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Whole Genome Sequencing (WGS) for food safety










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    Article
    Investing in Food Safety for Developing Countries:Opportunities and Challenges in Applying Whole-Genome Sequencing for Food Safety Management 2019
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    Whole-genome sequencing (WGS) has become a significant tool in investigating foodborne disease outbreaks and some countries have incorporated WGS into national food control systems. However, WGS poses technical challenges that deter developing countries from incorporating it into their food safety management system. A rapid scoping review was conducted, followed by a focus group session, to understand the current situation regarding the use of WGS for foodborne disease surveillance and food monitoring at the global level and identify key limiting factors for developing countries in adoptingWGSfor their food control systems. The results showed that some developed nations routinely use WGS in their food surveillance systems resulting in a more precise understanding of the causes of outbreaks. In developing nations, knowledge of WGS exists in the academic/research sectors; however, there is limited understanding at the government level regarding the usefulness of WGS for food safety regulatory activities. Thus, the incorporation of WGS is extremely limited in most developing nations. While some countries lack the capacity to collect and analyze the data generated from WGS, the most significant technical gap in most developing countries is in data interpretation using bioinformatics. The gaps in knowledge and capacities between developed and developing nations regarding the use of WGS likely introduce inequality in the international food trade, and thus, relevant international organizations, as well as the countries that are already proficient in the use of WGS, have significant roles in assisting developing nations to be able to fully benefit from the technology and its applications in food safety management.
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    Applications of Whole Genome Sequencing (WGS) in food safety management 2016
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    Recent advances in Whole Genome Sequencing (WGS) technology have the potential to play a significant role in the area of food safety. WGS provides rapid identification and characterization of microorganisms, including antimicrobial resistance (AMR), with a level of precision not previously possible. With the rapidly declining cost of this technology, WGS applications in food safety management, including the opportunities it provides for enhanced integration of information from other sectors, suc h as human and animal health, could contribute to enhanced consumer protection, trade facilitation, nutrition and food security. However, the level of understanding of the concepts and potential use of WGS in food safety management vary among countries. This document aims to take the first steps in addressing these gaps, and providing answers to some of the questions which food safety officials (particularly those in developing countries) need to ask and consider if they are to make informed dec isions about WGS and its potential value in food safety management in their context. Four real-life case studies are presented to highlight key benefits and potential drawbacks of WGS in food safety management. Benefits and drawbacks are explained in detail, including the issues related to global data sharing. The document discusses challenges in employing WGS within the regulatory framework in both developed and developing countries, and highlights considerations for countries with limited capa city and resources. A simple exercise to enable developing countries to assess the feasibility of incorporating WGS into national food control systems through a step-by-step approach is described. While WGS can significantly contribute to improving food safety management, it still relies on the appropriate interpretation of laboratory data in the context of epidemiological evidence; WGS alone will not suffice. Despite the challenges, WGS is poised to become standard methodology in some places fo r the identification and characterization of foodborne pathogens. Finding appropriate mechanisms for data sharing will be an important element of its application. In all of this, there is a strong need at the global level to ensure that situations in developing countries are fully taken into account, and that the technology advances in an appropriate direction, in order for WGS to become an effective tool for all.
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    A Silver Lining of the Pandemic: Whole-Genome Sequencing and Food Safety
    The benefits of whole-genome sequencing are far ranging
    2021
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    With the coronavirus disease 2019 (COVID-19) pandemic, whole-genome sequencing (WGS) has proven once again to be an efficient tool for outbreak investigations. The first sequence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was published on January 10, 2020.1 WGS was continuously used to investigate the virus’s genetic variants and their spread, to understand the impacts of mutations, and to monitor emerging lineages.2 The sequenced data and relevant information have been made available on open-source platforms, leading to scientific collaboration and accelerating research on the virus. A prominent example of such collaboration is the “Nextstrain” project3 with its online platform, which has enabled scientists to upload real-time data and facilitated further scientific analyses. While interpretations of the information on such platforms may have been used for decision making,4 one of the most redeeming values of the open platform is that it connects scientists to the general public, as this is a scientific communication tool with effective visuals.5 This confirms the importance of securing an enabling environment for global WGS data sharing, which was discussed extensively at a meeting convened by the Food and Agriculture Organization of the United Nations (FAO) in 2016.6 The scope of the meeting was on WGS applications, particularly for food safety management, which deals with various types of pathogenic microbes.

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