# Molecular epidemiology of Salmonella Enteritidis in humans and animals in Spain

## TL;DR

This study analyzed Salmonella Enteritidis isolates from Spain to understand their genetic diversity, antimicrobial resistance patterns, and sources, revealing distinct phylogenetic groups and resistance dynamics.

## Contribution

The study provides new insights into the molecular epidemiology and antimicrobial resistance dynamics of Salmonella Enteritidis in Spain across multiple sources and years.

## Key findings

- Human isolates predominantly clustered in clade I with pan-susceptible phenotypes and no AMR determinants.
- Clade II strains from animal/food/environment sources showed high fluoroquinolone resistance and carried ARGs and plasmid replicons like IncX1.
- Human isolates had unique resistance genes (e.g., extended-spectrum beta-lactamase) not found in animal isolates.

## Abstract

Salmonella Enteritidis, the most prevalent serovar-causing human gastroenteritis, has been traditionally linked to poultry sources. Although antimicrobial resistance (AMR) is not common in this serovar, increasing levels of resistance to fluoroquinolones and ampicillin have been reported in the last few years. Here, 298 isolates retrieved from different sources (human, livestock, wildlife, food, and environment) and years (2002–2021) in Spain were analyzed to evaluate their diversity, the distribution of AMR-conferring genes (ARGs), and mutations and reconstruct the epidemiology of infection due to this serovar. Isolates were clustered in two major clades (I and II), with strains in clade I (including 61.5% of all human isolates) displaying a pan-susceptible phenotype and not carrying AMR determinants. In contrast, clade II included 80.7% of isolates from animal/food/environmental sources, with the majority (69.8%) harboring mutations in the quinolone resistance determinant regions (QRDR). ARGs, although rare, were mostly found in clade II strains that also carried plasmid replicons, among which IncX1 was the most common. Although higher levels of phenotypic resistance were found in animal isolates, extended-spectrum beta-lactamase, plasmid-mediated AmpC, and carbapenemase-encoding genes were only found among human isolates. In summary, the majority of human and animal isolates from Spanish sources in our collection were classified in different phylogenetic branches, suggesting that additional sources are contributing to the occurrence of foodborne infections in Spain. Furthermore, the different distributions of virulence factors and ARGs in isolates from different sources and their association with specific plasmids suggest the presence of different dynamics contributing to the selection of resistant strains.