UTI research: DNA sequencing helps to fight UTI

So you have a urinary tract infection (UTI) and go to a doctor. At this point, you are probably in pain and want quick relief. The doctor most likely will prescribe you an antibiotic and take your urine sample to run the tests and confirm that his diagnosis was correct. It takes a couple of days for the lab to grow the bacteria in your sample and test which antibiotics kill them. Most likely you can’t wait that long and therefore you will be prescribed a broad spectrum antibiotic, targeting the bacteria most likely to be responsible, and then the doctor might adjust treatment once the lab results come through. Unfortunately, this approach also means that your doctor is “teaching” your bacteria how to resist antibiotics. And this is where UTI research could help us to change the way we deal with harmful bacteria.

As you might know, every living organism has DNA. Bacteria have DNA as well. This is basically a unique blueprint that makes up the distinguished traits of the living organism. DNA sequencing is a process of uncovering that “blueprint” to identify what characteristics the organism possesses. A research team from the University of East Anglia used a new small DNA sequencing device called Nanopore MinION from Oxford Nanopore Technologies to investigate UTIs quickly – without culturing the bacteria.

“We found that this device, which is the size of a USB stick, could detect the bacteria in heavily infected urine – and provide its DNA sequence in just 12 hours. This is a quarter of the time needed for conventional microbiology,” said one of the researchers, Justin O’Grady.

Within 12 hours the device can tell you what type of bacteria you have and also detect antibiotic resistance – allowing doctors to prescribe the right antibiotics.

“Swift results like these will make it possible to refine a patient’s treatment much earlier – and that is good for the patient, who gets the ‘right’ antibiotic,” O’Grady said.

“There are still challenges to be overcome. The approach is currently best suited to difficult cases, whereas improving hospitals’ antibiotic stewardship requires new diagnostics to be deployed widely.

“Our method currently only works with heavily-infected urine and can’t yet predict those resistances that arise by mutation – changes to existing genes – rather than the acquisition of new resistance genes. However, the technology is developing rapidly, with progressive improvements even during our studies, and it is likely that these limitations can be overcome.

“It is crucial that we do overcome them, because the old approach of using an ever broader range of antibiotics is no longer viable, given the shortage of new drugs, and the growing diversity and complexity of antibiotic-resistant bacteria” he added.

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