Urinary tract infections are among the most common reasons for prescribing antibiotics. 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. But it also means that a growing number of patients with bacteria which is resistant even to a broad range of drugs, go undertreated. Sometimes this can be fatal.
Researchers used a 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.
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.
The new method can also detect antibiotic resistance - allowing patients to be treated more effectively and improving stewardship of diminishing antibiotic reserves.
Both the type of bacteria and its acquired resistance genes were identified reliably, agreeing with resistance profiles found by conventional laboratory testing.