One Step Closer to Personalized Antibiotic Treatment

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.

Eric van der Helm, Lejla Imamovic, Mostafa M. Hashim Ellabaan, Willem van Schaik, Anna Koza, Morten O.A. Sommer.
Rapid resistome mapping using nanopore sequencing.
Nucleic Acids Res 2017 gkw1328. doi: 10.1093/nar/gkw1328.

Most Popular Now

HIMSS IMPACT Big Data in Medicine

20 - 21 Novemebr 2017, Potsdam, Germany. Big Data looks set to become a game-changer for healthcare and is likely to have a groundbreaking effect in all areas - from health...

The Digital Revolution in Medicine is Ta…

13 - 16 November 2017, Düsseldorf, Germany. The MEDICA HEALTH IT FORUM at the world’s leading medical trade fair, MEDICA 2017, taking place in Düsseldorf with over 5,000 exhibitors, offers an...

FDA Selects Participants for New Digital…

Today, the U.S. Food and Drug Administration announced the names of the companies selected to participate in a first-of-its kind pilot program that will help revolutionize digital health regulation in...

Future50: Nominate the Top Healthcare IT…

HIMSS Europe has launched Future50 supported by IBM Watson Health, a new flagship initiative that aims to identify and bring together the top 50 leaders in European Healthcare IT in...

UBM Strengthens Focus on Medtec Europe f…

17 - 19 April 2018, Stuttgart, Germany. UBM announced today the continuation of its strategy to ensure Medtec Europe is the preeminent, stand alone, European-focussed, medical technology platform by deciding to...

Smartphone Apps Launched for Atrial Fibr…

Novel smartphone and tablet applications (apps) for atrial fibrillation patients and healthcare professionals have been launched by heart experts. The objectives and design of the apps are outlined in a...

New Self-Powered Paper Patch could Help …

A new paper-based sensor patch developed by researchers at Binghamton University, State University of New York could allow diabetics to effectively measure glucose levels during exercise. Today's most widespread methods...

MEDICA App COMPETITION 2017

For the 6th time, MEDICA 2017 will see the world's largest live competition for the best App-based Medical Mobile Solution for use in the daily routine of a patient, a...

Up to $20,000 Available to the Digital H…

MSD is looking for innovators to solve 7 health-related challenges aiming to support physician education or patient disease management. The 3 digital solutions with the most outstanding value will receive...

IBM Research and UC San Diego Collaborat…

IBM (NYSE: IBM) and the University of California San Diego have announced a multi-year project to enhance quality of life and independence for aging populations through the new Artificial Intelligence...