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Preventive controls for the hygienic production of sprouted seeds

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This document provides information about good agricultural practices (GAP) and good hygienic practices for the production of sprouted seeds that may be consumed raw. It sets out specific recommendations for the production of sprouts and general recommendations for the growing of seeds destined for sprout production.


For the purpose of this document, the following definitions apply.

Seed distributor:
Any person responsible for the distribution of seeds (handling, storage and transportation) to sprout growers. Seed distributors may deal with single or multiple seed producers and can be producers themselves.
Seed producer:
Any person responsible for the management of activities associated with the primary production of seeds including post-harvest practices.
Seed lot:
A quantity of seeds produced and handled under uniform conditions with as little variation as possible (e.g., seeds grown under similar agricultural
Spent irrigation water:
Water that has flowed over and through the sprouts.
Sprout lot:
A quantity of sprouts produced and handled under uniform conditions with as little variation as possible and harvested on the same day (e.g., sprouts produced from a single seed lot, germinated, grown and harvested at the same time using the same disinfection and growing methods and type of equipment).
Sprout grower:
Any person responsible for the management of the activities associated with the production of sprouted seeds.
Sprouted seed:
Any seed that has been sprouted for human consumption. This includes seeds grown in soil.

Seed production

Microbial and chemical contamination may occur during the cultivation and harvesting of seeds in fields or during storage and transportation. The safety of sprouts is highly influenced by the degree of preventive measures used on farm to avoid contamination of seeds. It is recommended that seeds used for sprout production be produced using good agricultural practices (GAP) at all stages during the planting, growing, harvesting, cleaning, storage and transportation. Sprout growers can recommend that seed producers adopt GAP and provide evidence that the product was grown according to specifications.

Natural fertilizer

Composting and other treatments (including environmental conditions) may reduce but may not eliminate pathogens in manure, bio solids and other natural fertilizers. It is particularly important to prevent microbial contamination during the production of seeds because of the potential for pathogens to grow during the sprouting process.

Agricultural water

Water used for irrigation and other agricultural uses is a potential source of microbial contamination.



Seeds for sprouting should be free to the extent possible from foreign matter including soil, insect fragments, bird and rodent droppings, metal and glass fragments. Conditioning utilizes a variety of equipment to remove soil, weed seeds and other debris from seeds. Conditioning should be carried out in a hygienic manner employing practices that minimize potential sources of contamination.


Packaging of seeds for sprouting should be carried out in a hygienic manner.

Analyses, documentation and records

Seed distributors should analyse each lot for the presence of microbial pathogens of concern such as Salmonella spp. and E. coli O157:H7 using internationally accepted analytical methods. Microbial analysis of seeds may help identify highly contaminated lots. Seed producers and sprout growers should be aware that negative results do not guarantee pathogen free seeds because of analytical and sampling limitations. It is important to use random sampling techniques, sufficient sample sizes and sub sample numbers to represent the lot as best as possible.

Seed producers should keep all records on agricultural activities current, such as the site of production, suppliers' information on agricultural inputs, lot numbers of agricultural inputs, irrigation data, agricultural chemical and fertilizer usages, water quality data, cleaning schedules for premises, facilities, equipment and containers, and details of disposition of rejected lots.

Control of sprouting production

Prevention of cross-contamination

During sprout production, effective measures should be taken to prevent cross-contamination of seeds and sprouts. To prevent cross-contamination, sprout growers can consider the following.

Incoming seeds

As a sprout grower:

Control of incoming seeds

Each bag should be examined at its arrival to minimize the potential for introducing obvious contaminants into the establishment. If certificates of analysis are not provided by seed producers or distributors, sprout growers should analyse the seed lots for the presence of microbial pathogens of concern as described in Analyses, documentation and records above.

Seeds storage

The storage area for seeds should be clean, dry, and protected against pests and separate from the rest of the facility. It should not be used to store equipment, chemicals or personal items.

Specific steps in sprout production

All steps involved in antimicrobial treatment for seeds (e.g., initial rinse and disinfection) should be carried out in an area separate from the germination and packaging areas and designed to avoid contamination of sprouts by non-disinfected seeds or chemical disinfectants.

Initial rinse

The seeds should be rinsed thoroughly before the antimicrobial treatment to remove dirt and increase the efficiency of the antimicrobial treatment.

Antimicrobial treatment for seeds

If seeds for sprouting have been grown under GAP and stored and transported in closed containers, the likelihood of being contaminated with pathogenic bacteria is minimized but not eliminated. Seeds should undergo an antimicrobial treatment to reduce the potential for pathogenic microorganisms. There is currently no treatment available that can guarantee pathogen free seeds. An antimicrobial treatment for seeds that can achieve a minimum 3 log reduction of the microbial pathogens of concern should be considered. Examples of such treatments are the use of 2,000 ppm of calcium hypochlorite or sodium hypochlorite for 15-20 minutes or 6-10% hydrogen peroxide for 10 minutes. Other antimicrobial treatments for seeds may be evaluated by the Food Directorate, Health Products and Food Branch, Health Canada, if enough data is provided.

During the antimicrobial treatment, sprout growers can consider the following.

Rinse after antimicrobial treatment

Rinse the seeds thoroughly with potable water after the antimicrobial treatment. Repeat rinsing sufficiently with potable water to eliminate disinfectant.

Pre-germination soak

Soaking is often necessary to improve germination. When soaking, the sprout grower can consider the following.


During germination, it is critical to keep the environment and equipment clean to avoid potential contamination. All equipment should be cleaned and sanitized before each new batch.


All equipment should be cleaned and sanitized before each new batch. Harvesting should be done with cleaned and sanitized tools dedicated for this use.

Final rinse and cooling

A final water rinse will remove hulls and may reduce microbial contamination on sprouts. Cold water will lower sprout temperature and slow down potential microbial growth. When the final rinse is being carried out, the following can be considered.

Bulk cooling


Packaging design and materials should provide adequate protection for sprouts to minimize contamination, prevent damage, and accommodate proper labelling. Packaging materials should be clean, non-toxic and pose no threat to the safety and suitability of sprouts under the specified conditions of storage and use. There should be no unnecessary delays between harvesting and packaging.

Storage of finished product

The cold storage room used for sprouts should allow for adequate maintenance and cleaning; prevent pest access and harbourage; and consistently provide an environment which minimizes microbial growth (e.g., by temperature control and air circulation).

Analysis of spent irrigation water and finished product

Sprout growers should have a sampling plan to ensure the consistent collection of samples in an appropriate manner. Spent irrigation water is the water that has flowed over and through the sprouts and is a good indicator of the types of microorganisms in the sprouts themselves. It should be analysed for microbial pathogens of concern by collecting a representative sample from each production lot or batch. Finished product samples may also be collected and analysed.

Sample collection and testing of the spent irrigation water and sprouts

Microbial testing of spent irrigation water is considered to be one of the most practical and acceptable testing techniques currently available. Health Canada recommends that sprout growers regularly test the spent irrigation water, because water that has flowed over and through the sprouts is a good indicator of the types of microorganisms in the sprouts themselves, including pathogens of microbial concern (Salmonella spp., E. coli O157:H7). Sprouts should not be tested in place of spent irrigation water unless the production methods make it impossible to test the spent irrigation water. However, the recommendation to test spent irrigation water does not preclude additional testing of sprouts (either sprouts collected during production or finished product). Representative samples should be collected from each production lot and analysed for microbial pathogens of concern.

More guidance about general sampling techniques can be found in Sampling procedures guidance.

Sampling equipment and containers

Equipment and containers used to collect samples should be clean and sterile. They may be purchased pre-sterilized or, alternatively, they may be sterilized at 121°C (250°F) for 30 minutes in an autoclave, prior to use. Heat-resistant, dry materials may be sterilized in a dry-heat oven at 140°C (284°F) for 3 hours. Once sterilized, the sampling equipment and containers should be protected from contamination at all times before and during use. Ensure that the used sampling equipment, containers and the collected samples do not contaminate remaining sterile equipment and containers.

The type of sample containers to be used depends on whether spent irrigation water or sprout samples are being collected. Containers may include pre-sterilized plastic bags, bottles, tubes, cups and flasks. They should be dry, leak-proof, wide-mouthed, and of a size suitable for the samples. Containers should also seal properly to ensure the integrity of the sample. The containers should be properly labelled prior to collecting the sample.

When to sample

Samples of spent irrigation water can be collected as early as 48 hours after the start of sprouting. If the seeds are pre-soaked (e.g., soaked in water for a short time and then transferred to growing units for sprouting), include the pre-soak time. Early results will allow the sprout growers to take corrective actions sooner, thus minimizing the potential for one lot of sprouts to contaminate other lots.

Procedures for sample collection

Sample collection of spent irrigation water and sprouts should be done on site by trained personnel. Aseptic sampling procedures should be used to avoid contaminating the sample and the product being sampled.

Personnel should wear a clean lab coat, hair net and sterile gloves. Hands should be washed immediately prior to putting on sterile gloves. The sterile gloves should be put on in a manner that does not contaminate the outside of the glove. During sample collection, hands should be kept away from the mouth, nose, eyes and face. After sample collection, the gloves should be properly discarded.

The sterile sample container should be opened only sufficiently to allow for the sample to be collected. The sample should be placed directly in the container. Once the sample is collected, it should immediately be closed and sealed. If collecting samples in a container with a lid, the lid should not be completely removed. The lid should not be held separately or placed on a counter.
The sample container should be filled no more than ¾ full to prevent overflow. The air from the container should not be expelled when sealing, particularly for plastic bags

Once collected, the samples should be delivered to the laboratory promptly. The sample should be kept at an appropriate temperature, preferably between 0 and 4°C (32° to 40°F). To avoid cross-contamination from melting ice, sealed coolant packs should be used.

Pooling samples from different sprout lots may reduce the number of lab analyses to be performed, however if a presumptive positive is found, all sprouts lots represented by the pooled sample are suspect. The suspect sprout lots should either be discarded or each sprout lot should be analysed separately to determine which lot(s) is (are) contaminated.

Sample size

The volumes given below for spent irrigation water and sprouts represent a sufficient sample size to test for the presence of the microbial pathogens of concern (i.e., Salmonella spp., and E.coli O157:H7).

A. Spent irrigation water

One (1) litre of water should be aseptically collected as the water leaves a drum or tray(s) during the irrigation cycle. Spent irrigation water samples should be collected directly into clean, sterile, pre-labelled containers.


One (1) litre of spent irrigation water may be collected from the drum.

Trays with common trough

One (1) litre of spent irrigation water may be collected at the common trough.

Trays with no common trough

If there is no common trough, spent irrigation water samples from individual trays should be collected and pooled. If the tray is large, spent irrigation water samples from different areas of the tray should be collected.

When Ten (10) or fewer trays make up a production lot, approximately equal volumes of spent irrigation water should be collected from each of the 10 trays to make a total sample volume of one (1) litre. For example:

When there are Ten (10) or more trays, collect ten (10) spent irrigation water samples throughout the entire production lot. For example: if there are 20 trays in a production lot, collect samples from every other tray in the rack, moving from top to bottom, side to side, and front to back.

B. Sprouts

Five (5) sample units of approximately 200 grams each should be aseptically collected from different locations in the drum or growing trays, to ensure the sample collected is representative of the lot. The sample units should be collected throughout the entire production lot (e.g., from top to bottom, side to side, and front to back of the drum or trays). Each 200 gram sample unit should be placed directly into individual clean, sterile, pre-labelled containers.

Microbial testing procedures

All microbial testing for pathogens should be conducted in an external, certified, independent laboratory, and consider the following criteria:

The testing procedures described below can be used to obtain results as simply and quickly as possible on the presence or absence of the microbial pathogens of concern (i.e., Salmonella spp. and Escherichia O157:H7). These methods are described in the Health Canada (HC) Compendium of Analytical Methods.

Please keep in mind that seasonal or regional differences in water quality, type of seed being sprouted, and variations in sampling and analytical conditions may all impact on the effectiveness of the screening tests.

Test kits

Escherichia coli O157:H7:

  1. MFLP-87 VIP EHEC. Biocontrol Systems, Inc., Bellview, WA.
  2. MFLP-94/95 Reveal E. coli O157:H7, Neogen Corp., Lansing, MI.
  3. MFLP-91 Tecra UVA method for E. coli O157:H7.
  4. Any other methods listed in the Compendium for E. coli O157:H7.

Salmonella spp.:

  1. MFHPB-24 Vidas SLM method, Biomerieux, Montreal.
  2. MFLP-96 Reveal kit for Salmonella.
  3. MFLP-97 Alert kit for Salmonella.
  4. MFLP-35 Tecra VIA for Salmonella.
  5. Any other methods listed in the Compendium for Salmonella spp.

General laboratory instructions

Follow instructions in each method.

Dividing samples into sample units for analysis

Spent irrigation water

Total of one (1) L of spent irrigation water should be collected. Two (2) 100 ml sample units should be analysed for the presence of E. coli O157:H7. Two (2) 375 ml sample units should be analysed for the presence of Salmonella spp. Any unused portion of spent irrigation water should be stored under refrigeration pending completion of the analysis.


Total of five (5) sample units of 200 g of sprouts should be collected. For each sample unit, one 25 g sample unit should be analysed for the presence of E. coli O157:H7 and one 25 g sample unit should be analysed for the presence of Salmonella spp. Unused portions of the sprout sample units should be stored under refrigeration pending completion of the analysis.

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