Draft Genome Sequence of Streptococcus suis S10, a Virulent Strain Used in Experimental Pig Infections

Here, we report the draft whole-genome sequence of Streptococcus suis strain S10, isolated from the tonsils of a healthy pig. S. suis S10 belongs to the highly virulent serotype 2, which includes isolates that cause infectious diseases, including meningitis, in pigs and human.

S treptococcus suis bacteria are commonly part of the porcine tonsillar microbiota (1), comprising carriage strains and strains that cause infectious disease in pigs and humans (2). Here, we report the genome sequence of S. suis strain S10, sampled in 1992 from porcine tonsils, which has been used for experimental infections of pigs (3).
S. suis S10 was cultured without agitation at 37°C with 5% CO 2 in Todd-Hewitt Broth (THB) (Oxoid, UK). Genomic DNA was extracted from 2 ml of exponentially growing bacteria that were lysed in Nuclei Lysis solution (Promega) with proteinase K and protein precipitation solution (Promega) following the manufacturer's protocol. DNA was precipitated in isopropanol and purified using phenol-chloroform-isoamyl alcohol following the protocols described by Barker (4). DNA purity and quality were assessed by gel electrophoresis and spectrometric analysis (ND-1000; NanoDrop Technologies).
DNA library preparation using the Illumina Nextera XT kit following the manufacturer's protocol and genomic DNA sequencing using an Illumina HiSeq 2500 instrument on a paired-end library (125 cycles) were carried out at BaseClear B.V. (Leiden, The Netherlands). FASTQ sequence files were generated using the Illumina CASAVA pipeline 1.8.3. A BaseClear in-house pipeline carried out quality assessment of paired-end reads by Illumina Chastity filtering, removal of reads containing adapters, PhiX control signal, and FASTQC Quality Control Tool 0.10.0. CLC Genomics Workbench 8 trimmed lowquality bases and assembled reads into contigs. KmerGenie (5) determined the optimal k-mer size. SSPACE Premium Scaffolder 2.3 (6) linked contigs and placed them into scaffolds. GapFiller 1.10 (7) closed gapped regions within scaffolds. For all in silico analyses, default parameters were used.
Sequencing generated 4,268,836 paired-end reads (average length, 126 bases) from which 2,011,091 bases were aligned (266.38-fold coverage). Filtered reads were assembled in 32 gap-closed scaffolds. Quast (8) showed that the GC content was 41.25%, the N 50 and L 50 values were 170,355 and 5, and the N 75 and L 75 values were 86,491 and 9. The number of uncalled bases per assembled 100 kbp was 0.10.
In contig_00009, Phage Search Tool Enhanced Release (PHASTER) (13) predicted a complete prophage containing 64 coding sequences (CDS) spanning a region of 62,145 base pairs (Fig. 1). The predicted S10 phage contains a candidate virulence gene with high identity (E value, 7EϪ164) with the S. mitis (14) and S. pneumoniae (15) phage-encoded gene pblB, which encodes a platelet adhesin that plays a role during multiple steps in endocardial infection, including direct binding of bacteria to platelets.
The genome sequence of S. suis S10 will enable the research community to make targeted gene deletion mutants.
Data availability. The genome sequence of strain S. suis S10 has been deposited at the European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI); the raw reads have been deposited at the European Nucleotide Archive (ENA) under the study identifier PRJEB30600.

ACKNOWLEDGMENTS
This work was funded as part of the ITN project TRAIN-ASAP, funded by the Marie Curie Actions under the Seventh Framework Programme for Research and Technological Development of the EU (grant agreement no. 289285). S. suis strain S10 was obtained from Hilde Smith, Wageningen Bioveterinary Research, Wageningen University & Research, The Netherlands. region shown is part of the largest S10 region that did not align to S. suis strain P1/7. Att, attachment site; Hyp, hypothetical protein; Int, integrase; Oth, other protein; PLP, phage-like protein.