Exploring the prophage biology of Salmonella enterica serovar Typhimurium ST313

In the past 30 years, Salmonella bloodstream infections have become a significant health problem in sub-Saharan Africa and are responsible for the deaths of ~390,000 people each year. The disease is largely caused by a recently described sequence type of Salmonella Typhimurium: ST313. Comparative genomic analysis showed that the ST313 lineage is closely-related to the ancestral gastroenteritis-associated Typhimurium sequence type ST19, but carries a distinct prophage repertoire. I hypothesised that prophages contribute to the biology of this clinically-relevant ST. In this thesis I show that the African ST313 representative strain D23580 contains 5 full length prophages. Prophage BTP1 and BTP5 are undescribed, novel prophages specific to African ST313 strains, whilst Gifsy-2, ST64B and Gifsy-1 are well-characterised prophages found in other strains of S. Typhimurium. Of the five prophages, only BTP1 and BTP5 showed evidence for functional phage production, and mutations responsible for the inactivation of Gifsy-2, ST64B and Gifsy-1 were identified. The BTP1 prophage spontaneously induced at a prolific rate, estimated to result in the phage-mediated lysis of approximately 0.2% of the lysogenic cell population. A GFP reporter system was developed to visualise the spontaneous induction of the BTP1 prophage at the single-cell level. Though the BTP5 phage could not be studied using traditional plaque assay methodology, there was evidence that the BTP5 prophage was capable of forming viable BTP5 phage that could lysogenise naïve hosts. I analysed the genomes of recently discovered ST313 isolates from the UK and show that ST313 in the UK represents a distinct population of antibiotic susceptible strains associated with gastrointestinal infection. Additionally, analysis of the UK-ST313 genomes indicated that the BTP1 and BTP5 prophages were acquired independently by the two African ST313 lineages, showing convergent evolution to acquire and conserve the BTP1 and BTP5 prophages. Finally I present evidence that the prophages, in particular BTP5, effect the global gene expression of ST313, and the ST313-td gene of BTP1 mediates lysogenic conversion by functioning as a superinfection immunity factor against infection by Salmonella phage P22. The implications of these findings for understanding the pathogen in terms of ecological niche, host range and invasiveness in humans is discussed.