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 very closely-related to the ancestral gastroenteritis-associated Typhimurium sequence type, but carries two novel prophages.

An RNA-seq-based transcriptomic analysis revealed extensive expression of the late genes of novel prophage BTP1 during in vitro growth, suggesting spontaneous induction of the phage in a sub-set of the bacterial population. We found that the abundance of infective BTP1 virions equals the number of bacterial cells in non-induced cultures. A GFP-based reporter system allowed visualisation and quantification of bacteria undergoing spontaneous prophage induction. Genomic and TEM characterisation showed that BTP1 is a lambdoid podoviridae which closely resembles Salmonella phage P22. The transcriptome of BTP1 revealed expression of a number of putative cargo genes.

Spontaneous prophage induction is a well-documented phenomenon in bacteria, but has not been well-studied in clinically-relevant strains. The impact of spontaneous prophage induction on bacterial pathogens and disease is not well understood. Our data pose interesting questions about the potential fitness costs and benefits of novel prophages in epidemic S. Typhimurium ST313.