Following the massive European E. coli outbreak linked to sprouts grown from contaminated seeds this spring, the European Commission requested that the European Food Safety Authority (EFSA) conduct an analysis of the specific threats facing the safety of sprouts and how best to combat them. 


Last week the European Food Safety Authority (EFSA) released the results of its report. The  scientific opinion looks at how sprouted seeds are most likely to be contaminated, what pathogens they carry, and what can be done to avoid future outbreaks. 

The assessment found that there are several specific concerns related to sprouted seeds. Not only are they most often consumed raw, without a cooking step to kill bacteria, but they are grown in a warm, humid environment conducive to bacteria growth.

Because of this, a concentration of as little as 4 bacteria per kilogram on seeds can be sufficient to produce an outbreak when the pods are sprouted. 

Sprouts also have a greater risk of exposure to harmful pathogens, since seeds used for sprouting are usually stored longer than those used for growing fruits and vegetables, possibly exposing them to dust, contaminated water or animal feces for longer periods of time, says the EFSA analysis. Once bacteria contaminate seeds, they can survive for at least 56 weeks.

While the majority of previous outbreaks have arisen from sprouts contaminated in the seed phase, history has shown that sprouts can also become contaminated in the growing or processing phase by irrigation water, contaminated human hands, or a variety of other environmental sources.  

Not only do sprouts create an ideal environment for bacteria growth, but outbreaks caused by sprouts can often be more widespread than incidents of illness caused by other foods, because the seeds are often divided into many sections and sold widely. This also means that an outbreak caused by contaminated sprouts can be harder to trace back to the point of origin, since seed lots can be scattered to various regions.

“Epidemiological data shows that a single contaminated seed lot may be used by several sprouting plants, even in different countries, causing widespread related outbreaks,” says the report.  

Reducing the Risk

EFSA’s evaluation reveals that the best way to avoid a sprout-related outbreak (which are most often caused by E. coli or Salmonella and – less often – Listeria bacteria) is to prevent contamination of sprouting seeds in the first place. 

“Measures to prevent introduction of pathogens in sprouted seed production…remains of the foremost importance,” it says.

The report recommends several measures to protect seeds intended for human consumption. 

 “Diseased or damaged seeds, which may be more susceptible to microbial contamination, should not be used for the production of sprouts for human consumption,” the report says.

Studies have shown that bacteria on a seed’s surface can travel to its interior if the seed is punctured, according to the analysis. 

Broken seeds are also dangerous because once inside the pod, bacteria can grow into the tissues of the plant, and can also be more difficult to remove in a seed cleaning process.


Seeds to be used for production should be kept in a dry storage area away from walls to avoid contamination by rodents, and should be clearly labeled as seeds to be sprouted and consumed, separated from seeds used for other purposes.  

EFSA recommends that seeds be cleaned of dirt before used for growing, and notes that while a disinfection step can help reduce the presence of bacteria on seeds, “no chemical method of disinfection has been able to ensure pathogen-free for all seed types.”

Microbial Testing

While testing of seed or sprout samples can be useful in identifying the presence of bacteria, it can also create a false sense of security if no bacteria is found, since such a small percentage of an overall seed lot is usually tested.

“A negative sample result does not ensure the absence of the pathogen in the tested lot, particularly where it is present at low or heterogeneous prevalence.”

Since a tiny amount of bacteria can eventually lead to an outbreak, sometimes a low but still dangerous amount of E. coli or Salmonella could go undetected. 

This problem, however, can be mitigated by pooling and sprouting seeds to allow bacteria to multiply before testing for pathogens. 

The EFSA report also recommends setting an acceptable threshold for pathogens found on sprouts that are ready for consumption. While these criteria currently exist for Salmonella and Listeria, there is no established threshold for pathogenic E. coli. The report recommends setting these microbiological criteria for E. colis O157, O26,O103, O111, O145 and O104 (the strain associated with the European outbreak this spring). 

Existing Sprout Safety Steps

The EFSA scientific opinion also reiterates existing standards for growing fresh produce, and specifically for sprouts, found in the Good Agricultural Practices (GAPs) guidelines, Good Handling Practices (GHP), Good Manufacturing Practices (GMP) and Hazard Analysis and Critical Control Point (HACCP) principles. Each of these sets of recommendations offers scientific-based recommendations on how to produce ready-to-eat sprouts safely.  

EFSA’s recommendations are intended for everyone along the sprout supply chain, from producer to consumers to those who grown their own at home.