title: Short-term genome stability of serial Clostridium difficile ribotype 027 isolates in an experimental gut model and recurrent human disease.
abstract: BACKGROUND
  Clostridium difficile whole genome sequencing has the potential to identify related isolates, even among otherwise indistinguishable strains, but interpretation depends on understanding genomic variation within isolates and individuals.
  
  
  METHODS
  Serial isolates from two scenarios were whole genome sequenced. Firstly, 62 isolates from 29 timepoints from three in vitro gut models, inoculated with a NAP1/027 strain. Secondly, 122 isolates from 44 patients (2-8 samples/patient) with mostly recurrent/on-going symptomatic NAP-1/027 C. difficile infection. Reference-based mapping was used to identify single nucleotide variants (SNVs).
  
  
  RESULTS
  Across three gut model inductions, two with antibiotic treatment, total 137 days, only two new SNVs became established. Pre-existing minority SNVs became dominant in two models. Several SNVs were detected, only present in the minority of colonies at one/two timepoints. The median (inter-quartile range) [range] time between patients' first and last samples was 60 (29.5-118.5) [0-561] days. Within-patient C. difficile evolution was 0.45 SNVs/called genome/year (95%CI 0.00-1.28) and within-host diversity was 0.28 SNVs/called genome (0.05-0.53). 26/28 gut model and patient SNVs were non-synonymous, affecting a range of gene targets.
  
  
  CONCLUSIONS
  The consistency of whole genome sequencing data from gut model C. difficile isolates, and the high stability of genomic sequences in isolates from patients, supports the use of whole genome sequencing in detailed transmission investigations.
authors.affiliation: NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, Oxfordshire, United Kingdom. david.eyre@ndm.ox.ac.uk
authors.forename: David W
authors.initials: DW
authors.lastname: Eyre
authors.forename: A Sarah
authors.initials: AS
authors.lastname: Walker
authors.forename: Jane
authors.initials: J
authors.lastname: Freeman
authors.forename: Simon D
authors.initials: SD
authors.lastname: Baines
authors.forename: Warren N
authors.initials: WN
authors.lastname: Fawley
authors.forename: Caroline H
authors.initials: CH
authors.lastname: Chilton
authors.forename: David
authors.initials: D
authors.lastname: Griffiths
authors.forename: Alison
authors.initials: A
authors.lastname: Vaughan
authors.forename: Derrick W
authors.initials: DW
authors.lastname: Crook
authors.forename: Tim E A
authors.initials: TE
authors.lastname: Peto
authors.forename: Mark H
authors.initials: MH
authors.lastname: Wilcox
mesh_terms: D016360:Clostridioides difficile / Q000235:genetics* / Q000302:isolation & purification; D003015:Clostridium Infections / Q000382:microbiology*; D041981:Gastrointestinal Tract / Q000382:microbiology*; D005798:Genes, Bacterial; D014644:Genetic Variation; D042822:Genomic Instability; D006801:Humans; D008954:Models, Biological; D012008:Recurrence