Testing for bacterial genes – Can it help find early infection in Cystic Fibrosis?
Dr Zina Alfahl and team are carrying out a study in the Children’s CF unit in Galway University Hospital (GUH) to develop tests for bacterial genes in samples from children with CF. The hope is that testing for bacterial genes will help find bacteria causing infection in the lung of people with CF before they can be found with the methods that are generally used at the moment. Dr Alfahl, Lecturer in Bacteriology, University of Galway is leading the study with support from Professor Martin Cormican (Professor of Bacteriology, University of Galway & Consultant Microbiologist, Galway University Hospital) and Dr Mary Herzig (Consultant Paediatrician, Galway University Hospital. They are able to do this study with the support of parents and children who attend the CF clinic in GUH who agreed that we can use leftover material after their usual tests are complete. Thanks also to the staff of the Microbiology Laboratory in Galway University Hospital for storing the leftover material and preparing it for use in the study.
Understanding New Advances in Detecting Lung Infections
CF affects the movement of salt and water in and out of cells, leading to problems with glands that produce mucus, tears, sweat, saliva and digestive juices. Normally, these secretions are thin and slippery, helping to protect the body's tissues. However, in PWCF, these secretions become thick and sticky, making it difficult for them to move through the body. This can clog tubes, ducts and passageways, and also create an environment where bacteria can thrive. Now there are treatments that can correct a lot of the underlying problem with movement of salt and water for many people but they don’t work for everyone and do not solve all the problems.
Why Is This Important?
The thick mucus in PWCF can lead to lung infections that are very difficult to clear. Long-term infection can cause inflammation, lung damage and breathing difficulties. Although CF affects many parts of the body, it is usually the infection and inflammation to the person’s lung that causes most harm. Protecting the lungs of children from CF from infection and finding and treating any bacterial infection before it gets firmly established is therefore a critical part of protecting the health of people with CF.
The Challenge of Detecting Harmful Bacteria
Many types of bacteria normally live in the mouth, nose and throat. These include one Haemophilus influenzae and another called Staphylococcus aureus. Pseudomonas aeruginosa is a bacteria that is very common in the environment and that can also live in the mouth and throat. When these bacteria stay in the nose and throat they usually do no harm. In people with CF bacteria from the mouth and throat can spread more easily into the lower airways and lungs. These bacteria do not belong to the lungs. In the lungs, they can cause infection and inflammation. This can damage the lungs and this damage makes it easier for more infection to follow. Over time this causes increasing breathing difficulties.
Today, most labs test for harmful bacteria in the lower airways by growing bacteria from samples. These tests are useful but they are not perfect. The best samples come directly from the lower airways. Samples from the upper airways are a mix of fluids from the upper and lower airway so it is hard to tell if the bacteria in the sample came from the mouth, throat or the lung. Sometimes bacteria that grow in the lung may not grow in the lab. New treatments such as Kaftrio help to reduce fluids in the airways and make them more normal. This has big benefits but because there is less fluid in the airways it is harder to get a good sample to test for bacteria.
A New Approach: Testing for bacterial genes
In recent years, tests that find bacterial genes without the need to grow the bacteria have become more common. These genetic tests are already used a lot to test for bacteria that cause diseases like tuberculosis as well as many other infection. The PCR test you will have heard so much about during COVID is a test of virus genes. Testing for genes by PCR is often faster than waiting for bacteria to grow and can find bacteria that will not grow at all in the lab. Our research aims to use these advanced genetic methods to test for bacteria that cause infections in the airways of people with CF. Our first step is to develop a test method that works well. The next step will be to see if testing for genes can find infection earlier than the usual method of growing bacterial. The methods we are using does not look at the genes of the person. There is genetic information from the person in the sample but because we use a method that targets the bacterial genes we do not produce any information about the human genes.
How Will This Help?
We hope that this could improve tests to find infection and help start treatment earlier. Early treatment of infection helps protect the lung and means less time in hospital. We also hope that genetic testing will work better on the smaller samples that come from the airways of people on the new treatments.
Would you like to be involved?
This project is only possible with the support of children with CF and their parents who have agreed that we can use the left over material from their sample after the usual tests are finished. We are looking to set up a panel of patients and public to make sure that we take the view the people most affected in the way we carry out the study and the way we report our findings. If you would like to help, please get in touch.
Finally, we would like again to thank the fantastic participants and their parents/guardians, and everyone in the children’s CF clinic and the Microbiology Laboratory in GUH and also Dr Louise O’Connor in University of Galway. We would like to express our heartfelt thanks to all involved in this work so far.