In October 2025, consumers across the nation were advised to check their refrigerators for millions of eggs voluntarily recalled due to potential Salmonella contamination. The announcement, affecting products from the Black Sheep Egg Company and others, highlighted a persistent public health challenge. For the average person, the warning was straightforward: check the carton and throw away affected products. Behind this simple public message, however, lies a remarkably complex and divided regulatory system. The effort to control Salmonella, a pathogen causing an estimated 1.3 million illnesses in the U.S. each year, is split between two federal agencies with different mandates, philosophies, and tools. This division shapes everything from farm and production facility inspections to the very definition of what makes a food product unsafe.
The U.S. Department of Agriculture’s Food Safety and Inspection Service (FSIS) and the Food and Drug Administration (FDA) share the immense responsibility for keeping the American food supply safe. Their jurisdictions were carved out by historical statutes, leading to a system where the agency overseeing a food product depends not on the pathogen in question, but on the type of food it contaminates. In general, the FSIS regulates the safety of meat, poultry, and some egg products, while the FDA oversees virtually everything else, including whole shell eggs, produce, dairy, and processed foods. This split has led to divergent regulatory approaches for controlling the same pathogen, sparking ongoing scientific and legal debates about the most effective path forward for public health.
The Jurisdictional Divide: A Historical Perspective
The roots of America’s dual food safety system run deep, stemming from different eras of public concern and congressional action. The FSIS derives its authority from the Federal Meat Inspection Act, the Poultry Products Inspection Act, and the Egg Products Inspection Act. These laws charge the agency with ensuring that meat, poultry, and processed egg products are “wholesome, not adulterated, and properly marked, labeled, and packaged.” A core feature of the FSIS system is the presence of its inspectors in over 6,000 slaughter and processing plants nationwide, who conduct daily inspections and monitor compliance.
The FDA’s regulatory scope, under the Federal Food, Drug, and Cosmetic Act, is far broader. It is responsible for the safety of most other foods sold in the United States, a portfolio that includes seafood, fresh fruits and vegetables, shell eggs, spices, cheese, and packaged foods. Unlike the continuous inspection model of FSIS, the FDA typically relies on periodic inspections of facilities and a focus on responding to outbreaks when they occur. For shell eggs, for instance, the FDA sets preventive controls for farms, including requirements for biosecurity, pest control, and testing for Salmonella Enteritidis, a common serotype associated with eggs.
This jurisdictional line can seem counterintuitive to consumers. The FSIS regulates open-faced meat and poultry sandwiches, but the FDA oversees closed-faced sandwiches because they are considered “processed foods.” The FSIS has authority over pepperoni pizza, while the FDA regulates cheese pizza. Most relevant to Salmonella, the FSIS regulates liquid, frozen, and dried egg products, while the FDA is responsible for the safety of shell eggs in their cartons. This division means that the regulatory response to Salmonella can look very different depending on which side of the line a food product falls.
The FSIS Approach: Continuous Inspection and a Shifting Paradigm
For decades, the FSIS approach to Salmonella in raw meat and poultry has been guided by a fundamental principle: these products are not considered sterile, and the consumer bears the final responsibility of cooking them thoroughly to kill any pathogens. Consequently, Salmonella has not historically been classified as an “adulterant” in raw poultry products. An adulterant is a substance that legally renders a product unfit for human consumption, allowing the agency to mandate a recall. Instead, FSIS has used a system of performance standards to measure and push for incremental improvement within the industry.
The cornerstone of this system has been the Salmonella verification testing program, established in 1996. Under this program, the FSIS sets a maximum allowable percentage of positive Salmonella samples for specific raw products, such as chicken carcasses or ground turkey, over a 52-week window. Establishments that fail to meet these performance standards are subject to more in-depth evaluations of their food safety systems. While this approach has contributed to a reduction in the prevalence of Salmonella in raw poultry products, public health data has revealed a stubborn paradox. Despite these lower contamination rates, the national incidence of human Salmonella illnesses has not declined correspondingly over the past two decades. This disconnect has forced a profound rethinking of the agency’s strategy.
In a significant policy shift, FSIS announced in May 2024 that it was declaring Salmonella an adulterant in a specific category of poultry for the first time: not ready-to-eat (NRTE) breaded stuffed chicken products. This decision was based on research showing that consumers often rely on visual cues like color rather than thermometers to determine if these products are fully cooked, leading to undercooking and illness. The new rule deemed these products adulterated if they contained Salmonella at levels of 1 Colony Forming Unit per gram (CFU/g) or higher.
Building on this move, FSIS proposed a more ambitious regulatory framework in August 2024. The proposal aimed to declare raw chicken carcasses, parts, and comminuted (ground) chicken and turkey products adulterated if they were contaminated with any Salmonella at a level of 10 CFU/g or higher, or if they contained any detectable level of specific, highly virulent serotypes, including Enteritidis, Typhimurium, and I 4,[5],12:i:-. This represented a potential landmark change, moving from a system based on prevalence rates to one with enforceable, product-specific safety thresholds.
However, this bold proposal faced significant headwinds. The agency received over 7,000 comments from industry trade associations, consumer groups, scientists, and small farmers. Critics raised concerns about the scientific basis for the 10 CFU/g threshold, the potential for overwhelming economic impacts on small producers, and questions about FSIS’s legal authority to make such a determination. In a telling development, FSIS announced the withdrawal of the proposed framework in April 2025, stating that the comments had “raised several important issues that warrant further consideration.” The agency remains committed to reducing Salmonella illnesses but is now back to the drawing board, assessing its next steps.
The FDA Approach: Preventive Rules and Outbreak Response
On the other side of the regulatory divide, the FDA’s strategy for managing Salmonella risk, particularly in shell eggs, has been built on a foundation of prevention and farm-based controls. The FDA’s “Egg Rule,” which came into effect in stages beginning in 2010, is a quintessential example of its preventive approach. The rule targets the most common egg-associated serotype, Salmonella Enteritidis, and is expected to prevent approximately 79,000 illnesses and 30 deaths each year.
The rule mandates that shell egg producers with 3,000 or more laying hens implement a suite of specific measures. These include procuring chicks from SE-monitored breeder flocks, testing the pullet (young hen) environment for SE at 14-16 weeks of age, and conducting regular testing of the poultry house environment for SE when laying hens are 40-45 weeks old. If an environmental test comes back positive, the producer must begin testing eggs from the affected flock. The rule also lays out detailed requirements for biosecurity – such as limiting visitors and protecting against cross-contamination – and pest control, requiring monitoring and control of rodents and flies. Furthermore, it mandates strict refrigeration requirements throughout storage and transportation to inhibit bacterial growth.
This approach contrasts with the FSIS model by focusing on controlling the pathogen’s introduction and spread at the farm level, before the eggs are ever packaged. When outbreaks do occur, the FDA’s role shifts to investigation and response. The ongoing outbreak of Salmonella Enteritidis linked to eggs from Country Eggs, LLC, first posted in August 2025, demonstrates this process. The FDA, in collaboration with the CDC and state partners, uses epidemiological interviews with sick people to identify a common food exposure. Traceback efforts then work to pinpoint the source, leading to voluntary recalls by the company, as was the case with the Country Eggs recall affecting 95 people across 14 states.
The FDA’s regulatory tools, however, also have limits. The agency generally cannot declare a pathogen in a raw agricultural commodity like shell eggs an “adulterant” in the same way it can for a processed food. Its authority often rests on demonstrating that a food was prepared, packed, or held under unsanitary conditions that may have caused it to become contaminated. This was evident in the October 2025 recall of over six million eggs from Black Sheep Egg Company, which was initiated after FDA inspections found 40 environmental samples positive for Salmonella, including seven different strains known to cause human illness. The contamination within the facility itself provided the regulatory leverage for action.
Table: Key Differences in USDA-FSIS and FDA Regulation of Salmonella
| Regulatory Aspect | USDA-FSIS (Meat & Poultry) | FDA (Shell Eggs & Produce) |
| Core Regulatory Philosophy | Continuous inspection in facilities; shifting from performance standards toward enforceable product standards | Preventive, farm-based controls and facility standards; outbreak response and traceback |
| Key Regulatory Tools | HACCP plans, sanitation SOPs, Salmonella performance standards, recent moves to declare specific products adulterant | The “Egg Rule” (preventive controls on farm), Facility registration, Good Manufacturing Practices, outbreak investigations |
| Approach to Raw Products | Historically, not an adulterant; consumer cooking is the final kill step. This is now being debated and tested | Pathogens in raw ag commodities are not typically declared adulterants; action is based on insanitary conditions |
| Example of Recent Action | Proposed (and later withdrawn) framework to set enforceable limits for Salmonella in raw poultry | Enforcement of the “Egg Rule” and oversight of recalls linked to shell eggs, as seen in the 2025 Country Eggs outbreak |
The Central Debate: The Science and Law of an “Adulterant”
At the heart of the recent regulatory turmoil at FSIS lies a contentious scientific and legal question: Should certain levels or types of Salmonella in raw meat and poultry be legally considered adulterants? This debate was the core of the withdrawn 2024 proposal and continues to shape the future of food safety policy.
The traditional argument against declaring Salmonella an adulterant in raw products has rested on two pillars. First, it is a microorganism that is naturally present in the gut of livestock and poultry. Second, and most critically, it is universally accepted that proper cooking will destroy the pathogen. Therefore, the legal and regulatory view has been that the presence of Salmonella does not automatically render a raw product “injurious to health” as required by the law’s definition of adulteration. The responsibility for ensuring safety has been seen as a shared one, with the industry reducing contamination and the consumer delivering the final kill step through cooking.
This long-held view, however, is being challenged by a growing body of consumer behavior research. Observations indicate that many consumers do not follow recommended food safety practices. They may not use a meat thermometer to verify that poultry has reached the safe internal temperature of 165°F, instead relying on visual cues like color or juice clarity, which are unreliable indicators of safety. Furthermore, cross-contamination in home kitchens – where bacteria from raw meat or poultry are transferred to ready-to-eat foods like salads via hands, utensils, or cutting boards – is a major cause of illness. From this perspective, the pathogen itself, not consumer mishandling, is the primary cause of preventable harm, justifying a stricter regulatory stance.
The scientific debate is also becoming more nuanced. FSIS’s 2024 proposal reflected a modern understanding that not all Salmonella serotypes are created equal. Some, like Enteritidis and Typhimurium, are more frequently associated with severe human illness and possess higher virulence. The proposed framework attempted to account for this by targeting these specific “serotypes of public health significance” for stricter treatment, a concept that is likely to remain central to future regulatory efforts even as the specific thresholds are reevaluated.
Analysis and Next Steps
The recent withdrawal of the FSIS’s proposed Salmonella framework is more than a regulatory setback; it is a testament to the immense complexity of controlling a pervasive pathogen within a divided food safety system. What is new is the intensified struggle to modernize a decades-old approach in the face of stagnant illness rates. The push to declare specific Salmonella serotypes as adulterants represents a significant shift from a philosophy of process control to one of product liability, a move that has proven scientifically compelling to public health advocates but legally and economically fraught for the industry. Simultaneously, the FDA continues to grapple with the limitations of its own tools, as seen in the recent high-profile egg recalls, where action is often reactive, following the emergence of outbreaks and positive environmental tests.
This ongoing debate matters because the stakes are measured in human health – over a million illnesses annually – and economic stability for food producers large and small. The burden of illness falls disproportionately on the most vulnerable: children, the elderly, and those with compromised immune systems. For the food industry, the uncertainty surrounding potential new adulterant classifications creates a challenging planning environment, while small farmers fear that costly testing and control requirements could threaten their viability. Consumers, caught in the middle, face confusing messages about food handling and an ever-present, though often invisible, risk.
Moving forward, the path is unlikely to be a simple one. FSIS must now go back to the drawing board to craft a strategy that is both legally defensible and scientifically robust, a process that will require more data and broader consensus. All stakeholders, from federal agencies and industry groups to consumer advocates and academic scientists, must grapple with the practical challenges of implementing a more targeted, serotype-based policy. This includes investing in the rapid diagnostic technologies that would be needed for such a system to function in real-time at processing plants. For consumers, the imperative remains the consistent practice of safe food handling: using a thermometer, preventing cross-contamination, and heeding recall notices. The tale of two agencies is far from over, and its next chapter will be written in the ongoing effort to bridge the gap between regulatory authority and public health reality.
