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Adaptive nanopore sequencing on miniature flow cell detects extensive antimicrobial resistence

View ORCID ProfileAdrian Viehweger, View ORCID ProfileMike Marquet, Martin Hölzer, Nadine Dietze, Mathias 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 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 on a new type of low-cost nanopore flow cell as a highly multiplexed assay covering 1,147 antimicrobial resistance genes. Using this method, we detected four types of carbapenemase in a single isolate of Raoultella ornithinolytica (NDM, KPC, VIM, OXA). Further investigation revealed extensive horizontal gene transfer within the underlying microbial consortium, increasing the risk of resistance spreading. Real-time sequencing could thus quickly inform how to monitor this case and its surroundings.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://osf.io/wt7gc/

Copyright 
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 August 29, 2021.
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Adaptive nanopore sequencing on miniature flow cell detects extensive antimicrobial resistence
Adrian Viehweger, Mike Marquet, Martin Hölzer, Nadine Dietze, Mathias Pletz, Christian Brandt
bioRxiv 2021.08.29.458107; doi: https://doi.org/10.1101/2021.08.29.458107
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Adaptive nanopore sequencing on miniature flow cell detects extensive antimicrobial resistence
Adrian Viehweger, Mike Marquet, Martin Hölzer, Nadine Dietze, Mathias Pletz, Christian Brandt
bioRxiv 2021.08.29.458107; doi: https://doi.org/10.1101/2021.08.29.458107

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