The genomic diversity of Salmonella Enteritidis from poultry and human clinical cases in Israel

Salmonella Enteritidis, a leading cause of foodborne illness worldwide, is often linked to poultry. Despite the limited genetic variation of the serotype, distinct lineages have been shown to circulate at both national and global scales, and invasive and antimicrobial-resistant strains have emerged. In Israel, despite active surveillance and mitigation measures in the poultry sector, the pathogen persists in commercial layer hen flocks and continues to cause human clinical infections. We aimed to characterize the genetic diversity and antimicrobial resistance (AMR) determinants of S . Enteritidis isolates from poultry and human clinical cases in Israel and to compare these findings with the genetic diversity of this serotype found globally. Whole-genome sequencing was performed on S . Enteritidis isolates from surveillance samples collected from layer hen flocks ( n =48) and human clinical cases ( n =29) between 2019 and 2022 and compared to a representative global dataset of sequences ( n =115). We identified a genetically diverse S . Enteritidis population in Israel. A dominant clade I and a smaller clade IV were ST11 and closely related to each of the major ‘Atlantic’ and ‘Global’ lineages circulating globally. These clades demonstrated shared circulation between poultry and human populations which may suggest poultry-associated transmission. In addition, three smaller distinct Israeli clades were not part of the global clades. These included clades II and III of ST11 and clade V of ST183, a rarely described sequence type in poultry. Mutations in the gyrA gene (D87G, D87Y and S83F) conferring resistance to fluoroquinolones were present in both human (6.9%) and poultry (10.4%) isolates from Israel, highlighting the importance of continued antimicrobial resistance surveillance in this serotype. These findings establish a genomic baseline to support control and mitigation policy for S . Enteritidis in Israel and contribute to the understanding of its genomic diversity globally.