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Rapid resistome mapping using nanopore sequencing

View ORCID ProfileEric van der Helm, View ORCID ProfileLejla Imamovic, View ORCID ProfileMostafa M Hashim Ellabaan, View ORCID ProfileWillem van Schaik, Anna Koza, View ORCID ProfileMorten O. A. Sommer
doi: https://doi.org/10.1101/067652
Eric van der Helm
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2870 Hørsholm, Denmark
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Lejla Imamovic
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2870 Hørsholm, Denmark
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Mostafa M Hashim Ellabaan
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2870 Hørsholm, Denmark
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Willem van Schaik
2Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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Anna Koza
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2870 Hørsholm, Denmark
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Morten O. A. Sommer
1Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2870 Hørsholm, Denmark
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  • For correspondence: msom@bio.dtu.dk
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Abstract

The emergence of antibiotic resistance in human pathogens has become a major threat to modern medicine and in particular hospitalized patients. The outcome of antibiotic treatment can be affected by the composition of the gut resistome either by enabling resistance gene acquisition of infecting pathogens or by modulating the collateral effects of antibiotic treatment on the commensal microbiome. 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 patient. The accuracy of the poreFUME pipeline is >97 % sufficient for the reliable 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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 04, 2016.
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Rapid resistome mapping using nanopore sequencing
Eric van der Helm, Lejla Imamovic, Mostafa M Hashim Ellabaan, Willem van Schaik, Anna Koza, Morten O. A. Sommer
bioRxiv 067652; doi: https://doi.org/10.1101/067652
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Rapid resistome mapping using nanopore sequencing
Eric van der Helm, Lejla Imamovic, Mostafa M Hashim Ellabaan, Willem van Schaik, Anna Koza, Morten O. A. Sommer
bioRxiv 067652; doi: https://doi.org/10.1101/067652

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