Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing

Schmidt, K., Mwaigwisya, S., Crossman, L. C., Doumith, M., Munroe, D., Pires, C., Khan, A. M., Woodford, N., Saunders, N. J., Wain, J., O'Grady, J. and Livermore, D. M. (2017) Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. Journal of Antimicrobial Chemotherapy, 72 (1). pp. 104-114. ISSN 0305-7453

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    Abstract

    Objectives: The introduction of metagenomic sequencing to diagnostic microbiology has been hampered by slowness, cost and complexity. We explored whether MinION nanopore sequencing could accelerate diagnosis and resistance profiling, using complicated urinary tract infections as an exemplar. Methods: Bacterial DNA was enriched from clinical urines (n = 10) and from healthy urines ‘spiked’ with multiresistant Escherichia coli (n = 5), then sequenced by MinION. Sequences were analysed using external databases and bioinformatic pipelines or, ultimately, using integrated real-time analysis applications. Results were compared with Illumina data and resistance phenotypes. Results: MinION correctly identified pathogens without culture and, among 55 acquired resistance genes detected in the cultivated bacteria by Illumina sequencing, 51 were found by MinION sequencing directly from the urines; with three of the four failures in an early run with low genome coverage. Resistance-conferring mutations and allelic variants were not reliably identified. Conclusions: MinION sequencing comprehensively identified pathogens and acquired resistance genes from urine in a timeframe similar to PCR (4 h from sample to result). Bioinformatic pipeline optimization is needed to better detect resistances conferred by point mutations. Metagenomic-sequencing-based diagnosis will enable clinicians to adjust antimicrobial therapy before the second dose of a typical (i.e. every 8 h) antibiotic.

    Item Type: Article
    Additional Information: Date of Acceptance: 21/08/2016 © The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
    Uncontrolled Keywords: minion nanopore sequencing, diagnostics,uti,antibiotic resistance genes,host dna depletion
    Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
    Depositing User: Pure Connector
    Date Deposited: 04 Oct 2016 13:01
    Last Modified: 23 Jan 2019 14:03
    URI: https://ueaeprints.uea.ac.uk/id/eprint/60673
    DOI: 10.1093/jac/dkw397

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