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).本数据集仓库包含与上述已发表论文相关的处理后数据、基因组组装结果、系统发育分析文件、基因组特征谱以及分析脚本。本研究针对从两家运营鲜切水果与鲜切生菜生产线的鲜切食品加工设施的三次消毒前采样批次中分离得到的99株单核细胞增生李斯特菌（Listeria monocytogenes），对其基因组多样性及毒力相关特征展开探究。所有分离株均完成全基因组测序（Whole-genome sequencing, WGS），并通过多位点序列分型（Multi-Locus Sequence Typing, MLST）、核心基因组多位点序列分型（core genome Multi-Locus Sequence Typing, cgMLST）、高质量单核苷酸多态性系统发育分析（high-quality SNP, hqSNP）以及毒力、抗菌药物耐药性与移动遗传元件筛选开展分析。 本仓库未包含原始测序读段，相关数据可在欧洲核苷酸档案馆（European Nucleotide Archive, ENA）中获取，研究登录号为PRJEB109318（二级登录号ERP190100）。