Lineage-aware comparative genomics of the Salmonella Enteritidis plasmidome in low-moisture food and non-LMF reservoirs

Overview

This repository contains the code, curated metadata, processed tables, figures, and manuscript-linked outputs for a lineage-aware comparative genomics study of Salmonella Enteritidis from low-moisture food (LMF) and non-LMF reservoirs.

Main finding

After controlling for lineage using SNP cluster stratification, we found no consistent reservoir-specific enrichment of plasmid replicons, plasmid backbones, acquired AMR determinants, or accessory gene functions in LMF-associated isolates. Genomic variation was structured primarily by lineage rather than reservoir origin.

Repository structure

• metadata/ source cohort metadata files
• data/processed/ intermediate and processed analysis tables
• data/intermediate/ bulky working outputs
• scripts/notebooks/ analysis notebooks
• results/figures/ final figure files
• results/tables/ manuscript-linked supplementary tables
• manuscript/ manuscript files
• docs/ supporting documentation
• workflow/ workflow files

Notes

This repository is organized to separate raw or intermediate analysis material from final manuscript outputs.