One step closer to personalized antibiotic treatment

February 10, 2017

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. Therefore, knowing the resistome -- i.e. the pool of resistance genes present in the gut microbiota -- can improve treatment immensely.

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 1-2 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 faecal 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.

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.

Every year 700,000 people die of resistant infections, in particular hospitalized patients; and the problem seems to be growing. For many 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 hospitalisation.

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 Dollars.

"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.
-end-


Technical University of Denmark

Related Antibiotics Articles from Brightsurf:

Insights in the search for new antibiotics
A collaborative research team from the University of Oklahoma, the Memorial Sloan Kettering Cancer Center and Merck & Co. published an opinion article in the journal, Nature Chemical Biology, that addresses the gap in the discovery of new antibiotics.

New tricks for old antibiotics
The study published in the journal Immunity reveals that tetracyclines (broad spectre antibiotics), by partially inhibiting cell mitochondria activity, induce a compensatory response on the organism that decreases tissue damage caused during infection.

Benefits, risks seen with antibiotics-first for appendicitis
Antibiotics are a good choice for some patients with appendicitis but not all, according to study results published today in the New England Journal of Medicine.

How antibiotics interact
Understanding bottleneck effects in the translation of bacterial proteins can lead to a more effective combination of antibiotics / study in 'Nature Communications'

Are antivitamins the new antibiotics?
Antibiotics are among the most important discoveries of modern medicine and have saved millions of lives since the discovery of penicillin almost 100 years ago.

Hygiene reduces the need for antibiotics by up to 30%
A new paper published in the American Journal of Infection Control (AJIC), finds improved everyday hygiene practices, such as hand-washing, reduces the risk of common infections by up to 50%, reducing the need for antibiotics, by up to 30%.

Antibiotics: City dwellers and children take the most
City dwellers take more antibiotics than people in rural areas; children and the elderly use them more often than middle-aged people; the use of antibiotics decreases as education increases, but only in rich countries: These are three of the more striking trends identified by researchers of the NRW Forschungskolleg ''One Health and Urban Transformation'' at the University of Bonn.

Metals could be the link to new antibiotics
Compounds containing metals could hold the key to the next generation of antibiotics to combat the growing threat of global antibiotic resistance.

Antibiotics from the sea
The team led by Prof. Christian Jogler of Friedrich Schiller University, Jena, has succeeded in cultivating several dozen marine bacteria in the laboratory -- bacteria that had previously been paid little attention.

Antibiotics not necessary for most toothaches, according to new ADA guideline
The American Dental Association (ADA) announced today a new guideline indicating that in most cases, antibiotics are not recommended for toothaches.

Read More: Antibiotics News and Antibiotics Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.