Support data for "Population genomics uncovers global distribution, antimicrobial resistance, and virulence factors of the Streptococcus suis"

<i>Streptococcus suis</i> is a major bacterial pathogen in pigs and an emerging zoonotic pathogen. Nevertheless, the lack of a global collection has hindered understanding of its epidemiological characteristics. In order to deepen the understanding of <i>S. suis</i> population characteristics, we investigated the phylogenetic structure, genomic features, transmission, antimicrobial resistance and virulence of <i>S. suis </i>including 195 non-duplicated newly sequenced isolates and 7,359 publicly available genomes. Applying cgMLST scheme and UMAP embedding approach, a total of 20 high-density clusters were identified. All clusters were characterized by significant geographical dispersion, suggesting the intricate global distribution of <i>S. suis</i>. Subsequently, the focus was directed towards three predominant serotypes (serotype 2, 1/2 and 9). Genome reduction occurred in global clusters rather than local epidemic clusters in SS2 and SS1/2. The loss of 89K pathogenicity island (PAI) is a contributing factor to the reduction process in SS2. Meanwhile, the transmission patterns exhibited marked differences. China has been identified as the primary epicenter of SS2 transmission, while Europe and Japan have been recognized as the primary hotspots for SS1/2 transmission. Concurrently, SS9 manifested remarkably distinct characteristics. Two SS9 clusters have been identified in China and European countries, respectively, and no genetic relationship has been observed between them, indicating local expansion in each region of SS9. Furthermore, the distribution of ARGs and VFs across different clusters, continents and hosts was identified. Overall, this study provides much-needed insights into ecological and evolutionary dynamics of <i>S. suis</i>, which has the potential to improve infection control strategies and public health policy.