PhD student Nathaniel Wand has developed a method to extract data from images of DNA barcodes, allowing the identification resistance profiles in bacteria such as MRSA from mixed samples, in a much shorter time than traditional diagnostic methods.
A new technique developed by scientists in the Physical Sciences for Health Centre at the University of Birmingham can identify the resistance profile of bacteria in a much shorter time than traditional diagnostic methods. The technique can be used to identify whether the bacteria causing an infection such as MRSA is resistant to certain drugs and antibiotics, and therefore identify treatments most likely to be effective.
By labelling the bacterial DNA at specific points and then imaging a sample of the DNA spread on a surface so that the DNA strands are extended, it is possible to read a ‘DNA barcode’, where the positions of the label reveal the DNA sequence, in the same way as the bars in a barcode provide an identifying pattern.
Currently, when a patient presents with a bacterial infection, the infection is diagnosed by taking a sample from the patient, growing bacteria from it and then using genetic sequencing to identify the type of bacteria present and the presence of markers of resistance. Although considered the gold-standard for diagnosing bacterial infections this process is time-consuming, taking several days to produce the results, and requires specialist equipment and expert laboratory personnel. This means the provision of the most appropriate treatment for a patient can be delayed while their infection is being identified. There is a clear need for techniques that are able to provide the same information in a shorter time period.
Work conducted by PhD student Nathaniel Wand has proven that the DNA barcoding technique is able to identify DNA fragments in a mixed sample, containing segments such as those which provide a marker of resistance in MRSA, which would be very beneficial to identify in a healthcare setting. The time taken to make the identification is currently less than a day, however with further development and streamlining of the technique this will be further reduced.
Project leader Dr Rob Neely says “Nat has developed a method for searching through the DNA barcodes we produce. He’s applied the kind of technology that Google use to compare images to our DNA barcodes and this has made a step-change in the way that we can pull the information we need from a huge dataset. In a hospital, this would mean a doctor is able to search for a specific organism in a DNA sample from the mapping data. It could all be done in a matter of hours from collecting the sample through to diagnosis.”
Our hope is that eventually, the computational analysis designed and developed in this project for extracting information from images of DNA barcodes will contribute to a system able to be deployed in hospitals to aid in the profiling of infections. This will decrease the time taken to identify and deliver beneficial treatments to patients, and therefore improve the treatment of bacterial infections.
