Pangenome-based network analysis reveals subpopulations of Salmonella Infantis pESI-like plasmids that differ temporally and regionally

Authors: Anderson, Christopher; Villanueva, Paul; BRADSHAW, DAVID - Oak Ridge Institute For Science And Education (ORISE); Bearson, Bradley - Brad; Bearson, Shawn

Submitted to: American Society for Microbiology
Publication Type: Abstract Only
Publication Acceptance Date: 2/28/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The increasing carriage of pESI megaplasmids encoding antimicrobial, heavy metal, and disinfectant resistance is a primary driver in the emergence of Salmonella enterica serovar Infantis (S. Infantis) as a global health threat. The evolution of pESI variants with additional virulence and fitness genes raises food safety concerns about multidrug-resistant S. Infantis strains with enhanced persistence in food-producing animals. Understanding the plasticity of pESI-like plasmids is crucial for effective risk management. Here, we describe a framework to delineate the gene content and spread of subpopulations of pESI-like plasmids. By annotating genes commonly found on pESI plasmids, we identified 5,545 S. Infantis isolates with pESI-like plasmids originating from poultry-associated samples collected by the USDA Food Safety and Inspection Service between 2016-2022. A network was constructed based on plasmid pangenome relatedness, and subpopulations of pESI-like plasmids were identified through the Louvain network community detection algorithm. The diversity of pESI-like subpopulations increased from 2016 to 2022, and the frequency of the plasmid subpopulations was significantly associated with sampling year and geographical region. The proportion of the most frequently detected pESI-like subpopulation decreased from 79.5% in 2016 to 27.2% in 2022, while the next two largest subpopulations increased from 2.7% and 13.7% relative abundance to 25.0% and 33.4% in the same timeframe. Further, the estimated genome size and gene content, including genes conferring resistance to sulphonamides, tetracyclines, trimethoprim, and cephalosporins, differed between subpopulations. In 2021 and 2022, subpopulations with smaller estimated genome sizes and fewer antimicrobial resistance genes have become more prevalent in the West and Northeast regions. Selective pressures within various environments may drive the acquisition or loss of advantageous or metabolically costly genetic elements, respectively, and our findings demonstrate how pangenome analysis can be leveraged to better understand the evolution of the genetic content of pESI-like plasmids in S. Infantis.