Food Safety: ARS National Program 108 Retrospective Review: Accomplishment Report: 2016-2020 Action Plan United States Department of Agriculture Research, Education & Economics Agricultural Research Service Office of National Programs October 2019 2 Table of Contents Page Table of Contents 3 Executive Summary 4 Program Review 8 • Action Plan 9 • Report 26 • Return on Investments 27 • Appropriated Projects 31 Problem Statement: Major Accomplishments & Impact 37 1. Population Systems 38 2. Systems Biology 63 3. Microbial Contaminants: Technologies for Detection & Characterization 86 4. Chemical & Biological Contaminants: Detection & Characterization Methodology; Toxicology & Toxinology 112 5. Intervention and Control Strategies 172 6. Predictive Microbiology/Modeling; Data Acquisition & Storage; Genomics Database 220 7. Antimicrobial Resistance 246 Examples of Externally Funded Projects 273 This Report was compiled in-part from material provided by Program scientists, and from documents within the Office of National Programs including: Action Plans, Project Plans, Annual Reports, and technology transfer and budget office databases. To all those who contributed our graciously expressed thanks. Special thanks go to Nadine Kessler our Program PA, for all her invaluable assistance. 3 Executive Summary Background In the Executive Summary for the 2011-2015 Food Safety Program Retrospective Review and the 2016-2020 Food Safety Program Action Plan, it was noted that the United States (U.S.) Administration had emphasized its commitment to change by overhauling the U.S. food safety system and moving towards more preventative regulatory strategies. The formation of the President’s Food Safety Working Group (FSWG) and the development and implementation of the FDA-Food Safety Modernization Act (FSMA) and its various components, were underway, and were concrete examples of initiatives that were expected to be cornerstones of these changes, of which ARS was to play a critical part. Thus, expectations for the 2016-202o Agricultural Research Service (ARS) Food Safety Program were high. FSMA was implemented by the Food and Drug Administration (FDA), despite the fact that some components were still under revision, for example, the Produce Safety Rule. Closer relationships were developed between the U.S. Department of Agriculture (USDA) agencies (ARS, Food Safety Inspection Service (FSIS)) and with the Department of Health and Human Services (DHHS) (FDA, Centers for Disease Control (CDC)) at the research level. However, sadly and unfortunately other Administration initiatives fell by the wayside such as the FSWG, whose goal was to coordinate federal food safety efforts. The disbanding of the FSWG was strongly noted with deep concern in the recent U.S. Government Accountability Office (GAO) [GAO-19-157SP High-Risk Series Report]. A positive outcome was the “Formal Agreement between USDA and FDA Relative to Cooperation and Coordination” signed by the USDA Secretary and the FDA Commissioner on Jan 30, 2018. Produce safety is one of the focus areas/issues of shared concern. https://www.fda.gov/food/domestic-interagencyagreements-food/formal-agreement-between- usda-and-fda-relative-cooperation-andcoordination This loss in coordination efforts, that is the ability “to participate in a centralized, collaborative mechanism on food safety” (GAO) was and is difficult to understand. The safety of the food (and feed) supply continues to be of critical concern to certain sectors of government (for example, USDA, DHHS) and yet almost no effort has been made by Administrations to eliminate/or alleviate these concerns. Thus, “food safety and the safety of the food supply still remain highly visible agriculture and public health priorities, now for more than four decades”. [pp. 195-197: GAO-19-157SP High-Risk Series]. Rationale Foodborne outbreaks and consequential illnesses are a major cause of morbidity and mortality, as well as economic devastation (including trade), both nationally and internationally. The data provided by the CDC indicates that in the U.S. as a result of foodborne illness (FBI), about 1 in 6 Americans (~48 million) people get sick annually, ~128,000 are hospitalized and ~3,000 die. Cost estimates (in 2014) by the USDA Economic Research Service (ERS) are in excess of $15.6 billion. 4 Although high, these data are likely an underestimate since they only account for a limited number and type of microorganisms, and not unknown agents, biological toxins, or chemical contaminants/residues (https://www.cdc.gov/foodborneburden/2011-methods.html.) The CDC data also do not indicate the long-term sequelae of any illnesses and their public health impact, which are likely more extensive. For example, illnesses such as rheumatoid disease, autoimmune thyroid disease, inflammatory bowel disease, autoimmunity, renal disease, neural/ neuromuscular diseases, organ impairment, heart/vascular diseases, nutritional/ gastrointestinal disorders, and personality changes or behavioral disorders. The cost/burden of these illnesses remains unknown, and likely inestimable since most are lifelong. Contrary to the CDC, other (academic research) data suggests at the national level (the U.S.), there are 76+ million illnesses at a potential cost of $150+ billion. Internationally (world-wide), the incidence of FBI is estimated at 600+ million cases. Thus (1 in 10) people get FBI. Incidents for example are: ~96 million cases of campylobacterosis and ~80 million cases of salmonellosis. The cost (burden) worldwide is incalculable. Regardless of which data are used for public health policy, these are staggering numbers which cannot be sustained. What can be consistently said, and is of concern both nationally and internationally, is that multi-state and multi-country outbreaks are increasing, and are thus, affecting greater numbers of people. Regrettably, the cause of many of the increased outbreaks remain unresolved. Fortunately however, with the recent implementation and use of culture- independent diagnostic tests (CIDTS) and whole genome sequencing (WGS) by U.S. regulatory and public health agencies, there is now a real potential for faster and greater resolution of foodborne illness events. Continuing Issues Food safety is and must continue to be seen as a continuum, not a linear process. It is the intertwining of factors associated with food animals, plants, the environment and humans, that creates opportunities for contamination through infection, intoxication or transmission, by bacterial, viral, and parasitic pathogens; and chemical contaminants, residues, or toxins. Within this continuum there are additional research issues of concern: for example, intensive food production, the globalization of the food supply and resulting international trade, climate change, food integrity (adulteration), changes in pathogenicity, changes in consumption habits, travel, and immigration of people. ARS food safety research must continue to be conducted and evolve, to address many of these issues, especially through the development of improved technologies; being cognizant and pragmatic of the challenges because of the complexity of the production, processing and distribution processes. Food Safety Program (NP108) Two decades ago ARS began the Office of Scientific Quality Research (OSQR) and implemented the external Program and project review process. Since that time (year 2000) each of the ARS Food Safety Program’s 5-year [Strategic] Action Plans has been considered a progressive step toward the ultimate goal of providing the necessary technological tools (in the broadest sense) to increase the safety of the food [and feed] supply. As technologies advanced, the data improved 5 and increased in complexity. Thus, each new 5-year cycle provided further opportunity to formulate more complex hypotheses and study new areas of research such as: population and systems biology; development, validation and subsequent implementation of more rapid, sensitive and quantifiable detection methods; development, evaluation and subsequent implementation of better intervention and control strategies; predictive microbiology and modeling; genomics; metagenomics and microbiome analyses; and antimicrobial resistance. The ARS Food Safety Program continued to strive to provide data for policy change (regulations/guidelines), and to develop and validate new technologies that could be utilized by regulatory, public health, and/or defense agencies, and industry. The ultimate goal is to ensure the safety of the food supply for the American consumer. Nonetheless, to be successfully conducted, scientific research requires a balance between the pursuit of an individual hypothesis and studies on a problem that will have outcomes and impact. This was and still is critically important in times of challenging fiscal and personnel resources, albeit very apparent during the past decade. Program Funding Status With regards to ARS, over time there has been a reduction in actual research funds for the Program for a variety of reasons, including budget cut-backs due to sequestration. In 2005 the Food Safety Research Program had 77 appropriated funded projects, compared with 51 projects in 2019. For the next round of OSQR under the 2021-2025 Action Plan we anticipate 43 projects. Regretfully, the Program cannot sustain such reductions and losses, and will be refocused to address issues/needs of high priority. 2016-2020 Action Plan In developing the 2016-2020 Action Plan; ongoing research activities and technology developments