Genome-Wide Comparative Functional Analyses Reveal Adaptations of Salmonella sv. Newport to a Plant Colonization Lifestyle

Outbreaks of salmonellosis linked to the consumption of vegetables have been disproportionately associated with strains of serovar Newport. We tested the hypothesis that strains of sv. Newport have evolved unique adaptations to persistence in plants that are not shared by strains of other <i>Salmonella</i> serovars. We used a genome-wide mutant screen to compare growth in tomato fruit of a sv. Newport strain from an outbreak traced to tomatoes, and a sv. Typhimurium strain from animals. Most genes in the sv. Newport strain that were selected during persistence in tomatoes were shared with, and similarly selected in, the sv. Typhimurium strain. Many of their functions are linked to central metabolism, including amino acid biosynthetic pathways, iron acquisition, and maintenance of cell structure. One exception was a greater need for the core genes involved in purine metabolism in sv. Typhimurium than in sv. Newport. We discovered a gene, <i>papA</i>, that was unique to sv. Newport and contributed to the strain's fitness in tomatoes. The <i>papA</i> gene was present in about 25% of sv. Newport Group III genomes and generally absent from other <i>Salmonella</i> genomes. Homologs of <i>papA</i> were detected in the genomes of <i>Pantoea, Dickeya</i>, and <i>Pectobacterium</i>, members of the Enterobacteriacea family that can colonize both plants and animals.