Understanding the role of phages against Streptococcus suis in microbial ecology and biocontrol

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dc.check.chapterOfThesisI wish to place an embargo the whole thesis with a lift date of 31st December 2027en
dc.check.date2027-12-31
dc.check.infoControlled Access
dc.contributor.advisorMahony, Jennifer
dc.contributor.advisorexternalKenny, John G.
dc.contributor.advisorexternalManzanilla, Edgar Garcia
dc.contributor.authorOsei, Emmanuel Kuffouren
dc.contributor.funderDepartment of Agriculture, Food and the Marine, Ireland
dc.contributor.funderTeagasc
dc.date.accessioned2026-02-18T14:52:36Z
dc.date.available2026-02-18T14:52:36Z
dc.date.issued2025
dc.date.submitted2025
dc.descriptionControlled Access
dc.description.abstractBacterial pathogens compromise the sustainability of livestock farming and public health through production losses, welfare concerns, and contamination of food products. The growing problem of antimicrobial resistance further complicates disease control along the farm-to-fork continuum. Streptococcus suis, a major zoonotic pathogen of pigs, exemplifies these challenges. Bacteriophage (phage) biocontrol offers a promising adjunct or alternative to conventional antibiotics due to their ability to specifically target and kill bacteria, yet several pathogens remain underexplored in the veterinary context, in particular, S. suis. This thesis uses in vitro characterisation, genomics, and metagenomics to investigate phage-S. suis interactions, as well as the therapeutic potential of S. suis-infecting phages. A comprehensive review of phage applications within food production sector revealed that only one “lytic” phage had previously been isolated and sequenced against S. suis. This prompted an analysis of prophage prevalence and anti-viral defence systems encoded in S. suis using publicly available genomes. Despite limited reports on virulent phages, several diverse prophages were identified across different serotypes and geographical origins. Additionally, we found that unlike other streptococci in which CRISPR systems are nearly universally encoded, less than one-third of S. suis genomes encoded it. The Irish S. suis landscape was explored through serotyping and whole-genome sequencing of isolates from diseased pigs collected between 2005–2022. Serotype 9 emerged as the leading cause of infection among diagnostic submissions. Phylogenetic analysis showed Irish isolates were dispersed throughout the global S. suis population rather than forming a distinct clade. However, a stable endemic clonal lineage was identified, with members showing minimal genetic variation over a decade. Genomic analysis of the prophage load and anti-viral defence arsenal of the Irish isolates echoed earlier findings, suggesting an ongoing phage pressure. Restriction-modification systems were almost ubiquitous in the genomes, and a high diversity of prophages were identified that showed no obvious associations with specific serotypes or sequence types (STs). CRISPR spacer analysis and phylogenomic reconstruction revealed evolutionary links between phage lineages infecting different streptococci, particularly, Streptococcus thermophilus. The resolution of the Irish S. suis population structure enabled the selection of representative strains for subsequent phage screening. Two phages, named Bonnie and Clyde, were isolated and characterised. They infect 58% of S. suis strains tested, including representatives of seven different serotypes and thirteen STs. Both phages demonstrated remarkable pH stability. Clyde could supress bacterial growth in vitro within two multi-strain mixes designed to simulate multi-serotype infections. Genomic analysis revealed that both phages represent novel species within two distinct novel genera. Furthermore, AlphaFold predictions of phage adhesion devices revealed two distinct lineages: S. thermophilus phage-like (Bonnie) and S. suis phage-like (Clyde). The structural similarities between the adhesion devices of Bonnie and S. thermophilus phages supported earlier observations about evolutionary links between phages infecting different streptococcal species. Although two phages were isolated and characterised, phage screening attempts were mostly unsuccessful despite the identification of a reservoir of prophages within the genomes of isolates. This raised questions about whether extracellular S. suis phages exist in the pig oral environment. To address this question, microbiome and viromics approaches were used. First, we characterised the overall microbiome and DNA virome and found that both exhibit coordinated age-associated restructuring. Secondly, using paired bulk and virus-like particle (VLP) sequencing, 32 viral species predicted to target S. suis were identified. The majority of these phages were predicted to be virulent (n=18) compared to non-prophage temperate (n=14), with virulent phages having significantly smaller genomes. S. suis phage abundance peaked during early post-weaning stage, which coincides with the period when S. suis colonisation is the most dynamic and clinical outbreaks often occur. This thesis significantly expands our understanding of S. suis-phage interactions through in-depth characterisation of Bonnie and Clyde, and genomic analysis of prophage diversity and anti-viral defence systems. In addition, it establishes a framework for streamlining phage discovery by identifying viral populations enriched under specific host conditions to focus future isolation efforts. Finally, the first national-level genomic characterisation of S. suis provides a critical baseline for tracking pathogen evolution and informing future intervention strategies.en
dc.description.statusNot peer revieweden
dc.description.versionAccepted Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationOsei, E. K. 2025. Understanding the role of phages against Streptococcus suis in microbial ecology and biocontrol. PhD Thesis, University College Cork.
dc.identifier.endpage178
dc.identifier.urihttps://hdl.handle.net/10468/18548
dc.language.isoenen
dc.publisherUniversity College Corken
dc.relation.projectDepartment of Agriculture, Food and the Marine, Ireland (Improved Pig Health through the Novel Application of SynBio in Phage Therapy (2020US-IRL201))
dc.rights© 2025, Emmanuel Kuffour Osei.
dc.rights.urihttps://creativecommons.org/licenses/by-nc/4.0/
dc.subjectAnti-viral defenceen
dc.subjectAntimicrobial resistanceen
dc.subjectBacteriophageen
dc.subjectGenomicsen
dc.subjectFooden
dc.subjectPhage therapyen
dc.subjectMicrobiomeen
dc.subjectPigen
dc.subjectStreptococcus suisen
dc.subjectViromicsen
dc.subjectZoonosisen
dc.titleUnderstanding the role of phages against Streptococcus suis in microbial ecology and biocontrol
dc.typeDoctoral thesisen
dc.type.qualificationlevelDoctoralen
dc.type.qualificationnamePhD - Doctor of Philosophyen
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