Husbandry & Biosecurity

Husbandry & Biosecurity

This section identifies possible on-farm risks related to the husbandry and biosecurity procedures, poultry housing and equipment contamination and farm staff training.

Contamination from shed equipment

Presence of yolk

Robust husbandry and biosecurity tactics for cage, barn and free range poultry production and egg grading areas include reducing or eliminating any yolk and or broken eggs on equipment and in facilities.

This is particularly important for equipment that has regular or sustained contact with eggs, including egg belts and hen nest pads.

Egg yolk is an excellent growth medium for Salmonella and can directly contaminate eggs. Antibodies in the yolk have been shown to have little effect on the growth of some types of Salmonella, but some research indicates there can be inhibitory effects from other types.

It is vital to ensure at-risk equipment, facilities and areas are cleaned and sanitised regularly.

Leaking eggs can contaminate equipment
Egg yolk contaminating shed equipment

Manure belts

Poultry manure is a potential source of pathogens such as Salmonella. Manure belts should be emptied and cleaned at least twice weekly. This will prevent faecal material building up and coming into contact with hens and eggs.

For cage and barn systems, it is important hens in low tiers can not reach up and peck the manure belt used for the cage above. This risks ingestion of faecal matter containing Salmonella.

Poultry operators are encouraged to check the manure belt scrapers are functioning every time the manure belt is moved and to clean this effectively. Scrapers are key to removing or reducing faecal build-up on the manure belt, minimising organic matter and limiting bacterial load in the housing facilities.

Replacement motors for manure belts should be readily available to ensure fast turnaround in the event of breakdown.

Manure belt scrapers need to be maintained
Ensure manure belt scrapers are doing an effective job
Make sure that manure doesn’t build up to the bottom of cages
Manure belts are a potential source of Salmonella

Manure dryer (if applicable)

If used in a poultry housing facility, the manure dryer must be maintained appropriately.

Dryers can be useful to ensure minimal moisture levels in manure. Low moisture levels can limit, and potentially inhibit bacterial growth. This can help to reduce the overall bacterial load in the hen housing and reduce risks of spreading Salmonella.

No specific research has been conducted to determine if drying of manure belt will reduce Salmonella, although it is recognised that Salmonella will typically grow rapidly in high moisture conditions, so manure dryers may help with this.

If used, manure air belt dryers need to be maintained

Hen housing, equipment and health in single batch ‘all-in, all-out’ systems

In between poultry batch depopulation and repopulation in cage, barn and free range ‘all-in, all-out’ production systems, it is recommended to undertake:

  • Thorough cleaning
  • Disinfection
  • Any necessary chick or pullet vaccinations
  • Routine maintenance of housing, equipment and amenities.

This can help to control and eradicate any endemic pathogens, such as Salmonella, between flock depopulation and chick or pullet arrival in these single age operations.

Hen housing should be dry cleaned of organic materials first, followed by a wet wash with a free-rinsing foaming agent, a high pressure wash to remove the soils and a rinse. A sanitiser may be applied, preferably one that is active in organic matter.

The type of chemicals used will depend on what needs cleaning. These need to be compatible with each other, if used on the same surface, and with the material of the shed and equipment.

A good chemical can be simply applied and penetrate all components of the egg production system, and then rinsed off.

It is recommended cleaning chemicals are:

  1. Able to solubilise or emulsify fats, which requires sequestrants or emulsifier
  2. Penetrate soil, dirt and faeces, requiring a surfactant
  3. Breakdown proteins, such as yolk and albumin,
  4. Maintain these components in the solution for rinsing.

Cleaning should be carried out quickly or in sections, to avoid chemicals and extraneous matter from drying up.

In free range areas, the extent of disease risk reduction and eradication is determined by how resilient pathogens are. Agents such as mycoplasma, infectious bronchitis virus (IBV) and external parasites (including northern fowl mite) survive for only a limited time in the natural environment and away from the host.

Most other avian pathogens and intestinal worm eggs require hot dry conditions for destruction by desiccation. This means, in some seasonal conditions, endemic disease and pest pathogens may persist between poultry batches in free range systems. In these circumstances, a vaccination program is recommended before entry of pullets.

Vaccinations and a worming program can help to protect pullets against a broad spectrum of avian endemic diseases before transfer and are recommended for all poultry production systems as part of a biosecurity program.

Prior to chick or pullet delivery, trucks, dollies and chick boxes should be cleaned and disinfected.

Stock transporters need to wear clean protective clothing and footwear prior to each delivery and sanitise their hands regularly. A log of staff movements is also advisable.

If chick or pullet delivery trucks need to visit several farms during one delivery run, measures are needed to minimise the risk of infectious agents spreading between properties. Options can include visiting designated rearing farms first and mixed rearing and production farms last. This will ensure off-loading equipment and chick boxes are confined to the clean and disinfected placement shed.

When carrying out repair and maintenance tasks between poultry batches in cage, barn or free range systems, try to avoid entry by any external contractors who have had contact with poultry or other birds on the day of stock entry to the facility or free range area. Emergencies are an exception, but contractors should enter only after showering and changing into clean clothes and boots.

Concrete floors are able to be high pressure washed
Sanitising vehicles is essential to reduce site contamination

Hen housing and equipment in multi-age operations

Cleaning and sanitising areas or tiers of housing that have been depopulated is necessary in multi-age poultry systems. An effective sanitiser needs to penetrate organic matter to reduce bacterial load before new hens are introduced.

It is best-practice to dry or wet clean flooring, equipment and other amenities regularly and good drainage is required for any water used in the process.

It can be challenging to clean cage and barn housing and internal equipment of dust, dander and other extraneous materials (such as faeces) when hens remain in a section. But dry cleaning and even better, wet cleaning where hens had been depopulated, it is possible and will significantly reduce risks and incidence of Salmonella (and total bacterial load).

The types of chemicals for this process should be fit-for-purpose and compatible if used on the same surface, shed facilities and equipment.  These should be simple to apply and penetrate all the components of the egg production system, and then rinsed off. 

It is recommended cleaning chemicals are:

  1. Able to solubilise or emulsify fats, which requires sequestrants or emulsifier
  2. Penetrate soil, dirt and faeces, requiring a surfactant
  3. Breakdown proteins, such as yolk and albumin,
  4. Maintain these components in solution for rinsing.

 Cleaning should be carried out quickly or in sections, to avoid chemicals and extraneous matter from drying up.

Some sanitisers are approved for misting in the presence of animals and are a potential option for partially sanitising a multi-age shed. Alternatively, a sanitiser can be applied to a whole vacant tier as a foam or low pressure spray without contacting hens in other tiers.

Depopulated areas of sheds need to be cleaned/sanitised
Cleaning down depopulated areas of the sheds

Egg collection belts and conveyors

Frequent egg collection and maintaining clean, hygienic belts, conveyors and other equipment in grading and processing areas is vital to reducing transmission of diseases, such as Salmonella, to eggs.

Extended egg contact with faeces, dust, other extraneous matter and egg internal contents (from broken eggs) on belts, conveyors and other equipment increases the risk of Salmonella on the eggshell and its potential translocation through the shell.

Faeces, in particular, are a reservoir for Salmonella and yolk (from broken eggs) is the ideal growth medium.  If there is bacteria and organic matter, such as yolk, present, Salmonella typically continues to grow before eggs reach cold chain storage. Research has found in the presence of organic matter, Salmonella can grow on eggs at ambient temperatures of up to 15°C.

Regular egg collection will prevent eggs building-up, especially on conveyors and belts. It is recommended eggs are collected at least once every 24 hours in cage, barn and free range production systems. Collection can be more frequent, as often as every two hours in peak lay times and if hens are laying ‘floor eggs’.  

This can help to reduce egg breakages and bacterial growth in the egg internal contents, especially the yolk. Regular collection also boosts egg recovery rates and profitability for producers.

Assess whether it is possible to run egg belts prior to hen laying each day, so dust can be removed before eggs are laid. If birds are not yet in production, egg belts can still be run every day to minimise build-up of dust and faeces and acclimatise the hens.

If appropriate for the system, collection belts can be dry cleaned of faeces and internal egg material when running. This is best done using a clean brush that does not damage the belt material or vacuuming.

Daily dry cleaning can be followed by sanitisation and ensure belts and conveyors are cleaned and dried before having contact with eggs. Spot cleaning of belts and conveyors can be carried out with paper towels (or equivalent) to remove visible, robust material, followed by spraying with a cleaner or sanitiser.

At shed clean-out, the belt should be wet washed, or high-pressure washed, and sanitised. It must then be dried before having contact with eggs. Salmonella growth significantly increases where there is water or moisture and can persist in high levels in dust.

Egg belts are an ideal place to test for Salmonella in a facility, as bacteria can persist on these and the conveyors. Some materials such as cloth and plastic used for conveyors are able to retain more bacteria than others.

If operators use egg grading floors that are connected to several hen houses with conveyor belts, it is important the outside sections are effectively covered so that eggs do not get wet from rain or fog.

For centralised, stand-alone grading floors where eggs or equipment come from multiple sheds and farms, it is important to sanitise regularly and always between facilities.

In these operations, strict biosecurity measures are needed for vehicles, personnel and egg handling equipment, including fillers, trolleys and pallets. This can help minimise risks of disease such as Egg drop syndrome (EDS) infection and spread of bacteria across layer farms.

Reusing cardboard egg fillers is particularly problematic in transmitting diseases between properties. Where multiple properties use a shared grading floor, either sanitised plastic fillers or heat sanitised cardboard fillers should be used. Another, less preferred option is to use marked fillers with a property identification.

Leaking eggs can contaminate equipment
Cracked egg from mechanical stress
DSC 0893
Outdoor conveyors should be covered
Extraneous matter can contaminate eggs and equipment
Bird housing and egg packing areas of the shed should be cleaned
High pressure hosing removes caked on organic matter
Reusing cardboard fillers is a disease risk

Egg collection containers

Containers used to collect eggs should be cleaned and sanitised at least once every day. It is vital these containers are free from extraneous matter, including faeces and egg yolk from any broken eggs. Faeces are a reservoir for Salmonella and yolk is the ideal growth medium.

Bacteria can build-up on collection containers, especially if there is organic matter present. This risks contaminating eggs from subsequent collections, or increasing the disease load if eggs already have bacteria on the surface.

Visible organic matter can be brushed-off containers after each egg collection, or at least once each day.

Alternatively, a wet cleaning, sanitising and then drying process should be used at least once every day to prevent bacterial build-up.

Containers must be dry before being used for the next egg collection, as water/moisture can facilitate bacterial growth and the movement of bacteria into the egg.

There is also a need to clean any container equipment used to transport eggs from hen production areas to the grading/processing floor.

If operators use internal vehicles to combine eggs from several facilities, these should be considered to have a high disease status - equivalent to that of the farms ‘dirtiest’ production shed. 

Egg collection trays need to be clean and dry
Dirty fillers are a risk

Egg unloaders

Maintaining a regular cleaning schedule is key to preventing the build-up of debris and organic matter from all equipment used in poultry production systems, including unloaders.

Before coming into contact with eggs, unloaders need to be dry and free of extraneous matter, such as dust, faeces and egg yolk from any broken eggs.

This can be difficult during the production day. But it is important to assess and implement effective tactics to reduce build-up, as faeces are a reservoir for Salmonella, and yolk is an ideal growth medium for the bacteria.

Growth of Salmonella is also significantly higher when there is moisture present and high levels of dust.

Eggs can easily break during the unloading part of the automated collection process, making it particularly crucial for unloaders to be well maintained and subjected to a regular and thorough cleaning schedule.

If wet cleaning is performed, ensure unloaders are dried again before subsequent contact with the next batch of eggs.

Shed equipment should be kept yolk free
Egg unloaders should be clean, and free of extraneous matter - dust, dirt

Sources of shed contamination

Pre-hen placement housing cleanliness

For all production systems - cage, barn and free range – the aim should be to provide a clean environment for hens and minimise stress and disease opportunity.

Robust hygiene and cleaning practices prior to, during and in-between hen placement underpin industry best-practice management for cage, barn and free range poultry production systems.

The objective is to ensure facilities, landscapes and amenities are maintained to the highest possible standards to minimise risks of Salmonella (and other pathogens) entry, contamination and spread in a flock or on eggs.

Keys to success in meeting this objective include undertaking effective cleaning of housing and amenities and limiting access to all production areas by pests, insects, other animals, wild birds and humans that can carry disease.

Any Salmonella testing is best carried out before the arrival of new hens to a facility and further to this it is recommended to do a thorough visual assessment of housing areas to check there is no organic matter build-up. Any bacteria present in organic matter can infect new hens placed in the housing.

For an all-in/all-out poultry housing system, it is recommended the facilities are cleaned well before hen placement.  Sterilising housing between flocks is not required in commercial poultry systems, except for breeder operations. But efforts need to be made to reduce bacterial loads in the housing.

When cleaning the facilities, it is crucial the water quality does not limit the effectiveness of the products used. It is best to use fresh disinfectants and remove organic matter before disinfection.

In a free range production operation, to further reduce disease risks it is recommended to avoid having debris, trees, shrubs and other amenities near to poultry facilities that could attract vermin, insects or wild birds. Adequate drainage is also needed to prevent accumulation and stagnation of water.

Hen pre-placement measures for free range areas include minimising manure and removing any litter material in the area and on adjoining land. After entry, if moveable housing is used, hens may require regular rotation to acclimatise.

Hens can ‘shed’ Salmonella for a months after initial infection when stressed and this can increase the percentage of flock disease infection and persistence. 

Cleaned shed and equipment
All equipment should be thoroughly cleaned
Cleaned shed prior to placement
High pressure cleaning equipment

Receiving chicks / pullets

Chicks and pullets for egg production should be sourced from suppliers using industry best-practice Salmonella disease risk management strategies. This can help to minimise risks of disease transmission between properties and flocks, and Salmonella incidence at laying sites.

It is recommended chick and pullet suppliers provide a certificate or statement outlining the Salmonella management techniques used in their operations or results of any Salmonella testing of their flocks.

It is possible to control any Salmonella infection and shedding of pathogens in chicks and pullets with vaccination, but often this requires repeat doses. Pullets, especially, may need multiple vaccinations to complete the required schedule and ensure maximum vaccine efficacy.

There are two live, attenuated Salmonella Typhimurium vaccines registered for use in Australian poultry; any other vaccines are not prohibited for use unless expressly approved by national veterinary authorities the AVPMA.

Preparing to vaccinate a chick

Presence of dust / feathers / faeces

Regular dry cleaning of barn and cage poultry housing is required to remove dust, feathers, dander, faeces and other extraneous material from equipment, floors and amenities. This is especially important during the egg-laying period to prevent potential disease contamination from debris build-up, hen infections and overall Salmonella bacterial load in the hen housing.

Dry cleaning can be done by sweeping or vacuuming and hens can be trained early to get used to the associated noises and movement.

Using compressed air systems effective for removing or reducing dust and organic matter build-up from housing, but can increase bacteria spread by aerosol through the facility and hen flock.

Wet cleaning is recommended after a flock exits the facility, if possible. Cleaning products need to be fit-for-purpose and compatible if used on the same surface, such as concrete and aluminium. These products must be able to:

  1. Penetrate soils, dirt and faeces, which requires a surfactant
  2. Breakdown proteins, such as yolk and albumin
  3. Maintain efficacy in soluble form
  4. Solubilise/emulsify fats, which requires sequestrants/emulsifier

Effective application involves penetrating and then easily rinsing-down all parts of the egg production system so there is minimal risk of re-attachment of material back to equipment, flooring or amenities. Cleaning should be fast, or carried out in sections to avoid chemicals and extraneous matter from drying.

Build-up of dust, feathers, faeces and other materials tends to be particularly problematic in building and equipment joins, such as where walls join the floor or where one component meets another. It is important to target these areas regularly for cleaning.

There are approved sanitisers available for misting in the presence of animals and these may be useful for partially sanitising a multi-age poultry shed. Alternatively, a sanitiser can be applied to a whole vacant tier as a foam or low pressure spray - without contacting hens in other rows.

Dirt and dust should be cleaned
Regular cleaning of equipment is needed
Cleaning grading areas is also important
Wet cleaning at end of flock

Vehicle and equipment movement on to farm

Limiting and controlling the movement of vehicles, equipment and machinery in a poultry operation is key to minimising the risks of introducing or spreading contaminants such as Salmonella or diseases.

A perimeter fence around the property and robust fencing around all cage, barn or free range production area is best practice. The main entrance must be capable of being closed to vehicle traffic. A lockable entry gate is the best option and, ideally, this should be locked at all times. Signage on the gate or fencing should clearly identify the site as a biosecurity area, “Biosecure Area - No Entry Unless Authorised” or similar wording.

Having designated vehicles for poultry production areas is recommended and it is best to avoid dead bird retrieval, waste removal, feed delivery and other deliveries coming through the perimeter or facility fence.

If entry to the site by vehicle is needed, a quarantine plan is important to limit potential environmental contamination. This can include strategies such as:

  • Restricting vehicle movement to only one way in one day
  • Installing a designated vehicle sanitising station
  • Ensuring machinery, equipment or vehicles are clean and decontaminated
  • Have a visitor log for all visitor to the site

If there are multiple poultry production sites or geographic locations in a single farming business, it is important to minimise the potential for vehicles to cross-contaminate flocks. 

Vehicles for picking up or dropping off chicks, pullets and spent hens should only transfer one single age flock in any one day from a particular production area.

Pick-up vehicles, modules and crates should be thoroughly cleaned and disinfected between loads and farms. A thorough inspection of the vehicle and trailer should be undertaken prior to farm entry and movements of the driver and crew validated.

Where chick delivery trucks need to visit several farms during one delivery run, it is important to reduce the risk of infectious agents spreading between properties. Ideally, this requires visiting designated rearing farms first and mixed rearing and production farms last. Part of the process should involve restricting off-loading equipment and chick boxes to clean and disinfected placement sheds.

Vehicles carrying new litter should come from reputable companies and not be used for carting used litter and manure. Trucks carrying manure and used litter should not be used for backloading grain without prior thorough cleaning.

Biosecurity sign should be at all site entry points
Robust perimeter fencing
Dedicated vehicle sanitation station

Human traffic

Production, service and grading staff, contractors, poultry suppliers, other service providers, visitors and family members pose risks of introducing or spreading contaminants and diseases to cage, barn and free range operations.

It is recommended to limit human traffic in poultry production areas, except for regular farm staff, as Salmonella can persist on clothing, hair, skin and footwear. Salmonella can also be transferred from domestic birds, farm environments and laboratories to humans, who can then spread infection back to hens or eggs.

Industry best-practice is to ensure regular staff, and visitors to poultry areas use dedicated farm boots, or wash these in boot dips, farm clothing, over-suits and hairnets and sign in using a visitor log.

Regular farm staff should walk through hen areas regularly to acclimate the flock to human movement and not stress the hens. However, production area staff, including those on grading floors, should not move between various operational areas without considering the biosecurity risks. Movement should occur from ‘clean sites’ to ‘dirty sites’ and not the reverse.




1. Chicks 2. Pullets

3. Younger

single age

4. Older

single age

5. Multi-age


In an egg production facility, unless specific avian disease testing indicates otherwise, the pullet area is considered a clean site, followed by a single age production area and then a multi-age area.

External contractors and service providers to the poultry operation need to have an overview of biosecurity policies and responsibilities on entry. This can include stipulations for drivers to:

  • Wear clean, site-specific protective clothing and footwear prior to each delivery
  • Sign in and out of a visitor log
  • Sanitise their hands before entering production areas
  • Stay close to their trucks and trailers.

 External feed suppliers should be certified and use hygiene policies that are acceptable to the poultry producer. It is recommended to trace movements of delivery personnel, by using delivery dockets, visitor logs and feed company records.

Boot dips should be prominent, signage directing visitors
Visitors should be dressed in full PPE to reduce risk
Sanitising vehicles is essential to reduce site contamination

Boot dips

A boot dip is required at the entrance to cage, barn and free range poultry areas. It needs to incorporate facilities for scraping the soles of boots and washing with an effective disinfectant, used according to label instructions and the disinfectant is changed regularly.

It is important to ensure the correct concentration of disinfectant is used for all boot dips. This should be checked regularly with test strips.

A pre-dip or boot scraping implement may be needed to remove mud and excess dirt to ensure the boot dip remains effective, especially for boot treads.

Rain might compromise the disinfectant potency of the boot dip and in wet weather, it might be necessary to check it more regularly or cover it. The quality and/or ‘hardness’ of water used in boot dips can also affect the disinfectant efficacy and should be checked.

Dry boot dips might be an alternative to wet dipping. These use dry or aerosol disinfectants.

It is valuable to consider using dedicated farm or flock-specific boots for staff and visitors if practical.

Shed specific boots, kept where they can be scraped and cleaned
Boot dips should be prominent, signage directing visitors

Farm staff training

Farm staff and visitor biosecurity (including domestic birds)

To stop contamination and disease agents, such as Salmonella, entering cage, barn or free range poultry production areas, robust farm staff training programs are needed, along with strict biosecurity protocols for staff and visitors.

Salmonella can persist on human clothing, hair, skin and footwear. Hen contact with these vectors needs to be minimised and some options to achieve this include:

  • Using dedicated farm, facility and shed boots
  • Using boot covers or boot dips
  • Having dedicated farm clothing or over-suits
  • Using hairnets.

Farm staff and visitors must not have access to a poultry facility if they have been to another farm, or been in contact with hens from outside the farm, on any given day. They must not have handled avian pathogens within the previous 48 hour period.

Where possible, farm staff should be prohibited from owning domestic birds at their residence and visitors must declare if they own birds, or have had recent contact before entering a poultry farm.

Salmonella can be transferred from domestic and wild birds, farm environments and laboratories to humans and their environment. If farm staff or visitors become infected in this manner, the infection can potentially be transferred to hens or eggs.

Domestic animals, including cats, dogs and rodents, are known to carry Salmonella and can potentially transmit disease pathogens to humans, hens and eggs.  

Protective equipment should be worn in sheds
Shed specific boots, kept where they can be scraped and cleaned
Boot dips should be prominent, signage directing visitors
shutterstock 1149378164b

Farm staff training

All staff working in poultry operations, including egg production, grading and processing areas, must be trained in food safety. At least one regular staff member should be made responsible as a food safety manager.

Strict training protocols, procedures and reviews will help reduce the risks of Salmonella being transmitted from human sources to eggs during handling, collection, storage, transport and food preparation.

Staff should be made aware of the importance of biosecurity measures to the reputation and profitability of the poultry business and wider industry. They should be encouraged to regularly assess and review tasks to identify areas that could be improved.

Humans can carry pathogenic Salmonella in their gut and this is a potential contaminant to hens, especially if they have returned from international travel or have an intestinal upset. In these situations, it is advised they do not contact hens or eggs for at least 48 hours after symptoms cease.

It is common for about 50 per cent of adults infected with Salmonella to continue to excrete the bacteria for up to five weeks and about 10 per cent can excrete the bacteria for more than nine weeks. A regular toilet cleaning schedule should be used at the production facility, along with ensuring hand sanitising facilities are available throughout the area.

The poultry industry has produced a comprehensive training resource, called the National Farm Biosecurity Technical Manual for Egg Production. It is advisable to have a readily-available copy of this on the property and to instruct staff on relevant chapters. 


 Salmonella can be transferred to human hands from any contaminated hen faeces.

Staff that handle faeces, nest box material, equipment or other material likely to be contaminated with faeces must wash and sanitise their hands after completing the task. This is particularly important before handling hens or eggs from another housing facility, or new poultry entering the facility.

Strict hygiene practices can help prevent cross-contamination and spread of bacteria. Optimal hand cleaning techniques include a combination of hand washing (to clean) and alcohol-based gel (to sanitise). Improper, or ineffective hand-washing can lead to bacterial cross-contamination. Antibacterial wipes or gel could be used as part of this procedure.

Handling ungraded eggs

There is a risk of Salmonella being present on the eggshells of ungraded and unwashed eggs. Staff handling these eggs must wash and sanitise their hands after completion of the task.

This is particularly important before handling hens or eggs from other housing or production areas, to prevent cross-contamination and spread of bacterial infection.

The best hand hygiene technique includes a combination of hand washing (to clean) and alcohol-based gel (to sanitise). Improper or ineffective hand-washing can lead to bacterial cross-contamination.

Maintained washing facilities should be supplied for farm staff
Appropriate training, signage and biosecurity needs to be observed by grading area staff

Time between when egg is laid and its collection

Producers are advised to collect eggs at least once every 24 hours. More frequent collection is recommended if hens are laying ‘floor eggs’. This could be as often as every two hours during peak time of lay during the day.

Infrequent collection increases risks of eggs being in extended contact with faeces and other extraneous matter, including internal egg contents from broken eggs. This increases potential for any Salmonella on the eggshell to penetrate and contaminate the internal egg contents.

Faeces are a reservoir for Salmonella, and yolk is the ideal growth medium.  Salmonella can continue to grow before the egg enters cold chain storage and has been found to persist at temperatures of 15°C if organic matter is present.

Regular egg collection will prevent a build-up of egg numbers in the facility, which can result in breakages and lead to bacterial growth. It will also boost egg recovery rates, leading to better productivity and profits.

After lay, eggs should be transported and stored correctly
Irregular egg collection can lead to bunching, and cracked eggs

Staff handling dead or live hens and pre-graded eggs

Hand sanitising facilities need to be available for staff who handle live or dead hens, faeces, equipment that is likely to be contaminated with faeces and/or pre-graded egg. Pre-graded eggs, especially, have a higher risk of Salmonella persisting on the eggshell surface.

Salmonella can be transferred to human hands from any contaminated live or dead hens, faeces, dust and pre-graded eggs. This potentially leads to human infections and a risk of re-infection back to hens.

Robust hygiene practices minimise bacteria spread and are particularly important for staff and other personnel who have contact with hens and eggs from multiple facilities.

It is best practice to combine hand washing (to clean) and alcohol-based gel or antibacterial wipes (to sanitise). Ineffective hand washing can lead to a high risk of bacterial cross-contamination. 

Poultry flocks should be assessed daily for dead hens so these can be removed quickly. Dead hens can attract insects and rodents that can transmit Salmonella.

Disposal and storage of dead hens needs to ensure there is no accessibility by these pests. Practices also need to meet any applicable hygienic containment and environmental compliance requirements.

Hand sanitising facilities should be readily available for all farm staff

Personal health, hygiene and behaviour

Any staff working in poultry operations and who are ill should not handle eggs, prepare or handle raw egg products and foods for up to 48 hours after recovering from symptoms.

Good personal hygiene and behaviour should be standard practice when handling whole eggs and any egg products. This includes avoiding coughing and sneezing onto eggs or egg products and ensuring regular hand washing, especially when suffering from gastrointestinal upsets.

Pathogens can potentially spread to other humans from contaminated eggshell or internal egg content, which provide ideal conditions for bacterial growth. Humans can also carry pathogenic Salmonella a-symptomatically and potentially infect others through contaminated food, direct or indirect contact.

Research has shown both symptomatic and asymptomatic food handlers have caused (or are suspected to have caused) food-borne illness outbreaks.

The Australian Government Department of Health has produced a set of guidelines outlining how to manage food handlers during Salmonella outbreaks. It advises that food handlers infected with Salmonella should be excluded from work until symptoms have ceased (in Victoria and Tasmania) or for up to 48 hours after symptoms cease (in the ACT, NSW, QLD, SA, NT and WA).

It should be noted that humans can shed Salmonella for weeks or months after infection and appropriate precautions may be needed.

Staff should observe good hygiene
Washing facilities should be readily available for staff

Hen stress

Typical periods of hen stress include during transport, at the onset of lay, when routines change, if there is pre-existing disease, moulting or if there are adverse environmental conditions, such as heat, rain or high humidity.

When stressed, the hen’s immune system is suppressed and it can shed Salmonella. This can lead to transmission and spread of the bacteria.

Hens infected with Salmonella can shed the bacteria for more than a month after initial infection, which can lead to the persistence of Salmonella in a flock. Salmonella can also persist in the hen’s gut without active shedding and then be shed during a stress event.

Using procedures that minimise hen stress and better manage situations, where stress is unavoidable, can help to boost productivity. This can include vaccination programs.

Stress can limit cuticle deposition, which provides the egg with a natural barrier to bacterial penetration through the shell.

In free range systems with moveable housing, hens may need to be moved regularly, as often as once per week, to acclimatise to this activity. This can help to reduce the incidence of stressful events throughout the laying period.

Differences in Salmonella infection rate and shedding have also been attributed to hen age and breed.

Good staff husbandry reduces stress on hens
Shelters can reduce heat stress on ranging birds

Rodent and pest control

Pest control

All poultry housing, free range poultry areas and egg grading facilities should have a robust and regularly monitored pest control program to minimise biosecurity, contamination and Salmonella transmission risks.

The aim is to limit vermin, insects, rodents, livestock, foxes, wild dogs, cats and wild birds from accessing production and grading areas, as these are potential disease vectors and pose a high biosecurity risk.

In free range operations, trees, shrubs and other amenities in the immediate vicinity should not be attractive to vermin, animals or wild birds. These areas should be free from debris and have dust control strategies.

It is also essential to keep the areas around poultry production facilities free from debris, dust and vegetation to discourage wild birds, insects and rodents. Vegetation buffers for environmental compliance should not be compromised.

A baiting program may be necessary to minimise the potential introduction of infectious agents and pathogens to poultry areas by vermin, especially rodents. This decision can be based on a thorough risk assessment of facilities.

Debris beside sheds promotes pests
Mesh screening used to prevent pest entry
Mini vents should also exclude pest entry

Perimeter fence and other fencing

Animals such as pigs, cows, sheep, turkeys, domesticated and wild dogs, cats, foxes, wild and domesticated birds and other chickens can be carriers of some types of Salmonella. These animals risk infecting the environment and poultry flocks in cage, barn and free range operations, especially if there is hen contact with faecal material.

For cage, barn and free range egg production systems, fencing is needed to either enclose the poultry site or the whole farming property (via a perimeter fence). This clearly defines a biosecurity zone and minimises risks of unwanted entry by land animals.

The main entrance to a poultry production area should display appropriate signage and be capable of being locked or closed to vehicle traffic. It is recommended that signage clearly shows the facility is a “Biosecure Area No Entry Unless Authorised”. It is valuable to direct all site visitors to contact the producer or operator before proceeding inside the perimeter fence, including a visitor log book to monitor movements.

It is recommended farm staff and visitors do not have access inside the perimeter fence if they have had contact with hens from another property. Stringent hygiene practices for staff and visitors are also a key tactic to minimise the risks of infection from Salmonella.

If the property has other livestock, the poultry production area must have a stock-proof fence. Nearby grazing is permitted only if there is separation by a stock-proof barrier. Robust perimeter and internal fencing will prevent other livestock and debris from coming into contact with free range hens.

Adequate fencing can also deter humans from entering poultry facilities. This is important, as people can be a source of Salmonella to poultry and eggs if they have been infected from other people, other poultry operations, domestic birds, farm environments, laboratories or overseas travel.

Movement of all vehicles, equipment and machinery on the farm should be restricted to outside the poultry area perimeter fence. This includes for operations such as dead bird retrieval, waste removal, feed delivery and other deliveries.

If vehicle movement cannot be directly controlled, other management strategies can be used, including:

  • Having designated vehicles and equipment for use inside the fence
  • Allowing vehicle movement only one way in one day
  • Installing a designated vehicle sanitising station
  • Ensuring machinery, equipment or vehicles entering the property are clean.
Electrified fence to reduce predator/pest risk
Biosecurity sign at site entry
Range perimeter fencing
Fence deep in soil to eliminate pest entry

Animals - domestic and wild

Hen housing and ranging areas need to be secure to prevent entry from domestic, livestock and wild animals.

Chickens, turkeys, domesticated and wild dogs, cats, foxes, pigs, cows, sheep, wild birds (including ducks, pigeons, finches and sparrows) and other wild animals can be carriers of various types of Salmonella. These animals pose a risk of infecting hens with Salmonella if they contaminate the production environment, feed or drinking water sources of the hens.

Risks of hen disease infection increases if there is contact with or ingestion of faecal material from infected animals.

Tactics to deter other animals from coming into contact with hens in houses or free range areas include:

  • Installation of robust fencing
  • Stock-proof fences where necessary
  • Minimising surrounding vegetation
  • Reducing the attractiveness of nearby water reservoirs to waterfowl (such as ducks)
  • Not having irrigated grass or pastures nearby
  • Putting netting over dams
  • Using an active duck repelling program if needed. 

If animals such as dogs or alpacas are used to protect hens, these should be tested for Salmonella before their introduction to the flock and re-tested regularly.

In egg grading areas, it is important to prevent animal access to minimise risks of contamination to equipment that can then cross-contaminate eggs.

Maintain short grass, and a buffer zone between sheds and thicker vegetation
Guard animals should be tested for Salmonella
Waterfowl and wild birds are a risk
Animal decoys may be used to deter wild animals

Insects and rodents

Maintaining a clean production area, free from debris, spilled feed or grain, long grass, other vegetation, pools of stagnant water, animal faecal material and dust, are vital tactics to minimise insect and rodent pressure in cage, barn and free range systems.

For hen housing, insects such as flies, beetles and cockroaches, and rodents, such as mice and rats, need to be deterred from entering the facilities. This will reduce risks of Salmonella infection from direct hen contact with these pests and indirect contact from feed and water contamination.

It is particularly important to control rodents in poultry housing, as there is a correlation between Salmonella load in a hen population and the density of the rodent population. Preventing rodents from accessing egg grading areas minimises risks of Salmonella contamination on eggs, grading equipment and packaging.

Control of rodents may require a baiting program. As part of this, it is advised to maintain bait control records (date, time and type of active ingredient used).

Bait stations used for all poultry production areas are ideally:

  • Numbered for recording and monitoring
  • Placed at regular intervals around the sheds or free range areas
  • Mapped, checked and re-baited weekly (more frequently in high-risk seasons).

 Hens should not have access to the baits, to avoid any ingestion of rodenticide. Bait stations need to be secure, tamper-proof and designed to minimise access by other mammals, native wildlife and birds. It is recommended more bait stations are used in areas with visible signs of increased rodent activity.

Other procedures, such as trapping and sonic sound aversion systems, may help to control rodents.

Alternative style of bait station
Bait stations should be placed at regular intervals
Bait stations should be impenetrable to chickens or wildlife
Feed spills should be quickly and thoroughly cleaned up to reduce pest presence

Sources of feed and water contamination

Raw ingredients / feed contamination during pelleted feed production, storage and transport

Raw poultry feed ingredients and pelleted feed can harbour human pathogenic Salmonella and become a source of Salmonella contamination in the food chain.

Heat treatment processes for pelleted feed are not typically sufficient to destroy all Salmonella that might be present, but can reduce bacterial load.

During this process, there is the risk of a ‘biofilm’, or protective ‘coat’, forming by Salmonella. This will protect the pathogen until it has optimal conditions again and can continue to grow.

Some types of Salmonella are also more resistant than others and can be recovered after heat treatment. The level of heat resistant Salmonella is affected by the rate at which the heat is applied. Typically, the slower the temperature rise, the greater the increase in heat resistant bacteria.

Feed can be re-contaminated with Salmonella after heat treatment in pre-processing dust, unclean air intake during pellet cooling, out-loading bins, augers and exposure to insects, rodents and wild animals.

All raw ingredient feed batches and heat-treated feed batches that are received on-farm must be sourced from an approved supplier. These should be accompanied by supplier testing records or a letter outlining how the supplier manages Salmonella risks.

It is preferable if each batch of raw ingredients and feed is tested for Salmonella, but this is often not practical. Contaminated raw ingredients and feed should not be provided to hens.

Not all Salmonella found in raw ingredients and feed is transferred to hens or humans. Mash feed is a higher risk than heat-treated pelleted feed.

Trucks used to transport raw materials and hen feed should be cleaned regularly. Trucks transporting heat-treated feed should not be used to transport raw ingredients without an appropriate cleaning schedule in between.

It should be noted that imported raw ingredients and feed pose a risk of introducing Salmonella Enteritidis into layer farms.

Mash feed is a higher risk than pellets
Pellet feed

Contamination with human effluent (feed and water)

Hen feed and water cannot be in contact with human effluent, sewage or improperly treated effluent water at any time.

Humans can carry pathogenic Salmonella in the gut for extensive periods without symptoms after recovering from gastroenteritis.

Any effluent water used in the poultry operation from town treatments, or on-premises storage and treatments, can be contaminated with Salmonella and exposes hens to risk of infection through drinking water and feed.

There are a range of regionally-specific guidelines for microbiological limits for discharge requirements in treated effluent water that is released into water systems and it is advised to check these closely.

If there is effluent water or a water treatment plant close to the poultry operation, a check is needed to determine if rodents, insects and wild animals able to access this water are also able to access the property.

It should be noted that improperly treated effluent water accessed for hen use was a significant contributor to Salmonella Enteritidis spread in the USA.

A high proportion of gastroenteritis in overseas travellers that return to Australia is due to Salmonella Enteritidis. Salmonella Enteritidis is present in the Australian community and sewerage systems, and it is important to prevent transfer to hens. Keeping a log of visitors, and restricting access from those who have recently travelled (last 7 days) is important.

Feed formulation

Feed formulation for hens should aim to ensure production of eggs with high quality, strong eggshells.

Thin eggshells will crack or micro-crack more easily and potentially facilitate bacteria transmission into the egg internal contents. Other factors that affect the quality of the eggshell include hen breed, age and health status.

There are commercial feed additives for hens reported to reduce potential Salmonella load in feed, and others that potentially impact on the ability of various bacteria to grow or persist in the hen gut. But the efficacy of any feed additive to reduce Salmonella is affected by the Salmonella status of the flock and the quality of nutritional management.

There is limited research to determine the interactivity and efficacy of various in-feed additives (such as organic acids) and probiotics on the gut flora of the hen and, by extension, Salmonella presence.

High quality strong egg shells reduce risk
Micro-cracks can result from mechanical stresses


Poultry operators need to provide hens with drinking, cooling and cleaning water of the same standard suitable for other livestock. The use of quality water supply, free from potential avian pathogens, is an essential part of  good biosecurity.

Surface water can be contaminated with Salmonella by rodents, other animals, wild birds and environmental factors.

In most cases, treated town water will be appropriate for use in poultry operations. But in rural areas where this is impossible, dam or tank water must be assessed and treated with chlorine or an acceptable alternative. This includes town water reservoirs on-farm.

Effective treatment of surface water to reduce contamination and eliminate avian disease agents can be technically challenging and the process should be monitored regularly. It is recommended a trained person test farm water supplies, and it may be necessary to get professional advice about the best treatments to ensure quality for use.

It is advised to conduct on-farm water testing several times each year for microbial counts to ensure there is a good understanding of the risks posed by the water source and to implement robust management.

Water with a high level of organic matter, or low or high acidity (measured in pH), cannot typically be effectively sanitised (chlorinated) without an appropriate pre-treatment. Filtration may also be required.

Ultraviolet treatment of water is limited to low flow rate, clean water with no turbidity.

For chlorinated water supply, the treatment must achieve a level of 1.0 – 2.0 ppm free available chlorine (FAC) at the continuous point of use. It should be noted that effectively chlorinated water may, after sitting in storage for extended periods, test negative for FAC. Provided the water storage is sealed, this is satisfactory and this can occur for manually treated multiple water tanks, or for early morning water entering the shed immediately after lights go on.

When chlorinating water, it is advised there is a minimum of two hours contact time with chlorine prior to use. As water quality varies, the effective level of FAC required during these two hours can change. One of the most accurate ways to determine if the chlorine level is effective is to measure the Oxidation Reduction Potential (ORP) of treated water. This should be about 650 mv and carried out with reading the pH of the water (which may require adjustment). The 650 mv recommendation also applies for any oxidative chemical used for sanitising water.

Chlorine dioxide water sanitisation systems are becoming more popular for poultry producers and can have advantages over using chlorination using sodium hypochlorite.

The effectiveness of water treatment systems, including alternative systems (such as ultraviolet), must be validated before use and production area records kept to demonstrate the effectiveness of water treatment.

Producers are advised to download the National Water Biosecurity Manual for Poultry Production below for more detail about water biosecurity.

Young birds are more vulnerable to pathogens
Water should be clean, free from any pathogens

Water line cleanliness

Water lines and accompanying equipment should be cleaned and checked regularly, depending on the system and its set-up.

Assessing water quality can also help determine the best cleaning process, as it can impact on the effectiveness of chemicals used.

Organic matter can build-up in water lines, especially if the water quality is poor. This material can harbour Salmonella, which can also persist and grow in water.

Salmonella can form an undesirable ‘biofilm’, or protective ‘coat’, in water when there are sub-optimal environmental conditions. A biofilm protects the Salmonella until conditions improve and it continues to grow again.

Drinker lines should be regularly checked
Drinker lines need to be clean free of organic matter

Other sources of shed contamination

Extraneous material in nest box during production

It is recommended to check hen nest boxes at least once every 24 hours and remove or reduce faeces load, without spreading faeces to eggs during cleaning.

Eggs contacting faeces for any length of time, or rolling over faeces during grading or processing, are at high risk of Salmonella contamination. If there is moisture present, this risk is heightened and bacteria can potentially penetrate the eggshell.

It is recommended to assess whether eggs are able to roll away from nest areas immediately, or if modifications can be made to the nests to allow eggs to roll away quickly. Limiting faecal contamination on eggs will lead to fewer issues during grading and (if applicable) washing.

Faecal contamination levels can be reduced if hen nests are closed at night and the nests and egg conveyor are cleared before hens sleep.

Preventing hens roosting in the nest boxes at night can substantially lower quantities of extraneous matter building-up.

Prevent hens from roosting in nest boxes
Faeces in nest box should be removed ASAP

Nest box material not maintained during production

Nest box material should be cleaned-out or replaced before poultry enters a facility. It is advisable to use a non-absorbent material that can be easily cleaned or replaced as needed.

It is particularly important for nest box material that has contact with eggs to be free of extraneous matter, including faeces and egg yolk.

The cleaning, replenishing or replacement schedule for nest boxes will depend on the efficacy of the material used in reducing the incidence of eggs rolling through it and lying on faeces and other extraneous material that can harbour Salmonella.

Commonly used effective next box material includes sand, shell grit, straw, sawdust, wood shavings, carpet, plastic mats, fake turf and steel mesh. To prevent bacteria embedding into the material and proliferating, it is important the material is not absorbent.

Nest box material should be kept dry and unable to contact any water sources, as moisture significantly increases Salmonella growth and risk of cross contamination to eggs.

Plastic nest pad inside nest box
Nesting material should be regularly checked and replaced

Nest pads not cleaned / replaced regularly during production

Nest pads should be checked for faeces every day and regularly cleaned or replaced. Pads that have contact with eggs also need to be free of other extraneous matter, including dust and egg yolk, which can contain Salmonella.

If extraneous matter, especially faeces, is present on nest pads and contacts eggs for an extended period, there is a high risk of bacterial transfer into the egg internal content. Faeces are a reservoir for Salmonella and yolk is an ideal growth medium for the bacteria.

After hens are removed from housing, a cleaning and sanitising program is needed for nest pads before the next batch arrives. It is also advised to have spare pads ready to replace those removed for cleaning.

Plastic nest pads need to be clean
Plastic nest pad inside nest box

Presence of yolk

Egg yolk is an excellent growth medium for Salmonella and must not be present on equipment that is in regular contact with eggs. This includes egg belts, hen nest material and hen nest pads.

The aim is to limit the potential for direct egg contamination from any spilled yolk stemming from broken eggs during production, grading and processing.

To achieve this, particularly on equipment that has sustained contact with eggs, regular cleaning and sanitising is needed.

Leaking eggs can contaminate equipment
Egg yolk contaminating shed equipment

Eggs not laid in the dedicated nest boxes

Hens can be trained to use nest boxes for egg production by discouraging laying elsewhere, such as directly on the floor. Any ‘floor eggs’ laid have a higher risk of bacterial contamination due to contact with much more dirt, dust, faeces and moisture than eggs laid in controlled areas, such as nests.

Some poultry breeds tend to lay more eggs on the floor than others. But most breeds can be trained to lay eggs in the nest boxes by:

  • Enticing them in before the start of lay
  • Preventing entry during non-lay times, such as at night
  • Discouraging laying in areas that are not optimal, such as on the floor, outside in the dirt, mud and faeces.

It is essential to give hens adequate time to learn to use the nests. Tactics include:

  • Minimal outside stimulation in the pre-lay and start of lay periods
  • Electric fencing for areas of unwanted eggs
  • Bright lights for areas of undesirable egg laying
  • Stimulation in the boxes prior to lay
  • Nest lights
  • Closing boxes at night

Nest lights can be used to train birds to explore the nests, but should not be left on during peak laying periods during the day.

When hens have learned how to use the nest boxes, and floor egg issues are under control, the design of the range and facilities can be adjusted for optimum efficiency. This includes the feed and drinking water systems, which are best located inside the cage, barn or other housing to limit hens going outside and laying eggs.

Diffusion of bacteria into eggs can also occur due to differences in temperature between the internal egg contents and the external environment. This is true for eggs that condensate, or come into contact with wet shed contaminants.

This is particularly risky for ‘floor eggs’, or eggs laid into faeces, and especially when the egg is laid into a wet environment, or is in contact with water at a lower temperature than its internal content temperature (an egg is laid at about 41°C).

Research has found it is easier to artificially contaminate eggs with a wet solution of faeces containing Salmonella than with a dry faecal sample. But the rate of bacterial penetration into the egg depends on factors such as hen age, eggshell quality, health status, diet, breed and type of Salmonella.

It is recommended to consider pulping any floor eggs to reduce the Salmonella risk for human consumption.

Lighting in scratch areas helps eliminate floor eggs
Floor eggs are a higher risk, and should be pulped
Nest lighting can be used to encourage laying in nest boxes
Electric fence to prevent laying in corners

Water / moisture on eggs

Best-practice husbandry and biosecurity measures for all poultry operations includes ensuring eggs are kept dry at all times during production, grading, processing, transport, storage and food preparation. The exception is during a strictly controlled washing process.

Water can facilitate movement of Salmonella into the egg. The rate of this diffusion will be mainly determined by the quality of the eggshell and cuticle.

Any cooling systems used in production facilities should not allow eggs, or equipment contacting eggs, to become persistently wet or produce condensation (referred to as ‘sweating’). To limit condensation issues, temperature must be maintained when eggs reach required storage temperatures.

It is recommended eggs are slowly cooled to final storage temperature through the on-farm process, and not subjected to wide temperature fluctuations.

Once cooled, eggs should stay refrigerated
Condensating or sweaty eggs are a risk

Wet floor eggs / dry floor eggs

Eggs laid on the floor of housing facilities (called ‘floor eggs’) are at a significantly higher risk of Salmonella contamination than those laid in controlled areas. This is due to exposure to dirt, dust, faeces and moisture.

Water or moisture exposure facilitates the growth of Salmonella and its penetration into the egg. Wet ‘floor eggs’ can be a concern, as these eggs in contact with the floor (or another wet environment) are likely to be internally contaminated. These eggs should not be graded for human consumption.

Dry ‘floor eggs’ should be processed separately to non-floor eggs to limit the risk of cross-contamination to clean eggs. Dry ‘floor eggs’ can be cleaned using a closely monitored, verified, washing or sanitisation process to remove the additional contamination that is present, regardless of whether this is visible or not.

Some hen breeds are more likely to lay eggs on the floor than other breeds. More research is needed to assess the efficacy of specific interventions to reduce ‘floor eggs’, which are affected by flock management, climate and weather changes.

Diffusion of bacteria into eggs can occur due to differences in temperature between the internal egg and the outer environment.

Research into Salmonella diffusion into eggs has found it is easier to artificially contaminate eggs with a wet solution of faeces containing Salmonella, as opposed to a dry faecal sample.

Floor eggs should be processed separately (and pulped)