used more broadly.

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