Streptococcus suis (S. suis) is an emerging zoonotic pathogenic bacterium capable of infecting piglets and human. Here, we isolated a S. suis srtain WH1609 from piglets brain with obvious bacterial meningitis symptoms in China, which belongs to serotype 9 according to multiplex PCR and agglutination test. The strong pathogenicity of strain WH1609 was reproduced successfully in BABL/C mouse model. The LD50 in mice reached 179 CFU/mouse, which means at least 1000 times virulence more than any strain of S. suis. To elucidate the genetic determinants of meningitis caused by the strain, whole genome sequencing was undertaken. Comparative genomic analysis revealed that WH1609 genome exhibits a high level gene gain and loss, especially in multi drug resistance and genomic islands (GI) addition. A candidate GI was investigated at genomic level which shares low homogeneity with other GIs of S. suis, consistent with its potential role in streptococcal toxic shock syndrome (STSS) and high virulence.