title: Recombinational switching of the Clostridium difficile S-layer and a novel glycosylation gene cluster revealed by large-scale whole-genome sequencing.
abstract: BACKGROUND
  Clostridium difficile is a major cause of nosocomial diarrhea, with 30-day mortality reaching 30%. The cell surface comprises a paracrystalline proteinaceous S-layer encoded by the slpA gene within the cell wall protein (cwp) gene cluster. Our purpose was to understand the diversity and evolution of slpA and nearby genes also encoding immunodominant cell surface antigens.
  
  
  METHODS
  Whole-genome sequences were determined for 57 C. difficile isolates representative of the population structure and different clinical phenotypes. Phylogenetic analyses were performed on their genomic region (>63 kb) spanning the cwp cluster.
  
  
  RESULTS
  Genetic diversity across the cwp cluster peaked within slpA, cwp66 (adhesin), and secA2 (secretory translocase). These genes formed a 10-kb cassette, of which 12 divergent variants were found. Homologous recombination involving this cassette caused it to associate randomly with genotype. One cassette contained a novel insertion (length, approximately 24 kb) that resembled S-layer glycosylation gene clusters.
  
  
  CONCLUSIONS
  Genetic exchange of S-layer cassettes parallels polysaccharide capsular switching in other species. Both cause major antigenic shifts, while the remainder of the genome is unchanged. C. difficile genotype is therefore not predictive of antigenic type. S-layer switching and immune escape could help explain temporal and geographic variation in C. difficile epidemiology and may inform genotyping and vaccination strategies.
authors.affiliation: Nuffield Department of Clinical Medicine, Oxford Biomedical Research Centre, John Radcliffe Hospital, UK. kate.dingle@ndcls.ox.ac.uk
authors.forename: Kate E
authors.initials: KE
authors.lastname: Dingle
authors.forename: Xavier
authors.initials: X
authors.lastname: Didelot
authors.forename: M Azim
authors.initials: MA
authors.lastname: Ansari
authors.forename: David W
authors.initials: DW
authors.lastname: Eyre
authors.forename: Alison
authors.initials: A
authors.lastname: Vaughan
authors.forename: David
authors.initials: D
authors.lastname: Griffiths
authors.forename: Camilla L C
authors.initials: CL
authors.lastname: Ip
authors.forename: Elizabeth M
authors.initials: EM
authors.lastname: Batty
authors.forename: Tanya
authors.initials: T
authors.lastname: Golubchik
authors.forename: Rory
authors.initials: R
authors.lastname: Bowden
authors.forename: Keith A
authors.initials: KA
authors.lastname: Jolley
authors.forename: Derek W
authors.initials: DW
authors.lastname: Hood
authors.forename: Warren N
authors.initials: WN
authors.lastname: Fawley
authors.forename: A Sarah
authors.initials: AS
authors.lastname: Walker
authors.forename: Timothy E
authors.initials: TE
authors.lastname: Peto
authors.forename: Mark H
authors.initials: MH
authors.lastname: Wilcox
authors.forename: Derrick W
authors.initials: DW
authors.lastname: Crook
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D016360:Clostridioides difficile / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D019143:Evolution, Molecular; D014644:Genetic Variation; D016680:Genome, Bacterial; D006031:Glycosylation; D006801:Humans; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; C070683:surface layer protein A, Bacteria