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Real-time strain typing and analysis of antibiotic resistance potential using Nanopore MinION sequencing

Minh Duc Cao, Devika Ganesamoorthy, Alysha G. Elliott, Huihui Zhang, Matthew A. Cooper, Lachlan Coin
doi: https://doi.org/10.1101/019356
Minh Duc Cao
1Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
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Devika Ganesamoorthy
1Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
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Alysha G. Elliott
1Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
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Huihui Zhang
1Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
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Matthew A. Cooper
1Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
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  • For correspondence: m.cooper@imb.uq.edu.au l.coin@imb.uq.edu.au
Lachlan Coin
1Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
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  • For correspondence: m.cooper@imb.uq.edu.au l.coin@imb.uq.edu.au
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Abstract

Clinical pathogen sequencing has significant potential to drive informed treatment of patients with unknown bacterial infection. However, the lack of rapid sequencing technologies with concomitant analysis has impeded clinical adoption in infection diagnosis. Here we demonstrate that commercially-available Nanopore sequencing devices can identify bacterial species and strain information with less than one hour of sequencing time, initial drug-resistance profiles within 2 hours, and a complete resistance profile within 12 hours. We anticipate these devices and associated analysis methods may become useful clinical tools to guide appropriate therapy in time-critical clinical presentations such as bacteraemia and sepsis.

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Posted May 20, 2015.
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Real-time strain typing and analysis of antibiotic resistance potential using Nanopore MinION sequencing
Minh Duc Cao, Devika Ganesamoorthy, Alysha G. Elliott, Huihui Zhang, Matthew A. Cooper, Lachlan Coin
bioRxiv 019356; doi: https://doi.org/10.1101/019356
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Real-time strain typing and analysis of antibiotic resistance potential using Nanopore MinION sequencing
Minh Duc Cao, Devika Ganesamoorthy, Alysha G. Elliott, Huihui Zhang, Matthew A. Cooper, Lachlan Coin
bioRxiv 019356; doi: https://doi.org/10.1101/019356

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