Antimicrobial resistance (AMR) is recognised to be a major threat to modern medicine. Better and faster diagnostic tests are key to improved treatment of infections. However, identification of what bacteria or virus (pathogen) is causing the disease and what antimicrobial treatment to use is complex, typically requiring days to weeks and involving multiple steps.
In contrast, pathogen sequencing (looking at the DNA) can identify what pathogen is present, whether it can be treated or not and whether it is similar to any other pathogens that have been seen previously. Sequencing can do this quickly, potentially within hours.
The Infectious Disease group at Oxford, supported by the Biomedical Research Centre (BRC), is working towards overcoming problems to use of sequencing for diagnosis by developing methods to get bacterial or viral DNA from a sample, rather than waiting for it to grow. We wish to establish a use of computers to look at health records and sequence data so medical doctors can use results directly to treat patients. For this, we aim to identify whether a bacteria or virus is present that could cause the patient symptoms. If so, can we identify whether antibiotics could be used. As antibiotics do not work on viruses, this reduces the number of antibiotics prescribed which is important to reduce antimicrobial resistance. A previous study funded by the BRC showed that a reduction in use of a particular antibiotic reduced infections by a type of Clostridium difficile.
In the new BRC programme we aim to sequence as fast as possible directly from a sample. This requires improvement of laboratory methods to extract pathogen DNA from a sample without growing the bacteria and to remove any human DNA that may be present. It also includes methods to reduce the total amount of DNA needed to sequence. Once DNA is obtained from cells, the group uses computer programs to look at the sequence quickly and accurately. Our researchers aim to create new ways to detect infections from this DNA data and work with specialists in other disciplines to modify and expand computational methods. Combining these data with electronic health records allows doctors to detect whether pathogens are increasing within the hospital or community or whether new ones are causing infections. We aim to find out whether bacteria are resistant or more capable of causing serious disease (virulent). This improves treatment and helps England’s health system monitor what infectious diseases are present (national surveillance).
Lecture by Derrick Crook, Professor of Microbiology and Consultant Physician, about how our hospitals are working hard to reduce infection and what that means for patients and healthcare staff. He explains how his team are tracking patients and the history of their treatment over time in the hospital by retrieving and using old records. They are also tracking the progress of different bugs over a number of years.