DNA sequencing USB stick-sized device can help treat urinary infections

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Published: September 21, 2015 10:55:39 PM

A DNA sequencing device the size of a USB stick can help treat urinary tract infections (UTIs) more quickly and efficiently, scientists say.

A DNA sequencing device the size of a USB stick can help treat urinary tract infections (UTIs) more quickly and efficiently, scientists say.

Researchers from the University of East Anglia, UK, used the new device called MinION to perform nanopore sequencing to characterise bacteria from urine samples four times more quickly than using traditional methods of culturing bacteria.

The new method can also detect antibiotic resistance, allowing patients to be treated more effectively.

“Urinary tract infections are among the most common reasons for prescribing antibiotics,” said Professor David Livermore, from UEA’s Norwich Medical School.

“These ‘ascending’ UTIs cause a growing burden of hospitalisations, mostly of elderly patients. At worst, infection spills into the bloodstream, leading to a condition called urosepsis, which can be fatal,” Livermore said.

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

“As a result, doctors must prescribe a broad range antibiotics, targeting the bacteria most likely to be responsible, and then adjust treatment once the lab results come through. This means that some patients are over-treated, which of course contributes to the problem of antibiotic resistance,” he said.

Researchers used the device developed by 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 Dr Justin O’Grady, from UEA’s Norwich Medical School.

“Both the type of bacteria and its acquired resistance genes were identified reliably, agreeing with resistance profiles found by conventional laboratory testing.

“Swift results like these will make it possible to refine a patient’s treatment much earlier – and that’s good for the patient, who gets the ‘right’ antibiotic, and for society – which can better manage or ‘steward’ its limited supply of antibiotics.

“This technology is rapid and capable not only of identifying the bacteria in UTIs, but also detecting drug-resistance at the point of clinical need,” said O’Grady.

“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 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,” said O’Grady.

The findings were presented at an international four-day medical conference in San Diego, run jointly by the American Society for Microbiology’s Interscience Conference of Antimicrobial Agents and Chemotherapy (ICAAC) and the International Society of Chemotherapy (ICC).

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