What Whole Genome Sequencing Capabilities Can Mean for Food Safety

The U.S. Centers for Disease Control and Prevention estimate that over 48 million people get sick from foodborne illnesses each year, with the potential for these illnesses to wreak havoc on public health, economies, and the world’s food supply chain. With so much at stake, improving foodborne illness surveillance and response is a top priority for stakeholders across the globe. 

Recently, technological advancements in the field have culminated in the World Health Organization’s November 2023 guidelines on using whole genome sequencing (WGS) for food safety. The wider adoption of whole genome sequencing opens a new frontier in surveillance and protecting the public from foodborne illnesses. 

What is whole genome sequencing?

Whole genome sequencing is a technology that allows investigators to analyze an organism’s entire DNA sequence. In food safety, this testing reveals the genetic makeup of an organism (particularly foodborne pathogens), including all genes and non-coding sequences.

Whole genome sequencing provides both a comprehensive view of an organism's genetic blueprint and insight into how it evolved over time. Currently, the technology is most used by public health officials to investigate pathogens and monitor outbreaks, but some food and beverage companies have already established infrastructure for it. It’s expected to become more widely adopted as the technology becomes more cost effective and easier to deploy. 

How Whole Genome Sequencing Is Revolutionizing Food Safety 

When applied to food safety and foodborne illness outbreak investigation, whole genome sequencing creates many possibilities that simply haven’t been available before. 

More Precise Pathogen Identification 

Whole genome sequencing allows investigators to compare the genetic makeup of an organism to a reference database, helping to quickly and accurately identify specific strains of foodborne pathogens. This capability helps investigators understand the exact nature of the agent behind an outbreak. 

Enhanced Pathogen Traceability 

In addition to improving identification, whole genome sequencing helps investigators quickly pinpoint the origin of the pathogen, including linking seemingly disparate cases of foodborne illness. 

By comparing the genetic profiles of pathogens isolated from different individuals, investigators can uncover genetic similarities between different strains that indicate a common source of contamination — something traditional epidemiological methodologies are unable to provide insight into. As a result, WGS allows officials to quickly track individual cases to their source. 

Faster Outbreak Response 

Since investigators can compare the genetic profiles of pathogens from different cases and identify links to a common source, WGS allows officials to identify and recall contaminated food products more efficiently than traditional methods, preventing further cases of illness. WGS can even reveal genetic markers of antimicrobial resistance or virulence to develop more informed response strategies. 

Enabling Global Outbreak Surveillance 

Whole genome sequencing provides a highly detailed genetic fingerprint of pathogens, allowing investigators to easily compare strains worldwide and track the spread of foodborne illnesses across borders. WGS has facilitated the formation of networks like the CDC’s PulseNet, and the FDA’s GenomeTrakr. 

These networks facilitate data sharing between U.S. agencies but are increasingly incorporating international partners, such as the European Food Safety Authority, for truly global outbreak monitoring. 

What’s Next for Whole Genome Sequencing 

As whole genome sequencing becomes more widely used and institutionalized, it could lead to major changes in food safety laws and processes over time. Food and beverage manufacturers need to keep the technology on their radar for potential application in their operations and to stay ahead of food safety trends and regulatory headwinds. 

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