title: Draft genome sequences of the type strains of Shigella flexneri held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence.
abstract: BACKGROUND
  Public Health England (PHE) holds a collection of Shigella flexneri Type strains isolated between 1949 and 1972 representing 15 established serotypes and one provisional type, E1037. In this study, the genomes of all 16 PHE Type strains were sequenced using the Illumina HiSeq platform. The relationship between core genome phylogeny and serotype was examined.
  
  
  RESULTS
  The most common target gene for the detection of Shigella species in clinical PCR assays, ipaH, was detected in all genomes. The type-specific target genes were correctly identified in each genome sequence. In contrast to the S. flexneri in serotype 5 strain described by Sun et al. (2012), the two PHE serotype 5 Type strains possessed an additional oac gene and were differentiated by the presence (serotype 5b) or absence (serotype 5a) of gtrX. The somatic antigen structure and phylogenetic relationship were broadly congruent for strains expressing serotype specific antigens III, IV and V, but not for those expressing I and II. The whole genome phylogenies of the 15 isolates sequenced showed that the serotype 6 Type Strain was phylogenetically distinct from the other S. flexneri serotypes sequenced. The provisional serotype E1037 fell within the serotype 4 clade, being most closely related to the Serotype 4a Type Strain.
  
  
  CONCLUSIONS
  The S. flexneri genome sequences were used to evaluate phylogenetic relationships between Type strains and validate genotypic and phenotypic assays. The analysis confirmed that the PHE S. flexneri Type strains are phenotypically and genotypically distinct. Novel variants will continue to be added to this archive.
authors.forename: Philip M
authors.initials: PM
authors.lastname: Ashton
authors.forename: Kate S
authors.initials: KS
authors.lastname: Baker
authors.forename: Amy
authors.initials: A
authors.lastname: Gentle
authors.forename: David J
authors.initials: DJ
authors.lastname: Wooldridge
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Thomson
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Dallman
authors.affiliation: Gastrointestinal Bacteria Reference Unit, Public Health England, 61 Colindale Ave, NW9 5HT London, England. claire.jenkins@phe.gov.uk.
authors.forename: Claire
authors.initials: C
authors.lastname: Jenkins