title: Detection of the plasmid-mediated mcr-1 gene conferring colistin resistance in human and food isolates of Salmonella enterica and Escherichia coli in England and Wales.
abstract: In response to the first report of transmissible colistin resistance mediated by the mcr-1 gene in Escherichia coli and Klebsiella spp. from animals and humans in China, we sought to determine its presence in Enterobacteriaceae isolated in the UK.
  
  
  
  The PHE archive of whole-genome sequences of isolates from surveillance collections, submissions to reference services and research projects was retrospectively analysed for the presence of mcr-1 using Genefinder. The genetic environment of the gene was also analysed.
  
  
  
  Rapid screening of the genomes of ∼24 000 Salmonella enterica, E. coli, Klebsiella spp., Enterobacter spp., Campylobacter spp. and Shigella spp. isolated from food or humans identified 15 mcr-1-positive isolates. These comprised: 10 human S. enterica isolates submitted between 2012 and 2015 (8 Salmonella Typhimurium, 1 Salmonella Paratyphi B var Java and 1 Salmonella Virchow) from 10 patients; 3 isolates of E. coli from 2 patients; and 2 isolates of Salmonella Paratyphi B var Java from poultry meat imported from the EU. The mcr-1 gene was located on diverse plasmids belonging to the IncHI2, IncI2 and IncX4 replicon types and its association with ISApl1 varied. Six mcr-1-positive S. enterica isolates were from patients who had recently travelled to Asia.
  
  
  
  Analysis of WGS data allowed rapid confirmation of the presence of the plasmid-mediated colistin resistance gene mcr-1 in diverse genetic environments and plasmids. It has been present in E. coli and Salmonella spp. harboured by humans in England and Wales since at least 2012.
authors.affiliation: National Infection Service, Public Health England, London NW9 5EQ, UK.
authors.forename: Michel
authors.initials: M
authors.lastname: Doumith
authors.affiliation: National Infection Service, Public Health England, London NW9 5EQ, UK.
authors.forename: Gauri
authors.initials: G
authors.lastname: Godbole
authors.affiliation: National Infection Service, Public Health England, London NW9 5EQ, UK.
authors.forename: Philip
authors.initials: P
authors.lastname: Ashton
authors.affiliation: National Infection Service, Public Health England, London NW9 5EQ, UK.
authors.forename: Lesley
authors.initials: L
authors.lastname: Larkin
authors.affiliation: National Infection Service, Public Health England, London NW9 5EQ, UK.
authors.forename: Tim
authors.initials: T
authors.lastname: Dallman
authors.affiliation: National Infection Service, Public Health England, London NW9 5EQ, UK.
authors.forename: Martin
authors.initials: M
authors.lastname: Day
authors.affiliation: National Infection Service, Public Health England, London NW9 5EQ, UK.
authors.forename: Michaela
authors.initials: M
authors.lastname: Day
authors.affiliation: National Infection Service, Public Health England, London NW9 5EQ, UK.
authors.forename: Berit
authors.initials: B
authors.lastname: Muller-Pebody
authors.affiliation: National Infection Service, Public Health England, London NW9 5EQ, UK.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Ellington
authors.affiliation: National Infection Service, Public Health England, London NW9 5EQ, UK.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: de Pinna
authors.affiliation: National Infection Service, Public Health England, London NW9 5EQ, UK.
authors.forename: Alan P
authors.initials: AP
authors.lastname: Johnson
authors.affiliation: National Infection Service, Public Health England, London NW9 5EQ, UK.
authors.forename: Katie L
authors.initials: KL
authors.lastname: Hopkins
authors.affiliation: National Infection Service, Public Health England, London NW9 5EQ, UK neil.woodford@phe.gov.uk.
authors.forename: Neil
authors.initials: N
authors.lastname: Woodford
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D002648:Child; D002675:Child, Preschool; D003091:Colistin / Q000494:pharmacology*; D019295:Computational Biology; D024881:Drug Resistance, Bacterial; D004739:England; D004755:Enterobacteriaceae / Q000187:drug effects* / Q000235:genetics / Q000302:isolation & purification; D004756:Enterobacteriaceae Infections / Q000382:microbiology*; D005260:Female; D005516:Food Microbiology; D005798:Genes, Bacterial; D006801:Humans; D008297:Male; D008875:Middle Aged; D010957:Plasmids; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA; D014852:Wales; D055815:Young Adult
chemical_list: D000900:Anti-Bacterial Agents; D003091:Colistin