LiSEQ – whole-genome sequencing of a cross-sectional survey of Listeria monocytogenes in ready-to-eat foods and human clinical cases in Europe

Anaïs Painset; Jonas T. Björkman; Kristoffer Kiil; Laurent Guillier; Jean-François Mariet; Benjamin Félix; Corinne Amar; Ovidiu Rotariu; Sophie Roussel; Francisco Perez-Reche; Sylvain Brisse; Alexandra Moura; Marc Lecuit; Ken Forbes; Norval Strachan; Kathie Grant; Eva Møller-Nielsen; Timothy J. Dallman

doi:10.1099/mgen.0.000257

LiSEQ – whole-genome sequencing of a cross-sectional survey of Listeria monocytogenes in ready-to-eat foods and human clinical cases in Europe

Anaïs Painset, Jonas T. Björkman, Kristoffer Kiil, Laurent Guillier, Jean-François Mariet, Benjamin Félix, Corinne Amar, Ovidiu Rotariu, Sophie Roussel, Francisco Perez-Reche, Sylvain Brisse, Alexandra Moura, Marc Lecuit, Ken Forbes, Norval Strachan, Kathie Grant, Eva Møller-Nielsen, Timothy J. Dallman (Corresponding Author)

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Abstract

We present the LiSEQ ( Listeria SEQuencing) project, funded by the European Food Safety Agency (EFSA) to compare Listeria monocytogenes isolates collected in the European Union from ready-to-eat foods, compartments along the food chain (e.g. food-producing animals, food-processing environments) and humans. In this article, we report the molecular characterization of a selection of this data set employing whole-genome sequencing analysis. We present an overview of the strain diversity observed in different sampled sources, and characterize the isolates based on their virulence and resistance profile. We integrate into our analysis the global L. monocytogenes genome collection described by Moura and colleagues in 2016 to assess the representativeness of the LiSEQ collection in the context of known L. monocytogenes strain diversity.

Original language	English
Article number	000257
Number of pages	11
Journal	Microbial Genomics
Volume	5
Issue number	2
Early online date	18 Feb 2019
DOIs	https://doi.org/10.1099/mgen.0.000257
Publication status	Published - Feb 2019

Keywords

phylogeny
human
Listeria monocytogenes
whole-genome sequencing
food
genetic diversity
Human
Whole-genome sequencing
Genetic diversity
Phylogeny
Food
STRAINS
ALIGNMENT
RESISTANCE
SURVEILLANCE
RISK-ASSESSMENT

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1099/mgen.0.000257Licence: CC BY

LiSEQ – whole-genome sequencing of a cross-sectional survey of Listeria monocytogenes in ready-to-eat foods and human clinical cases in Europe
© 2019 The Authors | Published by the Microbiology Society. This is an open access article published by the Microbiology Society under the Creative Commons Attribution License https://creativecommons.org/licenses/by/4.0/deed.ast.
Final published version, 1.73 MBLicence: CC BY

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Painset, A., Björkman, J. T., Kiil, K., Guillier, L., Mariet, J-F., Félix, B., Amar, C., Rotariu, O., Roussel, S., Perez-Reche, F., Brisse, S., Moura, A., Lecuit, M., Forbes, K., Strachan, N., Grant, K., Møller-Nielsen, E., & Dallman, T. J. (2019). LiSEQ – whole-genome sequencing of a cross-sectional survey of Listeria monocytogenes in ready-to-eat foods and human clinical cases in Europe. Microbial Genomics, 5(2), [000257]. https://doi.org/10.1099/mgen.0.000257

Painset, A, Björkman, JT, Kiil, K, Guillier, L, Mariet, J-F, Félix, B, Amar, C, Rotariu, O, Roussel, S, Perez-Reche, F, Brisse, S, Moura, A, Lecuit, M, Forbes, K, Strachan, N, Grant, K, Møller-Nielsen, E & Dallman, TJ 2019, 'LiSEQ – whole-genome sequencing of a cross-sectional survey of Listeria monocytogenes in ready-to-eat foods and human clinical cases in Europe', Microbial Genomics, vol. 5, no. 2, 000257. https://doi.org/10.1099/mgen.0.000257

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title = "LiSEQ – whole-genome sequencing of a cross-sectional survey of Listeria monocytogenes in ready-to-eat foods and human clinical cases in Europe",

abstract = "We present the LiSEQ ( Listeria SEQuencing) project, funded by the European Food Safety Agency (EFSA) to compare Listeria monocytogenes isolates collected in the European Union from ready-to-eat foods, compartments along the food chain (e.g. food-producing animals, food-processing environments) and humans. In this article, we report the molecular characterization of a selection of this data set employing whole-genome sequencing analysis. We present an overview of the strain diversity observed in different sampled sources, and characterize the isolates based on their virulence and resistance profile. We integrate into our analysis the global L. monocytogenes genome collection described by Moura and colleagues in 2016 to assess the representativeness of the LiSEQ collection in the context of known L. monocytogenes strain diversity.",

keywords = "phylogeny, human, Listeria monocytogenes, whole-genome sequencing, food, genetic diversity, Human, Whole-genome sequencing, Genetic diversity, Phylogeny, Food, STRAINS, ALIGNMENT, RESISTANCE, SURVEILLANCE, RISK-ASSESSMENT",

author = "Ana{\"i}s Painset and Bj{\"o}rkman, {Jonas T.} and Kristoffer Kiil and Laurent Guillier and Jean-Fran{\c c}ois Mariet and Benjamin F{\'e}lix and Corinne Amar and Ovidiu Rotariu and Sophie Roussel and Francisco Perez-Reche and Sylvain Brisse and Alexandra Moura and Marc Lecuit and Ken Forbes and Norval Strachan and Kathie Grant and Eva M{\o}ller-Nielsen and Dallman, {Timothy J.}",

note = "Funding information This work was funded by EFSA, contract number C/EFSA/BIOCONTAM/2014/01-CT 1 on “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{\textquoteright}, EFSA-Q-2014-00 026. Acknowledgements A. P., T. D. and K. G. are affiliated to the National Institute for Health Research – Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at University of Liverpool in partnership with Public Health England, in collaboration with the University of East Anglia, the University of Oxford and the Quadram Institute. A. P., T. D. and K. G. are based at Public Health England. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, the Department of Health or Public Health England.",

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AU - Kiil, Kristoffer

AU - Guillier, Laurent

AU - Mariet, Jean-François

AU - Félix, Benjamin

AU - Amar, Corinne

AU - Rotariu, Ovidiu

AU - Roussel, Sophie

AU - Perez-Reche, Francisco

AU - Brisse, Sylvain

AU - Moura, Alexandra

AU - Lecuit, Marc

AU - Forbes, Ken

AU - Strachan, Norval

AU - Grant, Kathie

AU - Møller-Nielsen, Eva

AU - Dallman, Timothy J.

N1 - Funding information This work was funded by EFSA, contract number C/EFSA/BIOCONTAM/2014/01-CT 1 on “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-Q-2014-00 026. Acknowledgements A. P., T. D. and K. G. are affiliated to the National Institute for Health Research – Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at University of Liverpool in partnership with Public Health England, in collaboration with the University of East Anglia, the University of Oxford and the Quadram Institute. A. P., T. D. and K. G. are based at Public Health England. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, the Department of Health or Public Health England.

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N2 - We present the LiSEQ ( Listeria SEQuencing) project, funded by the European Food Safety Agency (EFSA) to compare Listeria monocytogenes isolates collected in the European Union from ready-to-eat foods, compartments along the food chain (e.g. food-producing animals, food-processing environments) and humans. In this article, we report the molecular characterization of a selection of this data set employing whole-genome sequencing analysis. We present an overview of the strain diversity observed in different sampled sources, and characterize the isolates based on their virulence and resistance profile. We integrate into our analysis the global L. monocytogenes genome collection described by Moura and colleagues in 2016 to assess the representativeness of the LiSEQ collection in the context of known L. monocytogenes strain diversity.

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KW - phylogeny

KW - human

KW - Listeria monocytogenes

KW - whole-genome sequencing

KW - food

KW - genetic diversity

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KW - Whole-genome sequencing

KW - Genetic diversity

KW - Phylogeny

KW - Food

KW - STRAINS

KW - ALIGNMENT

KW - RESISTANCE

KW - SURVEILLANCE

KW - RISK-ASSESSMENT

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DO - 10.1099/mgen.0.000257

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JO - Microbial Genomics

JF - Microbial Genomics

SN - 2057-5858

IS - 2

M1 - 000257

ER -

LiSEQ – whole-genome sequencing of a cross-sectional survey of Listeria monocytogenes in ready-to-eat foods and human clinical cases in Europe

Abstract

Keywords

UN SDGs

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