MinION used to identify pathogen and antimicrobial resistance in less than four hours

A paper published today by researchers at the University of East Anglia (UEA) uses the MinION DNA sequencer to characterise pathogens and profile antibiotic resistance in infection within four hours from an original urine sample.

In the paper, published today in the Journal of Antimicrobial Chemotherapy, the researchers have achieved a turnaround time from 'sample to answer' of less than four hours for urinary tract infections (UTIs). In a press release the researchers compare this to traditional methods that “take two to three days to characterise bacteria and test their antimicrobial resistances from a urine sample…” Dr Justin O’Grady from UEA said “Getting results this fast would allow clinicians to adjust antimicrobial very early, even before the second dose is given – most antibiotics are given around once every eight hours.”

The research team also note:

“While most UTIs are mild, serious cases can lead to hospitalisation. At worst, bacteria can enter the bloodstream causing urosepsis, a life-threatening condition. In this case antibiotics are vital and must be given urgently.

Faster prediction of whether the UTI is caused by a highly-resistant type of bacteria will allow precise tailoring of treatment. The patient will get an antibiotic that is sure to be active against their pathogen, and society's limited antibiotic resource will be better managed. This will help in the fight against increasing antibiotic resistance, one of the biggest challenges facing society today.

As highlighted in the O’Neill report in May of this year, overuse of antimicrobials and the resulting increase in antibiotic resistance could - if all antibiotics fail - lead to the loss of 10 million lives a year by 2050 if no action is taken. This government-commissioned report stresses the potential of rapid diagnostics to improve both treatment and antibiotic stewardship and called on the governments of the richest countries to “mandate now that by 2020, all antibiotic prescriptions will need to be informed by up-to-date surveillance information and a rapid diagnostic test wherever one exists”.

Prof David Livermore from UEA’s Norwich Medical School said: “Identifying specific pathogens and resistance to antibiotics as quickly as possible is the key to reducing the number of patients who are ‘over treated’ with broad-spectrum antibiotics while waiting for results to come through from the micro lab – a process that presently takes a couple of days'.

“This 'carpet-bombing' approach -of giving a broad spectrum antibiotic whilst you wait for results -leads to poor antibiotic stewardship. It's vital that we move beyond it. The way to do so lies in accelerating lab investigation. That way, treatment can be refined earlier. This will benefit the patient, who gets an effective antibiotic, and society, whose diminishing stock of antibiotics is better managed.”

Oxford Nanopore is developing an analysis workflow to support any researcher characterising anti microbial resistance. Read about it here.