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Whole-genome sequencing: Paving the way forward globally to better understand food systems

The First FAO/WHO/AU International Food Safety Conference Addis Ababa, 12-13 February 2019















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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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    Document
    Drafting the technical paper on Applications of Whole Genome Sequencing (WGS) for Food Safety Management 2016
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    The expert workshop on practical applications of Whole Genome Sequencing (WGS) for food safety management was held to develop a paper with concrete case studies on the use of WGS for food safety management in the regulatory frameworks at the national level. The experts presented different case studies, practical applications and lessons learnt from implementing WGS for food safety management. WGS could be an effective tool that allows the identification and characterization of microorganisms wit h a high level of precision not previously possible. The experts stated that WGS could be a cost-efficient alternative for countries with existing subtyping capabilities or countries that have existing infrastructure and want to implement WGS. Through the case studies presented by the experts, along with various benefits and potential drawbacks, it was recognized that there are several regulatory and technical challenges associated with the actual implementation of WGS in food safety managemen t. Interpretation of data and validation, comfort level among partners on appropriate use of data, intellectual property, and isolate ownership can be drawbacks related to implementation of the technology. Another challenge that needs to be addressed, especially in developing countries is the confidence in the use of databases and fear of trade barriers. At the end of the workshop, the first draft of the technical background paper was successfully developed. All key elements identified on the f irst day were incorporated into the paper and some suggestions were made for FAO and WHO for the next steps.
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    Book (stand-alone)
    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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