Molecular characterization of pESI-like megaplasmids in Salmonella Infantis from poultry in Lebanon.

Abstract

UNLABELLED: Salmonella enterica serovar Infantis has emerged as a globally disseminated multidrug-resistant (MDR) pathogen, largely driven by the spread of the plasmid of emerging Salmonella Infantis (pESI)-like megaplasmid. In our study, we investigated the prevalence, antimicrobial resistance (AMR) phenotypes, and genomic features of S. Infantis isolates collected from poultry farms in Lebanon. A total of 72 isolates were recovered during a nationwide surveillance effort, among which 67 (93%) were MDR based on antimicrobial susceptibility testing (disk diffusion and broth microdilution) results, including resistance to critically important agents such as quinolones, and highly important classes such as tetracyclines and sulfonamides. Whole-genome sequencing was performed on 19 isolates selected through a stratified approach to encompass all identified AMR phenotypes; this analysis revealed a conserved pESI-like backbone together with MDR-associated determinants, including sul1, tet(A), and aadA. Plasmid marker analysis confirmed the presence of pESI in the majority of isolates, with plasmid-associated genes (ardA and trbA) and replicon markers (IncP and IncFIB(pN55391)) among the most prevalent. Comparative plasmid alignments with representative pESI sequences from Italy, Turkey, and the United States revealed strong conservation of the backbone alongside regional variation in AMR gene content. These findings highlight the role of poultry production systems in Lebanon as reservoirs for pESI-like megaplasmids and MDR S. Infantis, underscoring the zoonotic and public health risks posed at the human-animal-environment interface. Strengthened surveillance, antimicrobial stewardship, and biosecurity interventions are urgently needed to mitigate the spread of MDR S. Infantis within agriculture and beyond. IMPORTANCE: The emergence of plasmid of emerging Salmonella Infantis (pESI)-like megaplasmids has transformed Salmonella Infantis into a globally distributed multidrug-resistant (MDR) clone with the capacity to persist in livestock and disseminate resistance genes across ecological boundaries. Our study provides the first genomic characterization of pESI-positive S. Infantis from poultry farms in Lebanon, a region with high antimicrobial usage and limited stewardship frameworks. By integrating phenotypic susceptibility testing and whole-genome sequencing, we demonstrate that Lebanese isolates harbor conserved pESI-like backbone markers together with antimicrobial resistance determinants, aligning them with internationally circulating lineages. Comparative analysis with isolates from Italy, Turkey, and the United States highlights both the evolutionary stability and geographic diversity of pESI. These findings emphasize the urgent need for integrated surveillance and stewardship strategies to curb the spread of MDR S. Infantis and reduce the zoonotic risk at the human-animal-environment interface.