By Jonathan Deeds

from GeneWatch 26-5
Nov-Dec 2013

DNA sequencing provides public health officials with an important tool which can be used to help ensure that seafood products are safe and properly labeled. When the FDA is investigating either a foodborne illness outbreak linked to a seafood product or a seafood mislabeling case, the Agency wants to have a high degree of certainty when confirming the identity of the product in question - no small task, given that there are over 1,700 species of fish and shellfish potentially found in the U.S. marketplace. In almost all cases, DNA sequencing can provide that certainty. The benefits of using DNA to identify species aren't just limited to public health officials; it can be an invaluable tool for industry when it comes to ensuring that the proper food safety measures are in place during processing and that the product is properly labeled.

Historically, regulatory seafood species identifications either relied on visual examination of the external characteristics of the product, which are often removed during processing, or crude protein profiling methods that were sometimes difficult to interpret or did not work on heavily processed products due to protein degradation. Despite its limitations, protein based seafood identification methods were the regulatory standard for many years. Techniques involving DNA were sometimes used in high profile cases but its routine use was restricted by the cost and technical skill required to perform the analyses. As a result, it was not typically utilized during regulatory investigations. In 2003, a series of publications by a research group at the University of Guelph in Ontario Canada first highlighted the concept of "DNA Barcoding" for the FDA. This use of short fragments of DNA, generated and analyzed under a standardized set of conditions, seemed like an ideal alternative to the protein based methods of the day. Advances in sequencing technology and techniques, which reduced both the cost and expertise required to perform these tests, allowed the FDA to modernize many of its food analysis laboratories around the country to include DNA testing. Working with many of the pioneers of DNA Barcoding, including the Canadian Center for DNA Barcoding and the Smithsonian Institution, the FDA has developed a standardized protocol for DNA Barcode generation allowing the Agency to fully replace the older protein based methods in its regulatory investigations.

An early example of FDA's use of DNA analysis of seafood was during a 2007 investigation of several foodborne illness outbreaks in Illinois, California, and New Jersey. The illnesses were linked to fish that had been illegally imported into the U.S. from China as "headless monkfish" and sold in several Korean retail establishments and restaurants as "Bok." DNA analysis revealed that the fish were in fact a species of pufferfish that was not allowed for import. The meat of that particular species of fish is known to be highly contaminated with the pufferfish toxin tetrodotoxin, making safe preparation of the species impossible. DNA barcoding is now used regularly to confirm the species of seafood associated with foodborne illness outbreaks. This has already resulted in a better understanding of food safety hazards associated with specific species of seafood, which in turn helps FDA to further refine its guidance for controlling these hazards and hopefully prevent outbreaks from occurring.

Use of this technology need not be limited to regulatory officials. Proper species identification by the seafood processing industry is essential because the controls necessary to ensure the safety of seafood during processing are determined by the species of seafood being processed. Proper labeling of seafood is also dependent on knowing the species of seafood. To assist the seafood industry in labeling their products in a manner that is truthful and not misleading, FDA has published a guidance document called "The Seafood List." It contains a list of seafood species potentially found in U.S. commerce, the acceptable market names for each species, and guidance for developing acceptable market names for new species. With the increased globalization of the seafood trade, new species are always being introduced into the U.S. marketplace. If there is ever any question as to the identity of the fish a processor receives, DNA sequencing can provide the answer and help ensure that it is safely processed and properly labeled.

As the technology progresses and sequencing equipment becomes smaller, more affordable, and more transportable, its use by regulators and industry members will likely increase further. The ability to perform this analysis outside of centralized laboratories and directly at the point of importation or processing will further ensure the safety and accurate labeling of seafood in the U.S.


Jonathan Deeds, PhD, is a Research Biologist at the U.S. FDA's Center for Food Safety and Applied Nutrition.

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