̽��ֱ�� of Cambridge - pneumonia

DNA test can quickly identify pneumonia in patients with severe COVID-19, aiding faster treatment

sc604 — Fri, 15 Jan 2021 06:00:00 +0000

For patients with the most severe forms of COVID-19, mechanical ventilation is often the only way to keep them alive, as doctors use anti-inflammatory therapies to treat their inflamed lungs. However, these patients are susceptible to further infections from bacteria and fungi that they may acquire while in hospital – so called ‘ventilator-associated pneumonia’.

Now, a team of scientists and doctors at the ̽��ֱ�� of Cambridge and Cambridge ̽��ֱ�� Hospitals NHS Foundation Trust, led by Professor Gordon Dougan, Dr Vilas Navapurkar and Dr Andrew Conway Morris, have developed a simple DNA test to quickly identify these infections and target antibiotic treatment as needed.

̽��ֱ��test, developed at Addenbrooke’s hospital in collaboration with Public Health England, 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. This approach, based on higher throughput DNA testing, is being rolled out at Cambridge ̽��ֱ�� Hospitals and offers a route towards better treatments for infection more generally. ̽��ֱ��results are reported in the journal Critical Care.

Patients who need mechanical ventilation are at significant risk of developing secondary pneumonia while they are in intensive care. These infections are often caused by antibiotic-resistant bacteria, and are hard to diagnose and need targeted treatment.

“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 co-author Dr Andrew Conway 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.

Normally, confirming a pneumonia diagnosis is challenging, as bacterial samples from patients need to be cultured and grown in a lab, which is time-consuming. ̽��ֱ��Cambridge test takes an alternative approach by detecting the DNA of different pathogens, which allows for faster and more accurate testing.

̽��ֱ��test uses multiple polymerase chain reaction (PCR) which detects the DNA of the bacteria and can be done in around four hours, meaning there is no need to wait for the bacteria to grow. “Often, patients have already started to receive antobiotics before the bacteria have had time to grow in the lab,” said Morris. “This means that results from cultures are often negative, whereas PCR doesn’t need viable bacteria to detect – making this a more accurate test.”

̽��ֱ��test – which was developed with Dr Martin Curran, a specialist in PCR diagnostics from Public Health England’s Cambridge laboratory – runs multiple PCR reactions in parallel, and can simultaneously pick up 52 different pathogens, which often infect the lungs of patients in intensive care. At the same time, it can also test for antibiotic resistance.

“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 lead author Mailis 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. ̽��ֱ��researchers anticipate that similar approaches would benefit patients if used more broadly.

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

Reference:
Mailis Maes et al. ‘Ventilator-associated pneumonia in critically ill patients with COVID-19.’ Critical Care (2021). DOI: 10.1186/s13054-021-03460-5

Researchers have developed a DNA 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.

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

Andrew Conway Morris

Official U.S. Navy Page

Lt. Cmdr. Michael Heimes checks on a patient connected to a ventilator at Baton Rouge General Mid City campus

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Towards a ‘super-vaccine’ for swine bacterial diseases

bjb42 — Mon, 01 Mar 2010 09:27:59 +0000

Among the most serious diseases in pigs are those that are caused by bacteria that live in their throats, airways or tonsils and can cause severe lung infections such as pneumonia. Infected animals either die quickly or fail to grow normally, resulting in substantial economic costs to the worldwide pig industry and adding to food security concerns. Because the infections are difficult to diagnose, and current vaccines have limited efficacy, antibiotics are now in widespread use in efforts to reduce infection.

A new five-year, £5.6 million grant awarded by the Biotechnology and Biological Sciences Research Council (BBSRC) under its strategic longer and larger grant (LoLa) scheme, which supports research projects requiring ‘big’ science approaches and longer timescales, aims to develop a new vaccine and a diagnostic tool to combat the four most common bacteria that cause infections in pigs.

̽��ֱ��grant has been awarded to a consortium of researchers at the ̽��ֱ�� of Cambridge, Imperial College London, the London School of Hygiene and Tropical Medicine, and the Royal Veterinary College, as well as Huazhong Agricultural ̽��ֱ�� in China, and involves three UK government-funded agencies. ̽��ֱ��consortium also receives support from Pfizer Animal Health.

‘This combined expertise has generated a new opportunity that is highly synergistic and where real progress is possible,’ said Professor Maskell, Head of the Department of Veterinary Medicine and leader of the Cambridge component. ‘It’s also a perfect marriage between fundamental biological research and applied clinical outcomes.’

‘As a first step, we are isolating bacteria from pigs and assembling the largest ever sequenced collection of these types of bacteria,’ explained co-investigator Dr Dan Tucker. ‘From this, we’ll design and assemble appropriate super-vaccines and single-platform diagnostic tests. Crucially, these will immunise and test pigs for all four pathogens at the same time.’ In the final year of the project, field trials will be carried out in China, where dedicated facilities for this type of work are already set up.

Commenting on the timeliness of the BBSRC funding, Professor Maskell added: ‘Technical innovations and the availability of genome data have progressed to such an extent, and continue to do so, that only recently has it become possible to embark on this type of programme to find effective vaccines and diagnostics.’

For more information, please contact Professor Duncan Maskell (djm47@cam.ac.uk), Marks & Spencer Professor of Farm Animal Health, Food Science and Food Safety at the Department of Veterinary Medicine (www.vet.cam.ac.uk/).

A new multidisciplinary research programme aims to develop a single vaccine that will combat four major respiratory pathogens of pigs.

It’s a perfect marriage between fundamental biological research and applied clinical outcomes.

Professor Duncan Maskell

̽��ֱ��Pug Father from Flickr

Prize Pig

Biotechnology and Biological Sciences Research Council

̽��ֱ��Biotechnology and Biological Sciences Research Council (BBSRC) is the UK’s principal research funder across the biosciences. Its current Chair is Sir Tom Blundell, who is also Director of Research and Emeritus Professor in Cambridge’s Department of Biochemistry.

Over the past decade, BBSRC has helped achieve a step change in bioscience. Descriptive, single-problem research is increasingly being replaced by generic, predictive and systems approaches, informed by the physical, computational and social sciences. ̽��ֱ��result is that the UK has kept its world-lead in fundamental bioscience, and enhanced its capability to generate the new knowledge needed to tackle global challenges such as food security, sustainable energy and healthier ageing.

BBSRC research at Cambridge exemplifies this combination of excellence and impact. A grants and fellowships portfolio of over £50 million supports research in more than 20 departments, ranging from predictive modelling of disease epidemiology, the role of short interfering RNAs in cell regulation, data standards and software for macromolecular analysis, to mechanisms of predator vision and defensive colouration in birds. BBSRC also funds around 100 postgraduate research students including some registered with the ̽��ֱ�� at the Babraham Institute.

Cambridge hosts one of six programmes that comprise the BBSRC Sustainable Bioenergy Centre, which is a £26 million investment bringing together academics and industry to investigate sustainable methods for producing biofuels. Dr Paul Dupree in the Department of Biochemistry leads the Cambridge programme, with partners at Newcastle ̽��ֱ�� and Novozymes A/G, which seeks to improve the release of sugars from plant cell walls. An important resource for the Dupree lab, and many others across Cambridge, has been the protein-analysis capabilities of the Cambridge Centre for Proteomics, a long-term recipient of BBSRC funding.

Research projects requiring ‘big’ science approaches and longer timescales are supported by BBSRC under its strategic longer and larger (LoLa) grant scheme. One such grant to develop a pig super-vaccine was recently awarded to a consortium of researchers based at five universities, including Cambridge’s Department of Veterinary Medicine.

Ways to improve the manufacturability of viral vectors for therapeutics are currently being pursued with funding from the BBSRC-led Bioprocessing Research Industry Club.

BBSRC-funded research at Cambridge has also turned into notable innovations. One example is the massively parallel Solexa sequencing technology invented by Professor Shankar Balasubramanian and Professor David Klenerman in the Department of Chemistry, resulting in the spin-out company Solexa, which was purchased by Illumina for $600 million in 2007. ̽��ֱ��technology is revolutionising bioscience by improving the cost and speed of DNA sequencing by 1,000–10,000 fold on previous technologies. In recognition of this work, Professor Balasubramanian was recently named BBSRC Innovator of the Year 2010.

For more information and to download the BBSRC 2010–2015 Strategic Plan, please visit www.bbsrc.ac.uk/

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