Why Whole Genome Sequencing Is Not the Right Tool for Routine Pathogen Testing
November 27, 2018
This is an excerpt from a piece we wrote and published in Food Dive. You can read the full article here.
A misconception has run amok in the food safety industry. You’ve likely heard the terms “whole genome sequencing” and “next-generation sequencing” a lot lately. It’s common even for industry insiders to use the terms interchangeably. However, while the technologies are related, they’re not the same.
Next-generation sequencing (NGS) is the overarching descriptor for sequencing millions of data points in parallel from one sample or multiple samples per machine run. Whole genome sequencing (WGS) is one application of next-generation sequencing. In other words, WGS is a special type of NGS, but NGS isn’t limited to WGS. NGS platforms can also support non-WGS applications like targeted sequencing or shotgun metagenomics.
In fact, for routine pathogen testing, WGS is not the right tool for food manufacturers. Targeted sequencing would be more helpful. Since it can get confusing, it’s helpful to break down the distinctions between WGS and targeted sequencing through the lens of routine pathogen testing.
Whereas whole genome sequencing looks at the entire genome, targeted NGS looks at many sites within several genetic markers. While this might sound like a limited PCR test, it’s different in a few fundamental ways. PCR-based tests only look at one genetic marker (or, in case of multiplex PCR, at a couple of genetic markers) rather than multiple genetic markers as is done in targeted NGS. As a result, the accuracy of PCR tests is lower than that of targeted NGS.
The other fundamental difference between PCR and a targeted sequencing-based approach is that PCR can only flag the presence or absence of a genetic marker. On the other hand, sequencing can read every single building block of a targeted region, benchmark that against a previously verified reference, and confirm whether the target matches the reference across all those hundreds to thousands of building blocks. That is why PCR-based tests can also miss or misidentify pathogens, resulting in higher rates of false negatives and false positives, while sequencing can deliver the highest degree of certainty.
NGS solutions are a clear way forward for the industry, outperforming PCR and WGS in virtually every category. NGS platforms give food labs and manufacturers more control over the testing process, insofar as users can choose the depth of molecular characterization of pathogens. In 24 hours, NGS platforms can do speciation, serotyping, and strain-typing all in one test–at the same price per sample as PCR.
To read the full post at Food Dive, click here.