Compact DNA sequencing device hastens treatment of urinary infections

A new DNA sequencing device the size of a USB stick can treat urinary tract infections, or UTI, more quickly and efficiently, according to scientists. Called Nanopore MinION, the device performs nanopore sequencing to characterise bacteria from urine samples four times more quickly than using traditional methods of culturing bacteria. It can also detect antibiotic resistance, which allows patients to be treated more effectively.

Urinary tract infections are among the most common reasons for prescribing antibiotics, the research team from the University of East Anglia, or UEA, in the UK, said. While most infections are mild and only affect the lower urinary tract, a few are more troublesome, which can cause a growing burden of hospitalisations, mostly of elderly patients.

In worst cases, the study notes that infection can spill into the bloodstream, leading to a condition called urosepsis, which can be fatal. In 2014, there were more than 30,000 cases of Escherichia coli bloodstream infection recorded in England, mostly with a urinary origin.

In the study, the research team used the Nanopore MinION from Oxford Nanopore Technologies to investigate UTIs quickly without culturing the bacteria. They found that the device 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, the team claimed, which will make it possible to refine a patient’s treatment much earlier. In addition to benefitting the patient, this will also be good for the society, since it will lead to better management or stewardship of the limited supply of antibiotics.

According to Professor David Livermore from UEA’s Norwich Medical School, antibiotics are vital to treat UTI. However, he said that it takes two days to grow the bacteria in the lab and test which antibiotics kill.

“As a result, doctors must prescribe a broad range of antibiotics, targeting the bacteria most likely to be responsible, and then adjust treatment once the lab results come through,” he said. Livermore pointed out that because of this, some patients are overtreated, which contributes to the problem of antibiotic resistance. It also means that a growing number of patients with bacteria resistant even to a broad range of drugs go undertreated, which can be fatal. With the new device, these gaps are addressed, the team claimed.

The researchers admit that there are still challenges to be overcome, since the approach is currently best suited to difficult cases. They say that the method currently only works with heavily-infected urine and cannot yet predict those resistances that arise by mutation or changes to existing genes. However, the team claims that technology is developing rapidly with progressive improvements even during studies, and it is likely that these limitations can be overcome.

Contact the writer at feedback@ibtimes.com.au or tell us what you think below.