Genomics of Irish swine-derived Streptococcus suis: population structure, prophages and anti-viral defence mechanisms

<i>Streptococcus suis</i> is a major pig pathogen with zoonotic potential, posing an occupational risk to farmers and meat handlers. We characterized 110 <i>S</i>. <i>suis</i> strains from diseased pigs in Ireland (2005-2022) using whole-genome sequencing to investigate population structure and phage-host dynamics. We identified 15 distinct serotypes, with serotypes 9 and 2 being the most dominant. <i>In silico</i> multi-locus sequence typing revealed high diversity within the collection, identifying several sequence types (STs), including 26 novel STs. Investigation of strain-level genomic clustering using PopPUNK against global <i>S. suis</i> genomes showed that the Irish isolates were phylogenetically dispersed across the broader global <i>S. suis</i> population rather than clustering in a single clonal group. The majority of Irish isolates fall within the ten established pathogenic lineages, including the highly virulent zoonotic lineage 1. A locally persistent clonal lineage was identified among Irish isolates, showing minimal genetic variation over a decade.Prophage analysis revealed novel viral taxa that were interspersed among known streptococcal phages, rather than clustering distinctly. Restriction-modification systems were the predominant anti-viral defence systems identified across genomes. CRISPR-Cas systems were present in limited strains but showed substantial targeting bias toward full-length prophages, indicating ongoing phage pressure. CRISPR spacers matched non-<i>S. suis</i> streptococcal phages, and phylogenomic analysis revealed that <i>Vansinderenvirus</i> phages clustered with <i>S. suis</i> rather than other <i>Streptococcus thermophilus</i> phages, suggesting evolutionary connections between phage lineages infecting different streptococci.This study presents the first comprehensive genomic characterization of <i>S. suis</i> in Ireland, revealing a diverse population with significant implications for animal and human health.