Developing genome typing strategies for the emerging zoonotic pathogen <i>Streptococcus parasuis</i>

The reported human infections with the emerging zoonotic pathogen <i>Streptococcus parasuis</i> are steadily rising. Rapid and standardized genotyping tools specific to <i>S. parasuis</i> are critically needed for epidemiological surveillance and identification of strains with zoonotic potential. This study developed a whole-genome sequence (WGS)-based typing strategy, encompassing average nucleotide identity, a minimum core genome (MCG) typing scheme, and a multilocus sequence typing (MLST) scheme using 255 <i>S</i>. <i>parasuis</i> genomes isolated from eight countries between the 1980s and 2024. The <i>S. parasuis</i> population was categorized into 12 MCG clusters based on 72,172 SNPs in non-recombining regions distributed across an MCG comprising 607 genes, forming two distinct lineages. The rapid MCG typing program accurately assigned 92.5% of <i>S. parasuis</i> genomes to their corresponding MCG clusters by identifying 4,509 cluster/subcluster-specific SNPs. To elucidate the clonal relationships among <i>S. parasuis</i> genomes, an MLST scheme was developed, defining 161 sequence types (STs) based on the allelic profiles of seven housekeeping <i>loci</i> (<i>aroA</i>, <i>cpn60</i>, <i>gki</i>, <i>mutS</i>, <i>sdhA</i>, <i>recA</i>, and <i>thrA</i>). Thirty-two STs that shared identical alleles at 6 <i>loci</i> were assigned to 10 complex clones, whereas 100 STs that shared identical alleles at 4 or more <i>loci</i> were grouped into 9 ST clades. The MCG typing scheme and the MLST scheme demonstrated sufficient discriminatory power, with Simpson's diversity index values of 0.8864 and 0.9821, respectively. This study characterized the <i>S. parasuis</i> population and provided a rapid, reproducible, and expandable WGS-based typing strategy for taxonomic identification, epidemiological surveillance, and evaluation of the zoonotic potential of <i>S. parasuis</i>.IMPORTANCEOur study provides valuable insights for developing effective prevention and control strategies for <i>Streptococcus parasuis</i> infections, by revealing the structural characteristics and phylogenetic relationship of <i>S. parasuis</i> population, by developing a whole-genome sequence-based typing strategy applicable for epidemiological surveillance, transmission investigation, and zoonotic potential evaluation.