title: Determining Streptococcus suis serotype from short-read whole-genome sequencing data.
abstract: Streptococcus suis is divided into 29 serotypes based on a serological reaction against the capsular polysaccharide (CPS). Multiplex PCR tests targeting the cps locus are also used to determine S. suis serotypes, but they cannot differentiate between serotypes 1 and 14, and between serotypes 2 and 1/2. Here, we developed a pipeline permitting in silico serotype determination from whole-genome sequencing (WGS) short-read data that can readily identify all 29 S. suis serotypes.
  
  
  
  We sequenced the genomes of 121 strains representing all 29 known S. suis serotypes. We next combined available software into an automated pipeline permitting in silico serotyping of strains by differential alignment of short-read sequencing data to a custom S. suis cps loci database. Strains of serotype pairs 1 and 14, and 2 and 1/2 could be differentiated by a missense mutation in the cpsK gene. We report a 99 % match between coagglutination- and pipeline-determined serotypes for strains in our collection. We used 375 additional S. suis genomes downloaded from the NCBI's Sequence Read Archive (SRA) to validate the pipeline. Validation with SRA WGS data resulted in a 92 % match. Included pipeline subroutines permitted us to assess strain virulence marker content and obtain multilocus sequence typing directly from WGS data.
  
  
  
  Our pipeline permits rapid and accurate determination of S. suis serotype, and other lineage information, directly from WGS data. By discriminating between serotypes 1 and 14, and between serotypes 2 and 1/2, our approach solves a three-decade longstanding S. suis typing issue.
authors.affiliation: Public Health Ontario Toronto Laboratory, 661 University Avenue, Toronto, ON, M5G 1M1 Canada.
authors.forename: Taryn B T
authors.initials: TB
authors.lastname: Athey
authors.affiliation: Public Health Ontario Toronto Laboratory, 661 University Avenue, Toronto, ON, M5G 1M1 Canada.
authors.forename: Sarah
authors.initials: S
authors.lastname: Teatero
authors.affiliation: Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculty of Veterinary Medicine, University of Montreal, St-Hyacinthe, QC, Canada.
authors.forename: Sonia
authors.initials: S
authors.lastname: Lacouture
authors.affiliation: Bacterial and Parasitic Diseases Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan.|The United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Takamatsu
authors.affiliation: Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculty of Veterinary Medicine, University of Montreal, St-Hyacinthe, QC, Canada.
authors.forename: Marcelo
authors.initials: M
authors.lastname: Gottschalk
authors.affiliation: Public Health Ontario Toronto Laboratory, 661 University Avenue, Toronto, ON, M5G 1M1 Canada. nahuel.fittipaldi@oahpp.ca.|Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada. nahuel.fittipaldi@oahpp.ca.
authors.forename: Nahuel
authors.initials: N
authors.lastname: Fittipaldi
mesh_terms: D016667:Bacterial Capsules; D001426:Bacterial Proteins; D001483:Base Sequence; D004269:DNA, Bacterial / Q000235:genetics; D018390:Gene Targeting; D005798:Genes, Bacterial; D056426:Genetic Loci; D016680:Genome, Bacterial; D060885:Multiplex Polymerase Chain Reaction; D011135:Polysaccharides, Bacterial / Q000145:classification / Q000235:genetics / Q000276:immunology / Q000302:isolation & purification; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D065288:Serogroup; D012703:Serotyping; D017011:Streptococcus suis / Q000145:classification / Q000235:genetics* / Q000276:immunology / Q000302:isolation & purification*; D014774:Virulence / Q000235:genetics; D037521:Virulence Factors
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D011135:Polysaccharides, Bacterial; D037521:Virulence Factors
keywords: Serotyping; Short-reads; Streptococcus suis; Whole-genome sequencing