Genomic insights into the prevalence and genetic diversity of Salmonella in chicken eggs in Saudi Arabia

TL;DR

This study uses genomic analysis to understand Salmonella contamination in chicken eggs in Saudi Arabia, revealing differences in contamination sources and antibiotic resistance.

Contribution

The first comprehensive genomic characterization of Salmonella in chicken eggs in Saudi Arabia, linking environmental and internal contamination with antimicrobial resistance.

Findings

Salmonella was detected in 9% of samples, with higher contamination on eggshells than inside.

Egg content isolates showed higher antimicrobial resistance and clinically significant serovars.

Multidrug resistance genes were identified, indicating potential spread of resistant strains through the food chain.

Abstract

Salmonella enterica remains one of the leading causes of foodborne illness globally, with poultry and eggs recognized as major transmission vehicles. In Saudi Arabia, data integrating genomic epidemiology with conventional microbiological surveillance in eggs remain limited. This study aimed to provide the first comprehensive genomic characterization of Salmonella isolated from chicken eggs in the Kingdom, assessing prevalence, serovar distribution, virulence determinants, and antimicrobial resistance (AMR) profiles to better inform food safety risk assessment within a One Health framework.

A total of 260 chicken eggs were collected and analyzed using conventional microbiological culture methods for Salmonella detection. Confirmed isolates underwent whole-genome sequencing (WGS) to determine serovar identity, virulence-associated genes, and antimicrobial resistance determinants. Comparative genomic analyses were conducted to evaluate differences between isolates recovered from eggshell surfaces and egg contents, with particular focus on multidrug resistance (MDR) genes, plasmid-mediated β-lactamases, and fluoroquinolone resistance determinants.

Salmonella was detected in 9% of the analyzed samples. Contamination was more frequently identified on eggshells than within egg contents, suggesting a substantial contribution of environmental exposure during handling and distribution. Twelve distinct serovars were identified, with Salmonella Enteritidis and Salmonella typhimurium predominating.Eggshell isolates demonstrated broader serovar diversity but carried fewer antimicrobial resistance determinants. In contrast, isolates recovered from egg contents were associated with clinically significant serovars and exhibited a higher prevalence of antimicrobial resistance genes. Whole-genome analysis revealed multidrug resistance profiles, including plasmid-mediated β-lactamase genes and fluoroquinolone resistance determinants, indicating the potential for dissemination of resistant strains through the food chain.

The findings demonstrate dual contamination pathways in eggs: external contamination linked to environmental handling factors and internal contamination associated with serovars of greater clinical relevance and elevated AMR gene burden. The detection of multidrug resistance determinants highlights the risk of horizontal transmission of resistance elements across foodborne bacteria.These results underscore the importance of integrating genomic surveillance into national food safety systems to strengthen risk assessment, guide targeted control measures, and support antimicrobial resistance monitoring. Within the Saudi context, implementing WGS-based surveillance aligns with One Health principles and enhances preparedness against emerging foodborne AMR threats.

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