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. 2019 May 21;10:1107. doi: 10.3389/fmicb.2019.01107

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Copyright © 2019 Collineau, Boerlin, Carson, Chapman, Fazil, Hetman, McEwen, Parmley, Reid-Smith, Taboada and Smith.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Summary figure of the steps at which whole-genome sequencing (WGS) can contribute to improve quantitative microbial risk assessment (QMRA) of foodborne antimicrobial resistance (AMR). White boxes represent steps of a farm-to-fork risk assessment as conventionally recommended by the Codex Alimentarius Guidelines (Codex Alimentarius, 2011). Black boxes highlight areas where additional pieces of information may be provided by WGS data analysis. Solid arrows: direct connections between elements of the QMRA. Dash arrows: additional connections to be considered in cases where AMR is addressed as an indirect hazard (European Food Safety Authority [EFSA], 2008).