title: Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes.
abstract: OBJECTIVE
  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 DNA was prepared and sequenced using the MinION as instructed by the manufacturer, and Illumina MiSeq and PacBio sequencing was performed using established methods.
  
  
  RESULTS
  An evaluation of the accuracy of the MinION 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.
authors.affiliation: Department of Medicine, University of Cambridge, Cambridge, UK.
authors.forename: Kim
authors.initials: K
authors.lastname: Judge
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Simon R
authors.initials: SR
authors.lastname: Harris
authors.affiliation: Department of Medicine, University of Cambridge, Cambridge, UK.
authors.forename: Sandra
authors.initials: S
authors.lastname: Reuter
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.affiliation: Department of Medicine, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Hinxton, UK Public Health England, Clinical Microbiology and Public Health Laboratory, Cambridge, UK sjp97@medschl.cam.ac.uk.
authors.forename: Sharon J
authors.initials: SJ
authors.lastname: Peacock
mesh_terms: D004269:DNA, Bacterial; D024881:Drug Resistance, Bacterial; D005798:Genes, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods* / Q000592:standards; D006801:Humans; D055624:Methicillin-Resistant Staphylococcus aureus / Q000187:drug effects / Q000235:genetics; D015203:Reproducibility of Results
chemical_list: D004269:DNA, Bacterial