title: MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island.
abstract: Short-read, high-throughput sequencing technology cannot identify the chromosomal position of repetitive insertion sequences that typically flank horizontally acquired genes such as bacterial virulence genes and antibiotic resistance genes. The MinION nanopore sequencer can produce long sequencing reads on a device similar in size to a USB memory stick. Here we apply a MinION sequencer to resolve the structure and chromosomal insertion site of a composite antibiotic resistance island in Salmonella Typhi Haplotype 58. Nanopore sequencing data from a single 18-h run was used to create a scaffold for an assembly generated from short-read Illumina data. Our results demonstrate the potential of the MinION device in clinical laboratories to fully characterize the epidemic spread of bacterial pathogens.
authors.affiliation: Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK.
authors.forename: Philip M
authors.initials: PM
authors.lastname: Ashton
authors.affiliation: Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK.
authors.forename: Satheesh
authors.initials: S
authors.lastname: Nair
authors.affiliation: Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK.
authors.forename: Tim
authors.initials: T
authors.lastname: Dallman
authors.affiliation: 1] Department of Biomedical Sciences, University of Sassari, Sassari, Italy. [2] Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
authors.forename: Salvatore
authors.initials: S
authors.lastname: Rubino
authors.affiliation: National Reference Centre for Salmonellae and other Enterics, Robert Koch Institute, Wernigerode, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Rabsch
authors.affiliation: Norwich Medical School, University of East Anglia, Norwich, UK.
authors.forename: Solomon
authors.initials: S
authors.lastname: Mwaigwisya
authors.affiliation: Norwich Medical School, University of East Anglia, Norwich, UK.
authors.forename: John
authors.initials: J
authors.lastname: Wain
authors.affiliation: Norwich Medical School, University of East Anglia, Norwich, UK.
authors.forename: Justin
authors.identifier: 0000000154127152
authors.initials: J
authors.lastname: O'Grady
mesh_terms: D001482:Base Composition / Q000235:genetics; D002876:Chromosomes, Bacterial / Q000235:genetics; D018899:CpG Islands / Q000235:genetics*; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation* / Q000379:methods*; D058608:Nanopores; D010957:Plasmids / Q000235:genetics; D012485:Salmonella typhi / Q000235:genetics