Sprouts have been the subject of safety concerns in two areas. By far the biggest area of concern has been foodborne illness. According to the U.S. Food and Drug Administration (FDA), spouts have been associated with over 1,300 cases of food borne illness in the U.S between the years 1995-2000. This connection makes sense to me because the growing conditions for sprouts can also be ideal growing conditions for bacteria.
Over the past 10 years, the FDA has at times issued recommendations that all sprouts be cooked rather than being consumed in raw form due to the risk of foodborne illness, including illness related to Salmonella and E. coli 157:H7. The FDA has also issued guidelines to manufacturers for increasing the safety of sprouts. I believe that many producers of sprouts (particularly producers of certified organic sprouts) do a good job of implementing these safety rules and make sprouts that are nourishing, delicious, and safe. I encourage you to enjoy the special benefits of these sprouts! However, if you are planning to sprout your own seeds at home and add sprouts to your diet in this way, or if you are considering the purchase of sprouts of unknown quality, I consider doing so to be of much higher risk.
If you do decide to purchase sprouts in the grocery store, here are some additional steps that you can take in order to help increase their safety:
If you decide that you are interested in growing sprouts yourself at home, one excellent source of information is the University of California's "Growing Seed Sprouts at Home" safety manual.
The second area of safety concern—and a much smaller one—involves a non-protein amino acid called canavanine. Concerns about this amino acid are based primarily on animal studies and have usually involved alfalfa sprouts, alfalfa tablets, and alfalfa seeds. Some evidence exists for approaching canavanine in alfalfa sprouts as an aggravating substance with potentially unwanted health consequences for individuals diagnosed with lupus (systemic lupus erythematosus, or SLE).
There is also some evidence suggesting interference of canavanine with the metabolic pathways for another similar amino acid called arginine. I haven't seen any research to suggest that the canavanine in alfalfa sprouts is a problem for healthy individuals adding alfalfa sprouts to their salads or sandwiches. Since there are many vegetable seeds that can be sprouted—including broccoli sprouts, mung bean sprouts, sunflower seed sprouts, green pea sprouts, clover sprouts, and radish sprouts—we would still encourage you to consider the benefits of other high-quality sprouted vegetables, even if you choose to avoid alfalfa sprouts.
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