Part of the laboratory methods pillar, along with PCR and nucleic acid extraction.
What is whole genome sequencing (WGS)?
Whole genome sequencing (WGS) is a technique that reads the entirety — or nearly the entirety — of a microorganism's genetic material, instead of amplifying and detecting only a specific fragment as PCR does. Applied to food safety, WGS is mainly used to compare the complete genome of a bacterium isolated from a patient with that of environmental or food samples, in order to confirm whether they come from the same source.
How does it differ from PCR?
PCR answers a specific question: is this particular pathogen present in this sample? WGS answers a different question: is this Salmonella isolate found in a patient genetically the same as the one found in a processing plant hundreds of kilometers away? That is why the two technologies do not compete but are used at different stages: PCR for rapid routine detection, and WGS for the fine-grained investigation of an outbreak once a common source is already suspected.
Why did it become the surveillance standard?
Links geographically scattered cases
Before WGS, linking illness cases in different cities or countries depended almost exclusively on matches in patients' consumption histories, a slow and error-prone method. With WGS, two bacterial isolates with a practically identical genome can be linked to a common source even if the patients never had contact with each other or an obvious shared consumption history.
Speeds up the response
By confirming a common source with genetic evidence — instead of waiting for traditional epidemiological investigation to establish it — health authorities can order product recalls and alerts earlier, reducing the public's window of exposure.
Genomic surveillance networks
Programs such as PulseNet in the US or the sequencing networks of EFSA and ECDC in Europe maintain genomic databases that make it possible to compare a new isolate against thousands of historical profiles nearly in real time, something unthinkable with older typing methods.
Limitations
WGS requires more costly equipment and bioinformatics infrastructure than PCR, and its turnaround time — although much faster than traditional epidemiological investigation — is still longer than that of a routine PCR. That is why, in practice, WGS complements PCR rather than replacing it: PCR remains the first-line tool for rapid detection, while WGS comes into play once an outbreak is already suspected and its real scope needs to be confirmed.
Conclusion
Whole genome sequencing transformed how geographically scattered outbreaks are detected, making it possible to link cases that would previously have looked like isolated events. It does not replace PCR as a daily detection tool, but it became the standard for confirming, with genetic evidence, the real scope of an outbreak once one is already suspected.
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Frequently asked questions
Does WGS replace PCR in a food laboratory?
No. PCR remains the fastest and most affordable tool for routine detection. WGS is used at a later stage, to investigate already-suspected outbreaks and confirm whether different cases share a common source.
Can any laboratory perform WGS?
It requires sequencing equipment and specialized bioinformatics analysis infrastructure, so it tends to be concentrated in national or international reference laboratories, not in every plant or routine laboratory.
What is PulseNet?
It is a network of public health laboratories, originating in the US and replicated in other regions, that shares genomic profiles of foodborne pathogens to detect outbreaks that would otherwise appear as isolated, unconnected cases.