How DNA barcoding can prevent foodborne illness outbreaks

In 2012, when several hundred people fell ill in the U.S. amid a salmonella outbreak, the Food and Drug Administration was quickly able to isolate the exact strain of salmonella that had found its way into the contaminated sushi-grade tuna — and then trace it to the exact processing plant where the fish originated in India. (Not surprisingly, the FDA found 10 sanitation oversights, four of which were considered egregious.)

Then in 2014, the FDA managed to prevent a listeria outbreak from going beyond seven illnesses and one death when it traced the strain of the pathogen to soft cheeses manufactured by Ross Foods, which has since been shut down.

Both findings are thanks to DNA sequencing, which is helping not only to identify which species of animals we might be eating, but even which strains of foodborne pathogens might be present in our food.

The implications are broad. Knowing at a genetic level what we are eating isn’t just good for our health (think food allergies, high mercury levels, etc.) and for our wallets (how much are we really paying for tilapia?), but also for the animals (some of which are endangered or illegally hunted).

DNA sequencing is typically carried out in one of two ways: whole genome sequencing and partial sequencing. Both approaches are getting faster and more affordable every year, and may some day be able to be performed by regular consumers on tablets or smartphones.

When it comes to identifying one species from the next – i.e. determining if we are about to bite into beef or bush meat – we turn to DNA barcoding, first proposed back in 2003 by a Canadian researcher. By looking at a very short genetic sequence from one section of the genome, much in the way a supermarket scanner looks at the black stripes on the Universal Product Code (UPC), we can know with far greater certainty what sort of creature is before us than naked eye investigations of colors and shapes. To do this, partial sequencing is almost always sufficient.

One massive project, Barcode of Life, which was launched back in 2004, is a “DNA barcode reference library” that looks at a 648 base-pair gene region used as the standard barcode for nearly all animal groups. It’s in the mitochondrial cytochrome c oxidase 1 gene (“CO1”), and while looking at this region of the genome doesn’t work well in plants, where it evolves too slowly, it’s being used to identify 500,000 non-plant species.

But when it comes to identifying strains or subtypes of pathogens – say, of salmonella – whole genome sequencing is key. And this approach could soon be sped up by another large open-access database called Genome Trakr, which is organized by the FDA, the University of California, Davis, and Agilent Technologies with the goal of sequencing the entire genomes of 100,000 common foodborne pathogens. By distinguishing between precise strains quickly, outbreaks will ideally be cut off before spreading far and traced back to the source to prevent further contamination.

The project was launched in March of 2012, and is free for researchers and public health officials alike. And it’s continually expanding. Project director Bart Weimer, a microbiologist at UC Davis, said they’re now working on mapping 10,000 more genomes from China, with other collaborations in other countries in the works as well.

“A good library is essential,” Dr. Mark Stoeckle, a researcher at Rockefeller University who led high school students (including his own daughter) on a DNA barcoding mission in 2008 to sniff out mislabeled fish being sold in New York City (later dubbed sushigate), recently told me. “DNA sequencing is getting much cheaper, and not only cheaper but the ability to do it with a smaller machine … We’re not there yet in terms of as small as a cell phone, but one day I’m going to open the business section of the New York Times and someone will have done that.”

Such is the vision of Anthony Zografos, who founded DNATrek and has been inspired to create actual synthetic bar codes for foods. He recently told Scientific American that smartphone apps may eventually be able to tell us if the food we are about to bite into is what it says it is, or if it is contaminated.

Extracting DNA sequences from plants, DNATrek uses a colorless, odorless, tasteless material that can be mixed with, say, natural oils, and then sprayed on foods. They’re basically invisible bar codes readable by polymerase chain reaction testing. “When an outbreak occurs, polymerase chain reaction technology can read the DNA code in about 20 minutes in the laboratory, allowing immediate trace-back rather than weeks or months,” he said.

In the aftermath of sushigate, Dr. Peter Marko, a professor at Clemson University who used DNA sequencing back in 2004 to show that red snapper is often mislabeled, told the New York Times that “the technology is allowing us to ask questions that really would not have been possible in the past.”

Perhaps just as exciting is that as sophisticated as it is, the tech is now easy enough for a group of high school students to use. Pretty soon it may downsize so much in both price and equipment size that it will indeed be accessible to anyone with a smartphone.