Whole genome sequencing (WGS) has become the technology of choice for FDA, the Centers for Disease Control and Prevention (CDC), and the USDA Food Safety and Inspection Service (FSIS) to help protect consumers from foodborne illness. It can reveal the complete DNA makeup of an organism, thus enabling the differentiation between organisms with a precision that other technologies do not allow. Agencies can use WGS to determine what illnesses are part of an outbreak or narrow down the specific ingredient in a multi-ingredient food responsible for an outbreak; identify the geographic areas from where a contaminated ingredient may have originated; differentiate sources of contamination, even within the same outbreak; and link illnesses to a processing facility even before the food product vector has been identified. See, e.g., FDA, Examples of How FDA Has Used Whole Genome Sequencing of Foodborne Pathogens For Regulatory Purposes (WGS Examples).
In the context of past outbreaks, traditional epidemiological methods, such as slide agglutination tests and gel electrophoresis, have allowed health officials to find common subtyping patterns that show up both at production sites and in clinical samples collected from people with foodborne illnesses. However, some of these patterns contain different strains of bacteria, and this variety can make it nearly impossible to determine which strain is directly responsible for a given illness. By contrast, WGS can provide a greater specificity in cases where there are multiple strains by revealing the DNA sequences, and not just the patterns, involved, thereby ruling out which pathogens are not the cause of a particular illness. See, e.g., WGS Examples; FDA, Whole Genome Sequencing (WGS) Program.
Adoption of the technology has generated a new series of questions and conclusions. For example, following an outbreak in which Salmonella dublin was detected in ground beef, Senator Gillibrand, D-N.Y., and Representative DeLauro, D-Conn., recently asked the secretary of agriculture for greater transparency concerning microbiological testing data, generated using WGS from samples collected at US slaughter and processing facilities. See Kirsten Gillibrand and Rosa L. DeLauro, Letter to USDA’s FSIS, Congress of the United States, Nov. 15, 2019, at 1 (Senators’ Letter to FSIS). Specifically, based on an alert by the CDC stating that this salmonella strain is suspected to be linked to the death of one person and the hospitalization of several others, Sen. Gillibrand and Rep. DeLauro requested the disclosure of data on all collected samples, even if the facilities were not involved in the specific outbreak. See also Cathy Siegner, After Salmonella Outbreak, 2 Members of Congress Demand More Food Safety Transparency from USDA, FoodDive (Nov. 20, 2019). Sen. Gillibrand and Rep. DeLauro argued that such disclosure is necessary to identify links between pathogenic strains in facilities regulated by FSIS and patients with confirmed foodborne illness. In their request, they acknowledged that FSIS does not release these genetic data because it is concerned that disclosure would create public confusion or cause public health authorities to focus their attention on misleading claims, but argued that FSIS’s concerns are outweighed by the need for better food safety control.
Sen. Gillibrand and Rep. DeLauro’s request involves a wider scope of genetic data than just information from the specific facilities involved in the latest outbreak. For instance, they want FSIS to release sampling information and the name of each facility sampled that tested positive for the outbreak strain. Similarly, they requested the same type of information for turkey slaughter and processing facilities that tested positive for the outbreak strain associated with Salmonella infantis infections. Publication of such data, however, could have an unavoidable negative impact on all facilities that test positive for a specific strain but are not involved in any outbreak. It could also put pressure on the agency to take preemptive action against a facility based on speculation that it could be involved in a future outbreak.
There is understandable concern surrounding the potential for WGS data to be used incorrectly. The various sampling data collected by FSIS do not indicate product adulteration; they merely show whether a particular pathogen is present. This critical distinction between adulteration and the ongoing acceptance of certain pathogens as unavoidable in new products is fundamental to the FSIS food safety system. It is also a nuance that probably escapes the understanding of many consumers, raising the question of whether such disclosure would do more harm than good.