Use of whole genome sequencing is extremely limited in most developing nations, according to a study.

Researchers found while some countries lack the capacity to collect and analyse the data generated from whole genome sequencing (WGS), the main technical gap in most developing nations is in data interpretation using bioinformatics. The study was published in the Foodborne Pathogens and Disease journal.

A scoping review and a focus group session helped understand the use of WGS for foodborne disease surveillance and food monitoring globally and identify limitations for developing countries in adopting WGS for their food control systems. Experts from Ghana, Iran, the Philippines, Sudan, Tanzania, and Thailand were part of the focus group.

Underreporting of foodborne diseases and microbial contamination cases is common in developed and developing countries; however, the extremely low number of outbreaks reported by developing nations likely does not reflect the actual situation in these countries.

Differences between developed and developing nations
Results showed some developed nations routinely use WGS in food surveillance systems resulting in more precise understanding of outbreak causes. In developing nations, knowledge of WGS exists in the academic and research sectors; however, there is limited understanding at government level on the usefulness of it for food safety regulatory activities.

Gaps in knowledge and capacities between developed and developing nations regarding use of WGS will likely introduce an inequality in international food trade. International organizations and countries already proficient in WGS have significant roles in assisting developing nations to fully benefit from the technology and its applications in food safety management, said researchers.

The scoping review identified that more than 10 countries are using WGS for regulatory purposes compared to four that used it for food safety management in 2016. However, it also found these additional countries are developed nations. There were no data that any developing country had started using WGS in the government system and this was confirmed by the focus group.

All focus group participants said they are ready to use the technology to contribute to their national food control systems, but lack of commitment at higher levels of government has been a barrier to use.

While focus group members said well-equipped in-country labs are available for analysis of isolates, WGS needs to be conducted routinely if it is used as the basis for food surveillance systems, according to the study.

Is WGS cost-effective?
Some research institutes, such as the Pasteur Institute in France, have conducted WGS-related studies in developing countries to promote the technology. Before introducing WGS, it is essential for countries to have a systematic mechanism to collect isolates and metadata from clinical and food/environment samples.

“Assuming that it is already costly for developing countries to fully implement traditional methodologies to detect foodborne outbreaks, it is necessary to question whether incorporating WGS would be cost-effective in improving outbreak detection/reporting situations,” according to the study.

Universality of WGS has a benefit in efficiency and cost-per-sample has been decreasing. Although it could contribute to cost savings for identification of foodborne pathogens, overall cost may still be high as WGS requires relevant infrastructures and functioning equipment/personnel.

As of July 2018, between 11,000 and 18,000 scientific articles discuss the use of genomic technologies for identification, investigation, and/or prevention of foodborne disease outbreaks.

Case studies from the United States, Denmark, and England have shown how WGS can be incorporated into the food safety regulatory system for outbreak investigations with benefits, such as specificity, allowing improved case definition to enhance outbreak management; sensitivity, enabling linkage of apparently sporadic diseases occurring under the outbreak surveillance radar; and precision, determining the root cause of complex outbreaks.

Introduction of WGS in Kenya drew attention of decision makers to the importance of food safety and provided the basis for development of a national food control system. The Kenya Medical Research Institute introduced WGS to sequence strains from selected pathogens from clinical samples and the government was able to map disease hotspots to revise existing systems and identify high-risk foods.

Databases and platforms for WGS-data sharing include the U.S. FDA GenomeTrakr, European Nucleotide Archive, and deoxyribonucleic acid (DNA) Data Bank of Japan. Some initiatives, such as the Global Microbial Identifier (GMI), are trying to boost global data sharing.

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