AUTHOR=Abdelhamid Ahmed G. , Yousef Ahmed E. 

TITLE=Egg-associated Salmonella enterica serovar Enteritidis: comparative genomics unveils phylogenetic links, virulence potential, and antimicrobial resistance traits

JOURNAL=Frontiers in Microbiology

VOLUME=Volume 14 - 2023

YEAR=2023

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1278821

DOI=10.3389/fmicb.2023.1278821

ISSN=1664-302X

ABSTRACT=Salmonella enterica serovar Enteritidis (SE) remains a frequent cause of foodborne illnesses associated with consumption of contaminated hen eggs. Such food-pathogen association has been demonstrated epidemiologically but the molecular basis for this association has not been explored. Comparative genomic analysis was implemented to decipher the phylogenomic characteristics, antimicrobial resistance, and virulence potential of eggs-associated SE. Analyzing 1,004 genomes belonging to 841 sequence types of food-isolated SE strains suggests a high genomic similarity within the eggs-related lineage, which was phylogenetically close to SE strains isolated from poultry but was different from those isolated from beef. Core genome- and single nucleotide polymorphism (SNP)-based phylogeny of 74 SE strains of egg origin showcased two distinct sublineages. Time-scaled phylogeny supported the possibility of a common ancestor of eggs-related SE lineages. Additionally, genome mining revealed frequent antibiotic resistance, due to the presence of aac(6')-Iaa and mdsAB encoded on the genomes of eggs-associated SE strains. For virulence genes profiling, 103 to 113 virulence determinants were identified in the eggs-associated SE, which were comparable to 112 determinants found in human-associated SE, emphasizing the capacity of egg-associated strains to infect humans and cause disease. Findings of this study proved the genomic similarity of egg-associated SE strains, and these were closely related to poultry strains. The eggs-associated strains also harbor virulence genes equivalent to those found in human-associated SE strains. The analysis provided critical insights into the genetic structure, phylogenomics, and dynamics of virulence and antibiotic resistance of Salmonella Enteritidis circulating in eggs and emphasizing the necessity of implementing anti-Salmonella intervention strategies, starting at the production stage of the poultry supply chain.