Scientific Opinion on the risk posed by Shiga toxin-producing Escherichia coli (STEC) and other pathogenic bacteria in seeds and sprouted seeds


Panel on Biological Hazards
EFSA Journal
EFSA Journal 2011;9(11):2424 [101 pp.].
Panel members at the time of adoption
: Olivier Andreoletti, Herbert Budka, Sava Buncic, John D Collins, John Griffin, Tine Hald, Arie Havelaar, James Hope, Günter Klein, Kostas Koutsoumanis, James McLauchlin, Christine Müller-Graf, Christophe Nguyen-The, Birgit Nørrung, Luisa Peixe, Miguel Prieto Maradona, Antonia Ricci, John Sofos, John Threlfall, Ivar Vågsholm and Emmanuel Vanopdenbosch

The Panel wishes to thank the members of the Working Group on MRA in sprouts: Ana Allende, Gunnar Andersson, Paul Cook, Marie-Agnès Jacques, James McLauchlin, Kirsten Mooijman, Stefano Morabito, Christophe Nguyen-The for the preparatory work on this scientific opinion and, the hearing experts: Cynthia Andersson and Jelle Kuijper and EFSA staff: Maria Teresa da Silva Felício, Marta Hugas and Ernesto Liebana Criado for the support provided to this scientific opinion.

Opinion of the Scientific Committee/Scientific Panel
On request from
European Commission
Question Number
20 October 2011
15 November 2011
Last Updated
6 March 2012. This version replaces the previous one/s.
European Food Safety Authority (EFSA), Parma, Italy
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Sprouted seeds are young seedlings obtained from the germination of seeds. They are ready-to-eat foods which have caused large outbreaks. The bacterial pathogens most frequently associated with illness due to contaminated sprouted seeds are Salmonella and to a lesser extent STEC. Bacillus cereus, Listeria monocytogenes, Staphylococcus aureus and Yersinia enterocolitica have also been transmitted by sprouted seeds, albeit very rarely. Dry seed contaminated with bacterial pathogens has been identified as the most likely initial source of sprout-associated outbreaks; although other routes of contamination (e.g. during production due to poor practices) may also occur. In some outbreaks, contamination of seeds with as low as 4 Salmonella per kg was sufficient for the sprouts to cause disease. Seeds purchased by sprouts producers are usually not grown specifically for this purpose. They may be contaminated during production, harvest, storage and transport, and there may be difficulties in traceability of seeds from production to sprouting. Bacterial pathogens on seeds may survive for long periods during seed storage. There is so far no guarantee of a bactericidal step which is able to control contamination of seeds with bacterial foodborne pathogens acquired prior to germination. Due to the high humidity and the favourable temperature during sprouting, bacterial pathogens present on dry seeds can multiply on the sprouts. Contamination with pathogenic bacteria must be minimized by identification of seed crops intended for sprouted seeds production before planting, and application of GAP, GHP, GMP, HACCP principles at all steps of the production chain. The relevance of decontamination treatments of seeds and of microbiological criteria is also discussed.


The European Commission asked the Panel on Biological Hazards to issue a scientific Opinion on the public health risk of Shiga toxin-producing E. coli (STEC) and other pathogenic bacteria that may contaminate seeds and sprouted seeds and in particular the Panel was asked: (i) to assess the public health risk caused by STEC and other pathogenic bacteria that may contaminate both seeds and sprouted seeds intended for direct human consumption; (ii) to the extent possible, to identify risk factors contributing to the development of STEC and other pathogenic bacteria that may contaminate these seeds and sprouted seeds; (iii) to recommend possible specific mitigation options, and to assess their effectiveness and efficiency to reduce the risk throughout the food chain (from the seed production until final consumption); and lastly, (iv) to recommend, if considered relevant, microbiological criteria for seeds and sprouted seeds, water, and other material that may contaminate the seeds and sprouts throughout the production chain.

On the assessment of the public health risk, the BIOHAZ Panel concluded that sprouted seeds are ready-to-eat foods with microbial food safety concern due to the potential for certain pathogenic bacteria to contaminate the raw materials (seeds) and to grow during germination and sprouting, and to their consumption patterns (raw or minimally processed). The various types of sprouted seeds (sprouts, shoots, cress) may not represent the same risk for contamination with, and growth of, pathogenic bacteria. There is mostly data on risks from sprouts, and a scarcity of data for shoots and cress: for these final two categories the production is more comparable to that of fresh-cut leafy vegetables. Alfalfa and mung bean sprouts have been the most commonly consumed and most frequently implicated products in outbreaks. Salmonella and pathogenic Escherichia coli (including STEC) are the most commonly reported bacterial pathogens causing outbreaks associated with the consumption of contaminated sprouts. As found for Salmonella, very low contamination levels of dry seeds (e.g. 4 MPN/kg) can cause sprout associated-outbreaks. Other bacterial pathogens (e.g. Bacillus cereus, Staphylococcus aureus, Listeria monocytogenes and Yersinia enterocolitica) have also been implicated with sprout-associated outbreaks, although these have been reported very rarely. Epidemiological data shows that a single contaminated seed lot may be used by several sprouting plants, even in different countries, causing widespread related outbreaks. Due to limitations in available data, it has not been possible to carry out a quantitative microbiological risk assessment and estimate the proportion of foodborne infections attributable to the consumption of contaminated sprouted seeds. Large outbreaks involving these products (e.g. the outbreak in Germany 2011) illustrate the potential to cause major public health emergencies affecting previously healthy people and not limited to those considered particularly vulnerable to infections. Reliable methods for decontaminating all types of seeds or sprouted seeds are not currently available.

On the identification of risk factors, the BIOHAZ Panel concluded that pathogenic bacteria can be carried and transmitted by animals, humans and the environment, and they may contaminate seeds in the field and throughout the sprouted seed production chain. Seeds may be contaminated via diverse routes. The most relevant risk factors are associated with the effect of agricultural practices on seed production, storage and distribution: contaminated irrigation water and/or manure, presence of birds and rodents in storage facilities, dust and soil particles are potential sources of contamination. Processing conditions (e.g. temperature, humidity) prevailing during germination and sprouting of contaminated seeds favour the growth and dissemination of pathogenic bacteria and should be considered as major risk factors. The widespread distribution of seed lots is a risk factor that may increase the size and geographical spread of outbreaks. Poor traceability of the seed lots may delay the action taken by health authorities to control outbreaks. Poor traceability will also present difficulties for the sprouted seed producers to assess the hygienic quality of lots of seeds and consequently increases the risk of using contaminated seeds in the production process. Microbiological methods to detect emerging pathogens in seeds and sprouted seeds may not yet exist or be applied, posing an additional challenge in the identification of the source of outbreaks. There is limited information on risk factors during the production of shoots and cress compared to sprouts. Considering that sprouted seeds are ready-to-eat foods, contamination by asymptomatic carriers of pathogenic bacteria should not be excluded as a potential risk factor. Considering the above mentioned risk factors, it has been difficult to date to control the hygiene of the production process of sprouted seeds.

Regarding possible specific mitigation options, the BIOHAZ Panel indicated that food safety management based on HACCP principles should be the objective of operators producing sprouted seeds including GAP, GHP and GMP along the whole chain from seed production to the final sprouted product. The hazard analysis should include risk classification of commodities, regions of origin, and operators and suppliers of seeds. In seed and to some extent sprout production, it can be difficult to define critical control points (CCPs) including hazard control measures, critical limits and monitoring. Preventing seed contamination is particularly important because of the long survival of bacterial pathogens on seeds and their multiplication during sprouted seed production. This concerns both seeds intended for industrial and home sprouting. GAP and GHP concerning primary production, harvest and storage should be applied with a high level of stringency, similar to that applied for the primary production of fresh-produce, to minimize the risk of contamination with pathogenic bacteria. These include but are not limited to: (i) identifying seed crops intended for sprout production before planting; (ii) safe use of fertilizers and irrigation water; (iii) minimizing contamination of seeds with soil during harvest and preventing mechanical damage of seeds; (iv) ensuring that workers harvesting and handling seeds follow hygiene and health requirements; (v) ensuring that seeds are transported, processed and stored under conditions which will minimize the potential for microbial contamination; (vi) removing damaged seeds, from which it may be more difficult to remove pathogenic bacteria, or avoiding lots with too many damaged seeds; (vii) improving traceability of seed lots and minimizing, as far as possible, mixing of seed lots. Washing of seeds to remove dirt before sprouting is recommended. Measures to prevent introduction of pathogens in sprouted seeds production remain of the foremost importance. During sprouting, GMP, GHP and HACCP principles should be applied as for other ready-to-eat foods. Use of potable water is necessary during sprouting. Decontamination of seeds prior to sprouting, is currently practiced in some EU Member States as an additional risk mitigation measure as part of a combined intervention strategy. To date, no method of decontamination is available to ensure elimination of pathogens in all types of seeds without affecting seed germination or sprout yield. Decontamination of seeds would need to be optimised for each type of seed. The safety and efficacy of different seed decontamination treatments (e.g. chemical, heat treatment, irradiation alone or in combination) should be evaluated in a harmonised way at EU level. The consequence of any decontamination treatment on the background microflora and its potential impact on the pathogenic bacteria during sprouting should be taken into account. A chill chain for sprouts and shoots from end of production to consumption is necessary to limit growth of bacterial pathogens. Stakeholders, including consumers and also those practicing home-sprouting, at all parts of the production chain, should be informed of the food safety risk posed by sprouted seeds.

Regarding microbiological criteria, the BIOHAZ Panel indicated that as sprouted seeds are ready-to-eat foods, finding pathogenic bacteria in seeds used for sprouting or in sprouted seeds indicates a public health risk. Microbiological testing alone may convey a false sense of security due to the statistical limitation of sampling plans. 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. It is currently not possible to evaluate the extent of public health protection provided by specific microbiological criteria for seeds and sprouted seeds. This highlights the need for data collection to conduct quantitative risk assessment. Microbiological criteria including the design of sampling plans for pathogenic bacteria should be considered as one of the components of the food safety management system for the sprouted seed production chain. Existing food safety criteria and process hygiene criteria in Regulation (EC) 2073/2005 relevant to sprouted seeds or seeds are: a Salmonella food safety criterion, L. monocytogenes food safety criterion, and a total E. coli process hygiene criterion. Consideration should be given to the development of new or revision of the existing microbiological criteria for pathogens most frequently associated with outbreaks involving sprouts (Salmonella spp. and pathogenic E. coli). Currently, there are no criteria for pathogenic E. coli. If such criteria were to be proposed serotypes of concern and associated with severe human disease should be considered. Microbiological criteria for Salmonella, pathogenic E.coli and L. monocytogenes could be considered for seeds before the start of the production process, during sprouting and in the final product, to this respect: (i) detection and mitigation of a contamination problem earlier in the sprouted seed production chain (seeds) may have advantages as it avoids contamination being amplified during the full sprouting process; (ii) testing seeds alone does not permit to detect contamination which may come at a later stage in the production process. Therefore microbiological criteria could be useful during the sprouting process and/or for the final product; (iii) when considering a microbiological criterion for the final sprouted seeds, the time required for the detection methods for pathogenic bacteria combined with the short shelf-life may not allow to withdraw the product in the event of a non-compliance, and (iv) an additional value of testing would be to build up knowledge about the hygienic performance of seed and sprouted seeds producers. The Panel also indicated that when targets for seeds are considered it should be taken into account that low levels of Salmonella (4 MPN/kg) have been sufficient to cause sprouted seed associated-outbreaks. A 2-class sampling plan “absence in 25g”, n=5; c=0, as specified in EC Regulation 2073/2005 for sprouted seeds, will not give sufficient confidence to demonstrate absence of a target pathogen at these low levels in seeds. In order to increase probability of rejection of a positive lot it would be necessary to analyze kilogram quantities of the sample. In order to reduce the number of analytical samples when testing seeds, pooling strategies can be applied. Different approaches have been proposed; any pooling strategy needs to be validated and standardized taking into account the low level of contamination expected in the seeds. Seeds intended for home sprouting should be subjected to a sampling protocol for pathogens having at least the same level of stringency as for seeds intended for commercial sprout production. Ideally the inspection lot on which the sampling plan is applied should represent only one seed production lot. Testing seeds will be especially important if operators use new seed commodities or source seeds from new suppliers where a previous history of microbiological testing may be limited or lacking. Dust and debris from seed storage areas may also be regularly tested for Salmonella and STEC. Total E.coli counts may be included to provide evidence of faecal contamination. During the industrial sprouting process testing spent irrigation water for pathogenic bacteria has been proposed as an alternative strategy to the analysis of a large number of sprout samples. However, there are some uncertainties regarding the sensitivity of this strategy. Sampling could be conducted on sprouted seed production environments. It could be applied for pathogenic bacteria such as L. monocytogenes as well as indicator bacteria. There are currently no indicator organisms that can effectively substitute for the testing of pathogens in seeds, sprouted seeds or irrigation water. Testing for E. coli, Enterobacteriaceae and Listeria spp. can inform process hygiene control. Further work may be required to assess the value of tests for these indicator organisms. It is important to use standard methods for testing, preferably EN/ISO methods especially developed for analyzing microorganisms in seeds, spent water and sprouts. Due to the short shelf life of sprouted seeds rapid (e.g. molecular) methods for detection and/or typing of pathogenic bacteria are important to obtain timely information on the microbiological status of sprouted seeds. Alternative (rapid) methods should be validated according to EN/ISO methods (e.g. EN/ISO 16140).

Decontamination techniques, foodborne pathogenic bacteria, Salmonella, seeds, Shiga toxin-producing E. coli (STEC), sprouted seeds, microbiological criteria, mitigation options
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