Plasmid and whole genome sequencing of Enterobacteriaceae

MinION and MiSeq sequencing of three clinical isolates for antimicrobial resistance gene detection. We specifically evaluated the advantages of plasmid DNA sequencing using MinION for antimicrobial resistance gene detection and the value of supplementing MinION sequences with MiSeq reads for increasing assembly accuracy. With a MinION-only workflow full annotation of plasmid resistance gene content could be obtained in under 6 hours from a sub-cultured isolate, in less time than traditional phenotypic susceptibility testing.