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DNA testing may speed up, improve UTI treatment

By Stephen Feller
DNA testing may speed up, improve UTI treatment
Researchers confirmed E.coli in urinary tract infections and detected what antibiotics would be ineffective against the infection in about 12 hours -- a quarter of the time it takes using traditional testing methods. Photo by Oxford Nanopore Technologies

SAN DIEGO, Sept. 21 (UPI) -- Using a new USB-sized device, researchers are able to confirm the presence of bacteria causing a urinary tract infection four times faster than before and determine the best antibiotic for individual patients based on the test results.

The method of detection and testing only works for "heavily-infected urine" at this point, but researchers said the technology is progressing fast enough that they could see improvements during the study.

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Antibiotics are the most common way to treat UTIs. Speeding up the diagnosis and determining treatment options for UTIs will prevent the overuse of antibiotics, which can make some of them less effective, researchers said. Generally, selecting an antibiotic can be guesswork.

"This 'carpet-bombing' approach represents poor antibiotic stewardship, and it is vital that we move beyond it," David Livermore, a professor at the University of East Anglia, said in a press release. "The way to do so lies in accelerating laboratory investigation, so that treatment can be refined earlier, benefiting the patient, who gets an effective antibiotic, and society, whose diminishing stock of antibiotics is better managed."

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The researchers used a device called a MinION to do nanopore testing on 10 urine samples that had been spiked with Escherichia coli bacteria, as well as 10 infected clinical urine samples.

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In the two sets of urines, researchers tested for E.coli and genes that indicated what antibiotics the bacteria would be resistant to. The results of the tests were available in about 12 hours -- roughly a quarter of the time required for traditional lab tests.

In the spiked urine samples, the MinION identified the bacteria and resistance genes that indicated which antibiotic treatments would be least effective against them. In the clinical samples, six of 10 were identified as infected with E.coli. For those that were identified, researchers also were able to determine antibiotic treatments they expect would be effective against the bacteria.

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"Both the type of bacteria and its acquired resistance genes were identified reliably, agreeing with resistance profiles found by conventional laboratory testing," said Dr. Justin O'Grady, a professor at UEA. "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."

There is still work to do, the researchers said, as they can't yet predict genetic mutations of E.coli strains from the tests.

The MinION device, which can be plugged into a laptop using a USB cable, is designed to analyze DNA samples quickly for individualized treatment. It was shown in a study in June to be able to comparatively quickly decipher the full genome of the E.coli bacteria.

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The study was presented at ICAAC/ICC 2015.

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