Guidance for Industry
Prevention of Salmonella Enteritidis in 
Shell Eggs During Production, Storage, 
and Transportation 
    Additional copies are available from:  
Office of Food Safety 
Division of Plant and Dairy Food Safety, HFS-316 
Center for Food Safety and Applied Nutrition 
Food and Drug Administration 
5001 Campus Drive 
College Park, MD  20740 
(Tel) 240-402-2385  
 http://www.fda.gov/FoodGuidances   
You may submit electronic or written comments regarding this guidance at any time.  Submit 
electronic comments to http://www/regulations.gov.  Submit written comments on the guidance 
to the Division of Dockets Management (HFA-305), Food and Drug Administration, 5630 
Fishers Lane, rm. 1061, Rockville, MD 20852.  All comments should be identified with the 
docket number 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 
December 2011  Contains Nonbinding Recommendations 
 
Table of Contents 
 
 
 
I.    Introduction
 
II.    Background 
 
III.   Discussion 
  A.  Salmonella Enteritidis Prevention Measures 
  B.  Sampling and Testing for Salmonella Enteritidis 
C.  Recordkeeping  
IV.  References
 
 
  2 Contains Nonbinding Recommendations 
 
Guidance for Industry1
 
 
Prevention of Salmonella Enteritidis in Shell Eggs During 
Production, Storage, and Transportation
 
 
 
This guidance represents the Food and Drug Administration's (FDA's) current thinking on this 
topic.  It does not create or confer any rights for or on any person and does not operate to bind 
FDA or the public.  You can use an alternative approach if the approach satisfies the 
requirements of the applicable statutes and regulations.  If you want to discuss an alternative 
approach, contact the FDA staff responsible for implementing this guidance.  If you cannot 
identify the appropriate FDA staff, call the telephone number listed on the title page of this 
guidance.  
 
 
 
 
I.  Introduction 
 
The purpose of this document is to provide guidance to egg producers on certain provisions 
contained in FDAs July 9, 2009, final rule Prevention of Salmonella Enteritidis in Shell Eggs 
During Production, Storage, and Transportation (74 FR 33030), including how to implement 
Salmonella Enteritidis (SE) prevention measures, how to sample for SE, and how to maintain 
records documenting compliance with the final rule.   
  
FDA's guidance documents, including this guidance, do not establish legally enforceable 
responsibilities.  Instead, guidances describe the Agency's current thinking on a topic and should 
be viewed only as recommendations, unless specific regulatory or statutory requirements are 
cited.  The use of the word should in Agency guidances means that something is suggested or 
recommended, but not required.  
 
II.  Background 
 
FDA issued a final rule on July 9, 2009, requiring shell egg producers to implement measures to 
prevent SE from contaminating eggs on the farm and from further growth during storage and 
transportation (21 CFR part 118).  The egg rule was effective September 8, 2009.  The 
compliance date for the egg rule is July 9, 2010, for producers with 50,000 or more laying hens, 
and July 9, 2012, for producers with fewer than 50,000 but at least 3,000 laying hens.  Producers 
with fewer than 3,000 laying hens and those that sell all of their eggs directly to consumers are 
exempt from the egg rule. 
                                                 
1 This guidance has been prepared by the Division of Plant and Dairy Food Safety in the Center for Food Safety and 
Applied Nutrition at the U.S. Food and Drug Administration.  
  3 Contains Nonbinding Recommendations 
 
 
In the preamble in its July 9, 2009, final rule, FDA announced that it intended to provide 
guidance on recordkeeping and other provisions of the rule, including further specific 
recommendations for (1) biosecurity steps and options for achieving these steps, (2) monitoring 
for flies and on the level of fly activity considered acceptable, and (3) acceptable manure 
removal.  This guidance document is a follow-up to that commitment. 
 
This guidance provides recommendations on the following provisions: Salmonella Enteritidis 
(SE) prevention measures ( 118.4), environmental testing for Salmonella Enteritidis (SE) ( 
118.5), egg testing for Salmonella Enteritidis (SE) ( 118.6), sampling methodology for 
Salmonella Enteritidis (SE) ( 118.7), and recordkeeping requirements for the Salmonella 
Enteritidis (SE) prevention plan ( 118.10).  These provisions list the measures producers must 
take to comply with the rule.  This guidance offers more specific recommendations and options 
for several of the measures.  While each producer is required to comply with all applicable 
measures listed in  118.4, 118.5, 118.6, 118.7, and 118.10, producers should select and 
implement only those recommendations and options from this guidance that are most appropriate 
and will be most effective for their particular farm and situation.   
 
III.  Discussion 
 
A.  Salmonella Enteritidis Prevention Measures ( 118.4) 
 
1. Biosecurity ( 118.4(b)) 
 
FDAs egg rule defines biosecurity (see  118.3) as a program, including the limiting of visitors 
on the farm and in poultry houses, maintaining personnel and equipment practices that will 
protect against cross contamination from one poultry house to another, preventing stray poultry, 
wild birds, cats, and other animals from entering poultry houses, and not allowing employees to 
keep birds at home, to ensure that there is no introduction or transfer of [SE] onto a farm or 
among poultry houses.  Biosecurity practices should be designed to prevent SE from coming in 
contact with resident birds on the farm; the goal of biosecurity is to keep SE away from the birds 
and the birds away from SE. 
 
The egg rule requires, at a minimum, the following biosecurity measures:  
  Limiting visitors on the farm and in the poultry houses ( 118.4(b)(1)); 
  Maintaining practices that will protect against cross contamination when equipment is 
moved among poultry houses ( 118.4(b)(2)); 
  Maintaining practices that will protect against cross contamination when persons move 
between poultry houses ( 118.4(b)(3)); 
  Preventing stray poultry, wild birds, cats, and other animals from entering poultry houses 
( 118.4(b)(4)); and 
  Not allowing employees to keep birds at home ( 118.4(b)(5)). 
 
Further specific recommendations for biosecurity steps and options for achieving these steps are 
outlined below. 
  4 Contains Nonbinding Recommendations 
 
 
Biosecurity can be broken down into three components: isolation, traffic control, and sanitation.  
Isolation refers to time, distance, and physical barriers that reduce or prevent entry onto the farm 
and/or into the poultry houses.  Traffic control includes restricting human, equipment, and 
animal movement onto the farm, and movement patterns while on the farm.  Sanitation refers to 
the cleaning and disinfection of poultry houses, people, materials, and equipment.   
 
Isolation 
 
Isolation can be considered in terms of distance between farms or houses on a farm, physical 
barriers (cages, boot dipping stations), and time (the amount of time between depopulating and 
repopulating a house), all of which limit the spread of SE. 
 
Distance between farms or houses on a farm.  Layout and placement of houses within the farm is 
very important for minimizing the spread of SE.  For new farms or additional houses, egg 
producers should consider the distance that will be created from other farms, houses, and birds, 
such as pullets, other hens, and wild birds.  For existing houses and farms, egg producers should 
consider the actual distance from other farms, houses, and birds when determining appropriate 
prevention measures.  Wild birds, waterfowl, exotic pet birds, and domestic poultry can be 
important sources of Salmonella because closely related species are likely to carry agents that 
can also infect commercial chickens.  In addition, egg producers should give careful 
consideration to preventing airborne transmission of SE.  For example, air intakes of one poultry 
house that are located away from the outflow vents of other houses reduce the likelihood of 
airborne transmission of SE. 
 
Physical barriers.  Physical barriers are very effective at limiting the spread of SE.  Cages limit 
the fecal-to-oral mode of transmission between chickens because they reduce the amount of fecal 
material that accumulates where other chickens are exposed to it.  Although most fecal 
contamination of feed occurs from rodents defecating in the feed troughs, properly maintained 
feed storage silos help limit fecal contamination of feed by pests, which limits fecal-to-oral 
transmission of SE from pests to birds.  Securing buildings and removing feed and harborage for 
pests (including free-standing water and tall grasses) are effective at creating a barrier around the 
flock, thereby limiting the spread of SE.  Houses should be carefully inspected for possible 
routes of entry; if any are found, they should be repaired immediately. 
 
Human traffic also should be limited and controlled by the use of physical barriers.  SE can be 
carried on clothing, hair, exposed skin, and footwear.  Employees should wear freshly laundered 
clothing daily, and visitors should be provided with clean protective clothing.  Once a poultry 
house has tested positive for SE, it is especially important to consider physical barriers that will 
reduce the risk of cross-contamination among houses.  A properly maintained boot dipping 
station that includes a brush for the removal of organic material and a dip with a disinfecting 
agent can help prevent the exit of SE from the positive house on boots.  However, to be effective, 
all organic material should be removed from the surface of the boot before the boot is dipped 
into the disinfecting solution.  Disinfectants should be properly diluted and changed at least daily 
(or more often if baths collect a lot of dirt and manure) to be effective.  Dry foot baths utilizing 
dry and/or aerosol disinfectants may be used in lieu of boot dipping stations.  Other physical 
  5 Contains Nonbinding Recommendations 
 
barriers that producers should consider in the case of an SE-positive house are changing outer 
clothing upon exiting the positive house and, where practical, having dedicated equipment for 
the positive house.  These barriers reduce the risk of cross-contamination among houses when 
one or more houses on a farm has tested positive for SE.  If having dedicated equipment is not 
possible, shared equipment should be completely cleaned and disinfected upon removal from the 
positive house.  Although the common egg belt may be impractical to clean and disinfect, once a 
house has tested positive for SE, the egg belts in that house should be turned off to avoid 
commingling eggs from the positive house with eggs from other houses on the common egg belt.  
 
Time.  Ample time should be allowed between flocks in a house to prevent the transmission of 
SE.  Under normal conditions, two weeks is adequate for complete cleaning and disinfection of 
the poultry house.  However, the risk of infection from previous flocks should be considered 
when determining how much time needs to elapse between flocks.  Producers should consider 
longer down times if the environment or eggs of the previous flock in the house were found SE 
positive.  They may also wish to consider swabbing a cleaned and disinfected house to verify 
that it is SE negative prior to repopulating, if the environment or eggs of the previous flock in the 
house were positive for SE. 
 
Traffic Control 
 
People and equipment that come onto a farm can introduce SE.  One of the most effective ways 
to control human traffic is with the use of signs, fences, and gates (including locking gates).  
Buildings should remain locked to the extent possible to ensure that the biosecurity plan is 
followed by all visitors and nonfarm employees. 
 
Clothing should be provided for visitors, including maintenance and pest control personnel, as 
they come onto the farm.  These can be either disposable or reusable clothing that stays on the 
farm.  Coveralls that cover all street clothing including collars, cuffs, and wristwatches, and 
plastic or rubber boots or shoe covers that completely cover visitors shoes should be worn.  Hair 
should be covered with bouffant caps, beards covered with disposable beard covers, and hands 
washed or sanitized prior to entry into the house. 
 
Extra precautions should be taken for personnel or visitors arriving from other farms or from 
places considered potentially hazardous (e.g., laboratories, auctions).  All visitors should report 
to a central location and sign a log book before coming on the farm.  The log book should record 
the date, time, persons name, reason for visit, and types of places visited that day.  Farm 
personnel visiting laboratories, other farms, meetings, or restaurants where other producers, 
service personnel or backyard flock owners visit are at an increased risk of cross-contaminating 
the farm at which they are employed.   
 
Multiple farms should not share equipment, but if they do, it should be thoroughly cleaned and 
disinfected between farms.  Only clean and disinfected crates, egg cartons, pallets, and other 
equipment should be brought onto a farm, and business should only be conducted with other 
companies that also have high biosecurity standards. 
 
  6 Contains Nonbinding Recommendations 
 
Activities at each farm can be divided into dirty and clean ones.  Manure handling, dead bird 
disposal, disposal of trapped pests, and removal of breeding areas for pests are examples of dirty 
activities.  Examples of clean activities are egg handling, chick handling, movement of birds, and 
other activities involving contact with live birds.  When working with or in the presence of live 
birds, workers should always move from the youngest birds to the oldest.  Personnel and 
equipment used in dirty activities should be cleaned and disinfected before coming into contact 
with personnel and equipment involved in clean activities.  If equipment or personnel must be 
shared between the two types of activities, then they should always go from clean activities to 
dirty ones and not the reverse. 
 
Sanitation 
 
The goal of farm sanitation is to maintain a clean environment for the birds.  Sanitation reduces 
the likelihood of SE coming in contact with the birds, and is, therefore, an important component 
of biosecurity.  Daily attention should be paid to the proper management and disposal of dead 
birds, loose birds, spilled feed, manure, and refuse.  Dead birds should be removed and disposed 
of as quickly as possible.  Daily collection of mortality and disposal will reduce contact with 
insects, rodents, or other animals that could act as SE vectors.  New birds should always be 
placed in a cleaned and disinfected house.   
 
Spilled feed should not be allowed to amass in or around poultry houses, as it will attract insects, 
rodents, and wild birds, all of which can bring SE onto the farm and into the houses.  Poultry 
manure and litter should be managed properly so it does not attract flies and other insects or 
serve as a habitat for rodents that carry SE into the houses.  Manure should be kept as dry as 
possible to make it less attractive to flies and other insects.  Special attention should be given to 
preventing water system leaks and promptly repairing leaks when found.  Disposal of cracked 
eggs into the manure should be avoided since they are an attractive food source for both insects 
and rodents.  Poultry houses should be properly ventilated, as weather permits, since proper 
ventilation dilutes microbe populations and reduces disease buildup. 
 
Proper disposal of manure and all refuse on the farm is important in eliminating rodent harborage 
sites.  Trash and manure piles are also attractive to wild birds that may carry SE. 
 
(Refs. 3, 4, 10, and 15) 
 
2. Rodents, Flies, and Other Pest Control ( 118.4(c)) 
 
As part of a producers pest control program, the egg rule requires the following:  
  Monitoring for rodents by visual inspection and mechanical traps or glueboards or 
another appropriate monitoring method and, when monitoring indicates unacceptable 
rodent activity within a poultry house, using appropriate methods to achieve satisfactory 
rodent control ( 118.4(c)(1)); 
  Monitoring for flies by spot cards, Scudder grills, or sticky traps or another appropriate 
monitoring method and, when monitoring indicates unacceptable fly activity within a 
poultry house, using appropriate methods to achieve satisfactory fly control ( 
118.4(c)(2)); and 
  7 Contains Nonbinding Recommendations 
 
  Removing debris within a poultry house and vegetation and debris outside a poultry 
house that may provide harborage for pests ( 118.4(c)(3)). 
 
Monitoring for Rodents 
 
Some FDA recommended rodent monitoring methods, as well as characterizations of levels of 
rodent activity, are discussed below. 
 
Visual inspection: Visual inspection is conducted by walking through all areas of a poultry 
house.  Observation of any of the following is likely to indicate unacceptable rodent activity: live 
rodents, excessive dead rodents, rodent feces, gnaw holes, baited traps without bait, or nests in 
traps.   
 
Rodent indexing: The Rodent Index (RI) is based on the total number of rodents caught in a 
house in 7 days using 12 live catch traps and is used to estimate the rodent population. FDA 
recommends the following procedure for obtaining the RI: 
  Bait each of 12 live catch rodent traps with 0.5 oz. of chicken feed. 
  Place the traps in areas where recent signs of rodent activity are observed or in areas most 
likely to catch rodents, e.g., along cage walkways and against walls.  Use a minimum of 
15 feet distance between traps. 
  Check the traps after 2 to 4 days.  Remove, count, and record the number of rodents 
caught. 
  Move the traps that did not catch any rodents to a different location, a minimum of 15 
feet away.  Traps that caught a rodent are placed back in the same location. 
  Check the traps again 7 days after they were first placed. 
  Record the total number of rodents caught for the week. 
 
The following formula standardizes all rodent catches to a 1-week period using 12 live catch 
traps by adjusting for periods of time longer or shorter than 7 days and using more or fewer 
traps. 
 
Number of rodents for RI = (total number of rodents in traps  working traps set) x 12   x 7 
                   number of days traps are set 
 
The rodent population is then estimated by applying the number of rodents as determined using 
the formula above to the RI table below.  An RI of 1 or less is likely to indicate satisfactory 
rodent control.  If an RI greater than 1 is obtained, the producer should investigate to find out 
where rodents are entering the house.  Section 118.4(c)(1) requires that appropriate methods be 
taken to achieve satisfactory rodent control when monitoring indicates unacceptable rodent 
activity within a poultry house. 
 
Number of rodents caught in 7 days with 12 traps  RI  Description of RI 
0-10  1  Low 
11-25  2  Moderate 
26 or more  3  High 
 
  8 Contains Nonbinding Recommendations 
 
 
Monitoring for Flies 
 
Some FDA recommended fly monitoring methods, as well as characterizations of levels of fly 
activity, are discussed below.  Section 118.4(c)(2) requires that appropriate methods to achieve 
satisfactory fly control be taken when monitoring indicates unacceptable fly activity within a 
poultry house. 
 
Spot Card Method: Ordinary (3 inches x 5 inches) white index cards are attached to obvious fly 
resting surfaces. These are areas with large numbers of fly fecal and regurgitation spots. The 
number of spot cards will vary depending on the size of the house. At a minimum there should 
be five equidistant locations per house. After 7 days, the cards are collected, and the number of 
spots presumably made by flies is counted.  The average per card is calculated, giving a spot card 
index of the fly population.  A spot card index of 50 or fewer per card is likely to indicate 
satisfactory fly control. 
 
Fixed Sticky Tape Method: An ordinary sticky fly tape is hung above the cages in the front, 
center, and rear of the poultry house.  After 7 days, the tapes are removed and the number of flies 
trapped on the tapes is counted.  A weekly count of 50 or fewer flies per tape is likely to indicate 
satisfactory fly control. 
 
Moving Tape Method: In this method, an ordinary sticky fly tape is unrolled and extended full 
length.  The operator grasps the top of the tape by the string loop and suspends the tape by his 
side so that the bottom cardboard cylinder is about 2.5 to 5.0 cm from the floor while walking at 
a normal pace on an inside walkway between the cages.  After walking a 1,000-foot route that 
covers a representative sample of the house population of flies (approximately 5 minutes or two 
full rows), the operator counts and records the number of flies stuck on the tape.  A count of 75 
or fewer flies per tape is likely to indicate satisfactory fly control. 
 
Baited Traps: These may be gallon plastic milk jugs hung from the rafters on 18-24 inch wires.  
The jugs have 2-inch round openings cut in the upper part of the sides to allow flies attracted to 
bait placed on the inside bottom of the jug to enter.  A fly count of 250 or fewer flies per week is 
likely to indicate satisfactory fly control. 
 
Scudder Grill: A grill, often referred to as a Scudder grill, consists of 16 to 24 wooden slats, fastened 
at equal intervals to cover an area of approximately 0.8 square meters. The grill is placed where there 
are natural fly concentrations and the number of flies landing on the grill in a given period of time 
(usually 30 seconds or l minute) is counted. In each locality, counts are made on 3 to 5 or more of the 
highest fly concentrations found and the results averaged. A count of less than 20 on a Scudder grill 
is likely to indicate satisfactory fly control.   
 
Removing Debris 
 
A 3 foot area around a poultry house of gravel or other non-grass substance discourages rodents, 
as does maintaining grass at a short height (maximum of 6 inches) beyond the 3 foot area.  Old 
equipment, used boards, and discarded debris are rodent harborage areas and should be kept at 
  9 Contains Nonbinding Recommendations 
 
least 300 feet away from the house to discourage harborage of rodents.  In situations where 
poultry houses are located less than 300 feet from property lines, producers should practice  
additional vigilance to secure their property from rodent infestation. 
 
 
(Refs. 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, and 15) 
 
3. Cleaning and Disinfection ( 118.4(d)) 
 
FDAs egg rule requires that a poultry house be cleaned and disinfected according to the 
following procedures before new laying hens are placed in the house, if that house has had an 
environmental test or an egg test that was positive for SE at any point during the life of a flock 
that was housed in the poultry house prior to depopulation:  
  Remove all visible manure ( 118.4(d)(1)); 
  Dry clean the positive poultry house to remove dust, feathers, and old feed ( 
118.4(d)(2)); and 
  Following cleaning, disinfect the positive poultry house with spray, aerosol, fumigation, 
or another appropriate disinfection method ( 118.4(d)(3)). 
 
It is important that, once a poultry house has had an SE-positive environmental or egg 
test, a producer make every effort to rid the environment of SE before new laying hens are 
placed into that house to prevent the SE problem from being perpetuated in the replacement 
flock.  Although cleaning and disinfection is only required when a house has had an SE-positive 
test, FDA recommends that producers clean and disinfect every house between flocks.  
 
FDA recommends the following procedures for cleaning and disinfecting poultry houses 
between flocks: 
  Removal of all dead and live chickens, eggs, and other animals 
  Removal of all moveable equipment from the house to allow for thorough cleaning 
  Placement of fresh rodent bait; this is removed just prior to cleaning 
  Physical repair of rodent entry sites 
  Application of appropriate insecticides 
  Removal of all feed from troughs, hoppers, and feed bins; this is very important for 
rodent control; feed caked on troughs should be removed by scraping 
  Dry cleaning (by scraping, scooping, sweeping, compressed air, or other appropriate 
methods) of the upper part of the house, starting with the air inlets (inside and outside) 
and working downward; organic material should be moved into the pit for eventual 
removal 
  Physical removal of manure from dropping boards, cage curtains, cage cross 
members/bars, and floor joints such that no large, visible clumps of manure remain 
  Thorough dry cleaning of fans, housing, brush blades, and louvers 
  Removal of all manure and organic material from the pit 
  Follow-up of gross cleaning with scraping, scooping, and sweeping 
  Inspection of all areas for cleanliness and re-cleaning if necessary 
 
  10 Contains Nonbinding Recommendations 
 
Because manure is a reservoir for SE that has been shed by infected laying hens, once a poultry 
house has had an SE-positive environmental or egg test, it is important that all visible manure be 
removed ( 118.4(d)(1)).  Removing all visible manure before new laying hens are placed into a 
house will help prevent SE from infecting the replacement flock via the manure and rodents.  
Although the floor in a concrete-floored house could appear light grey after manure removal, 
there should not be any accumulation of manure in a house that has had the manure removed. 
 
Sanitation of water lines, 2 to 3 days prior to placement of new layers, is recommended as part of 
dry cleaning, as follows: 
  Water lines are filled with an 1870 ppm citric acid solution (2 pounds per gallon of stock 
metered at 1 ounce per gallon of water). 
  After 2 hours, lines are flushed thoroughly. 
  Next, lines are filled with a 20 ppm chlorine solution (13 ounces of chlorine bleach 
(5.25% sodium hypochlorite) per gallon of stock metered at 1 ounce per gallon of water). 
  After 2 hours, lines are flushed thoroughly until no smell of chlorine remains. 
 
Wet washing of the house is not required, but may be conducted following dry cleaning, if 
desired.  If wet washing, allow the house to dry thoroughly before disinfecting. 
 
Following cleaning, the house should be disinfected using spray, aerosol, fumigation, or another 
appropriate disinfection method.  Producers should choose a disinfectant that has action against 
Salmonellae and apply the disinfectant to all surfaces in an effort to kill any remaining SE that 
may be present on these surfaces.  To the extent that it is permitted under applicable local, State, 
and/or Federal environmental laws, FDA recommends that the disinfectant solution be applied to 
a 10-foot perimeter area outside the house as well. 
 
If a house tests positive for SE for two successive flocks, the producer should review the 
cleaning and disinfection procedures and should consider environmental testing of the house 
before restocking with new layers.  Producers should also consider a longer downtime between 
flocks in that house. 
 
(Refs. 4 and 10) 
 
B.  Sampling and Testing for Salmonella Enteritidis ( 118.5-
118.7) 
 
For the purposes of this section: 
  Row means a group of cages that runs the length of a house; when referring to manure, a 
row is the pile of manure that collects under one row of cages. 
  Bank means half of a cage row (one side of a row); when referring to manure, a bank is 
one side of the pile of manure that collects under one row of cages.  
  Tier means a level of cages in each row. 
 
1. Environmental Sampling 
 
  11 Contains Nonbinding Recommendations 
 
Section 118.7(a) of the egg rule states: Within each poultry house, you must sample the 
environment using a sampling plan appropriate to the poultry house layout.  FDAs 
environmental testing method, Environmental Sampling and Detection of Salmonella in Poultry 
Houses (April 2008), which is discussed in the preamble to the final rule and is incorporated by 
reference into  118.8(a), describes drag-swabbing the manure pit.  FDA understands that 
variations in poultry house design and/or unsuitable manure pit conditions could require 
adaptations for collecting representative environmental samples.  In those situations, we 
recommend one of the following alternative environmental sampling methods.  Any alternative 
environmental sampling method that is used must be equivalent to the method set out in 
Environmental Sampling and Detection of Salmonella in Poultry Houses (April 2008) in 
accuracy, precision, and sensitivity in detecting SE, as required by  118.8(a). 
 
For all methods described below, the swabs should be sterilized by autoclaving prior to 
sampling.  As an alternative, producers may wish to purchase pre-sterilized swabs.  You should 
moisten the swabs with canned evaporated milk, canned skim (fat-free) evaporated milk, or 
canned low-fat evaporated milk prior to sampling.  FDA recommends wearing sterile gloves 
when handling and moistening the swabs.  Additionally, you should disinfect the top of the can 
of milk as well as the can opener with 70% ethanol before opening the can.  You may place a 
swab over the opened can of milk to deter flies from contaminating the milk.  After sampling, 
each swab should be placed in its own individual sample bag and approximately 15 ml of the 
same media used for moistening the swab should be added to the bag to keep the swab moist 
during transport.  One swab equals one sample; samples (swabs) should not be pooled. 
 
High-Rise Poultry House (Pit Style Poultry House) 
 
This style of house has two stories; the top floor contains rows of cages that house the laying 
hens, and the bottom floor is the pit where the manure collects in a cone shaped pile under 
each row of cages.  Both sides (banks) of each manure cone should be sampled while walking 
the length of the row twice.  For example, walk from the front of the house to the back using one 
swab and then turn around and walk from the back of the house to the front using the same swab.  
Use one swab per bank, two swabs per row.  The area towards the top of the cone where the 
freshest manure is accumulated should be the area sampled (Figure 1).  Poles that can be easily 
sanitized may be used if it facilitates sampling.  If both sides of the cone are sampled at the same 
time, care should be taken to ensure that the swabs stay on the same side of the row on the trip to 
the end of the row and back.   
 
  12 Contains Nonbinding Recommendations 
 
Figure 1:  Sampling a high-rise poultry house (pit style poultry house) 
 
 
 
Manure Pits Unsuitable for Drag Swabbing 
 
A combination of egg belt and walkway swabbing should be utilized to obtain representative 
environmental samples if the manure pit is unsuitable for drag swabbing.  Examples of 
unsuitable conditions include manure that is piled very high or is liquid or semi-liquid.  Since 
this method is an alternative and the optimal sample (i.e., manure) is not able to be collected, a 
much more thorough sampling scheme should be followed.   
 
Egg belts: Hand-swab every egg belt in the house by swabbing approximately 6-10 inches every 
5-10 feet for the entire length of the belt and the de-escalator for the corresponding tier. Use a 
separate swab for each egg belt/tier (including de-escalators).  Continue this process until all egg 
belts in the house have been sampled. 
 
Walkways: Drag two swabs along the entire length of each walkway and back.  Care should be 
taken to maintain the swabs on the same side of the walkway on the walk to the end of the row 
and back.   
 
Shallow Pit Poultry House 
  13 Contains Nonbinding Recommendations 
 
 
Most shallow pit poultry houses have some type of manure scraper.  Some have scrapers under 
each tier, some have a floor scraper only, and some have a combination of both.  This style of 
house may be configured as a flush type house where water is flushed through the pit to aid in 
the removal of manure in conjunction with the main floor scraper blade or it may be a dry system 
where only the blades themselves remove the manure.  Only the solid manure on the scrapers 
should be sampled, as ammonia in the pit liquid may inhibit SE growth.  Sampling can take place 
either while the scraper assembly is running or while it is stationary.  Pits should have at least a 
24-hour supply of manure before being sampled; therefore, the scrapers should not be operated 
for at least 24 hours prior to sampling. 
 
When scraper is running: Attach two drag swabs onto the main manure scraper assembly, so that 
one drags on the left bank and the other on the right bank of that row, and run the scraper 
assembly to the opposite end of the house and back.  Care should be taken to attach the swabs in 
such a way that they are not buried under manure while the scrapers are being operated; instead, 
they should drag lightly over the manure.  
 
When scraper is stationary: Use hand swabs, i.e., gauze pads without the string attached, to swab 
the solid manure on all tiers of scraper blades.  The scraper blades under each tier should be 
sampled along with the corresponding side of the main pit scraper using one swab.  This 
swabbing method should be performed for each bank (left and right side) in a row.  If the 
shallow pit has a narrow walkway beneath it, use a drag pole to collect swab samples underneath 
the row of cages, as described for high rise poultry houses. 
 
Belted System Poultry House 
 
When sampling a belted system poultry house, each bank should be sampled.  Sampling should 
always occur from the topmost tier, in consecutive order, to the bottommost tier.  Use one swab 
for the left bank of all tiers in a row and a separate swab for right side of all tiers in a row.  Swab 
the area around the scraper blade on each tier (Figure 2).  If the belted system poultry house has a 
second story (often referred to as a stacked deck house), the process should be repeated on the 
second floor.  In situations where the upper tiers cannot be reached, some type of extension 
device should be used, such as a solid graphite rod with an alligator clip glued to one end or a 
metal broom handle that is capped at both ends.  The device should be sanitized between each 
bank of a row, between rows, and between houses.  You should avoid selecting anything with 
grooves, nooks, or crevices that may make sanitation difficult.    
 
Figure 2: Sampling scheme for a belted system poultry house (sample from top to bottom) 
 
  14 Contains Nonbinding Recommendations 
 
 
 
 
 
 
Colony Style Poultry House 
 
Colony style poultry houses are an open sided type of house that is encountered in parts of the 
country where year-round weather conditions are favorable (e.g., southern California and Texas).  
Colony style poultry housing usually consists of two rows of layer cages facing each other with a 
walkway separating the cage rows and a roof structure over the cages (Figure 3).  Usually a 
board is incorporated into the house structure near ground level at the rear of the cages.  This 
board allows manure to cone and stay dry.  The top level of this manure cone should be 
sampled with a drag swab attached to a pole with a short length of sterile string (Figure 4).  The 
entire length of one side of the house should be sampled with one drag swab.  This process 
should be repeated on the opposite side with a new drag swab.   
 
Figure 3: Colony style poultry house 
 
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Figure 4: Sampling areas for colony style poultry house 
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Single Deck Poultry House 
 
Single deck style poultry houses are typically an open-sided style of house usually encountered 
in the same geographic areas as colony style housing.  Like colony style houses, this style of 
house can only be used where annual weather permits.  In single deck style poultry housing, 
there may be one or multiple tiers of cages and the floor is usually concrete.  Manure collects on 
the floor, creating a row of manure (Figure 5).  This manure row should be sampled with a 
drag-swab attached to a pole with a short length of sterile string.  The whole length of each row 
should be sampled by dragging the swab the entire length of the row and back.  Individual drag 
swabs should be used to sample the left and right banks of each row for a total of two samples 
per row.   
 
Figure 5: Sampling areas for single deck poultry house 
 
  17 Contains Nonbinding Recommendations 
 
 
 
Cage-free Poultry House 
 
Sampling a cage-free poultry house should be based on the width of the house.  The following 
number of swabs should be collected per house, based on the width of the house, as follows:   
  55 or more feet wide = 12 swabs 
  46 - 54 feet wide = 10 swabs 
  37 - 45 feet wide = 8 swabs 
  28 - 36 feet wide = 6 swabs 
 
Divide the house in half physically and swab each half of the house with half the number of 
swabs required.  Use drag swab poles with multiple drag swabs on a pole, up to a maximum of 
three drag swabs per pole at one time.  Swab the litter and slat area the full length of the house. 
 
If a house has multiple floors, divide the number of swabs evenly to cover each floor equally. 
 
Aviary Poultry House 
 
Aviary poultry houses are a type of cage-free poultry house designed to allow more birds per 
square foot when compared to conventional cage-free operations.  Typical aviary systems have 
rows with platforms (Figure 6) that incorporate nest boxes, feeders, waterers, and perches.  
  18 Contains Nonbinding Recommendations 
 
There is typically a manure belt running under each platform level that conveys manure to the 
back end of the poultry house.  There are floor access areas or scratch areas between the 
platforms rows (See Figure 7).  This style of house may be sampled in one of two ways: drag 
swabbing the scratch areas (i.e., floor areas) or sampling the manure belts. 
 
Figure 6: Aviary poultry house platforms 
 
 
 
 
 
 
Scratch areas: Extreme care should be taken when using this sampling scheme because hens may 
pile and suffocate if sudden movements, loud noises, or any behavior that startles the hens is 
made.  To sample scratch areas, two drags swabs per row should be dragged the entire length of 
the row and back, keeping each swab on the respective side of the row (either right or 
left)(Figure 7).  All floor areas in the house should be sampled. 
 
Figure 7: Aviary poultry house scratch areas (i.e., floor areas) 
 
 
  19 Contains Nonbinding Recommendations 
 
 
Manure belts: Manure belts in an aviary poultry house are typically located at the back of the 
house and are similar to those found in belted system poultry houses except they are wider 
(Figure 8).  When this sampling scheme is used, the belts should not be operated for 24 hours 
prior to sampling to ensure fresh manure is sampled.  After the 24-hour wait, belts should be run 
one entire revolution to ensure fresh manure has come in contact with the scraper that knocks 
manure off the belts onto the main belt that leads out of the house.  Belts should then be sampled 
as described in the section for belted system poultry houses (Figure 2). 
 
Figure 8: Aviary poultry house manure belts 
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(Refs. 4 and 10) 
 
2. Egg Sampling 
 
When an environmental test is positive for SE, the egg rule ( 118.6(a)) requires either egg 
testing or diverting eggs to a treatment resulting in at least a 5-log reduction in SE.  Under the 
egg testing alternative, four 1,000-egg samples must be tested at two-week intervals ( 
118.7(b)(1)).  If all four tests are negative, no further testing is required ( 118.6(c)).  If any of 
the tests is positive, eggs must be diverted to a treatment that results in a 5-log reduction of SE 
(e.g., pasteurization) until four consecutive negative egg tests at two-week intervals are obtained 
( 118.6(d)).  Following a positive egg test, if a producer is later able to obtain four consecutive 
negative egg tests and return to table egg production, they must collect and deliver a 1,000-egg 
sample for testing to a laboratory once a month for the life of the flock ( 118.6(e)).  See Figure 
9. 
 
  21 Contains Nonbinding Recommendations 
 
Figure 9: Egg testing flowchart 
 
 
 
 
For each egg test, the producer must collect and deliver for testing a minimum of 1,000 intact 
eggs representative of a days production from the positive house ( 118.7(b)).  Since sample 
size is a minimum of 1,000 intact eggs, FDA recommends that several extra dozen eggs be 
collected to account for breakage during transport/shipping to the laboratory.  The sample should 
be collected from all areas of the positive house, including all banks, rows and tiers and should 
be obtained prior to egg belts being turned on or prior to the first collection in operations where 
hand collection is used.  FDA also recommends dividing the house into equal sections and using 
a systemic sampling approach to obtain a representative sample.  There are essentially two types 
of production systems, caged and cage-free systems with variability existing in house layout 
within each system.  FDA has developed the following guidance to assist producers in collecting 
an appropriate egg sample when required. 
 
Cage System 
 
Cage systems are the predominant system currently used in the U.S. egg industry.  In this system, 
cages can be configured in a variety of ways and are usually stacked several tiers high.  One of 
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the more common arrangements is in an inverted V configuration, referred to as an A frame 
configuration, with multiple rows, and several tiers.  The following is an example of how to 
collect a representative sample in this type of system. 
 
Example: This example is for a 5-row wide house with cages stacked 4 tiers high (see Figure 10).  
In this configuration, there are 10 banks, 5 rows, and 4 tiers.   
 
Figure 10: A five-row wide house with cages stacked four tiers high; cages arranged in an A 
configuration 
 
   
A 1,080-egg sample is collected (extra eggs account for breakage or eggs that are unsuitable for 
testing).  In this scenario, 216 eggs should be collected from each row (1,080 total eggs divided 
by 5 rows); this can be further divided into 108 eggs per bank (216 eggs per row divided by 2 
banks per row), and, ultimately, 27 eggs per tier on each bank (108 eggs per bank divided by 4 
tiers per bank). 
 
The 27-eggs-per-tier sample should include the entire length of the tier.  A random starting point 
can be selected, provided that the sample is representative of all areas in that tier.  Eggs should 
be collected in new egg flats to prevent cross contamination that could result from previously 
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used flats.  This sampling scheme would ensure collection of an appropriate sample 
representative of a days production. 
   
Cage-Free Systems 
 
Cage-free systems are utilized for production of specialty eggs such as organic or free-range 
eggs.  In this type of production system, eggs can be either hand-gathered or gathered via an egg 
belt.  If the eggs are completely hand-gathered (i.e., no egg belts), the producer should determine 
how many flats of eggs are produced in a day (an average number), then divide the average 
number of flats produced daily by the number of flats needed.  The answer will serve as a guide 
for which flats to collect for sampling.  For example, if a producer needs 1,080 eggs (36 flats) 
and his average production is 360 flats per day, he will collect every 10th flat for sampling. 
 
If eggs are collected via an egg belt, the producer should collect the egg sample from the first or 
second collection.  The producer should divide the number of eggs needed for the sample by 
three and also determine the length of time required per collection.  One-third of the eggs needed 
should be collected at the beginning of the collection, one-third from the middle of the 
collection, and one-third at the end of that egg collection.  For example, if 1,080 eggs are needed 
for the sample, 360 eggs would be collected at the beginning of the collection, another 360 eggs 
from the middle of the collection, and the remaining 360 eggs at the end of that collection.  The 
producer should collect eggs evenly from all collection tables, if more than one table is used.    
 
Unique Production Systems 
 
FDA recognizes the vast diversity in production systems and the need to develop sampling 
protocols for unique production systems.  In such situations, producers should follow these four 
basic principles of egg sampling: 
  1,000 minimum eggs sample (intact eggs); 
  Representative of days production; 
  Collected only from the house that tested positive; and  
  Collected from all potential egg laying areas of the positive house. 
 
(Refs. 4 and 10) 
 
C.  Recordkeeping ( 118.10) 
 
The egg rule requires producers to maintain a written SE prevention plan as well as records to 
document the effective implementation of that plan (118.10).  This written SE prevention plan 
should set forth a producer's plan to implement the regulation's prevention, testing, and diversion 
measures.  A written plan is necessary for producers to ensure that they have effectively and 
consistently implemented SE prevention measures.  Further, a written plan greatly facilitates 
FDA inspection.  SE prevention measures may be quite different among farms, given different 
facility design and size, and yet be equally effective in preventing SE contamination.  
Knowledge of the specific prevention measures taken on a farm, as discussed in an SE 
prevention plan, will assist FDA in assessing compliance with the prevention measures.    
 
  24 Contains Nonbinding Recommendations 
 
In addition, reviewing records of implementation of a facility's specific SE prevention measures 
is the best mechanism for FDA to use to determine whether preventive measures have been 
implemented over a period of time.  These required documents include records of 
implementation and compliance with all SE prevention measures ( 118.10(a)).  Keeping careful 
written records will help producers ensure that they have effectively and consistently 
implemented SE prevention measures and will also assist FDA in determining whether the plan 
is being followed and in identifying problems in the producers plan when a test is positive. If 
changes or modifications need to be made, recording such changes or modifications will help 
ensure such changes are implemented.   
 
FDAs egg rule requires producers to maintain the following records to document the SE 
prevention measures: 
  A written SE prevention plan, dated and signed (not initialed) by the administrator(s) of 
the plan ( 118.10(a)(1) and (b)(3)); 
  Documentation that pullets were SE-monitored or raised under SE-monitored conditions, 
including environmental testing records for pullets ( 118.10(a)(2)); 
  Records documenting compliance with the following (examples of each type of record 
are shown in parentheses):  
o  Biosecurity measures (examples: log-in sheets, inspection reports of boot-dipping 
stations, and cleaning and disinfection logs for equipment shared among houses) 
( 118.10(a)(3)(i)); 
o  Rodent and other pest control measures (examples: records showing dates of 
inspection, inspection findings, and steps taken to eliminate problems) ( 
118.10(a)(3)(ii)); 
o  Cleaning and disinfection procedures performed at depopulation, when applicable 
(examples: records showing names and concentrations of cleaning and sanitizing 
agents used) ( 118.10(a)(3)(iii)); 
o  Refrigeration requirements (examples: temperature logs or temperature recorder 
charts and times that allow for the calculation of 36 hours from time of lay) ( 
118.10(a)(3)(iv)); 
o  Environmental and egg sampling procedures, when applicable (examples: records 
showing dates and sampling procedures used) (118.10(a)(3)(v)); 
o  Results of SE testing, when applicable ( 118.10(a)(3)(vi)); 
o  Diversion of eggs, when applicable (example: records of where eggs were sent 
and dates sent) ( 118.10(a)(3)(vii)); 
o  Eggs at a particular farm being treated, when applicable (example: records of 
where eggs were sent and dates sent) ( 118.10(a)(3)(viii)); 
  Records of review and of modifications of the SE prevention plan and corrective actions 
taken ( 118.10(a)(4)). 
 
All records must include the following information: 
  Name of the producer and location of the farm ( 118.10(b)(1)); 
  Date and time of activity that the record reflects ( 118.10(b)(2)); and 
  Signature or initials of the person performing the operation or creating the record ( 
118.10(b)(3)). 
 
  25 Contains Nonbinding Recommendations 
 
General recordkeeping requirements: 
  Data and information reflecting compliance activities must be entered on records at the 
time the activity is performed or observed, and the records must contain the actual values 
observed (if applicable) ( 118.10(b)(4)).   
  Records must be retained for at least 1 year after the flock to which they pertain has been 
taken permanently out of production ( 118.10(c)). 
  These records, with the exception of the written SE prevention plan, may be stored 
offsite, provided they can be retrieved and provided at the producers place of business 
within 24 hours of request for official review ( 118.10(d)).  
  Electronic records are considered to be onsite if they are accessible from an onsite 
location ( 118.10(d)).  
 
IV.  References 
 
We have placed the following references on display in the Division of Dockets Management, 
Food and Drug Administration, 5630 Fishers Lane, rm. 1061, Rockville, MD 20852.  You may 
see them at that location between 9 a.m. and 4 p.m., Monday through Friday. 
 
 
1.  Axtell, R.C. Integrated Fly-control Program for Caged-poultry Houses. Journal of 
Economic Entomology. 63(2):400-405, 1970. 
 
2.  Beck, A.F. and E.C. Turner, Jr. A Comparison of Five House-fly (Diptera: Muscidae) 
Population Monitoring Techniques. Journal of Medical Entomology. 22(3):346-348, 1985. 
 
3.  Cardona, C.J. and Kuney, D.R. Chapter 28: Biosecurity on Chicken Farms.  In Commercial 
Chicken Meat and Egg Production, Fifth Edition, ed. Donald D. Bell and William D. Weaver, 
543-556. Springer Science + Business Media, Inc., 2002.  
 
4.  Davison, S.A., P.A. Dunn, D.J. Henzler, S.J. Knabel, P.H. Patterson, and J.H. Schwartz. 
Preharvest HACCP in the Table Egg Industry. Pennsylvania State University, 1997. 
 
5.  Gomez Villafane, I.E., F.R. Minarro, L. Valenzuela, and D. N. Bilenca. Experimental 
Assessment of Rodent Control on Two Poultry Farms of Central Argentina. Journal of Applied 
Poultry Research. 18:622-629, 2009. 
 
6.  Gomez Villafane, I.E., E. Muschetto, and M. Busch. Movements of Norway Rats (Rattus 
norvengicus) in Two Poultry Farms, Exaltacion de la Cruz, Buenos Aires, Argentina. 
Mastozoologia Neotropical, 15(2):203-208, 2008.  
 
7.  Hogsette, J.A., R.D. Jacobs, and R.W. Miller. The Sticky Card: Device for Studying the 
Distribution of Adult House Fly (Deptera: Muscidae) Populations in Closed Poultry Houses. 
Journal of Economic Entomology. 86(2):450-454, 1993. 
 
  26 Contains Nonbinding Recommendations 
 
8.  Lysyk, T.J. and R.C. Axtell. Comparison of Baited Jug-trap and Spot Cards for Sampling 
House Fly, Musca domestica (Diptera: Muscidae), Populations in Poultry Houses. 
Environmental Entomology. 14(6):815-819, 1985. 
 
9.  Lysyk, T.J. and R.C. Axtell. Field Evaluation of Three Methods for Monitoring Populations 
of House Flies (Musca domestica) (Diptera: Muscidae) and Other Filth Flies in Three Types of 
Poultry Housing Systems. Journal of Economic Entomology. 79:144-151, 1986. 
 
10.  Pennsylvania Department of Agriculture, Pennsylvania Egg Quality Assurance Program 
Operations Annex, 2009. 
 
11.  Rambo, G. Maryland Pesticide Applicator Training Manual: Rodent Control. 
 
12.  Scott, H.G. and K.S. Littig, Flies of Public Health Importance and Their Control, Training 
Guide-Insect Control Series, U.S. Department of Health, Education, and Welfare, Public Health 
Service, Communicable Disease Center, Atlanta, GA 30333. 
 
13.  Stafford, K.C., C.H. Collison, and J.G. Burg. House Fly (Diptera: Muscidae) Monitoring 
Method Comparisons and Seasonal Trends in Environmentally Controlled High-rise, Caged-
layer Poultry Houses. Journal of Economic Entomology. 81(5):1426-1430, 1988. 
 
14.  Turner, E.C. and P.L. Ruszler. Research Note: A Quick and Simple Quantitative Method to 
Monitor House Fly Populations in Caged Layer Houses. Poultry Science. 68:833-835, 1989. 
 
15.  United Egg Producers/United Egg Association. Recommended Security Measures: Farms, 
Production, and Processing Facilities.  
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