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Ted ElkinDeputy DirectorCenter for Food Safety and Applied Nutrition, FDA
FY 16-17: Agency Priority Goal
Reduce Foodborne Illness
Priority Goal
Goal Overview
With enactment of the 2011 Food Safety Modernization Act (FSMA) Congress mandated a paradigm shift to prevention – to establishing a modern system of food safety protection based not on reacting to problems but on preventing them from happening in the first place. FSMA has stimulated fundamental changes in FDA’s approach with establishment of preventive controls food safety standards. Key components of our implementation strategy include providing technical guidance and assistance to the industry, reorienting food safety staff to work in new ways, and improving surveillance of the food supply chain, so we can provide consistent, high quality oversight within the more technically sophisticated FSMA framework and better detect food safety problems when they occur. While prevention is the focus, food contamination events do occur.
Listeria monocytogenes (L.m.) infections are one of the leading causes of death from foodborne illness in the United States, resulting in an estimated 1,600 illnesses and 260 deaths each year. Outbreak investigations determine which foods are responsible for illness and can lead to important food safety improvements. For example, recent investigations identified previously unknown sources of L.m. illnesses—cantaloupe, ice cream, and caramel apples—and focused attention on preventing contamination of these products. However, finding the source of clusters of L.m. illnesses is difficult. Determining if the same strain of L.m is making people sick, meaning the illnesses likely came from the same food source, requires intensive investigation. Clusters of illnesses caused by L.m. strains with the same genetic fingerprint are often small. Figuring out what ill persons ate in common is often very difficult; especially when some are too sick for interviews or have died and the long incubation period makes it more difficult for patients to remember what and where they ate. More complete information from patient interviews, information about isolations of L.m. from food and the environment, and whole genome sequencing of strains can all help to detect outbreaks and identify their sources. When food sources and the cause of contamination are identified, food safety changes can be implemented throughout an industry and prevent future outbreaks.
Tracing foods to the source of contamination and determining how the contamination occurred is challenging. Ready-to-eat (RTE) foods can be contaminated if ingredients in the foods are contaminated with L.m. and are not treated to destroy viable cells of this pathogen, or if L.m. is allowed to contaminate the RTE food because of improper sanitary conditions or practices. For many RTE foods, contamination with L.m. can be avoided – e.g., through the application of current good manufacturing practices and sanitation. Sanitation controls include effective environmental monitoring programs designed to identify and eliminate L.m. in and on surfaces and areas in production and processing facility. As we learn from L.m. illness investigations and implement the preventive controls regulations, FDA will work with our food safety partners to better characterize the risks of L.m. contamination and provide guidance on how to better evaluate the hazards in food production and processing operations, and implement and monitor effective measures to prevent contamination.
As part of a shared vision to reduce foodborne L.m. illnesses, HHS’s Food and Drug Administration (FDA), the Centers for Disease Control and Prevention (CDC), and the United States Department of Agriculture’s Food Safety and Inspection Service (USDA-FSIS) have undertaken several activities to realize this vision. FDA recently released new preventive controls standards and is now working to increase industry’s application of preventive controls for L.m. hazards. FDA, CDC, National Institute of Health (NIH), and USDA-FSIS are collaborating to use genomic methods to help determine the food source of outbreaks and to determine the sources of L.m. in the food supply chain. Whole genome sequencing (WGS), combined with robust data from epidemiologic investigations, has the potential to greatly improve the detection and investigation of L.m. outbreaks and can even help link single, sporadic illnesses to foods, something rarely possible before. FDA and USDA-FSIS share regulatory responsibility for preventing L.m. contamination in food and as such will jointly report on their array of activities to reduce L.m. contamination at various points across the food supply chain. Collectively, these activities should help to reduce the overall burden of listeriosis in the population.
Findings from these efforts will ultimately advance the work of the Interagency Food Safety Analytics Collaboration, a tri-agency group of FDA, CDC, and USDA-FSIS, that is combining data from outbreaks with other information to determine the major sources of L.m. illness. The results of this work will significantly contribute to FDA’s and USDA-FSIS’s efforts in implementing more risk-informed food safety strategies and to better target resource allocations.
This Agency Priority Goal supports HHS Strategic Plan Goal 3, Objective E to reduce the occurrence of infectious disease and the Healthy People 2020 goal to reduce the incidence of L.m. infections. It also supports FDA Strategic Priorities, Goal 1, Enhance Oversight of FDA-Regulated Products and all the corresponding Objectives. Improving food safety is one of the CDC Director’s designated “Winnable Battles.” The indicator to strengthen collection of patient interview and laboratory data is consistent with a Quarterly Progress Report target for the CDC Director. And while FSIS does not fall under HHS, it is important to mention that this HHS Agency Priority Goal aligns with an outcome under USDA’s Strategic Goal 4 - to reduce the total number of Salmonella, L.m. and E.coli illnesses from USDA-FSIS regulated products and to FSIS’s Strategic Goal of preventing foodborne illness and protecting the public’s health.
Strategies
Our strategies for achieving the APG goal are multi-faceted and cover a life cycle from prevention, surveillance, detection, and response with lessons from investigations feeding into changes in practices in industry and Agency intervention measures for prevention.
USDA-FSIS joined the FDA/CDC/NIH APG in Q2, FY 2016. FDA and USDA-FSIS share regulatory responsibility for preventing L.m. contamination in food.
Improved preventive controls: With the finalization of preventive controls rules in 2015, FDA will emphasize controlling food safety hazards, such as L.m., in industry food production and processing facilities. FDA’s and USDA-FSIS’s approach will be to provide specific L.m. technical guidance to industry. Additionally, FDA will focus on providing guidance to regulatory food safety staff for more consistent and advanced science based assistance in interpreting the guidance.
With a focus on RTE foods that pose a higher risk of L.m. contamination and that support the growth of L.m., FDA and USDA-FSIS will increase regulatory focus at facilities producing ready-to-eat (RTE) foods that present a risk of listeriosis. FDA plans to increase its surveillance of food processing and production facilities through inspections coupled with environmental sampling for L.m. This will enhance early detection of potential human health risks and lead to actions that are likely to reduce risk of illness. In addition, environmental sampling will contribute to industry’s knowledge of L.m. harborage sites in both the short- and long-term thereby improving their ability to apply the necessary controls over L.m. hazards.
Interim progress on improving prevention controls is planned to be monitored by the following:
- increasing regulatory focus at facilities producing ready-to-eat (RTE) foods that present a risk of listeriosis.
- increasing the sharing of key technical materials with industry on practices/conditions resulting in L.m. contamination of food or the food production environment to help inform industry preventive control measures.
Improved surveillance and detection: As investigators work to identify more food safety gaps by finding the food sources for clusters with a small number of ill persons, obtaining the maximum amount of information about each illness becomes more essential. Interview data from patients and their families about what they ate before they became ill as well as molecular subtyping data (e.g., whole genome sequencing (WGS)) on their strains of L.m. are needed. Through funding and training, CDC works with state and local public health departments to complete interviews for all patients with listeriosis using the standardized Listeria Initiative form and to submit L.m isolates to public health laboratories for molecular subtyping.
CDC’s FoodNet surveillance system funds foodborne illness surveillance in 7 states and parts of three additional states. Data obtained from these sites is used to estimate the rate of foodborne infections nationwide. To track progress toward the goal, FoodNet data will be used to calculate the incidence of L.m. nationally on a quarterly and annual basis.
Whole genome sequencing of L.m. isolates is improving outbreak detection and investigation. By providing far higher resolution of the differences between isolates compared with the previous method (pulsed-field gel electrophoresis), WGS helps investigators better determine which clusters of illnesses are likely from a common food. Combining laboratory and epidemiologic data can sometimes link a single illness to a contaminated food. Through an inter-agency project recognized by a 2014 HHS Innovates Award, FDA, CDC, USDA-FSIS, and state and international partners perform WGS on all available L.m. isolates from patients, food, and the environment. All sequence data about L.m. strains are uploaded to NIH’s National Center for Biotechnology Information (NCBI) and shared publicly on the NCBI website. The public release allows for rapid information sharing among agencies and also allows researchers to use this vast trove of data to learn more about L.m., which might lead to improved prevention methods.
Interim progress on improving surveillance and detection is planned to be monitored by the following:
- increasing the number of sequenced L.m. isolates submitted from environmental and food samples to NCBI, with emphasis from FDA-funded state GenomeTrakr laboratories.
- increasing the capacity for screening new food/environmental isolates against the Listeria genome database.
- increasing the percentage of L.m. illnesses that have both epidemiological data reported to CDC’s Listeria Initiative and whole genome sequencing data from the clinical isolates.
Improved response leading to enhanced prevention: As NIH NCBI enhances its ability to screen sequenced L.m. isolates and FDA, CDC, and state partners increase the number of clinical, food, and environmental whole genome sequenced L.m. isolates, our ability to link illness and outbreak to the food that caused the illness will increase. Efforts have been underway to more consistently conduct tracebacks and share critical data to speed tracebacks among FDA, USDA-FSIS, and state food safety agencies. With these advances, FDA, USDA-FSIS and state partners’ investigations may be able to better identify the point in the food supply chain where the contamination occurred and also at food production or processing facilities; increasing the likelihood of determining how L.m. contamination occurred. As the practices and conditions that led to contamination are better understood, FDA and USDA-FSIS will expand their transfer of knowledge and technical guidance to industry to enable them to better evaluate L.m. risks and improve control measures.
Interim progress on improving response is planned to be monitored by the following:
- increasing the number of L.m. outbreaks in which a food source was identified through patient interviews, product tracebacks, and whole genome sequencing of isolates.
- increasing the number of L.m. illnesses that are linked to food sources through patient interviews, product tracebacks, and whole genome sequencing of isolates.
Progress Update
Improved preventive controls:
FDA conducted inspections and environmental sampling for Listeria at nine facilities that produce ready-to-eat (RTE) foods during the fourth quarter of FY 2016. In total for FY 2016, FDA has conducted 30 inspections that included environmental sampling for Listeria at facilities that produce ready-to-eat foods.
To enhance future prevention efforts, FDA shared with industry, academia, and others, lessons learned from outbreak investigations during a symposium on FSMA preventive controls for produce packing and cooling operations at a major food conference with over 3000 attendees. Also this quarter, FDA provided information to consumer advocacy groups about an L.m. outbreak associated with a novel food, frozen vegetables.
FSIS is updating the algorithms for two of FSIS’ sampling programs that test for L.m. in RTE foods based on certain risk factors. These updated algorithms will allow the Agency to prioritize inspections in the riskiest establishments, which will further strengthen the Agency’s zero tolerance policy for L.m. In the fourth quarter of FY 2016, FSIS cleared and will implement on October 1, 2016 an update to the Agency’s routine, risk-based program for sampling post-lethality-exposed RTE products and Agency clearance continues for the second RTE sampling algorithm update.
In January 2016, FSIS issued instructions for and launched a year-long pilot project to assess to what extent retailers are using the recommendation in the 2015 Best Practices Guidance for Controlling Listeria monocytogenes in Retail Delicatessens. The percentage of recommendations that retailers followed increased between the first and second quarters of the project, from 82 to 87% of product handling recommendations, 76 to 82% of cleaning and sanitizing recommendations, 96 to 97% of facility and equipment controls recommendations and 92 to 96% of employee practices recommendations. Results in the third quarter of the project, were similar to those in Q2.
Improved surveillance and detection:
In the fourth quarter of FY 2016, FDA submitted 439 Listeria isolates to NCBI. Of the 439 isolates, 184 were from state funded GenomeTrakr laboratories. In total for FY 2016, FDA has submitted 4,804 isolates to NCBI, of which 1,392 were from FDA-funded state GenomeTrakr laboratories
FDA did not have any outbreak related isolates during the fourth quarter. The total outbreak related isolates that were sequences by whole genome sequencing (WGS) for FY 2016 was 68. Fifty five were environmental isolates and 13 were product isolates.
NIH increased the capacity for screening new food/environmental isolates against the Listeria genome database by achieving a processing rate of 500 isolates per day, which was a 100% increase over the FDA baseline of 250 isolates per day. Moreover, in March 2016 NIH released beta access to a Web-based interface that will allow more efficient use of these data by FDA, CDC, USDA-FSIS and other partners.
USDA-FSIS sequenced and submitted to NCBI a total of 181 L.m. isolates in FY 2016.
In the fourth quarter of FY 2016, CDC linked epidemiological data with WGS data from isolates for 46% of L.m. illnesses, resulting in 52% of isolates linked to epidemiologic data in FY 2016. The percentage of linked cases may change if additional data are received.
Improved response leading to enhanced prevention:
In FY 2016, CDC and FDA identified the sources of 5 outbreaks through patient interviews, product tracebacks, and WGS of isolates.
These outbreaks caused 42 illnesses that occurred from 2013–2016. Sources identified in FY 2016 were a delicatessen, a grocery deli, bagged salad mixes, raw milk, and frozen vegetables.
There were no L.m. outbreaks associated with FSIS-regulated products in FY 2016.
Next Steps
Improved preventive controls:
FDA and USDA-FSIS will continue to increase their regulatory focus at facilities producing ready-to-eat (RTE) foods that present a risk of listeriosis. FDA plans to inspect and conduct environmental sampling at over 70 facilities producing ready-to-eat food in FY 2016. USDA-FSIS will continue to work towards clearance and implementation of updated sampling algorithms and continue the retail pilot.
FDA and USDA-FSIS will pursue greater sharing of L.m. testing results for dual jurisdiction establishments.
FDA and USDA-FSIS will also continue to increase the sharing of key technical materials with industry on practices/conditions resulting in L.m. contamination of food or the food production environment to help inform industry preventive control measures.
Improved surveillance and detection:
FDA will continue sequencing L.m. isolates submitted from environmental and food samples to NCBI, with emphasis from FDA-funded state GenomeTrakr laboratories.
NIH will increase screening capacity for new isolates by at least another 25%. In March 2016, NIH released beta access to a Web-based interface that will allow more efficient use of these data by FDA, CDC, USDA-FSIS and other partners. Once feedback has been collected from the FDA and CDC about the beta version of the interface, NIH anticipates a full release in Fall/Winter 2016.
CDC will continue to work with states to sequence human isolates of Listeria and submit the data to NCBI in real-time. CDC will continue to follow up regularly with state and local jurisdictions on any listeriosis illnesses that do not have epidemiological data linked with whole genome sequencing data.
Improved response leading to enhanced prevention:
CDC will continue to identify illness clusters through timely testing of clinical isolates. Additionally, CDC will continue to follow up with state and local jurisdictions weekly on any illnesses that do not have epidemiological data linked with whole genome sequencing data.
FDA and USDA-FSIS will continue working and collaborating with CDC, state, and local partners in identifying an outbreak vehicle through product tracebacks and whole genome sequencing of L.m. product and environmental isolates.
Collaboration will continue between FDA, CDC, USDA-FSIS, and states to share results of non-human isolates to facilitate identification of disease clusters.
Contributing Programs & Other Factors
FDA programs
Foods Program
The mission of the Foods and Veterinary Medicine Program is to protect and promote the health of humans and animals by ensuring the safety of the American food supply, animal feed and cosmetics, as well as the safety and effectiveness of animal drugs and devices. Foodborne illness and contamination events have a substantial impact on public health – an estimated 48 million foodborne illnesses occur every year resulting in an estimated 128,000 hospitalizations and 3,000 deaths.
Congress recognized the unique challenges faced by FDA in the area of food safety in the 21st century, and gave the Agency a modern legislative mandate to meet these challenges by enacting the FDA Food Safety Modernization Act of 2011 (FSMA). FSMA directs FDA to build a food safety system based on the public health principle of comprehensive prevention, an enhanced focus on risk‐based resource allocation, and partnership across the public and private sectors to minimize hazards from farm to table.
FDA Headquarters and Program Support
FDA Headquarters (HQ) provides Agency-wide program direction and administrative services to ensure that FDA's consumer and patient safety programs are effectively and efficiently managed. Specific to this Priority Goal, primary FDA components providing Agency-level oversight and advice to FDA leadership and programs: Office of the Commissioner, Office of the Chief Scientist, Office of Foods and Veterinary Medicine including Center for Food Safety and Applied Nutrition, and Office of Global Regulatory Operations and Policy.
CFSAN funds and supports the GenomeTrakr Network which is the first distributed network of labs to utilize whole genome sequencing for pathogen identification. It consists of 14 federal labs, 14 state health and university labs, 3 labs located outside of the U.S., and collaborations with independent academic researchers. Data curation and bioinformatic analyses and support are provided by the National Center for Biotechnology Information (NCBI) at the National Institutes of Health.
CDC programs
Emerging and Zoonotic Infectious Diseases
The Emerging and Zoonotic Infectious Diseases program aims to prevent disease, disability, and death caused by a wide range of infectious diseases. The program focuses on diseases that have been around for many years, emerging diseases (those that are new or just recently identified), and zoonotic diseases (those spread from animals to people). The program’s work is guided in part by a holistic "One Health" strategy, which recognizes the vital interconnectedness of microbes and the environment.
To carry out this mission, the program uses many different tactics: providing leadership in public health, conducting exemplary science, strengthening preparedness efforts, establishing public health policy, sharing vital health information with the public, and building partnerships
NIH/NCBI
NIH’s National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. NCBI has a multi-disciplinary research group composed of computer scientists, molecular biologists, mathematicians, biochemists, research physicians, and structural biologists concentrating on basic and applied research in computational molecular biology.
NCBI provides a centralized database (under the Agency’s Sequence Read Archive) and analytical tools to compare and search genomes that are submitted to the database.
United States Department of Agriculture’s Food Safety and Inspection Service
FSIS is the public health agency in the U.S. Department of Agriculture’s (USDA) responsible for ensuring that the nation’s commercial supply of meat, poultry, and processed egg products, whether domestic or imported, is safe, wholesome, and correctly labeled and packaged. The mission of FSIS is protecting public health and preventing foodborne illness from meat, poultry, and processed egg products. The Office of Public Health Science (OPHS), the Office of Policy and Program Development (OPPD), the Office of Field Operations (OFO), the Office of Investigation, Enforcement, and Audit (OIEA), and the Office of Data Integration and Food Protection (ODIFP) will be the primary FSIS program areas participating in activities related to this Agency Priority Goal since they are responsible for conducting activities such as illness outbreak investigation, laboratory analysis, policy development and implementation, sampling and inspection, and data analysis.
Other factors that might influence success
State health departments have responsibility for surveillance of human illness. They collect data about occurrence of L.m illnesses and they interview patients about foods consumed; they also obtain and test isolates from clinical laboratories. The speed and completeness with which these tasks are done and reported to CDC vary by state.
No Data Available
