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DNA testing device to improve urinary infection treatment

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Urinary tract infections could be treated more quickly and efficiently in future using a DNA sequencing device the size of a USB stick, according to UK researchers.

They used a new device to perform sequencing and characterise bacteria from urine samples four times more quickly than using traditional methods of culturing bacteria.

The new technology could also detect antibiotic resistance, said the researchers from the University of East Anglia.

“The old approach of using an ever broader range of antibiotics is no longer viable, given the shortage of new drugs”

Justin O’Grady

Professor David Livermore, from the university’s Norwich Medical School, noted that urinary tract infections were among the commonest reasons for antibiotic prescribing.

Though most infections were mild, he highlighted that serious cases of urosepsis could be fatal and that there were over 30,000 cases of Escherichia coli bloodstream infection recorded in England in 2014 – mostly with a urinary origin.

“Antibiotics are vital, especially if bacteria has entered the bloodstream, and must be given urgently,” he said. “Unfortunately it takes two days to grow the bacteria in the lab and test which antibiotics kill them.”

He added that, as a result, clinicians often initially prescribed a broad range of antibiotics that were then adjusted once the lab results came through.

“This ‘carpet-bombing’ approach represents poor antibiotic stewardship, and it is vital that we move beyond it,” he said.

The researchers used a new small DNA sequencing device – called Nanopore MinION from Oxford Nanopore Technologies – to investigate UTIs quickly, without culturing the bacteria.

“Swift results like these will make it possible to refine a patient’s treatment much earlier”

Justin O’Grady

Fellow study author Dr Justin O’Grady said: “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,” he said. “Swift results like these will make it possible to refine a patient’s treatment much earlier.”

However, he noted there were “still challenges” for the technology, but said it was likely they could be overcome.

“The approach is currently best suited to difficult cases, whereas improving hospitals’ antibiotic stewardship requires new diagnostics to be deployed widely,” he said.

“Our method currently only works with heavily-infected urine and can’t yet predict those resistances that arise by mutation,” he added.

“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,” said Dr O’Grady.

The study findings were unveiled over the weekend at an international conference in San Diego, run jointly by the American Society for Microbiology and the International Society of Chemotherapy.

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