Reducing antibiotic use and finding alternative treatments.

Where antibiotics are needed, it is important to get the right treatment to fight a specific infection, to reduce prescribing multiple antibiotics back-to-back. Professor Stefano Pagliara, Professor at the University of Exeter, aims to create ways to swiftly establish which antibiotics can work in each case, and how to ensure the treatment permeates the cell quickly and effectively. 

His team at Exeter’s multidisciplinary Living Systems Institute investigates how individual cells react in the presence of particular antibiotics, using microfluidics, microscopy and genomics. He explained: “Pathogens change their behaviour to escape the damaging effects of antibiotics. Traditionally, scientists have examined cells at population level, but to understand what really influences whether an antibiotic can penetrate the cell, or whether it has evolved resistance, we need to be able to capture differences in individual specialised cells, as well as study the response of an entire cell population."

Addressing the overuse of antibiotics is a critical component of combating AMR. Time-poor clinicians are under pressure to prescribe antibiotics, but often lack the evidence needed to help them make swift and accurate decisions. Exeter researchers are working to improve prescribing practices through innovative and evidence-based strategies. 

Professor Robert Beardmore and his team have used mathematical models to examine antibiotic management practices in hospitals and clinics. Through this approach, they uncovered issues in several analyses that inform the design of large-scale clinical trials. They found researchers had used computer models to make important predictions about antibiotics that could be misleading or even wrong. These flawed analyses informed the design of several inconclusive and failed clinical trials that cost millions of pounds. Professor Beardmore said: “This might sound all very academic or theoretical, but it isn’t; it’s a difficult topic

where issues with mathematical modelling need to be communicated to clinicians who do not typically have the background to understand all the ramifications.”

In an example of innovative work to reduce unnecessary antibiotic prescribing, Exeter’s academics worked with a UK health provider to assess the effectiveness of point-of-care testing for patients with an acute sore throat suspected to be Streptococcus A (Strep A). The pilot study found that 39-55 per cent of those who would have been ordinarily prescribed antibiotics according to NICE guidance did not actually require them.

Dr Rob Daniels, a senior clinical lecturer at the University of Exeter, said: “This type of rapid test could be the future – it's much more definitive than symptom scoring, helps us to avoid using antibiotics in viral sore throats and therefore target antibiotics to patients most in need.”

Professor Pagliara’s team has made progress in understanding how antibiotics overcome the complex labyrinth of barriers to penetrate the membrane of a cell, which affects whether they can work effectively. To add even more obstacles, the team discovered that cells in different metabolic states accumulate antibiotics to different extents – meaning they may react to antibiotic treatments very differently. The team also found that bacterial populations contain ‘sleeper cells’ that survive antibiotic treatment by remaining dormant, yet can wake up, and re-infect their host. Tracking individual bacteria that can escape antibiotics through these diverse routes could ultimately help target and eradicate such cells more effectively.

To date, the team has used several fluorescent analogues of the major antibiotic molecules used in the clinic. If the antibiotic penetrates the cell, the bacteria glows under the microscope. Using this technique to understand the chemical properties of drug molecules that accumulate in cells will provide crucial information for pharmaceutical companies, helping them design next-generation antibiotics. Analysing the chemical properties of drug molecules that accumulate in bacterial cells also provides insights that could lead to rapid diagnostic tests, allowing clinicians to quickly identify the most effective antibiotic for each patient. By understanding how antibiotics interact within bacteria, researchers can help develop tools to test patient samples and predict which treatments will work best, reducing trial-and-error in prescribing and improving patient outcomes. 

In the meantime, the team is developing a large interdisciplinary network, with private companies and clinicians, to combine expertise in a One Health approach.

“An important goal is to develop devices that could sit in clinical settings, enabling health professionals in every GP surgery and hospital to quickly test patient samples with several antibiotics. It could establish whether antibiotics will work and if so which to prescribe, with far more certainty that the chosen drug will be effective.” Professor Krasimira Tsaneva-Atanasova, Deputy Vice Chancellor for Research and Impact at the University of Exeter.

As bacterial pathogens evolve incredibly fast, Professor Robert Beardmore’s team use wet lab techniques to gather data on how bacterial genes and genomes respond to antibiotic treatments. This rapid evolution means they can increase resistance to antibiotics in just a week of treatment. These studies uncover some unusual findings too, including finding  that antibiotics can, in fact, harbour benefits to bacteria when they are treated. That recent study showed so-called ribosome-binding antibiotics provide benefits to bacteria when it is severely stressed due to a lack of nutrients needed for growth.

The team found that using a combination of more than one antibiotic can lead to a higher bacterial load than just one, work that was highlighted by Michal Laub for the Massachusettes Institute of Technology as a “beautiful demonstration of how easily our initial intuition can lead us astray”. They also won a Vivli Innovation Prize, funded by Pfizer, Vivli and Wellcome, for work showing that the variation in numbers that determine patient treatment recommendations could be harmonised, using artificial intelligence approaches.

Increasingly, antibiotics fail to work. A growing number of infections, including pneumonia, tuberculosis, gonorrhea, and salmonellosis, are becoming harder to treat, resulting in higher death rates, longer hospital stays and higher costs.  

“This is an urgent global problem, and we need alternatives to antibiotics to fight infections,” said Professor Ben Temperton, at the University of Exeter. He is one of a network of researchers at Exeter studying phage therapy. Bacteriophages are viruses that infect bacteria, and the Exeter team is now exploring whether they can be used to render an infection harmless. Phage therapy was first used successfully in 1919, yet despite early promise, research dried up in the West in the 1940s as the world began to adopt the quick medical fix of antibiotics. Now, phage research is resurging as part of the solution to antibiotic resistance.

More research is still needed to understand just how phage behave and how to make treatment more effective, which is a gap being addressed at Exeter. “Phages are incredibly good at killing bacteria,” said Dr Stineke Van Houte, Biotechnology and Biological Sciences Research Council (BBSRC) – UKRI Future Research Fellow at the University of Exeter. “Some scientists have already seen success in single patients, where phages have killed an infection in a patient with a heart condition when antibiotics have failed – but there is a long way to go before we might see this approach used in routine care. We are taking on some of the challenges of understanding phage better, towards that goal.”

Like the human immune system, some bacteria have their own CRISPR defence system, made up of proteins that fight off infection. As in human immune responses, this means that the virus infects the bacteria and is then killed. In the process, the bacteria’s CRISPR system learns to recognise and attack the virus in future.

However, bacteria have a second defence. They can also change their own cell surface to ward off infection, losing the receptor to which phages normally attach. Yet, unlike in CRISPR-based resistance, this cell surface defence comes with a cost to the development of the bacteria - the bacteria become less virulent, meaning they no longer cause disease, or the disease becomes less severe.  

Professor Edze Westra said: “Although the bacteria have fought off the virus, they are now less harmful. The question is, can we manipulate which defence mechanism the bacteria deploy?”

In findings published in Nature, which helped Professor Westra win both the 2020 Philip Leverhulme Prize and the 2020 Fleming Award, the team found that a number of variables are crucial, including the complex surrounding microbiome. By manipulating this in the lab, they found that the cell is more likely to implement its CRISPR defence in natural environments such as in living creatures than in previous lab experiments. 

The team is now investigating further how they can manipulate the defence mechanisms of cells, in a £4.6 million project funded by the Biotechnology and Biological Sciences Research Council (BBSRC).  

If bacteria do develop CRISPR immunity against a bacteriophage, Professor Westra and Dr Van Houte have discovered how phages can employ a new weapon in their armoury against the bacteria. In research published in Cell, they described experiments in which bacteria were killed by using phages that encode “anti-CRISPR” genes that target the bacterial immune response – although the phages need to be applied in high doses.

The team is working with scientists at the University of Liverpool to study the efficacy of phage in mice which are colonised by the bacterium Pseudomonas aeruginosa, which frequently leads to infection in the lungs of cystic fibrosis patients, in whom it is the leading cause of morbidity and death. 

Professor Westra concluded: “I certainly think phage will one day be used routinely in medicine in the UK. As we are working with living organisms, it will be much more complex than antibiotics currently. I would expect phage to make up part of the picture of treating infection, but it will not be a silver bullet'.”

Amid the vast array of both phage and bacteria, matching the right phage which can effectively treat infection is key. Professor Ben Temperton has amassed a huge library of phage, each documented to the bacteria it can kill. The library was built in part via a citizen science project which saw school children across the UK collecting samples from puddles and other sources.

As the UK government changes regulations to enable desperately needed clinical trials into phage, the library is uniquely positioned to work with the NHS – and has already exported samples to several countries. “It’s a really exciting time. Phage therapy has certainly been under-recognised, but combined with the research capacity of the NHS, there is so much potential to find a new way of treating infection,” Professor Temperton said.