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

Abstract

Salmonella enterica 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. Salmonella Enteritidis causes self-limited gastroenteritis in humans, which can progress to systemic infection in immunocompromised individuals. The Salmonella 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 Salmonella serotypes, and Salmonella Enteritidis infections are often related to the consumption of chicken meat and eggs. This study reports the whole-genome sequence of Salmonella 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 Salmonella 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 Salmon_118970_sal3 and Gifsy-2. The genome also contains two CRISPR systems. Comparative genome analysis with Salmonella Enteritidis ATCC 13076, Salmonella Typhimurium ATCC 13311, and Salmonella Typhimurium ATCC 14028 demonstrates that most unshared genes are related to metabolism, membrane, and hypothetical proteins. Finally, the phenotypic characterization evidenced differences among Salmonella 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 Salmonella Enteritidis PT4 578.

Keywords: Salmonella enteritidis; biofilm; foodborne pathogen; genome; rdar morphotype; virulence determinants.

Fig. 1.. Genome map of the chromosome of Salmonella Enteritidis PT4 578. The coding DNA sequences (CDS) on the heavy and light strands are depicted in dark green and light blue, respectively. Light purple marks denote tRNA genes, while pink represents rRNA genes. Resistance genes are in yellow. SPI-1 virulence factors are in orange and SPI-2 in blue. Regions of incomplete prophage are shown in red, while intact prophage regions are in green. The two inner tracks represent G+C content and GC skew. The DNAPlotter [69] generated the circular map.

Fig. 2.. Genetic organization of virulence factors in SPI-1 (a) and SPI-2 (b) in the Salmonella Enteritidis PT4 578 genome. The DNAPlotter [69] generated the linear map.

Fig. 3.. Genetic organization of CRISPR-Cas system in the Salmonella Enteritidis PT4 578 genome. The DNAPlotter [69] generated the linear map.

Fig. 4.. Venn diagram of clusters of orthologous proteins of Salmonella Enteritidis PT4 578 and shared with Salmonella Enteritidis ATCC 13076, Salmonella Typhimurium ATCC 14028, and Salmonella Typhimurium ATCC 13311 (a). Similarity matrix for pairwise genome comparisons, where the heatmap shows the ortholog cluster between any pair of genomes (b).

Fig. 5.. Swimming and swarming motilities of Salmonella Enteritidis PT4 578 (SEPT4578), Salmonella Enteritidis ATCC 13076 (SE13076), Salmonella Typhimurium ATCC 13311 (ST13311), and Salmonella Typhimurium ATCC 14028 (ST14028) at 28 °C for 10 and 40 h, respectively (a). Colony morphology of SEPT4578, SE13076, ST13311, and ST14028 in Congo red agar (b). Adhered cells of SEPT4578, SE13076, ST13311, and ST14028 on polystyrene microplates cultivated at 28 °C for 40 h (c). Error bars indicate a standard deviation, and the asterisk (*) and the different numbers mean significant difference (P<0.05).