The European Food Safety Authority (EFSA) assessed the risk of pathogenic bacteria that may contaminate seeds intended for sprouting and sprouted seeds (sprouts, shoots and cress) which are generally consumed raw or minimally processed. 
Pathogenic bacteria can contaminate seeds and grow during sprouting. Furthermore, preventing initial contamination during production, storage and distribution of seeds is of the foremost importance.
The Germany and France sprout-associated outbreaks in 2011 had been preceded by large outbreaks in the EU and worldwide commonly caused by Salmonella and pathogenic E. coli (including STEC). Very low levels of the bacteria - as little as 4 bacteria/kg - in seeds intended for sprouting have been sufficient to cause outbreaks. Other bacterial pathogens (e.g. Bacillus cereus, Listeria monocytogenes and Yersinia enterocolitica) have also been implicated in sprout-associated outbreaks, but very rarely.
These pathogenic bacteria can contaminate the seeds intended for sprouting during production, storage and distribution through, for example, contaminated irrigation water and soil particles. The high temperature and humidity needed for the germination and sprouting of seeds are also favourable conditions for pathogenic bacteria to further grow and spread.
Panel recommends additional safety measures for the sprouted seed production chain
Panel considers sprouted seeds as ready-to-eat foods and therefore recommends that general EU food safety hygiene rules should be applied across the whole chain from seed production to the final sprouted product. Food safety systems such as Hazard Analysis and Critical Control Point (HACCP) principles, Good Hygiene Practices (GHP), Good Agricultural Practices (GAP) and Good Manufacturing Practices (GMP) should be applied. The Panel concludes that preventing initial contamination of seeds intended for sprouting is of particular importance, as there are currently no methods to ensure elimination of pathogens in all types of seeds used for sprouting.
Suggested mitigation options include but are not limited to: identifying seed crops intended for sprout production before planting; safe use of fertilizers and irrigation water; minimizing contamination of seeds with soil during harvest and preventing mechanical damage of seeds; ensuring that workers harvesting and handling seeds follow hygiene and health requirements; ensuring that seeds are transported, processed and stored under conditions which will minimize the potential for microbial contamination; removing damaged seeds; and improving traceability and minimizing mixing of seed lots.
Operators producing sprouted seeds should strive to implement additional food safety management measures across the whole sprout production chain. Stakeholders at all parts of the production chain and consumers, including also those practising home-sprouting, should be informed of the food safety risk posed by sprouted seeds.
 EFSA assesses the public health risk of seeds and sprouted seeds.Press release 15 Nov 2011.