Prevalence and Genomic Insight of Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae (ESBL-E) Isolated from Food Sources in Saudi Arabia

Enterobacteriaceae are a diverse family of Gram-negative, rod-shaped, facultatively anaerobic bacteria that serve as important indicators of food safety. Many species within this family, including common foodborne pathogens, are major contributors to both community- and hospital-acquired infections. The widespread use of antibiotics in agriculture has facilitated the emergence and dissemination of antimicrobial-resistant bacteria in food products, livestock, and the environment. This study investigated the prevalence and genomic characteristics of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae isolated from food sources in Saudi Arabia. A total of 160 isolates preserved in the Saudi Food and Drug Authority (SFDA) biobank were screened for antimicrobial resistance using indicator β-lactam antibiotics according to CLSI guidelines. Phenotypic screening indicated that Escherichia coli O145, E. coli O157, Klebsiella pneumoniae, and Cronobacter sakazakii isolates were not ESBL producers. In contrast, ESBL production was detected among Salmonella spp. isolates, and 13 confirmed ESBL-producing Salmonella isolates were subsequently subjected to whole-genome sequencing (WGS). Genomic analysis identified the ESBL gene blaCTX-M-65, along with multiple antimicrobial resistance determinants, virulence-associated genes, and plasmid replicons, predominantly belonging to the IncFIB and IncX families. These findings provide important insights into the occurrence of ESBL-producing Enterobacteriaceae in food sources and highlight the value of integrating phenotypic and genomic approaches for antimicrobial resistance surveillance within food safety systems.