Ancient genomes lack the virulence-associated Ypf prophage present in modern pandemic strains.

is the causative agent of at least three major plague pandemics (Justinianic, Medieval and Modern). Previous studies on ancient genomes revealed that several genomic alterations had occurred approximately 5000-3000 years ago and contributed to the remarkable virulence of this pathogen. How a subset of strains evolved to cause the Modern pandemic is less well-understood. Here, we examined the virulence-associated prophage (Ypf), which had been postulated to be exclusively present in the genomes of strains associated with the Modern pandemic. The analysis of two new genomes from medieval/early modern Denmark confirmed that the phage is absent from the genome of strains dating to this time period. An extended comparative genome analysis of over 300 strains spanning more than 5000 years showed that the prophage is found in the genomes of modern strains only and suggests an integration into the genome during recent evolution. The phage-encoded Zot protein showed structural homology to a virulence factor of . Similar to modern , we observed phages with a common origin to Ypf in individual strains of other bacterial species. Our findings present an updated view on the prevalence of Ypf, which might contribute to our understanding of the host spectrum, geographical spread and virulence of responsible for the Modern pandemic.