AUTHOR=Emond-Rheault Jean-Guillaume , Jeukens Julie , Freschi Luca , Kukavica-Ibrulj Irena , Boyle Brian , Dupont Marie-Josée , Colavecchio Anna , Barrere Virginie , Cadieux Brigitte , Arya Gitanjali , Bekal Sadjia , Berry Chrystal , Burnett Elton , Cavestri Camille , Chapin Travis K. , Crouse Alanna , Daigle France , Danyluk Michelle D. , Delaquis Pascal , Dewar Ken , Doualla-Bell Florence , Fliss Ismail , Fong Karen , Fournier Eric , Franz Eelco , Garduno Rafael , Gill Alexander , Gruenheid Samantha , Harris Linda , Huang Carol B. , Huang Hongsheng , Johnson Roger , Joly Yann , Kerhoas Maud , Kong Nguyet , Lapointe Gisèle , Larivière Line , Loignon Stéphanie , Malo Danielle , Moineau Sylvain , Mottawea Walid , Mukhopadhyay Kakali , Nadon Céline , Nash John , Ngueng Feze Ida , Ogunremi Dele , Perets Ann , Pilar Ana V. , Reimer Aleisha R. , Robertson James , Rohde John , Sanderson Kenneth E. , Song Lingqiao , Stephan Roger , Tamber Sandeep , Thomassin Paul , Tremblay Denise , Usongo Valentine , Vincent Caroline , Wang Siyun , Weadge Joel T. , Wiedmann Martin , Wijnands Lucas , Wilson Emily D. , Wittum Thomas , Yoshida Catherine , Youfsi Khadija , Zhu Lei , Weimer Bart C. , Goodridge Lawrence , Levesque Roger C. 

TITLE=A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis

JOURNAL=Frontiers in Microbiology

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2017.00996

DOI=10.3389/fmicb.2017.00996

ISSN=1664-302X

ABSTRACT=<p>The <italic>Salmonella</italic> Syst-OMICS consortium is sequencing 4,500 <italic>Salmonella</italic> genomes and building an analysis pipeline for the study of <italic>Salmonella</italic> genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the <italic>Salmonella</italic> Foodborne Syst-OMICS database (SalFoS), at <ext-link ext-link-type="uri" xlink:href="https://salfos.ibis.ulaval.ca/" xmlns:xlink="http://www.w3.org/1999/xlink">https://salfos.ibis.ulaval.ca/</ext-link>. 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 <italic>Salmonella</italic> 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.</p>