Figure 4

Inferred genetic relationships among 108 serotype 9 S. suis strains investigated in this study based on core-genome analysis. The maximum likelihood phylogenetic tree was constructed based on 15 934 non-redundant core-genome SNP loci identified relative to the genome sequence of the ST16 serotype 9 reference strain GD-0088. The tree reveals that serotype 9 isolates are distributed across several distinct genomic clades, including four newly discovered genotypes, highlighting complex evolutionary dynamics. These patterns suggest that the cps9 Cps9 capsule may confer adaptive capabilities, although further research is needed to confirm such speculation. The tree is color-coded to indicate the country of origin for each strain, showcasing the geographical distribution across Belgium, France, Germany, the Netherlands, and the United Kingdom. The clade comprising ST16 organisms along with closely related STs 1520, 2772, and 2773 has been collapsed for simplicity, focusing the analysis on broader genomic diversity within serotype 9.