Genome sequencing and analysis of Salmonella enterica subsp. enterica serotype Enteritidis PT4 578: insights into pathogenicity and virulence

<i>Salmonella enterica</i> serotype Enteritidis is a generalist serotype that adapts to different hosts and transmission niches. It has significant epidemiological relevance and is among the most prevalent serotypes distributed in several countries. <i>Salmonella</i> Enteritidis causes self-limited gastroenteritis in humans, which can progress to systemic infection in immunocompromised individuals. The <i>Salmonella</i> pathogenicity mechanism is multifactorial and complex, including the presence of virulence factors that are encoded by virulence genes. Poultry products are considered significant reservoirs of many <i>Salmonella</i> serotypes, and <i>Salmonella</i> Enteritidis infections are often related to the consumption of chicken meat and eggs. This study reports the whole-genome sequence of <i>Salmonella</i> Enteritidis PT4 strain 578. A total of 165 genes (3.66%) of the 4506 coding sequences (CDS) predicted in its genome are virulence factors associated with cell invasion, intestinal colonization, and intracellular survival. The genome harbours twelve <i>Salmonella</i> pathogenicity islands (SPIs), with the SPI-1 and SPI-2 genes encoding type III secretion systems (T3SS) showing high conservation. Six prophage-related sequences were found, with regions of intact prophages corresponding to <i>Salmon_118970_sal3</i> and <i>Gifsy-2</i>. The genome also contains two CRISPR systems. Comparative genome analysis with <i>Salmonella</i> Enteritidis ATCC 13076, <i>Salmonella</i> Typhimurium ATCC 13311, and <i>Salmonella</i> Typhimurium ATCC 14028 demonstrates that most unshared genes are related to metabolism, membrane, and hypothetical proteins. Finally, the phenotypic characterization evidenced differences among <i>Salmonella</i> Enteritidis PT4 578 and the other three serotypes regarding the expression of the red, dry, and rough (rdar) morphotype and biofilm formation. Overall, the genomic characterization and phenotypic properties expand knowledge of the mechanisms of pathogenicity in <i>Salmonella</i> Enteritidis PT4 578.