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

TL;DR

This study provides the first comprehensive genomic analysis of Streptococcus suis in Ireland, revealing diverse strains and their potential risks to animal and human health.

Contribution

The study presents the first detailed genomic characterization of S. suis in Ireland, identifying novel serotypes, sequence types, and phage interactions.

Findings

Irish S. suis isolates show high genetic diversity with 15 serotypes and 26 novel sequence types identified.

Irish isolates are phylogenetically dispersed globally but cluster within known pathogenic lineages, including the zoonotic lineage 1.

CRISPR-Cas systems in some strains target prophages, suggesting ongoing phage pressure and evolutionary connections between phage lineages.

Abstract

Workflow illustrating isolation of Streptococcus suis from pig carcasses, DNA extraction and sequencing, followed by in silico analysis of population structure, prophage content and anti-viral defence systems.

Streptococcus suis is a major pig pathogen with zoonotic potential, posing an occupational risk to farmers and meat handlers. We characterized 110 S. suis 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. In silico 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 S. suis genomes showed that the Irish isolates were phylogenetically dispersed across the broader global S. suis 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-S. suis streptococcal phages, and phylogenomic analysis revealed that Vansinderenvirus phages clustered with S. suis rather than other Streptococcus thermophilus phages, suggesting evolutionary connections between phage lineages infecting different streptococci.

This study presents the first comprehensive genomic characterization of S. suis in Ireland, revealing a diverse population with significant implications for animal and human health.

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