Every year 700,000 people die of resistant infections, in particular
hospitalized patients; and the problem seems to be growing.
Taking antibiotics to fight an infection won't necessarily solve your
problems. Often, natural occurring bacteria in the gut harbor several
resistance genes. This means that the gut bacteria may exchange genes
with the infectious bacteria, resulting in antibiotic resistance.
‘With poreFUME, researchers will get an overview of the resistome in one-two days, and, hence, be able to start the treatment of the infection sooner and with better results than before.’
Therefore, knowing the resistome - i.e. the pool of resistance genes
present in the gut microbiota - can improve treatment immensely. Today, getting resistome-data from a patient takes weeks. In the
meantime, the resistome profile might change dramatically, and the
patient will suffer from failing health.
Now researchers from The Novo Nordisk Foundation Center for
Biosustainability - DTU Biosustain - at Technical University of
Denmark have developed a super-fast cheap method called poreFUME that
can shed light on the pool of resistance genes in the gut.
"With this method, you will get an overview of the resistome in one-two
days, and, hence, be able to start the treatment of the infection sooner
and with better results than before," says Eric van der Helm, Postdoc
at The Novo Nordisk Foundation Center for Biosustainability - DTU
Biosustain - at Technical University of Denmark.
The research has recently been published in the journal Nucleic Acid Research
The poreFUME method using nanopore sequencing is very rapid compared
to current methods, because it doesn't require growth of the fecal
bacteria, which takes time and can be difficult. Also, the data from the
device is streamed in real time, so the user doesn't need to wait until
the end of a 'run' to access information about the experiment.
patients, a quick assessment of their personal pool of resistance genes
in their feces can be lifesaving.
"Our research shows, that this method provides a promising
alternative to other sequencing methods and that it can be used to
rapidly profile the resistome of microbial communities in for instance
the gut. We are quite convinced, that rapid resistome profiling could
lead to personalized antibiotic treatment in high risk patients," says
Professor and co-author Morten Sommer from DTU Biosustain.
The study was carried out as a collaboration between DTU and
co-author Dr. Willem van Schaik from the University Medical Center
Utrecht, who provided access to an intensive care unit patient (ICU).
In this study, five feces samples from the ICU patient were
assessed. After lung transplantation surgery, due to Chronic obstructive
pulmonary disease (COPD), the patient was treated with four different
kinds of antibiotics to prevent and fight infections. Samples were
collected both upon admission to intensive care unit, during stay and
several months after hospitalization.
The results showed that the poreFUME method was 97% accurate, when
compared to standardized resistome profiling methods. This percentage is
sufficient when measuring the resistome.
Furthermore, the poreFUME method is much cheaper than current
methods, primarily due to the low cost of the so-called MinION; a small
handheld DNA-sequencing device, which scientists can start to use for
1,000 Dollars. In comparison, conventional so-called next generation
sequencing devices are priced at between 50,000 Dollars and 10 million
"If hospitals can purchase equipment for resistome profiling cheaper
than today, it opens up for better profiling of more patients and
hopefully fewer cases of bacterial resistance," says co-author and
Researcher Lejla Imamovic from DTU Biosustain.