Prophage {Phi}ESI promotes competitive dominance in the emergent Salmonella serovar Infantis lineage

Abstract

The global spread of multidrug-resistant Salmonella enterica serovar Infantis has been largely attributed to the pESI megaplasmid, yet additional factors underlying the ecological success of this lineage remain unclear. Here, we characterize {Phi}ESI (phage of emergent Salmonella Infantis), a temperate bacteriophage discovered during coculture of an emergent pESI-positive strain (PM57) and a non-emergent strain (DR006). Phage {Phi}ESI shows a siphovirus morphotype with a long tail and an elongated head, with a genome of 46,490 bp, which is integrated as a prophage in the 3-end of an Arg-tRNA gene in PM57, but is absent in DR006, which is susceptible to the {Phi}ESI-mediated lysis. The screening of {Phi}ESI genes across 20,429 global Salmonella Infantis genomes revealed an almost exclusive association of {Phi}ESI and {Phi}ESI-like phages with the emergent pESI-positive Salmonella Infantis lineage. Further bioinformatic analyses of complete chromosomes revealed diverse {Phi}ESI insertion profiles showing geographic clustering, and the presence of large-scale chromosomal inversions flanked by {Phi}ESI genes. Competition assays showed that PM57 outcompeted DR006 in coculture, coinciding with high viral loads that selectively targeted DR006, and susceptibility assays showed that strains lacking {Phi}ESI/{Phi}ESI-like prophages were susceptible to {Phi}ESI-mediated lysis. Together, our findings identify {Phi}ESI as a competitive factor associated with emergent Salmonella Infantis, able to selectively eliminate susceptible competitors. Our findings suggest that {Phi}ESI/{Phi}ESI-like prophages contributed to the persistence and global dissemination of the emergent Salmonella Infantis lineage. ImportanceEmergent multidrug-resistant Salmonella enterica serovar Infantis strains carrying pESI megaplasmids have spread worldwide, posing a global public health threat and a significant economic burden. Nevertheless, the factors contributing to the success of this foodborne pathogen, beyond pESI, remain poorly understood. Here, we describe {Phi}ESI, a novel temperate bacteriophage carried by the emergent lineage as a chromosomally integrated prophage. We show that {Phi}ESI provides a competitive advantage to emergent strains by selectively killing non-emergent competitors while protecting lysogens from reinfection. Our findings uncover the contribution of {Phi}ESI/{Phi}ESI-like bacteriophages to the success of emergent Salmonella Infantis, highlighting how lineage-associated prophages can shape the ecological success of pathogenic bacteria.