Comparative Patho-Genomics of Salmonella enterica Serovar Enteritidis Reveal Potential Host-Specific Virulence Factors

<i>Salmonella enterica</i> serovar Enteritidis (<i>S.</i> Enteritidis) is one of the most common causes of bacterial foodborne infections worldwide. It has an extensive host range, including birds and humans, making it one of the most adaptable <i>Salmonella</i> serovars. This study aims to define the virulence gene profile of <i>S.</i> Enteritidis and identify genes critical to its host specificity. Currently, there is limited understanding of the molecular mechanisms that allow <i>S.</i> Enteritidis to continue as an important foodborne pathogen. To better understand the genes that may play a role in the host-specific virulence and/or fitness of <i>S.</i> Enteritidis, we first compiled a virulence gene profile-based genome analysis of sequenced <i>S.</i> Enteritidis strains isolated from shell eggs in our laboratory. This analysis was subsequently used to compare the representative genomes of <i>Salmonella</i> serovars with varying host ranges and <i>S.</i> Enteritidis genomes. The study involved a comprehensive and direct examination of the conservation of virulence and/or fitness factors, especially in a host-specific manner-an area that has not been previously explored. Key findings include the identification of 10 virulence-associated clusters of orthologous genes (COGs) specific to poultry-colonizing serovars and 12 virulence-associated COGs unique to human-colonizing serovars. Virulence/fitness-associated gene analysis identified more than 600 genes. The genome sequences of the two <i>S.</i> Enteritidis isolates were compared to those of the other serovars. Genome analysis revealed a core of 2817 COGs that were common to all the <i>Salmonella</i> serovars examined. Comparative genome analysis revealed that 10 virulence-associated COGs were specific to poultry-colonizing serovars, whereas 12 virulence-associated COGs were present in all human-colonizing serovars. Phylogenetic analyses further highlight the evolution of host specificity in <i>S</i>. Enteritidis. This study offers the first comprehensive analysis of genes that may be unique to and possibly essential for the colonization and/or pathogenesis of <i>S.</i> Enteritidis in various and specific hosts.