Contains Nonbinding Recommendations 
 
 
Reducing Microbial Food Safety Hazards 
in the Production of Seed for Sprouting:   
Guidance for Industry   
 
 
Additional copies are available from: 
Office of Food Safety, HFS-300 
Center for Food Safety and Applied Nutrition 
Food and Drug Administration 
5001 Campus Drive 
College Park, MD 20740 
(Tel) 240-402-1700 
https://www.fda.gov/FoodGuidances  
 
 
You may submit electronic or written comments regarding this guidance at any time.  Submit 
electronic comments to https://www/regulations.gov.  Submit written comments on the 
guidance to the Dockets Management Staff (HFA-305), Food and Drug Administration, 5630 
Fishers Lane, rm. 1061, Rockville, MD 20852.  All comments should be identified with the 
docket number FDA-2018-D-4534 listed in the notice of availability that publishes in the 
Federal Register. 
 
 
 
U.S. Department of Health and Human Services 
Food and Drug Administration 
Center for Food Safety and Applied Nutrition 
 
 
 
May 2022 
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  Contains Nonbinding Recommendations 
 
 
Table of Contents 
I. Introduction ........................................................................................ 3
 
 
II. Background ....................................................................................... 3
 
III. Recommendations and Considerations.......................................... 5
 
IV. References ......................................................................................... 8
 
 
   
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  Contains Nonbinding Recommendations 
 
 
Reducing Microbial Food Safety Hazards 
in the Production of Seed for Sprouting 
Guidance for Industry1  
 
This guidance represents the current thinking of the Food and Drug Administration (FDA or we) 
on this topic.  It does not establish any rights for any person and is not binding on FDA or the 
public.  You can use an alternative approach if it satisfies the requirements of the applicable 
statutes and regulations.  To discuss an alternative approach, contact the FDA staff responsible 
for this guidance as listed on the title page.  
 
I. Introduction 
 
This guidance document is intended to inform the sprout seed industry (seed growers, 
conditioners, packers, holders, suppliers, and distributors) of FDAs serious concern with the 
continuing outbreaks of foodborne illness associated with the consumption of raw and lightly-
cooked sprouts and to provide our recommendations to firms throughout the production chain of 
seed for sprouting.  Throughout this guidance document, we refer to everything that can be 
sprouted, including beans, as seeds.   
 
The contents of this document do not have the force and effect of law and are not meant to bind 
the public in any way, unless specifically incorporated into a contract.  This document is 
intended only to provide clarity to the public regarding existing requirements under the law. FDA 
guidance documents, including this guidance, should be viewed only as recommendations, unless 
specific regulatory or statutory requirements are cited.  The use of the word should in FDA 
guidances means that something is suggested or recommended, but not required.   
 
II. Background  
 
In the United States, between 1996 and 2020, FDA has observed 52 reported outbreaks of 
foodborne illness associated with contaminated sprouts.  Together, it is estimated that these 
outbreaks resulted in more than 2,700 cases of illness (Refs. 1-6).  Seeds and sprouts can become 
contaminated with pathogens at any point along the supply chain, such as the seed farm, seed 
conditioner, seed supplier, transportation, sprout operation, sprout distributor, retailer, or 
consumer.  However, contaminated seed has historically been identified as the likely source of 
most sprout-related outbreaks and continues to be the most common source of sprout 
contamination (Refs. 7-10).  For example, between November 2015 and May 2016, 
contaminated seed was associated with a multistate outbreak of Salmonella (multiple serotypes) 
 
1 This guidance has been prepared by the Division of Produce Safety in the Office of Food Safety at the Center for 
Food Safety and Applied Nutrition at the U.S. Food and Drug Administration.  
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  Contains Nonbinding Recommendations 
 
 
infections linked to alfalfa sprouts, which sickened at least 26 people in 12 states (Ref. 11).  The 
outbreak investigation traced the underlying cause of the outbreak to a single contaminated seed 
lot, which had been sprouted by several different sprout operations throughout the United States 
(Ref. 11).  After positive test results for multiple serotypes of Salmonella were obtained from 
this seed lot and from sprouts grown from this seed lot, the entire seed lot was recalled (Ref. 11).  
In addition, based on the epidemiological information and traceback data from FDAs analysis of 
14 sprout outbreaks that occurred in the United States between 2012 and 2020, FDA found that 
contaminated seed was the likely cause of most sprout-related outbreaks during this timeframe 
(Ref. 10).   
 
In the Federal Register of November 27, 2015 (80 FR 74353), we issued a final rule entitled 
Standards for the Growing, Harvesting, Packing and Holding of Produce for Human 
Consumption (the Produce Safety Rule).  Subpart M of the Produce Safety Rule includes 
standards specific to sprout operations.  This subpart includes provisions to prevent the 
introduction of known or reasonably foreseeable hazards into or onto seed that will be used for 
sprouting, once seeds have been received at the sprout operation.  In addition, for those sprout 
operations subject to the Produce Safety Rule, we announced the availability of a draft guidance 
for the sprout industry on January 23, 2017, entitled Compliance With and Recommendations 
for Implementation of the Standards for the Growing, Harvesting, Packing, and Holding of 
Produce for Human Consumption for Sprout Operations (82 FR 7751).  However, we consider 
seeds for sprouting to be outside the definition of covered produce in the Produce Safety Rule, 
and activities such as growing, conditioning, and distributing seeds for sprouting to be outside 
the scope of covered activities in the Produce Safety Rule.  In addition, we recognize that the 
end use of seed may sometimes be unknown by the farmers who grow the seed and by the 
conditioners and distributors who handle the seed.  Therefore, we did not prescribe specific 
provisions in the Produce Safety Rule to prevent the introduction of known or reasonably 
foreseeable hazards into or onto seed during growing, harvesting, conditioning, or holding of 
seed for sprouting.   
 
We note that, although seeds for sprouting are not covered produce under the Produce Safety 
Rule, these seeds are food as defined in the Federal Food, Drug, and Cosmetic Act (FD&C 
Act) and are subject to regulation under the FD&C Act.2,3,4  Therefore, if a grower, holder, 
conditioner, packer, or distributor reasonably believes that its seeds will be used for sprouting, 
we recommend that the grower, holder, conditioner, packer, or distributor take steps that are 
reasonably necessary to prevent those seeds from becoming adulterated.  We also recommend 
that firms throughout the supply chain  from seed production and distribution through sprouting 
 review their current operations related to seeds for sprouting to determine whether such steps 
are in place.  We recommend firms throughout the supply chain follow the recommendations in 
this guidance, regardless of whether the seed for sprouting will be eventually treated to reduce 
microorganisms of public health significance.  Seed treatments may reduce, but not eliminate, 
pathogens on seed for sprouting; therefore, reduction of incoming microbial load through 
 
2 CPG Sec. 555.750 Seeds for Sprouting Prior to Food Use, i.e., Dried Mung Beans, Alfalfa Seeds, Etc. 
(https://www.fda.gov/ICECI/ComplianceManuals/CompliancePolicyGuidanceManual/ucm074562.htm).  
3 21 CFR Part 112.   
4 Section 201(f) of the FD&C Act defines food as (1) articles used for food or drink for man or other animals, 
(2) chewing gum, and (3) articles used for components of any such article. 
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  Contains Nonbinding Recommendations 
 
 
implementation of good agricultural practices (GAPs) in seed production is a key step in 
ensuring safety of seeds and sprouts.   
 
III. Recommendations and Considerations 
 
If You Grow, Condition, Pack, Hold, or Distribute Seeds for Sprouting: 
 
We recommend that everyone in the sprout seed supply chain become as informed as reasonably 
possible about the food safety practices, processes, and procedures followed by the firm(s) from 
which you source your seed; where your seed will go after it leaves your firm; and whether your 
seed is reasonably likely to be used to produce sprouts for human consumption.  Some firms may 
perform multiple operations, such as growing, conditioning, packaging, and distributing seeds, 
while other firms may perform a single type of operation. 
 
The practices and conditions appropriate for producing seed for sprouting most likely will 
necessitate a higher level of food safety precautions compared to practices and conditions for 
producing seed that will be used for other purposes.  In sprout-related outbreaks where seeds 
have been implicated as the source of contamination, the following have been identified as 
possible sources of contamination of the seed: rodent and bird activity within the seed 
conditioning operation; use of chicken manure to fertilize fields where seed was grown; transport 
in unclean vehicles; and use of irrigation water impacted by drainage from neighboring fields 
where manure was applied as a soil amendment.  Sampling of soil sediment and water undertaken 
by FDA in 2020 identified isolates of Salmonella in the agricultural environment, which were 
determined to be genetically related by Whole Genome Sequencing to clinical isolates from 2016 
and 2018 illness outbreaks associated with consumption of sprouts (Ref. 12).  The observed 
genetic association between pathogens found in the growing environment, and clinical cases 
from earlier outbreaks in which sprouts were implicated as a vehicle, highlight the importance of 
taking food safety precautions during the growing and production of seed for sprouting before 
the seed reaches the sprout grower.  
 
Specifically, we recommend that you: 
 
  Take steps to educate and train personnel, with a specific emphasis on personnel who 
handle seeds for sprouting or food contact surfaces of equipment and tools used for seeds 
for sprouting, or those engaged in the direct supervision such personnel, on the principles 
of food hygiene, food safety, and personal health and hygiene, and how these principles 
apply to their job duties.  Food contact surfaces are those surfaces that contact human 
food (e.g., seeds for sprouting) and those surfaces from which drainage, or other transfer, 
onto the food or onto surfaces that contact the food ordinarily occurs during the normal 
course of operations. 
  Provide adequate, readily accessible, clean, and well-maintained and -supplied toilet and 
hand-washing facilities to personnel who handle seeds for sprouting or food contact 
surfaces of equipment and tools used for seeds for sprouting, or are engaged in the direct 
supervision thereof, and ensure that wastes from those facilities do not serve as a source 
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  Contains Nonbinding Recommendations 
 
 
of contamination of the seeds for sprouting, food contact surfaces, or water sources and 
distribution systems used for seed for sprouting. 
  Encourage good hygiene practices, including: adequate personal cleanliness (through 
handwashing before starting work, when returning to work after breaks, immediately 
after using the toilet, and after handling trash, manure, or animals); personal behavior 
(including avoiding spitting, chewing, eating, and sneezing or coughing over unprotected 
seed); and communication (including providing notification to their supervisor if an 
employee has a health condition that presents a public health risk in the context of their 
normal work duties) among personnel who handle seeds for sprouting or food contact 
surfaces of equipment and tools used for seeds for sprouting, or are engaged in the direct 
supervision thereof. 
  Assess your operation for opportunities for seed for sprouting to become contaminated by 
other seeds or grains that are not for sprouting or human consumption and take steps that 
protect seed for sprouting from becoming contaminated by these other products.  For 
example, you could store seed for sprouting separately from seed for other uses.  If your 
operation uses the same equipment to process seed for sprouting and other commodities, 
consider ordering your operations from cleanest to dirtiest (i.e., if you use shared 
equipment, use it on seed for sprouting before using it on seed for other uses). 
  Ensure that food contact surfaces are cleanable, as appropriate to the manner in which the 
equipment will be used and the method of cleaning.  In many instances, dry cleaning 
(e.g., brushing, scraping, blowing with compressed air, suction with vacuum system to 
remove residual debris) may be preferable to wet cleaning (e.g., use of water and 
cleaning solutions, along with mechanical debris removal) to avoid the introduction of 
moisture into an otherwise low-moisture environment, which can facilitate pathogen 
growth and impact seed integrity.  However, there may be times when wet cleaning is 
preferable and feasible, for example when the equipment is frequently exposed to 
moisture naturally (e.g., it is left out in fields or in unenclosed buildings exposed to the 
elements).  
  Clean food contact surfaces as frequently as reasonably necessary to protect against 
contamination of seed for sprouting.  For example, if you intend to process seed for 
sprouting after processing other types of seed on the same equipment, you should clean 
the food contact surfaces of that equipment before use on seed for sprouting.   
  Evaluate your operation to determine which food contact surfaces can be sanitized, assess 
what options are available under the conditions of your operation for sanitizing such food 
contact surfaces, and determine under what circumstances sanitizing is necessary for 
these food contact surfaces (e.g., before their use to contact lots of seed for sprouting, or 
after events when they may have become contaminated, such as contact with flood waters 
or uncomposted manure). 
  Ensure that seed is transported in a manner that minimizes the likelihood of 
contamination with pathogens.  For example, choose transportation vehicles and 
equipment that are suitable for their intended use and cleanable, as appropriate to the 
manner in which the equipment will be used and the method of cleaning (e.g., dry 
cleaning); and take measures to segregate or use packaging to protect seeds for sprouting 
from contamination (e.g., contamination by other foods, seeds for uses other than 
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sprouting for human consumption, or other non-food items in the same load or previous 
loads). 
  Take appropriate follow-up actions if you know or have reason to believe the seed you 
have produced may be contaminated with a pathogen.  These actions may include, for 
example, informing sprout growers who purchased seed from the suspected lot(s) 
regarding the contamination; destroying or diverting remaining seeds from the lot(s) of 
concern to non-food uses; and investigating and addressing the potential source(s) of 
contamination, as necessary. 
 
Some seed producers may opt to test their seed for pathogens before distribution.  While testing 
lots of seed for sprouting for pathogens can help identify contaminated lots, we note that there 
are limitations to what the test results can tell you (for example, because contamination may be 
at low levels or unevenly distributed throughout the seed lot).  Laboratory analyses have 
frequently been unable to detect pathogens from lots of seeds that have been conclusively 
implicated as the vehicle in foodborne illness outbreaks because of low levels and lack of 
uniformity of pathogens (Ref. 13).  Therefore, testing seed is not a substitute for implementing 
GAPs and should not replace efforts to prevent seed from becoming contaminated during 
production.  In addition, we recognize that while a positive test can indicate seeds are 
contaminated, a negative test result is not a guarantee of the absence of pathogens in the lot of 
seeds.  You should not re-test lots of seed that have tested positive for a pathogen to demonstrate 
that the seed lot is not contaminated.  A positive test result is not negated by a subsequent 
negative test result. 
 
 
If You Grow Seed for Sprouting: 
 
We recommend that seeds for sprout production be grown using GAPs or in conformance with 
international standards such as the Codex Alimentarius International Code of Hygienic Practice 
for Fresh Fruits and Vegetables,5 including Annex II (Sprout Production), which addresses 
primary production of seeds for sprouting.  For example, we recommend the following: 
 
  You should determine at the time of planting whether a particular crop is intended for 
sprouting, so that you can follow the recommendations in this guidance while it is 
growing. 
  If you use biological soil amendments of animal origin (e.g., manure) in seed for 
sprouting growing fields, you should only use them in such a way that they do not 
contaminate the seed for sprouting, areas used for growing or handling seed for 
sprouting, food contact surfaces, or water sources and distribution systems used for seed 
for sprouting.  For example, you should treat any such soil amendments using a 
scientifically valid chemical, physical, biological, or combination process, such as static 
or turned composting, to ensure they do not contain pathogens of public health 
significance (e.g., Salmonella or E. coli O157:H7). 
 
5 http://www.fao.org/fao-who-codexalimentarius/sh-
proxy/en/?lnk=1&url=https%253A%252F%252Fworkspace.fao.org%252Fsites%252Fcodex%252FStandards%252
FCAC%2BRCP%2B53-2003%252FCXC_053e.pdf  
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  Contains Nonbinding Recommendations 
 
 
  You should assess the areas used for growing seed for sprouting for evidence of potential 
contamination of seed from domesticated or wild animals as needed during the growing 
season, based on the type of seed you use, your growing practices and conditions, and 
your past observations and experience (e.g., observation of animals, animal excreta, crop 
destruction).  If significant evidence of potential contamination is found (e.g., animal 
excreta on or near the crop, crop damage, or destruction by animals) you should evaluate 
whether or not the seed should be harvested.  If any seed should not be harvested because 
it is reasonably likely to be contaminated (e.g., it is visibly contaminated with animal 
excreta), we recommend that you take measures to help you later identify, and not 
harvest, the affected seed.  For example, you might mark the affected area in a manner 
that will ensure it is not harvested, even if weather events or other occurrences remove 
the excreta such that it is not visible later during harvest. 
  You should assess the areas used for growing seed for sprouting for adjacent land use 
considerations, such as the presence of nearby animal production facilities (e.g., 
concentrated feed operations, poultry farms, dairy farms) and related factors (e.g., slope 
of land, runoff controls, spreading manure) that could lead to contamination of the seed 
or irrigation water with untreated manure, and you should take steps to prevent such 
contamination. 
  You should ensure that water used for crop protection sprays or irrigation of areas where 
you grow seed for sprouting, in which there is contact with the seed, is safe and of 
adequate sanitary quality for its intended use.  For example, if you learn that your 
irrigation water has tested positive for a pathogen of public health significance, you 
should treat your water to eliminate the pathogen or change your water source.   
 
If You Pack or Hold Seed for Sprouting: 
   
We recommend that you pack and hold seed under sanitary conditions, including taking steps to 
control pests.  For example, we recommend: 
 
  Seed should be stored in closed or covered containers, in a clean, dry area dedicated to 
seed storage.  We recommend that containers be positioned off the floor and away from 
walls to reduce the possibility of contamination by rodents or other pests and to facilitate 
regular monitoring for pest problems. 
  You should use packaging for seeds that minimizes the potential for contamination. 
 
IV. References  
 
The following references marked with an asterisk (*) are on display at the Dockets Management 
Staff (HFA-305), Food and Drug Administration, 5630 Fishers Lane, Rm. 1061, Rockville, MD 
20852, and are available for viewing by interested persons between 9 a.m. and 4 p.m., Monday 
through Friday; they also are available electronically at https://www.regulations.gov.  References 
without asterisks are not on public display at https://www.regulations.gov because they have 
copyright restriction.  Some may be available at the website address, if listed.  References 
without asterisks are available for viewing only at the Dockets Management Staff.  FDA has 
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  Contains Nonbinding Recommendations 
 
 
verified the website addresses, as of the date this document publishes in the Federal Register, but 
websites are subject to change overtime.  
 
1.  DLima, C., et al.  Memorandum to the File  Produce Related Outbreaks and illnesses, 
December 2011.  Food and Drug Administration.*  
2.  Merriweather, S., et al.  Memorandum to the File  2011-2014 Produce Related Outbreaks 
and Illnesses, May 2015.  Food and Drug Administration.* 
3.  Gubernot, D., et al.  Memorandum of Record:  2015-2016 Sprout and Sprout-Derived 
Product Related Outbreak Data, July 28, 2016.  Food and Drug Administration.* 
4.  Fatica, Marianne K., et al. Memorandum of Record:  July-December 2016 Sprout Related 
Outbreak Data, February 16, 2017.  Food and Drug Administration.* 
5.  Fatica, Marianne K., et al. Memorandum of Record:  January 2017-August 2018 Sprout 
Related Outbreak Data, September 12, 2018.  Food and Drug Administration.* 
6.  Obenhuber, D., et al., Memorandum of Record: August 2018-August 2020 Sprout Related 
Outbreak Data, October 13, 2020.  Food and Drug Administration.*  
7.  National Advisory Committee on Microbial Criteria for Foods (NACMCF), Microbiological 
Safety Evaluations and Recommendations on Sprouted Seeds, International Journal of 
Food Microbiology 52 (1999):123-153.*  
8.  EFSA Panel on Biological Hazards (BIOHAZ); Scientific Opinion on the risk posed by 
Shiga toxin producing Escherichia coli (STEC) and other pathogenic bacteria in seeds and 
sprouted seeds.  EFSA Journal 2011;9(11):2424. [101 pp.] doi:10.2903/j.efsa.2011.2424. 
9.  Ferguson, D. D., J. Scheftel, A. Cronquist, K. Smith, A. Woo-Ming, E. Anderson, J. Knutsen, 
A. K. De, and K. Gershman.  Temporally distinct Escherichia coli O157 outbreaks 
associated with alfalfa sprouts linked to a common seed sourceColorado and Minnesota, 
2003, Epidemiology & Infection 133, no. 3 (2005): 439-447. 
10. Obenhuber, D., et al.  Memorandum of Record: 2012-2020 Sprout-Related Outbreak Data, 
July 20, 2020.  Food and Drug Administration.* 
11. Food and Drug Administration.  May 13, 2016.  FDA Investigated Multistate Outbreak of 
Salmonella Infections Linked to Alfalfa Sprouts.  Available at 
https://www.fda.gov/food/outbreaks-foodborne-illness/fda-investigated-multistate-outbreak-
salmonella-infections-linked-alfalfa-sprouts.  
12. Food and Drug Administration. May 2021.  Factors Potentially Contributing to the 
Contamination of Red Onions Implicated in the Summer 2020 Outbreak of Salmonella 
Newport.  Available at https://www.fda.gov/media/148440/download. 
13. Fett, W.F., M. Tortorello, and T. Fu.  Seed Sprouts: The State of Microbiological Safety.  
Microbiology of Fresh Produce edited by K.R. Matthews, pp. 167219. Washington, DC: 
ASM Press, 2006. 
 
 
 
 
 
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