Whole-genome sequencing reveals clonal connectivity of Listeria monocytogenes across hygienically separated processing lines within a fresh-cut produce facility prior to sanitation

This repository contains processed data, genome assemblies, phylogenetic files, genomic profiles, and analysis scripts associated with the above-named publication. The study investigated the genomic diversity and virulence-associated traits of Listeria monocytogenes isolates (n=99) recovered from two fresh-cut processing facilities (cut-fruit and cut-lettuce lines) across three pre-sanitation sampling campaigns. Whole-genome sequencing (WGS) was performed on all isolates and analysed using MLST, cgMLST, high-quality SNP (hqSNP) phylogenetics, and screening for virulence, antimicrobial resistance, and mobile genetic elements. Raw sequencing reads are NOT included in this repository. They are available in the European Nucleotide Archive (ENA) under study accession PRJEB109318 (secondary accession ERP190100).