Lineage-aware comparative genomics shows no consistent reservoir-specific plasmidome in low-moisture food associated Salmonella Enteritidis.

Foodborne outbreaks of Salmonella Enteritidis have been historically linked to poultry, but outbreaks associated with low-moisture foods (LMFs) are increasingly reported. Since plasmids encode stress-response and tolerance traits that support persistence in dry environments, this study evaluated whether LMF-associated (nuts, spices, grains, etc.) S. enteritidis isolates carry lineage-specific plasmidomes distinct from non-LMF (poultry/egg-associated and production-environment). A total of 2824 non-clinical records were curated from the NCBI Pathogen Detection database and organized into 51 SNP clusters (30 non-LMF, 11 LMF, 10 mixed). Reservoir comparisons were restricted to mixed clusters (319 non-LMF, 24 LMF at the metadata level) using 64 assemblies (24 LMF, 40 non-LMF). PlasmidFinder identified that most genomes contained IncF plasmid (IncFIB(S) 90.6%, IncFII(S) 89.1%), though global Fisher's exact tests and lineage-stratified CMH tests (FDR-adjusted) identified no replicon family enriched in LMF. MOB-suite reconstructed 88 plasmids from 63/64 genomes and assigned 11 backbone clusters dominated by AB461 (58/64 genomes). Plasmid counts, mobility profiles, and functional annotations were similar across reservoirs, with variations attributable to SNP clusters rather than isolation source. In the largest mixed lineage (PDS000218745.3; 9 LMF, 15 controls), no LMF-enriched plasmid gene products were detected. Shared accessory plasmids occurred in both reservoirs, including AB233 carrying mer operon genes and emrE, while rare LMF-only backbones (AB947; AA149; AA372 encoding TEM β-lactamase, toxN, mbeA, proQ) were isolate-specific. Pangenome analysis of 4899 gene clusters likewise found no accessory genes significantly enriched in LMF after lineage-stratified testing. Plasmid architecture was largely lineage-structured with limited evidence for association with LMF environments.