title: Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes.
abstract: Listeria monocytogenes (Lm) is a major human foodborne pathogen. Numerous Lm outbreaks have been reported worldwide and associated with a high case fatality rate, reinforcing the need for strongly coordinated surveillance and outbreak control. We developed a universally applicable genome-wide strain genotyping approach and investigated the population diversity of Lm using 1,696 isolates from diverse sources and geographical locations. We define, with unprecedented precision, the population structure of Lm, demonstrate the occurrence of international circulation of strains and reveal the extent of heterogeneity in virulence and stress resistance genomic features among clinical and food isolates. Using historical isolates, we show that the evolutionary rate of Lm from lineage I and lineage II is low (∼2.5 × 10-7substitutions per site per year, as inferred from the core genome) and that major sublineages (corresponding to so-called 'epidemic clones') are estimated to be at least 50-150 years old. This work demonstrates the urgent need to monitor Lm strains at the global level and provides the unified approach needed for global harmonization of Lm genome-based typing and population biology.
authors.affiliation: National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France.|Biology of Infection Unit, Institut Pasteur, 75724 Paris, France.|Inserm U1117, 75015 Paris, France.|Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France.|CNRS, UMR 3525, 75015 Paris, France.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Moura
authors.affiliation: Institut Pasteur-Hub Bioinformatique et Biostatistique-C3BI, USR 3756 IP CNRS, 75724 Paris, France.
authors.forename: Alexis
authors.initials: A
authors.lastname: Criscuolo
authors.affiliation: Applied-Maths, 9830 Sint-Martens-Latem, Belgium.
authors.forename: Hannes
authors.initials: H
authors.lastname: Pouseele
authors.affiliation: National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France.|Biology of Infection Unit, Institut Pasteur, 75724 Paris, France.|Inserm U1117, 75015 Paris, France.|Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France.|CNRS, UMR 3525, 75015 Paris, France.|Sorbonne Paris Cité, Cellule Pasteur, Paris Diderot University, 75013 Paris, France.
authors.forename: Mylène M
authors.initials: MM
authors.lastname: Maury
authors.affiliation: National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France.|Biology of Infection Unit, Institut Pasteur, 75724 Paris, France.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Leclercq
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
authors.forename: Cheryl
authors.initials: C
authors.lastname: Tarr
authors.affiliation: Statens Serum Institut, 2300 Copenhagen, Denmark.
authors.forename: Jonas T
authors.identifier: http://orcid.org/0000-0001-6120-0864
authors.initials: JT
authors.lastname: Björkman
authors.affiliation: Public Health England, London NW9 5EQ, UK.
authors.forename: Timothy
authors.initials: T
authors.lastname: Dallman
authors.affiliation: Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada.
authors.forename: Aleisha
authors.initials: A
authors.lastname: Reimer
authors.affiliation: Pasteur International Bioresources network (PIBnet), Mutualized Microbiology Platform (P2M), Institut Pasteur, 75724 Paris, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Enouf
authors.affiliation: Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France.|Institut Pasteur-Hub Bioinformatique et Biostatistique-C3BI, USR 3756 IP CNRS, 75724 Paris, France.|CNRS, UMS 3601 IFB-Core, 91198 Gif-sur-Yvette, France.
authors.forename: Elise
authors.initials: E
authors.lastname: Larsonneur
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
authors.forename: Heather
authors.initials: H
authors.lastname: Carleton
authors.affiliation: National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France.|Biology of Infection Unit, Institut Pasteur, 75724 Paris, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Bracq-Dieye
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
authors.forename: Lee S
authors.initials: LS
authors.lastname: Katz
authors.affiliation: Institut Pasteur-Hub Bioinformatique et Biostatistique-C3BI, USR 3756 IP CNRS, 75724 Paris, France.
authors.forename: Louis
authors.initials: L
authors.lastname: Jones
authors.affiliation: Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France.|CNRS, UMR 3525, 75015 Paris, France.
authors.forename: Marie
authors.initials: M
authors.lastname: Touchon
authors.affiliation: Public Health France, 94415 Saint-Maurice, France.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Tourdjman
authors.affiliation: Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada.
authors.forename: Matthew
authors.initials: M
authors.lastname: Walker
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
authors.forename: Steven
authors.initials: S
authors.lastname: Stroika
authors.affiliation: National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Cantinelli
authors.affiliation: National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France.
authors.forename: Viviane
authors.initials: V
authors.lastname: Chenal-Francisque
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
authors.forename: Zuzana
authors.initials: Z
authors.lastname: Kucerova
authors.affiliation: Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France.|CNRS, UMR 3525, 75015 Paris, France.
authors.forename: Eduardo P C
authors.initials: EP
authors.lastname: Rocha
authors.affiliation: Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada.
authors.forename: Celine
authors.initials: C
authors.lastname: Nadon
authors.affiliation: Public Health England, London NW9 5EQ, UK.
authors.forename: Kathie
authors.initials: K
authors.lastname: Grant
authors.affiliation: Statens Serum Institut, 2300 Copenhagen, Denmark.
authors.forename: Eva M
authors.initials: EM
authors.lastname: Nielsen
authors.affiliation: Applied-Maths, 9830 Sint-Martens-Latem, Belgium.
authors.forename: Bruno
authors.initials: B
authors.lastname: Pot
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Gerner-Smidt
authors.affiliation: National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France.|Biology of Infection Unit, Institut Pasteur, 75724 Paris, France.|Inserm U1117, 75015 Paris, France.|Sorbonne Paris Cité, Institut Imagine, 75006 Paris, Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Paris Descartes University, 75015 Paris, France.
authors.forename: Marc
authors.identifier: http://orcid.org/0000-0002-4491-1063
authors.initials: M
authors.lastname: Lecuit
authors.affiliation: Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France.|CNRS, UMR 3525, 75015 Paris, France.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Brisse
mesh_terms: D062665:Epidemiological Monitoring; D014644:Genetic Variation; D016680:Genome, Bacterial; D060005:Genotyping Techniques / Q000379:methods*; D014943:Global Health; D006801:Humans; D008089:Listeria monocytogenes / Q000145:classification* / Q000235:genetics*; D008088:Listeriosis / Q000453:epidemiology* / Q000382:microbiology*; D017720:Molecular Epidemiology / Q000379:methods; D058974:Phylogeography