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

Gait Assessed with Body-Worn Sensors may…

Body-worn sensors used at home and in clinic by people with mild Alzheimer's to assess walking could offer a cost-effective way to detect early disease and monitor progression of the...

Applications for the G4A Global Accelera…

Founded in 2013 in Berlin initially giving out grants to innovative healthcare apps, G4A Accelerator is now a global program dedicated to helping innovative health & care startups grow and...

Siemens Healthineers Fully on Track to M…

Siemens Healthineers AG has posted good business figures in the first quarter following its successful initial public offering on March 16, 2018. Year-over-year revenue was up four percent at EUR...

How to Build GDPR and HIPAA Compliant He…

The adoption of cloud and mobile technologies in healthcare is disrupting the services delivery models, and responsibilities and risks for involved actors. By their very nature, eHealth applications collect and...

Computers Equal Radiologists in Assessin…

Automated breast-density evaluation was just as accurate in predicting women's risk of breast cancer, found and not found by mammography, as subjective evaluation done by radiologists, in a study led...

The Big Ethical Questions for Artificial…

AI in healthcare is developing rapidly, with many applications currently in use or in development in the UK and worldwide. The Nuffield Council on Bioethics examines the current and potential...

Consultation: Transformation Health and …

The present report provides an analysis of the results of consultation activities carried out by the European Commission in preparation of a Communication on the Transformation of Health and Care...

Novartis Launches FocalView App, Providi…

Novartis announced the launch of its FocalView app, an ophthalmic digital research platform created with ResearchKit. FocalView aims to allow researchers to track disease progression by collecting real-time, self-reported data...

International Masters's in Medical Infor…

The Master of Science Program in Medical Informatics (MMI) at European Campus Rottal-Inn (ECRI)in Pfarrkirchen - a branch of the Deggendorf University of Applied Sciences (THD - Technische Hochschule Deggendorf)...

Data in the EU: Commission Steps Up Effo…

The European Commission is putting forward a set of measures to increase the availability of data in the EU, building on previous initiatives to boost the free flow of non-personal...

Philips Expands its Sleep & Respirat…

Royal Philips (NYSE: PHG, AEX: PHIA), a global leader in health technology, today announced that it has acquired NightBalance, a digital health scale-up company based in the Netherlands, that has...

A New Way to Watch Brain Activity in Act…

It's a neuroscientist's dream: being able to track the millions of interactions among brain cells in animals that move about freely, behaving as they would under natural circumstances. New technology...