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 DewarFlorence 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, 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

Research output: Contribution to journalArticle

19 Scopus citations

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.

Original languageEnglish (US)
Article number996
JournalFrontiers in Microbiology
Volume8
Issue numberJUN
DOIs
StatePublished - Jun 2 2017

Keywords

  • Antibiotic resistance
  • Bacterial genomics
  • Database
  • Foodborne pathogen
  • Next-generation sequencing
  • Phylogeny
  • Salmonella

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

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    Emond-Rheault, J. G., Jeukens, J., Freschi, L., Kukavica-Ibrulj, I., Boyle, B., Dupont, M. J., Colavecchio, A., Barrere, V., Cadieux, B., Arya, G., Bekal, S., Berry, C., Burnett, E., Cavestri, C., Chapin, T. K., Crouse, A., Daigle, F., Danyluk, M. D., Delaquis, P., ... Levesque, R. C. (2017). A Syst-OMICS approach to ensuring food safety and reducing the economic burden of salmonellosis. Frontiers in Microbiology, 8(JUN), [996]. https://doi.org/10.3389/fmicb.2017.00996