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Nanopore-Based Enrichment of Antimicrobial Resistance Genes – A Case-Based Study

View ORCID ProfileAdrian Viehweger, View ORCID ProfileMike Marquet, Martin Hölzer, Nadine Dietze, Mathias W. Pletz, Christian Brandt
doi: https://doi.org/10.1101/2021.08.29.458107
Adrian Viehweger
1Institute of Medical Microbiology and Virology, University Hospital Leipzig, Leipzig, Germany
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  • For correspondence: adrian.viehweger@medizin.uni-leipzig.de
Mike Marquet
2Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
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Martin Hölzer
3Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, Berlin, Germany
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Nadine Dietze
1Institute of Medical Microbiology and Virology, University Hospital Leipzig, Leipzig, Germany
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Mathias W. Pletz
2Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
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Christian Brandt
2Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
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Abstract

Rapid screening of hospital admissions to detect asymptomatic carriers of resistant bacteria can prevent pathogen outbreaks. However, the resulting isolates rarely have their genome sequenced due to cost constraints and long turn-around times to get and process the data, limiting their usefulness to the practitioner. Here we use real-time, on-device target enrichment (“adaptive”) sequencing as a highly multiplexed assay covering 1,147 antimicrobial resistance genes. We compare its utility against standard and metagenomic sequencing, focusing on an isolate of Raoultella ornithinolytica harbouring three carbapenemases (NDM, KPC, VIM). Based on this experimental data, we then model the influence of several variables on the enrichment results and predict a large effect of nucleotide identity (higher is better) and read length (shorter is better). Lastly, we show how all relevant resistance genes are detected using adaptive sequencing on a miniature (“Flongle”) flow cell, motivating its use in a clinical setting to monitor similar cases and their surroundings.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Minor revision

  • https://www.github.com/phiweger/adaptive

  • List of abbreviations

    ARG
    antimicrobial resistance gene
    ORF
    open reading frame
    MAG
    metagenome-assembled genome
    FNR
    false negative rate
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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 4.0 International license.
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    Posted January 04, 2023.
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    Nanopore-Based Enrichment of Antimicrobial Resistance Genes – A Case-Based Study
    Adrian Viehweger, Mike Marquet, Martin Hölzer, Nadine Dietze, Mathias W. Pletz, Christian Brandt
    bioRxiv 2021.08.29.458107; doi: https://doi.org/10.1101/2021.08.29.458107
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    Nanopore-Based Enrichment of Antimicrobial Resistance Genes – A Case-Based Study
    Adrian Viehweger, Mike Marquet, Martin Hölzer, Nadine Dietze, Mathias W. Pletz, Christian Brandt
    bioRxiv 2021.08.29.458107; doi: https://doi.org/10.1101/2021.08.29.458107

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