Diverse prophages of Salmonella enterica show potential role in disease and diversity
Kirstie Andrews 1*, Toby Landeryou 2, Janet Yakubu Nale 3
- Centre for Epidemiology and Planetary Health
- Department of Veterinary and Animal Science
- Scotland's Rural College
- Inverness
- United Kingdom
Janet Yakubu Nale janet.nale@sruc.ac.uk
Nontyphoidal salmonellosis is an important foodborne and zoonotic infection, causing significant global public health concern. Diverse Salmonella serovars are multi-drug resistant and encode for several virulence indicators, however, little is known on the role prophages play in driving these phenotypes. Here, we determined the potential contributions that prophages make to the diversity and pathogenicity of Salmonella. To do this, we explored 75 genomes from publicly available strains, representing the 15 most prevalent Salmonella serovars found in the United Kingdom. All prophage elements from the genomes of the strains were extracted using PHASTER tool and classified based on their completeness. The genomes of the intact prophages were further analysed for the presence of potential virulence factors using VFanalyzer platform within the Virulence Factor Database. Furthermore, we constructed phylogenetic relationships to reflect the genome diversity of the representative intact prophages using Mega 11. We identified 615 prophage elements from the genomes of the examined Salmonella strains and revealed that 195 prophages are intact, 332 incomplete and 88 were questionable. The prophages were found to be more prevalent in S. Heidelberg, S. Inverness and S. Newport (encoding 51-58 prophages each) compared to S. Agona, S. Braenderup, S. Bovismorbificans, S. Choleraesuis, S. Dublin, S. Enteritidis, S. Infantis, S. Java, S. Javiana, S. Stanley, S. Typhimurium and S. Virchow (with 29-53 prophages each). Cumulatively, 2760 virulence factors were detected in the genomes of the intact prophages and associated with cellular functionality being linked to effector delivery/secretion system (73%), adherence (22%), magnesium uptake (2.7%), resistance to antimicrobial peptides (0.94%), stress/survival (0.4%), exotoxins (0.32%) and antivirulence (0.18%). Various close and distant clusters were formed among the prophages suggesting different lineages and associations with prophages of other Enterobacteriaceae. Our data showed strong correlation between Salmonella prophages and numerous virulence factors, and contributing to diversity, pathogenicity and success of specific serovars. Further work would focus on how these prophages drive the evolution and selection of prevalent serovars responsible for salmonellosis in the United Kingdom.