Population genomics uncovers global distribution, antimicrobial resistance, and virulence factors of Streptococcus...

Streptococcus suis is a major porcine pathogen and an emerging zoonotic agent. Nevertheless, the lack of a global collection has hindered understanding of its epidemiological characteristics. Here, we provide a genomic overview of S. suis, encompassing 195 newly sequenced isolates and 7359 publicly available genomes. Applying cgMLST scheme and UMAP embedding approach, a total of twenty high-density clusters were identified. The clustering exhibited discordance with the serotype and MLST schemes due to recombination, indicating the limitations of classical identification methods. We also demonstrate that S. suis has an intricate global distribution and significant geographical dispersion. Serotype 2, 1/2, and 9 are top three predominant serotypes globally and displayed distinct genomic profiles. Genome reduction occurred in global clusters rather than local epidemic clusters in SS2 and SS1/2, and the loss of 89 K pathogenicity island (PAI) is a contributing factor to the SS2 reduction process. Various crucial transmission hubs and patterns have been identified for SS2 in China and SS1/2 in Europe and Japan. Concurrently, SS9 manifested remarkably distinct characteristics. Two SS9 clusters have been identified in China and Europe, respectively, and no genetic relationship was observed between them, indicating local expansion in each region of SS9. Moreover, the distribution patterns of resistance and virulence genes were closely correlated with different clusters. These results enhance our understanding of the antimicrobial resistance, pathogenicity, and transmission characteristics in a large international collection of S. suis genomes and demonstrate the genomic framework of epidemic clones at local and global scales.