Frontiers in Microbiology (Jun 2017)
A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis
- Jean-Guillaume Emond-Rheault,
- Julie Jeukens,
- Luca Freschi,
- Irena Kukavica-Ibrulj,
- Brian Boyle,
- Marie-Josée Dupont,
- Anna Colavecchio,
- Virginie Barrere,
- Brigitte Cadieux,
- Gitanjali Arya,
- Sadjia Bekal,
- Chrystal Berry,
- Elton Burnett,
- Camille Cavestri,
- Travis K. Chapin,
- Alanna Crouse,
- France Daigle,
- Michelle D. Danyluk,
- Pascal Delaquis,
- Ken Dewar,
- Ken Dewar,
- Florence Doualla-Bell,
- Ismail Fliss,
- Karen Fong,
- Eric Fournier,
- Eelco Franz,
- Rafael Garduno,
- Alexander Gill,
- Samantha Gruenheid,
- Linda Harris,
- Carol B. Huang,
- Hongsheng Huang,
- Roger Johnson,
- Yann Joly,
- Maud Kerhoas,
- Nguyet Kong,
- Gisèle Lapointe,
- Line Larivière,
- Stéphanie Loignon,
- Danielle Malo,
- Sylvain Moineau,
- Walid Mottawea,
- Walid Mottawea,
- Kakali Mukhopadhyay,
- Céline Nadon,
- John Nash,
- Ida Ngueng Feze,
- Dele Ogunremi,
- Ann Perets,
- Ana V. Pilar,
- Aleisha R. Reimer,
- James Robertson,
- John Rohde,
- Kenneth E. Sanderson,
- Lingqiao Song,
- Roger Stephan,
- Sandeep Tamber,
- Paul Thomassin,
- Denise Tremblay,
- Valentine Usongo,
- Caroline Vincent,
- Siyun Wang,
- Joel T. Weadge,
- Martin Wiedmann,
- Lucas Wijnands,
- Emily D. Wilson,
- Thomas Wittum,
- Catherine Yoshida,
- Khadija Youfsi,
- Lei Zhu,
- Bart C. Weimer,
- Lawrence Goodridge,
- Roger C. Levesque
Affiliations
- Jean-Guillaume Emond-Rheault
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
- Julie Jeukens
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
- Luca Freschi
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
- Irena Kukavica-Ibrulj
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
- Brian Boyle
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
- Marie-Josée Dupont
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
- Anna Colavecchio
- McGill University, MontréalQC, Canada
- Virginie Barrere
- McGill University, MontréalQC, Canada
- Brigitte Cadieux
- McGill University, MontréalQC, Canada
- Gitanjali Arya
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
- Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
- Chrystal Berry
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
- Elton Burnett
- McGill University, MontréalQC, Canada
- Camille Cavestri
- Université Laval, Québec CityQC, Canada
- Travis K. Chapin
- Institute of Food and Agricultural Sciences, University of Florida, GainesvilleFL, United States
- Alanna Crouse
- McGill University, MontréalQC, Canada
- France Daigle
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, MontréalQC, Canada
- Michelle D. Danyluk
- Institute of Food and Agricultural Sciences, University of Florida, GainesvilleFL, United States
- Pascal Delaquis
- Agriculture and Agri-Food Canada, SummerlandBC, Canada
- Ken Dewar
- McGill University, MontréalQC, Canada
- Ken Dewar
- Génome Québec Innovation Center, MontréalQC, Canada
- Florence Doualla-Bell
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
- Ismail Fliss
- Université Laval, Québec CityQC, Canada
- Karen Fong
- 0Food Safety Engineering, Faculty of Land and Food Systems, University of British Columbia, VancouverBC, Canada
- Eric Fournier
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
- Eelco Franz
- 1National Institute for Public Health and the EnvironmentBilthoven, Netherlands
- Rafael Garduno
- 2Canadian Food Inspection Agency, HalifaxNS, Canada
- Alexander Gill
- 3Bureau of Microbial Hazards, Health Canada, OttawaON, Canada
- Samantha Gruenheid
- McGill University, MontréalQC, Canada
- Linda Harris
- 4UC Davis Food Science and Technology, DavisCA, United States
- Carol B. Huang
- 5UC Davis School of Veterinary Medicine, DavisCA, United States
- Hongsheng Huang
- 6Canadian Food Inspection Agency, OttawaON, Canada
- Roger Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
- Yann Joly
- McGill University, MontréalQC, Canada
- Maud Kerhoas
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, MontréalQC, Canada
- Nguyet Kong
- 5UC Davis School of Veterinary Medicine, DavisCA, United States
- Gisèle Lapointe
- 7Food Science, University of Guelph, GuelphON, Canada
- Line Larivière
- McGill University, MontréalQC, Canada
- Stéphanie Loignon
- Université Laval, Québec CityQC, Canada
- Danielle Malo
- McGill University, MontréalQC, Canada
- Sylvain Moineau
- Université Laval, Québec CityQC, Canada
- Walid Mottawea
- McGill University, MontréalQC, Canada
- Walid Mottawea
- 8Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura UniversityMansoura, Egypt
- Kakali Mukhopadhyay
- McGill University, MontréalQC, Canada
- Céline Nadon
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
- John Nash
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
- Ida Ngueng Feze
- McGill University, MontréalQC, Canada
- Dele Ogunremi
- 6Canadian Food Inspection Agency, OttawaON, Canada
- Ann Perets
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
- Ana V. Pilar
- McGill University, MontréalQC, Canada
- Aleisha R. Reimer
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
- James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
- John Rohde
- 9Department of Microbiology and Immunology, Dalhousie University, HalifaxNS, Canada
- Kenneth E. Sanderson
- 0Department of Biological Sciences, University of Calgary, CalgaryAB, Canada
- Lingqiao Song
- McGill University, MontréalQC, Canada
- Roger Stephan
- 1Institute for Food Safety and Hygiene, University of ZurichZurich, Switzerland
- Sandeep Tamber
- 3Bureau of Microbial Hazards, Health Canada, OttawaON, Canada
- Paul Thomassin
- McGill University, MontréalQC, Canada
- Denise Tremblay
- Université Laval, Québec CityQC, Canada
- Valentine Usongo
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
- Caroline Vincent
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
- Siyun Wang
- 0Food Safety Engineering, Faculty of Land and Food Systems, University of British Columbia, VancouverBC, Canada
- Joel T. Weadge
- 2Biological and Chemical Sciences, Wilfrid Laurier University, WaterlooON, Canada
- Martin Wiedmann
- 3Department of Food Science, Cornell University, IthacaNY, United States
- Lucas Wijnands
- 1National Institute for Public Health and the EnvironmentBilthoven, Netherlands
- Emily D. Wilson
- 2Biological and Chemical Sciences, Wilfrid Laurier University, WaterlooON, Canada
- Thomas Wittum
- 4College of Veterinary Medicine, The Ohio State University, ColumbusOH, United States
- Catherine Yoshida
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
- Khadija Youfsi
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
- Lei Zhu
- McGill University, MontréalQC, Canada
- Bart C. Weimer
- 5UC Davis School of Veterinary Medicine, DavisCA, United States
- Lawrence Goodridge
- McGill University, MontréalQC, Canada
- Roger C. Levesque
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
- DOI
- https://doi.org/10.3389/fmicb.2017.00996
- Journal volume & issue
-
Vol. 8
Abstract
The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the Salmonella Foodborne Syst-OMICS database (SalFoS), at https://salfos.ibis.ulaval.ca/. Here, we present our strategy and the analysis of the first 3,377 genomes. Our data will be used to draw potential links between strains found in fresh produce, humans, animals and the environment. The ultimate goals are to understand how Salmonella evolves over time, improve the accuracy of diagnostic methods, develop control methods in the field, and identify prognostic markers for evidence-based decisions in epidemiology and surveillance.
Keywords
- Salmonella
- foodborne pathogen
- next-generation sequencing
- bacterial genomics
- phylogeny
- antibiotic resistance
