The Joint Food and Agriculture Organization of the United Nations (FAO)/World Health Organization (WHO) Expert Meetings on Microbiological Risk Assessment (JEMRA) recently published a technical report on the prevention and control of microbiological hazards in seeds for sprouts.

Experts reviewed publicly available literature and regulatory and industry guidelines to assess the current state of knowledge on controlling microbiological hazards in sprouts. Pathogens associated with sprouts and potential routes of contamination were identified and characterized. The experts also evaluated intervention measures at different points along the sprout supply chain, and the report highlights control measures that are most effective in reducing incidents of foodborne illnesses linked to sprouts.

The report is the third installment in a series on the prevention and control of microbiological hazards in fresh fruits and vegetables, supporting the work of the Codex Committee on Food Hygiene.

According to the report, sprouts have different food safety concerns from other fresh fruits and vegetables because the conditions under which sprouts are produced—time, temperature, humidity, pH and nutrients—are ideal for foodborne pathogen growth.

High risk foodborne pathogens for sprouts identified by JERMA include Shiga toxin-producing Escherichia coli (STEC), Salmonella, and Listeria monocytogenes. Outbreak investigations have demonstrated that foodborne pathogens found on sprouts most likely originate from the seed, but the contamination could also be attributed to the production environment.

Microbial Prevention and Control in Production, Handling, and Processing

Controlling and/or reducing microbial contamination of seeds for sprouting is difficult, given the diversity of growing and harvesting practices associated with seed production. Bacterial pathogens, if present on a seed, may survive for long periods of time during seed storage. Additionally, it may be difficult maintaining traceability of a seed from harvest to sprouting. However, JERMA identified interventions for reducing the risk of seeds contaminated by foodborne pathogens at various points during the growing and production of seeds:

  • Animal and human activities: Domestic animals should not graze in fields where crops are actively being grown for seed production, and wild animals should be excluded from the production area as much as possible
  • Manure, biosolids, and other natural fertilizers: Only adequately treated or composted manure should be utilized during seed production, and time between the application of manure and planting and harvest of seed should be maximized (60 days minimum), as bacterial pathogens die off over time
  • Agricultural water: Fit-for-purpose water should be used for irrigation and all other purposes, the microbiological quality of water used in production and processing of sprouts should be maintained and monitored, and the application method and timing of irrigation should be considered for their impact on risk
  • Equipment for growing and harvesting: Equipment should be cleaned and sanitized prior to harvest, and equipment should also be designed and maintained to minimize soil intake and seed damage, as well as to prevent the introduction of pathogens into seed
  • Seed handling: Control of moisture content during harvesting, threshing, and drying will decrease microbial growth and pathogen viability
  • Production environment: Proper storage, handling, and disposal of waste and effective pest control should be executed; facilities and operation flow should be designed to prevent raw material from coming into contact with the final product; and environmental monitoring should be conducted, especially for L. monocytogenes
  • Storage and transport: Temperature and humidity should be controlled, appropriate handler and equipment hygiene should be practiced, and animal and insect controls should be implemented
  • Seed: Seed should be sourced from producers or distributors that follow good agricultural practices (GAPs) and good hygiene practices (GHPs), and once received, seed should be inspected for physical damage and signs of contamination, and should be stored and handled properly
  • Seed treatment: Physical and chemical seed treatments to reduce the presence of pathogens is recommended; however, treatment can be challenging due to seeds’ low water activity and the need to preserve the viability of seeds and their ability to germinate
  • Microbiological testing: The likelihood of detecting the presence of pathogens in seeds for sprouting is extremely low, due to the commodity’s heterogeneous distribution and low numbers of pathogens contaminating a seed; however, spent sprout irrigation water has been identified as an appropriate target for microbial testing, and testing should be considered a verification that the seed used for sprouting and the production process does not contribute to sprout contamination.

JERMA states that preventive and control measures need to be put in place to avoid water, workers, the production environment, growth media, or seed from serving as the source of contamination or as a vehicle for cross-contamination. The production process should be based on a Hazard Analysis and Critical Control Points (HACCP) system, where all the steps are well-documented and potential critical control points can be identified and controlled.

Prevention and Control During Distribution and Point-of-Sale

The report states that the potential for bacterial growth and contamination can occur during transport distribution and at point-of-sale due to improper handling; poor personal hygiene; contamination through commingling with raw commodities, animals, or animal products; and exposure to unsanitary surfaces or water. Mitigation strategies include the training of operators and retailers; the use of clean, enclosed, refrigerated transport vehicles; a clean and sanitary point-of-sale environment; and fit-for-purpose water for cleaning, sanitizing, and cooling.

Sprouts should be kept at refrigeration temperature that will minimize microbial growth for the intended shelf-life of the product. The temperature of storage areas and transport vehicles should be monitored. Furthermore, for in-restaurant sprouting, interventions recommended for sprout operations should be considered, including seed sourcing programs, seed treatment (if appropriate), and the sampling and testing of spent sprout irrigation water (with samples to be tested by contract labs, in addition to cleaning and sanitizing food contact surfaces).

Records and Traceability

JERMA stresses that seed producers and suppliers should have a system to effectively identify seed lots, trace their associated production sites and agricultural inputs, and allow for the physical retrieval of the seed in the event of a suspected hazard. Sprout operations should ensure that records and traceability programs are in place to effectively respond to health risk situations.


Finally, the report states that all personnel involved in the production and handling of seed for sprouting or sprouts across the supply chain should receive training on the principles of food hygiene and food safety, as well as personal health and hygiene requirements. Seed producers, handlers, distributors and processors should be aware of GAPs and GHPs, and of their role and responsibility in protecting seed intended for sprouting from contamination.

Interventions designed to reduce microbiological hazards in sprouts can be highly technical and difficult to implement. Specific training related to seed sourcing and storage, seed treatment, sampling and microbial testing, cleaning and sanitizing, and record-keeping are required to ensure successful implementation. It is also important to develop a network of experts and technical support to enable the dissemination of accurate and complete information on safe production and handling of sprouts.