SRA

Streptococcus suis is a porcine pathogen responsible for major losses on pig farms in the Netherlands and serotype 9 has become the most prevalent serotype isolated from diseased pigs. Autovaccination with serotype 2 bacterin vaccine has been introduced succesfully, but a similar vaccination strategy with serotype 9 appears less effective. Recently it has been shown that serotype 9 strains isolated from pigs on farms without outbreaks for at least a year differ in gene content from invasive strains as indicated by comparative genome hybridization. However, it is not known which genetic factors are responsible for the virulent phenotype of these invasive isolates. Here, we present the results from a whole genome comparison of carriage and invasive serotype 9 isolates.Both carriage and invasive serotype 9 S. suis isolates were collected from farms across the Netherlands and 124 isolates were sequenced using Illumina sequencing. Sequence types (ST) were extracted from the sequencing reads using SRST2 and serotypes were confirmed using the Ssuis_serotypingPipeline. The genomes were assembled using SPAdes and annotated with Prokka. Roary was used to construct a core and pan genome and a Bayesian Analysis of Population Structure (BAPS) was used to determine population groups using the core genome nucleotide alignment. All phylogenetic trees were constructed with RAxML.We identified 14 novel ST’s, of which 10 among the 47 carriage isolates. BAPS grouped all isolates into 10 population groups of which one group contained 95% of all 77 invasive isolates. Isolates from this group belonged to ST16 or single locus variants of ST16. Carriage isolates demonstrated a much more diverse population structure consisting of 7 population groups containing only carriage isolates. Our data suggest up to 3 population groups existed on each farm. Interestingly, virulent isolates had larger genomes than the carriage isolates, which is in contrast to previous findings. Including other virulent isolates from the Netherlands including ST1 serotype 2 and ST20 serotype 2 showed that the ST16 serotype 9 isolates are closer related to virulent isolates compared to other carriage isolates. Comparison of the capsule locus revealed an insertion in the capsule locus in 5 out of 7 carriage groups which was absent in the invasive isolates. CpsK may be used as a diagnostic target for the detection of clinical serotype 9 isolates.Invasive S. suis serotype 9 isolates in the Netherlands can be attributed to the rise of a single clonal expansion. The sequencing of carriage isolates reveals a landscape of previously unknown Streptococcus suis strains, which differ from the disease causing isolates in genome structure. The results provide opportunities for the development of diagnostic tools as well as for vaccine development to detect and prevent invasive S. suis serotype 9 disease