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

Abstract

is a major pig pathogen with zoonotic potential, posing an occupational risk to farmers and meat handlers. We characterized 110 .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.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 globalgenomes showed that the Irish isolates were phylogenetically dispersed across the broader globalpopulation 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-streptococcal phages, and phylogenomic analysis revealed thatphages clustered withrather than otherphages, suggesting evolutionary connections between phage lineages infecting different streptococci.This study presents the first comprehensive genomic characterization ofin Ireland, revealing a diverse population with significant implications for animal and human health.