This report presents the results of the project "Closing gaps for performing a risk assessment on Listeria monocytogenes in ready-to-eat (RTE) foods: activity 3, the comparison of isolates from different compartments along the food chain, and from humans using whole genome sequencing (WGS) analysis". The main objective was to compare L. monocytogenes isolates collected in the EU from ready-to-eat (RTE) foods, compartments along the food chain and from human cases by the use of WGS. A total of 1,143 L. monocytogenes isolates were selected for the study, including 333 human clinical isolates and 810 isolates from the food chain. The isolates were whole genome sequenced. The phylogeny showed a clear delineation between L. monocytogenes lineages and between clonal complexes within lineages. A range of typing methods were applied to the sequence data, providing the framework to answer questions on genetic diversity and epidemiological relationships. Retrospective analysis of nine outbreaks showed that WGS is a powerful tool in national and international outbreak investigations as WGS can accurately rule isolates in or out of outbreaks. Source attribution models showed bovine reservoir to be the main source of human disease although other sources also contributed and generally confidence intervals were high. Numerous consistent genetic linkages between a priori unlinked strains were identified, some of which involved isolates from multiple countries. The presence of putative markers conferring the potential to survive/multiply in the food chain and/or cause disease in humans was explored by detecting the presence of putative virulence genes, AMR genes and factors conferring the ability to persist in the food processing chain. This study has demonstrated one of the major benefits of WGS, which is the ability to address a wide range of questions including those on virulence, antimicrobial resistance, source attribution, surveillance and outbreak detection and investigation, in a single experiment.