First Data on WGS-Based Typing and Antimicrobial Resistance of Human Salmonella Enteritidis Isolates in Greece

Abstract

Salmonella enterica subsp. enterica serotype Enteritidis (S. Enteritidis) is one of the major causes of foodborne infections and is responsible for many national and multi-country foodborne outbreaks worldwide. In Greece, human salmonellosis is a mandatory notifiable disease, with laboratory surveillance being on a voluntary basis. This study aims to provide the first insights into the genetic characteristics and antimicrobial resistance profiles of 47 S. Enteritidis human isolates using whole-genome sequencing (WGS) technology. The S. Enteritidis population was mainly resistant to fluoroquinolones due to gyrA point mutations, whereas one isolate presented a multi-resistant plasmid-mediated phenotype. ST11 was the most frequent sequence type, and phylogenetic analysis through the cgMLST and SNP methods revealed considerable genetic diversity. Regarding virulence factors, 8 out of the 24 known SPIs and C63PI were detected. Due to the observed variability between countries, it is of utmost importance to record the circulating S. Enteritidis strains' structure and genomic epidemiology at the national level. WGS is a valuable tool that is revolutionizing our approach to Salmonella by providing a deeper understanding of these pathogens and their impact on human health.

Keywords: S. Enteritidis; phylogenetic analysis; surveillance; whole-genome sequence-based typing.

Figure 1

The cgMLST-based phylogenetic tree of the 47 Salmonella Enteritidis strains isolated from human samples in 2023, Greece. The strain ID and year of isolation are given for each strain. The two cgMLST profiles 309241 and 207789, comprising quinolone-resistant isolates carrying the gyrA (D87Y) point mutation (black, dashed line rectangle), are highlighted in red and blue, respectively. The neighbor-joining tree based on S. Enteritidis cgMLST allelic profiles determined by the chewBACCA software version 3.5 [31]. The dendrogram was visualized with iTOL [32].

Figure 2

Single-Nucleotide Polymorphism (SNP)-based phylogenetic tree of the 47 Salmonella Enteritidis strains isolated from human samples in 2023, Greece. The strain ID and year of isolation are given for each strain. The quinolone-resistant S. Enteritidis isolates carrying the gyrA (D87Y) point mutation are marked with a black, dashed-line rectangle. The quinolone-resistant group of isolates comprises two cgMLST profiles, 309241 and 207789, which are highlighted in red and blue, respectively. SNP analysis was conducted using Snippy [33]; the maximum likelihood tree was constructed using RAxML [34] and visualized with iTOL [32].

Figure 3

A Single-Nucleotide Polymorphism (SNP)-based phylogenetic tree of 79 Salmonella Enteritidis strains; 47 were isolated from human samples in 2023, Greece, and 32 were downloaded from Enterobase. The strain ID, cgMLST profile, originating country, and year of isolation are given for each strain. Both the cgMLST profile and originating country are highlighted with different colors, explained in the respective legends. SNP analysis was conducted using Snippy [33]; the maximum likelihood tree was constructed using RAxML [34] and visualized with iTOL [32]. * Of the 44 S. Enteritidis cgMLST profile 318658 genomes found in Enterobase (accessed on 16 July 2024), 7 representative isolates were included in the phylogenetic tree.