title: Whole genome investigation of a divergent clade of the pathogen Streptococcus suis.
abstract: Streptococcus suis is a major porcine and zoonotic pathogen responsible for significant economic losses in the pig industry and an increasing number of human cases. Multiple isolates of S. suis show marked genomic diversity. Here, we report the analysis of whole genome sequences of nine pig isolates that caused disease typical of S. suis and had phenotypic characteristics of S. suis, but their genomes were divergent from those of many other S. suis isolates. Comparison of protein sequences predicted from divergent genomes with those from normal S. suis reduced the size of core genome from 793 to only 397 genes. Divergence was clear if phylogenetic analysis was performed on reduced core genes and MLST alleles. Phylogenies based on certain other genes (16S rRNA, sodA, recN, and cpn60) did not show divergence for all isolates, suggesting recombination between some divergent isolates with normal S. suis for these genes. Indeed, there is evidence of recent recombination between the divergent and normal S. suis genomes for 249 of 397 core genes. In addition, phylogenetic analysis based on the 16S rRNA gene and 132 genes that were conserved between the divergent isolates and representatives of the broader Streptococcus genus showed that divergent isolates were more closely related to S. suis. Six out of nine divergent isolates possessed a S. suis-like capsule region with variation in capsular gene sequences but the remaining three did not have a discrete capsule locus. The majority (40/70), of virulence-associated genes in normal S. suis were present in the divergent genomes. Overall, the divergent isolates extend the current diversity of S. suis species but the phenotypic similarities and the large amount of gene exchange with normal S. suis gives insufficient evidence to assign these isolates to a new species or subspecies. Further, sampling and whole genome analysis of more isolates is warranted to understand the diversity of the species.
authors.affiliation: Department of Veterinary Medicine, University of Cambridge Cambridge, UK.
authors.forename: Abiyad
authors.initials: A
authors.lastname: Baig
authors.affiliation: Department of Veterinary Medicine, University of Cambridge Cambridge, UK.
authors.forename: Lucy A
authors.initials: LA
authors.lastname: Weinert
authors.affiliation: Department of Veterinary Medicine, University of Cambridge Cambridge, UK.
authors.forename: Sarah E
authors.initials: SE
authors.lastname: Peters
authors.affiliation: Department of Paediatrics, University of Cambridge Cambridge, UK.
authors.forename: Kate J
authors.initials: KJ
authors.lastname: Howell
authors.affiliation: Department of Molecular Biology and Biotechnology, University of Sheffield Sheffield, UK.
authors.forename: Roy R
authors.initials: RR
authors.lastname: Chaudhuri
authors.affiliation: Department of Veterinary Medicine, University of Cambridge Cambridge, UK.
authors.forename: Jinhong
authors.initials: J
authors.lastname: Wang
authors.affiliation: School of Medicine, University of St Andrews St Andrews, UK.
authors.forename: Matthew T G
authors.initials: MT
authors.lastname: Holden
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Cambridge, UK.
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.affiliation: Section of Paediatrics, Department of Medicine, Imperial College London London, UK.
authors.forename: Paul R
authors.initials: PR
authors.lastname: Langford
authors.affiliation: Royal Veterinary College Hatfield, UK.
authors.forename: Andrew N
authors.initials: AN
authors.lastname: Rycroft
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine London, UK.
authors.forename: Brendan W
authors.initials: BW
authors.lastname: Wren
authors.affiliation: Department of Veterinary Medicine, University of Cambridge Cambridge, UK.
authors.forename: Alexander W
authors.initials: AW
authors.lastname: Tucker
authors.affiliation: Department of Veterinary Medicine, University of Cambridge Cambridge, UK.
authors.forename: Duncan J
authors.initials: DJ
authors.lastname: Maskell
keywords: MLST; Streptococcus suis; capsule; divergent; genome; phylogeny; recombination; virulence