Rapid resistome mapping using nanopore sequencing

Eric van der Helm, Lejla Imamovic, Mostafa M Hashim Ellabaan, Willem van Schaik, Anna Koza, Morten Otto Alexander Sommer

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The emergence of antibiotic resistance in human pathogens has become a major threat to modern medicine. The outcome of antibiotic treatment can be affected by the composition of the gut. Accordingly, knowledge of the gut resistome composition could enable more effective and individualized treatment of bacterial infections. Yet, rapid workflows for resistome characterization are lacking. To address this challenge we developed the poreFUME workflow that deploys functional metagenomic selections and nanopore sequencing to resistome mapping. We demonstrate the approach by functionally characterizing the gut resistome of an ICU (intensive care unit) patient. The accuracy of the poreFUME pipeline is with >97% sufficient for the annotation of antibiotic resistance genes. The poreFUME pipeline provides a promising approach for efficient resistome profiling that could inform antibiotic treatment decisions in the future.
Original languageEnglish
Article numbergkw1328
JournalNucleic acids research
Issue number8
Number of pages8
Publication statusPublished - 2017

Bibliographical note

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.


  • 2 Conference presentations

Functional Metagenomic Selections for Antibiotic Resistance Gene Profiling

Eric van der Helm (Invited speaker)

1 Jun 2017

Activity: Talks and presentationsConference presentations

Rapid resistome mapping using Nanopore sequencing

Eric van der Helm (Speaker)

4 May 2017

Activity: Talks and presentationsConference presentations

Press / Media

Ny metode kan give hurtigere måling af antibiotikaresistens i tarmen

Eric van der Helm


1 Media contribution

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