Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes

Kim Judge, Simon R. Harris, Sandra Reuter, Julian Parkhill, Sharon Peacock*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    62 Citations (Scopus)


    Objectives: Genome sequencing will be increasingly used in the clinical setting to tailor antimicrobial prescribing and inform infection control outbreaks. A recent technological innovation that could reduce the delay between pathogen sampling and data generation is single molecule sequencing. An example of this technology, which is undergoing evaluation through an early access programme, is the Oxford Nanopore MinION. Methods: We undertook a feasibility study on six clinically significant pathogens, comparing the MinION to the Illumina MiSeq and PacBio RSII platforms. Genomic DNAwas prepared and sequenced using theMinION as instructed by the manufacturer, and Illumina MiSeq and PacBio sequencing was performed using established methods. Results: An evaluation of the accuracy of theMinION based on sequencing of an MRSA isolate showed that error rates were higher in the MinION reads, but provided an even coverage across the entire genome length. The MinION detected all of the expected carbapenemases and ESBL genes in five Gram-negative isolates and the mecA gene in an MRSA isolate. Conclusions: The MinION can detect the presence of acquired resistance genes, but improvements in accuracy are needed so that antimicrobial resistance associated with mutations in chromosomal genes can be identified.

    Original languageEnglish
    Article numberdkv206
    Pages (from-to)2775-2778
    Number of pages4
    JournalJournal of Antimicrobial Chemotherapy
    Issue number10
    Publication statusPublished - Oct 2015

    Bibliographical note

    Publisher Copyright:
    © The Author 2015. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved.


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