title: Draft genomes of Shigella strains used by the STOPENTERICS consortium.
abstract: BACKGROUND
  Despite a significant global burden of disease, there is still no vaccine against shigellosis widely available. One aim of the European Union funded STOPENTERICS consortium is to develop vaccine candidates against Shigella. Given the importance of translational vaccine coverage, here we aimed to characterise the Shigella strains being used by the consortium by whole genome sequencing, and report on the stability of strains cultured in different laboratories or through serial passage.
  
  
  METHODS
  We sequenced, de novo assembled and annotated 20 Shigella strains being used by the consortium. These comprised 16 different isolates belonging to 7 serotypes, and 4 derivative strains. Derivative strains from common isolates were manipulated in different laboratories or had undergone multiple passages in the same laboratory. Strains were mapped against reference genomes to detect SNP variation and phylogenetic analysis was performed.
  
  
  RESULTS
  The genomes assembled into similar total lengths (range 4.14-4.83 Mbp) and had similar numbers of predicted coding sequences (average of 4,400). Mapping analysis showed the genetic stability of strains through serial passages and culturing in different laboratories, as well as varying levels of similarity to published reference genomes. Phylogenetic analysis revealed the presence of three main clades among the strains and published references, one containing the Shigella flexneri serotype 6 strains, a second containing the remaining S. flexneri serotypes and a third comprised of Shigella sonnei strains.
  
  
  CONCLUSIONS
  This work increases the number of the publically available Shigella genomes available and specifically provides information on strains being used for vaccine development by STOPENTERICS. It also provides information on the variability among strains maintained in different laboratories and through serial passage. This work will guide the selection of strains for further vaccine development.
authors.affiliation: Novartis Vaccines Institute for Global Health, s.r.l., a GSK Company, Siena, Italy.
authors.forename: Omar
authors.initials: O
authors.lastname: Rossi
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Kate S
authors.initials: KS
authors.lastname: Baker
authors.affiliation: Institut Pasteur, Paris, France.
authors.forename: Armelle
authors.initials: A
authors.lastname: Phalipon
authors.affiliation: Institut Pasteur, Paris, France.
authors.forename: François-Xavier
authors.initials: FX
authors.lastname: Weill
authors.affiliation: Novartis Vaccines Institute for Global Health, s.r.l., a GSK Company, Siena, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Citiulo
authors.affiliation: Institut Pasteur, Paris, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Sansonetti
authors.affiliation: Novartis Vaccines Institute for Global Health, s.r.l., a GSK Company, Siena, Italy.
authors.forename: Christiane
authors.initials: C
authors.lastname: Gerke
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Thomson
keywords: Genome; STOPENTERICS; Shigella; Vaccine