Taxonomic reassessment of genomes from a divergent population of Streptococcus suis by average nucleotide identity analysis

Streptococcus spp., including the emerging zoonotic pathogen S. suis, represent a dominant bacterial population in the porcine nasopharynx. Species identification within the Streptococcus genus remains challenging and frequently ambiguous, resulting in indistinct species boundaries. By employing comparative genomic analyses, a previous study categorized S. suis into a central population and divergent lineages, based on the single nucleotide polymorphisms (SNPs) within core genes and the presence or absence of accessory genes, indicating evolutionary divergence. The divergent lineages were designated as the “out population” in this study for clarity. The 16S rRNA gene sequences of seven putative novel Streptococcus strains isolated from the throats of healthy pigs in China exhibited 100 % similarity to that of the 684_17B strain of S. suis, which clustered in the out population. This study established a threshold average nucleotide identity (ANI) value of 93.17 % for the identification of authentic S. suis. All the 645 genomes from the out population fell below this threshold, indicating that they did not belong to S. suis. Further taxonomic assessment of the 645 genomes from the out population revealed 18 clusters based on pairwise ANI comparisons, using a 92.33 % threshold, determined by pairwise ANI comparisons among the 2422 genomes from the central population of S. suis. These clusters were identified as 12 novel Streptococcus spp. (Streptococcus sp. nov-1–12) and six known Streptococcus spp. by ANI comparisons with type or reference genomes of 98 known Streptococcus spp. The study provides a useful framework for the identification of authentic S. suis and the determination of Streptococcus sp. nov.