Exploring Foodborne Pathogen Ecology and Antimicrobial Resistance in the Light of Shotgun Metagenomics

  • Arnaud BridierEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1918)


In this chapter, applications of shotgun metagenomics for taxonomic profiling and functional investigation of food microbial communities with a focus on antimicrobial resistance (AMR) were overviewed in the light of last data in the field. Potentialities of metagenomic approach, along with the challenges encountered for a wider and routinely use in food safety was discussed.

Key words

Food safety NGS Shotgun metagenomic Antimicrobial resistance Foodborne pathogen ecology 


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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Fougères LaboratoryANSESFougèresFrance

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