title: Whole-genome sequencing to determine transmission of Neisseria gonorrhoeae: an observational study.
abstract: BACKGROUND
  New approaches are urgently required to address increasing rates of gonorrhoea and the emergence and global spread of antibiotic-resistant Neisseria gonorrhoeae. We used whole-genome sequencing to study transmission and track resistance in N gonorrhoeae isolates.
  
  
  METHODS
  We did whole-genome sequencing of isolates obtained from samples collected from patients attending sexual health services in Brighton, UK, between Jan 1, 2011, and March 9, 2015. We also included isolates from other UK locations, historical isolates from Brighton, and previous data from a US study. Samples from symptomatic patients and asymptomatic sexual health screening underwent nucleic acid amplification testing; positive samples and all samples from symptomatic patients were cultured for N gonorrhoeae, and resulting isolates were whole-genome sequenced. Cefixime susceptibility testing was done in selected isolates by agar incorporation, and we used sequence data to determine multi-antigen sequence types and penA genotypes. We derived a transmission nomogram to determine the plausibility of direct or indirect transmission between any two cases depending on the time between samples: estimated mutation rates, plus diversity noted within patients across anatomical sites and probable transmission pairs, were used to fit a coalescent model to determine the number of single nucleotide polymorphisms expected.
  
  
  RESULTS
  1407 (98%) of 1437 Brighton isolates between Jan 1, 2011, and March 9, 2015 were successfully sequenced. We identified 1061 infections from 907 patients. 281 (26%) of these infections were indistinguishable (ie, differed by zero single nucleotide polymorphisms) from one or more previous cases, and 786 (74%) had evidence of a sampled direct or indirect Brighton source. We observed multiple related samples across geographical locations. Of 1273 infections in Brighton (including historical data), 225 (18%) were linked to another case elsewhere in the UK, and 115 (9%) to a case in the USA. Four lineages initially identified in Brighton could be linked to 70 USA sequences, including 61 from a lineage carrying the mosaic penA XXXIV allele, which is associated with reduced cefixime susceptibility.
  
  
  CONCLUSIONS
  We present a whole-genome-sequencing-based tool for genomic contact tracing of N gonorrhoeae and demonstrate local, national, and international transmission. Whole-genome sequencing can be applied across geographical boundaries to investigate gonorrhoea transmission and to track antimicrobial resistance.
  
  
  BACKGROUND
  Oxford National Institute for Health Research Health Protection Research Unit and Biomedical Research Centre.
authors.affiliation: Nuffield Department of Medicine, University of Oxford, Oxford, UK.|National Institute for Health Research Biomedical Research Centre, Oxford, UK.|Oxford National Institute for Health Research Health Protection Research Unit.
authors.forename: Dilrini
authors.initials: D
authors.lastname: De Silva
authors.affiliation: St George's University Hospitals NHS Foundation Trust, London, UK.
authors.forename: Joanna
authors.initials: J
authors.lastname: Peters
authors.affiliation: Brighton and Sussex University Hospitals NHS Trust, Brighton, UK.|National Infection Service, Public Health England, UK.
authors.forename: Kevin
authors.initials: K
authors.lastname: Cole
authors.affiliation: Public Health England Sexually Transmitted Bacterial Reference Unit, Colindale, London, UK.
authors.forename: Michelle J
authors.initials: MJ
authors.lastname: Cole
authors.affiliation: Brighton and Sussex University Hospitals NHS Trust, Brighton, UK.
authors.forename: Fiona
authors.initials: F
authors.lastname: Cresswell
authors.affiliation: Brighton and Sussex University Hospitals NHS Trust, Brighton, UK.
authors.forename: Gillian
authors.initials: G
authors.lastname: Dean
authors.affiliation: National Infection Service, Public Health England, UK.
authors.forename: Jayshree
authors.initials: J
authors.lastname: Dave
authors.affiliation: Communicable Disease Surveillance Centre, Public Health Wales, Cardiff, UK.
authors.forename: Daniel Rh
authors.initials: DR
authors.lastname: Thomas
authors.affiliation: Health Protection Team, Public Health England North East, UK.
authors.forename: Kirsty
authors.initials: K
authors.lastname: Foster
authors.affiliation: Field Epidemiology Service Newcastle, Public Health England, Newcastle upon Tyne, UK.
authors.forename: Alison
authors.initials: A
authors.lastname: Waldram
authors.affiliation: Nuffield Department of Medicine, University of Oxford, Oxford, UK.|National Institute for Health Research Biomedical Research Centre, Oxford, UK.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Wilson
authors.affiliation: Department of Infectious Disease Epidemiology, Imperial College, London, UK.
authors.forename: Xavier
authors.initials: X
authors.lastname: Didelot
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, and Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA.
authors.forename: Yonatan H
authors.initials: YH
authors.lastname: Grad
authors.affiliation: Nuffield Department of Medicine, University of Oxford, Oxford, UK.|National Institute for Health Research Biomedical Research Centre, Oxford, UK.|Oxford National Institute for Health Research Health Protection Research Unit.|National Infection Service, Public Health England, UK.
authors.forename: Derrick W
authors.initials: DW
authors.lastname: Crook
authors.affiliation: Nuffield Department of Medicine, University of Oxford, Oxford, UK.|National Institute for Health Research Biomedical Research Centre, Oxford, UK.|Oxford National Institute for Health Research Health Protection Research Unit.
authors.forename: Tim Ea
authors.initials: TE
authors.lastname: Peto
authors.affiliation: Nuffield Department of Medicine, University of Oxford, Oxford, UK.|National Institute for Health Research Biomedical Research Centre, Oxford, UK.|Oxford National Institute for Health Research Health Protection Research Unit.
authors.forename: A Sarah
authors.initials: AS
authors.lastname: Walker
authors.affiliation: National Institute for Health Research Biomedical Research Centre, Oxford, UK.|Brighton and Sussex University Hospitals NHS Trust, Brighton, UK.|National Infection Service, Public Health England, UK.
authors.forename: John
authors.initials: J
authors.lastname: Paul
authors.affiliation: Nuffield Department of Medicine, University of Oxford, Oxford, UK.|National Institute for Health Research Biomedical Research Centre, Oxford, UK.|Oxford National Institute for Health Research Health Protection Research Unit.
authors.forename: David W
authors.initials: DW
authors.lastname: Eyre
mesh_terms: D000328:Adult; D000483:Alleles; D000900:Anti-Bacterial Agents / Q000627:therapeutic use; D020682:Cefixime / Q000627:therapeutic use; D018550:Cephalosporin Resistance / Q000235:genetics*; D002511:Cephalosporins / Q000627:therapeutic use; D005260:Female; D005838:Genotype; D006069:Gonorrhea / Q000188:drug therapy / Q000453:epidemiology* / Q000382:microbiology / Q000635:transmission; D006801:Humans; D008297:Male; D008826:Microbial Sensitivity Tests; D009344:Neisseria gonorrhoeae / Q000187:drug effects / Q000235:genetics*; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA; D006113:United Kingdom / Q000453:epidemiology
chemical_list: D000900:Anti-Bacterial Agents; D002511:Cephalosporins; D020682:Cefixime