title: Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION(TM) sequencing.
abstract: The recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This has great potential to shorten the sample-to-results time and is likely to have benefits such as rapid diagnosis of bacterial infection and identification of drug resistance. However, there are 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, strain typing and antibiotic resistance profile identification. Using four culture isolate samples, as well as a mixed-species sample, we demonstrate that bacterial species and strain information can be obtained within 30 min of sequencing and using about 500 reads, initial drug-resistance profiles within two hours, and complete resistance profiles within 10 h. While strain identification with multi-locus sequence typing required more than 15x coverage to generate confident assignments, our novel 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.
authors.affiliation: Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
authors.forename: Minh Duc
authors.initials: MD
authors.lastname: Cao
authors.affiliation: Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
authors.forename: Devika
authors.initials: D
authors.lastname: Ganesamoorthy
authors.affiliation: Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
authors.forename: Alysha G
authors.initials: AG
authors.lastname: Elliott
authors.affiliation: Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
authors.forename: Huihui
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Cooper
authors.affiliation: Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia. l.coin@imb.uq.edu.au.|Department of Genomics of Common Disease, Imperial College London, London, W12 0NN, UK. l.coin@imb.uq.edu.au.
authors.forename: Lachlan J M
authors.identifier: 0000-0002-4300-455X
authors.initials: LJ
authors.lastname: Coin
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000187:drug effects / Q000235:genetics / Q000302:isolation & purification*; D015373:Bacterial Typing Techniques / Q000379:methods; D003199:Computer Systems; D004269:DNA, Bacterial / Q000032:analysis; D024881:Drug Resistance, Bacterial; D005798:Genes, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D058608:Nanopores; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004269:DNA, Bacterial
keywords: Antibiotic resistance; Nanopore sequencing; Pathogen identification; Real-time analysis