Investing in Food Safety for Developing Countries: Opportunities and Challenges in Applying Whole-Genome Sequencing for Food Safety Management

Isabella Apruzzese, Eunyeong Song, Ernest Bonah, Vernadette S. Sanidad, Pimlapas Leekitcharoenphon, Julius John Medardus, Nagmeldin Abdalla, Hedayat Hosseini, Masami Takeuchi*

*Corresponding author for this work

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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 adopting WGS for their food control systems. The results showed that some developed nations routinely use WGS in their food surveillance systems resulting in 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, 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 use of WGS likely introduce an inequality in 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.
Original languageEnglish
JournalFoodborne pathogens and disease
Issue number7
Number of pages11
Publication statusPublished - 2019


  • Food and Agriculture Organization of the United Nations
  • Developing countries
  • Food safety
  • Foodborne disease surveillance
  • Next-generation sequencing
  • Whole-genome sequencing

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