Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION TM sequencing

  1. Minh Duc Cao
  2. Devika Ganesamoorthy
  3. Alysha G. Elliott
  4. Huihui Zhang
  5. Matthew A. Cooper
  6. Lachlan Coin

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Abstract

The recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This opens immense potential to shorten the sample-to-results time and is likely to lead to enormous benefits in rapid diagnosis of bacterial infection and identification of drug resistance. However, there are very few tools available for streaming analysis of real-time sequencing data. Here, we present a framework for streaming analysis of MinION real-time sequence data, together with probabilistic streaming algorithms for species typing, multi-locus strain typing, gene presence strain-typing and antibiotic resistance profile identification. Using three culture isolate samples as well as a mixed-species sample, we demonstrate that bacterial species and strain information can be obtained within 30 minutes of sequencing and using about 500 reads, initial drug-resistance profiles within two hours, and complete resistance profiles within 10 hours. Multi-locus strain typing required more than 15x coverage to generate confident assignments, whereas gene-presence typing could detect the presence of a known strain with 0.5x coverage. We also show that our pipeline can process over 100 times more data than the current throughput of the MinION on a desktop computer.

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  1. GigaScience

    Now published in GigaScience doi: 10.1186/s13742-016-0137-2

    Minh Duc Cao 1Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, QLD 4072 Brisbane, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDevika Ganesamoorthy 1Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, QLD 4072 Brisbane, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlysha G. Elliott 1Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, QLD 4072 Brisbane, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHuihui Zhang 1Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, QLD 4072 Brisbane, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMatthew A. Cooper 1Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, QLD 4072 Brisbane, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this site

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1186/s13742-016-0137-2 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.100473 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.100471

  2. Version published to 10.1101/019356 on bioRxiv