Gene sequencing will become more relevant as food safety standards increase.

Gene sequencing is having an impact on the food industry. The technology has advanced so rapidly in the past year, the speed and cost has dropped significantly. In fact, it is now feasible to use gene sequencing as a routine analytical test. There are many potential applications, and one relevant to the food industry is the ability to detect the presence and identity of pathogenic bacteria and viral particles in food or environmental samples.

Len Heflich, president, Innovation for Success
The entire DNA of all the organisms present are sequenced. Since every organism has DNA unique and specific to itself, the test will identify the genus, species and strain. This is very powerful information. The result is a strain-specific test with almost no risk of a false-positive finding. Microbiological tests can identify the genus and species of a microorganism but not the strain. In the past, other tests such as electrophoresis identified the strain, but identification of viral particles is not possible with classic techniques.


The fact that DNA testing produces results with no risk of false positives or negatives is a very important point. Microbiological testing delivers both false findings. With a positive finding, it is statistically impossible to prove that it is false. A false negative can be equally damaging as the test fails to detect a pathogen that is present. Having a more reliable and accurate test is valuable to all.

There are some issues with this new technology as well. For one, the test looks for DNA, and since both live and dead bacteria have DNA, the test cannot tell the difference. On one hand, for environmental testing, it is critically important to know if a pathogen is present. On the other hand, it matters greatly if the pathogen is dead or alive. This can be rectified by additional testing or by growing out the sample. Only live bacteria can grow.

This technology can identify DNA from viral particles as well. Because there are no other methods to test for the presence of viral particles, this is a major advance. We can expect to learn a lot as environmental testing now finds viral particles in places where they were not known to be present. The food industry will likely need to adjust practices and procedures in ways that currently cannot be anticipated. For example, a policy to prevent sick workers from handling food will be necessary but may not be sufficient if an ill worker can shed viral particles for a few days before and after they are free of symptoms. This is a difficult situation that is still far from a practical solution.

The Food and Drug Administration (FDA) and Centers for Disease Control (CDC) have begun using whole genome sequencing as part of the GenomeTrakr network. FDA is going back into their archives of positive pathogen samples taken from food manufacturing facilities, performing whole genome sequencing to identify the specific strains of pathogens present, and comparing these data to CDC’s database of the strains of pathogens reported to have caused illnesses during the same period. They are finding matches between strains found in manufacturing facilities and those found in sick people. This enables FDA to identify the product and manufacturing facility that is likely responsible for the reported illness. They are taking this information back to the manufacturing facilities, and if there is not definitive proof that the pathogen was eradicated, they may require the food manufacturer to recall product from the time of the finding, which could be up to five years ago. This is a potentially devastating outcome.

The bottom line is that the food industry needs to become acquainted with this new technology and begin using it to assess their own facilities before FDA does.