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

Abstract

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.

Whole‐genome sequencing reveals Listeria monocytogenes diversity and allows identification of long‐term persistent strains in Brazil

“…Existing national epidemiological surveillance programs actively detect and investigate clusters of cases, identify the origin of food contamination and implement control measures. Whole-genome sequencing (WGS) has recently emerged as a powerful tool for national and international outbreak investigations (Schmid et al, 2014;Ruppitsch et al, 2015;Moura et al, 2017;Nielsen et al, 2017;Van Walle et al, 2018). WGS allows an unprecedented subtyping resolution by analysis of the core genome, as well as the accessory genome.…”

Annual report of the Scientific Network on Microbiological Risk Assessment 2017

“…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 EFSA carried out a number of activities on Listeria monocytogenes in ready-to-eat foods. This report results from an outsourcing project and was published as an external scientific report (Møller Nielsen et al, 2017). The main objective of this tender was to compare L. monocytogenes isolates collected in the EU from ready-to-eat (RTE) foods, compartments along the food chain and from human listerioisis cases by the use of whole genome sequencing (WGS).…”

“…This report results from an outsourcing project and was published as an external scientific report (Møller Nielsen et al, 2017). The main objective of this tender was to compare L. monocytogenes isolates collected in the EU from ready-to-eat (RTE) foods, compartments along the food chain and from human listerioisis cases by the use of whole genome sequencing (WGS).…”

Stakeholder meeting on the draft scientific opinion on Listeria monocytogenes contamination of ready‐to‐eat foods and the risk for human health in the EU

“…In addition, by adapting the DR model to consider CC (if data allow) the number of cases due to meat and meat products would be reduced. (Møller Nielsen et al, 2017). The overall objective was to compare L. monocytogenes isolates collected in the EU from RTE foods, compartments along the food chain and humans using WGS analysis.…”

“…Factors considered as likely as not (33-66%) to increase human invasive starting from the retail stage. A report was published as the outcome of this activity (Pérez-Rodríguez et al, 2017 (Møller Nielsen et al, 2017). The overall objective was to compare L. monocytogenes isolates collected in the EU from RTE foods, compartments along the food chain and humans using WGS analysis.…”