Researchers using DNA sequencing to profile
antibiotic resistance in infection have achieved a
turnaround time from 'sample to answer' of less than
four hours for urinary tract infections (UTIs).
The nanopore MinION device is being researched by
the University of East Anglia (UEA) as a way to
speed up investigation of infection including UTIs –
one of the most common reasons patients are
Traditional culture methods take two to three days
to characterise bacteria and test their
antimicrobial resistances from a urine sample. Early
results from the UEA group’s method showed that the
Oxford Nanopore Technologies device can characterise
bacteria and predict their antimicrobial resistances
in just 12 hours from a urine sample.
This has now been shortened to as little as four
hours, as published in the Journal of Antimicrobial
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.
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
“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.”
Dr Justin O’Grady from Norwich Medical School said:
“This study is the first to use MinION sequencing to
rapidly diagnose pathogens and antimicrobial
resistance in clinical samples, without growing
them. Improvements in the sequencing technology,
data analysis and sample preparation mean we've
reduced the turnaround time to four hours.
“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.”
In the study, human cells were removed from
patients' urine samples, then the bacteria were
recovered and their DNA was sequenced by MinION.
Sequences were analysed and the results compared
with standard culture and antibiotic susceptibility
Dr O’Grady said: “Both the type of bacteria and the
acquired resistance genes were identified reliably,
agreeing with conventional laboratory testing.
“Challenges remain, though. The approach is
currently best suited to difficult cases, but
improving hospitals' antibiotic stewardship requires
new diagnostics to be deployed widely.
“Our method currently requires heavily-infected
urine and our rapid analysis can't yet predict those
resistances that arise by mutation – changes to
existing genes. But the technology is developing
rapidly and we expect to overcome these limitations
in the near future."
Faster resistance analysis for patients with blood
For more information
The Journal of Antimicrobial Chemotherapy
ID of bacterial pathogens and antimicrobial
resistance directly from clinical urines by
nanopore-based metagenomic sequencing
The University of East Anglia
Oxford Nanopore Technologies