Genetic diversity and mobile genetic element associated multidrug resistance in Salmonella enterica from broiler chickens in Egypt

Abstract

Abstract Salmonella enterica remains a leading foodborne zoonotic pathogen worldwide, with poultry serving as a major reservoir and vehicle for antimicrobial resistance dissemination to humans. This study investigated the genotypic basis and distribution of multidrug resistance (MDR) among 29 S. enterica isolates from broiler farms in Egypt, emphasizing the role of mobile genetic elements as integrons and the assessment of genetic relatedness using ERIC-PCR. Molecular screening revealed high prevalence of resistance determinants, including flo R (93.1%), tet A (86.2%), aph A1 (82.8%), cml A (75.9%), ere A (75.9%), sul I (62.1%), aad A1 (51.7%), dfr A1 (48.3%), aac (3)-IV (44.8%), tet B (41.4%), sul II (31.0%), aac (6′)-Ib-cr (24.1%), cat A1 (20.7%), fos A3 (20.7%), and qnr A (10.3%). High-risk serovars, including S. Jerusalem, S. Colorado, and S. Kentucky, harbored multiple resistance genes and exhibited pronounced XDR profiles. Notably, this study reports the detection of aph A1 and fos A3 in Salmonella isolates derived from broiler chickens, which may represent an early or uncommon finding in Egypt. Many resistance genes were associated with horizontally transferable class 1 integron, underscoring its key role in the dissemination of multidrug resistance (MDR) within poultry systems and along the food chain. ERIC-PCR genotyping segregated isolates into two major genetic groups with seven sub-clusters, reflecting clustering patterns and genetic diversity among the isolates, alongside notable heterogeneity in resistance, virulence, and biofilm-associated genes.Overall, poultry in Egypt represents a significant reservoir of genetically diverse and potentially transmissible MDR S. enterica , highlighting the need for enhanced antimicrobial stewardship and genomic surveillance to mitigate public health risks.