Between 2011 and 2023, non-dairy fermented foods caused 39 foodborne illness outbreaks in the United States, resulting in 509 illnesses, 132 hospitalizations, and four deaths. This is the first comprehensive analysis of its kind, revealing a significant blind spot in how we track and understand the safety of fermented foods.

Fermented and cultured foods represent roughly one-third of the human diet globally, yet foodborne illnesses linked to these products have been largely invisible in public health data. The reason is simple: when outbreaks occur, food safety agencies typically categorize them by the raw ingredient (like fish or meat) rather than by how the food was processed. This means fermented fish, fermented meat, and other cultured products get lumped together with their unfermented counterparts, making it nearly impossible to see the true burden of illness from fermentation itself.

Which Pathogens Are Causing the Most Harm?

Researchers from the FDA's Human Foods Program and the CDC's National Center for Emerging and Zoonotic Infectious Disease analyzed outbreak data to close this knowledge gap. What they found was striking: two pathogens dominated the outbreak landscape. Clostridium botulinum, a bacterium that produces a deadly nerve toxin, caused the most outbreaks at 16 (47 percent of single-cause outbreaks). Salmonella enterica, meanwhile, caused the most illnesses, accounting for 307 cases, or 64 percent of illnesses in single-cause outbreaks.

The specific food-pathogen combinations tell an important story. Botulinum contamination was most frequently linked to fermented aquatic animals, particularly traditional Alaskan foods like fermented seal and whale. Salmonella, on the other hand, was most dangerous when paired with cured pork products, causing 134 illnesses and 34 hospitalizations across just two outbreaks.

Why Are Traditional Alaskan Foods at Such High Risk?

Alaska accounted for 38 percent of all non-dairy fermented food outbreaks, with 15 of the 39 total outbreaks occurring in the state. The culprits included traditional foods like fermented black bear meat, fermented fish, fermented seal, and fermented whale. Researchers explained that Clostridium botulinum naturally occurs in coastal Arctic soils and fish, creating an inherent contamination risk. Additionally, some traditional preparation practices, such as rinsing meat in seawater or holding it on coastal rocks before fermentation, may increase exposure to the pathogen.

A particularly concerning shift has occurred in recent decades. The transition from traditional woven baskets to plastic containers for fermentation may inadvertently create an anaerobic (oxygen-free) environment where botulinum spores can germinate more effectively, researchers noted.

How to Safely Handle Fermented Foods at Home

• Use Proper Fermentation Practices: Ensure adequate salt content, correct temperature control, and appropriate fermentation duration to inhibit pathogenic bacteria while allowing beneficial microbes to thrive.
• Implement Preventive Controls: Use clean equipment, sanitized containers, and food-grade materials; avoid plastic containers that may create anaerobic conditions favoring botulinum growth.
• Avoid Shelf-Stable Whole Fish: Do not purchase or consume whole fermented fish unless the label explicitly states the fish has been eviscerated (gutted); uneviscerated fish pose a botulism risk.
• Cook Before Consuming: Since non-dairy fermented foods are typically eaten without further heating, proper fermentation is essential; if you have any doubt about preparation safety, discard the product.
• Watch for Warning Signs: Discard any fermented product with off-odors, unusual discoloration, or signs of mold growth that extends beyond the surface.

The researchers emphasized that because non-dairy fermented foods are intended to be consumed without further cooking, proper fermentation practices and the use of preventive controls are absolutely essential for food safety. Microbial contamination can occur at multiple stages: before or during fermentation (from contaminated starting materials or inadequate processing), after fermentation (from cross-contamination), or during consumer handling.

What About Deaths from These Outbreaks?

Of the four deaths reported in the study, two were attributed to botulinum toxin. One death was linked to fermented whale, and another to fermented fish heads. The remaining two deaths were caused by Listeria monocytogenes, a different pathogen, found in country-style deli ham and Italian-style deli meats. These deaths underscore the serious consequences of inadequate fermentation controls.

Notably, the analysis also identified emerging risks from plant-based and alternative fermented products. Four outbreaks were linked to meat and dairy alternatives, including cashew cheese (two outbreaks), tempeh, and fermented tofu. As consumers increasingly turn to plant-based fermented foods, ensuring safe fermentation practices across these newer product categories will be critical.

What Should Consumers Do Right Now?

The FDA and CDC analysis provides actionable guidance for anyone who consumes fermented foods. Avoid purchasing shelf-stable whole fish unless it is clearly labeled as eviscerated. If you ferment foods at home, follow established recipes and safety guidelines that specify proper salt concentrations, fermentation temperatures, and duration. If you buy fermented products commercially, check for any recalls, particularly those involving botulism risk or process-control deviations.

For parents, special caution is warranted with fermented infant formula. The study identified process-control issues in powdered infant formula, a particularly serious concern because infants have developing immune systems and are uniquely vulnerable to foodborne pathogens. Do not use any recalled infant formula; contact your pediatrician if your infant may have consumed a recalled product.

This landmark study fills a critical gap in food safety knowledge. By distinguishing fermented foods from their raw ingredient sources, public health agencies can now better track outbreaks, identify contamination patterns, and develop targeted prevention strategies. For consumers, the takeaway is clear: fermented foods can be nutritious and delicious, but only when prepared and handled with rigorous attention to safety.