Genomic analysis of prophage prevalence and diversity in the bovine mastitis pathogen Streptococcus uberis

The prevalence and diversity of prophages carried by the major global bovine mastitis pathogen, Streptococcus uberis, are poorly characterized. Bacteriophages (phages) are viruses which can infect and kill bacteria. Prophages, phages that have integrated into the bacterial genome, can have a profound impact on the fitness of their host cell. Here, we analysed the prophage content of 661 S. uberis genomes, including 345 newly sequenced isolates. Using PhiSpy, we identified 766 prophages, which formed 2 distinct clades postulated to correspond to full-length and satellite prophages, respectively. Putative full-length prophages had larger genomes and encoded more structural and lytic genes. Putative satellite prophages, which are reliant on helper phages for their replication and lysis, had smaller genomes, fewer structural genes and no lysins. Genomic and phylogenetic differences between the clades suggested that these satellite prophages were distinct from the full-length prophages, rather than being cryptic remnants of the latter. We identified a diverse repertoire of prophage-encoded endolysins with potential as novel therapeutics. Finally, we contextualized our S. uberis prophages within the broader phylogeny of Streptococcus phages, by aligning them with 1,078 publicly available phage genomes. The same division between putative full-length and satellite phages was maintained in this larger Streptococcus phage phylogeny of 1,844 phages. Our findings underline the prevalence and diversity of prophages within S. uberis and lay the foundations for furthering our understanding of phage-host interactions in this significant veterinary pathogen.