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Taboada EN, Graham MR, Carriço JA, et al. Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access. Front Microbiol. 2017;8:909doi: 10.3389/fmicb.2017.00909.
Taboada, E. N., Graham, M. R., Carriço, J. A., & Van Domselaar, G. (2017). Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access. Frontiers in microbiology, 8909. https://doi.org/10.3389/fmicb.2017.00909
Taboada, Eduardo N, et al. "Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access." Frontiers in microbiology vol. 8 (2017): 909. doi: https://doi.org/10.3389/fmicb.2017.00909
Taboada EN, Graham MR, Carriço JA, Van Domselaar G. Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access. Front Microbiol. 2017 May 23;8:909. doi: 10.3389/fmicb.2017.00909. eCollection 2017. PMID: 28588568; PMCID: PMC5440521.
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Front Microbiol. 2017 May 23;8:909. doi: 10.3389/fmicb.2017.00909. eCollection 2017.

Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access.

Frontiers in microbiology

Eduardo N Taboada, Morag R Graham, João A Carriço, Gary Van Domselaar

Affiliations

  1. National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada.
  2. Department of Biological Sciences, University of Lethbridge, LethbridgeAB, Canada.
  3. Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, WinnipegMB, Canada.
  4. Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de LisboaLisbon, Portugal.

PMID: 28588568 PMCID: PMC5440521 DOI: 10.3389/fmicb.2017.00909

Abstract

Public health labs and food regulatory agencies globally are embracing whole genome sequencing (WGS) as a revolutionary new method that is positioned to replace numerous existing diagnostic and microbial typing technologies with a single new target: the microbial draft genome. The ability to cheaply generate large amounts of microbial genome sequence data, combined with emerging policies of food regulatory and public health institutions making their microbial sequences increasingly available and public, has served to open up the field to the general scientific community. This open data access policy shift has resulted in a proliferation of data being deposited into sequence repositories and of novel bioinformatics software designed to analyze these vast datasets. There also has been a more recent drive for improved data sharing to achieve more effective global surveillance, public health and food safety. Such developments have heightened the need for enhanced analytical systems in order to process and interpret this new type of data in a timely fashion. In this review we outline the emergence of genomics, bioinformatics and open data in the context of food safety. We also survey major efforts to translate genomics and bioinformatics technologies out of the research lab and into routine use in modern food safety labs. We conclude by discussing the challenges and opportunities that remain, including those expected to play a major role in the future of food safety science.

Keywords: food safety; genomic epidemiology; molecular typing; next-generation sequencing; open data access

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