Canadian Poultry Magazine

Ask the Vet: Health challenges in alternative housing

By Tom Inglis   

Features Ask the Vet Health

Do cage-free housing systems (free-run and free-range) present any unique health challenges? If so, how can they be prevented or managed?

Cage-free systems present unique poultry health challenges. PHOTO: Egg Farmers of Canada

Alternative housing systems have gained in popularity over the past few years due to an increase in outside influences. Consumers have become more involved with farm-to-fork and have driven the egg industry to adopt modifications on how birds are housed throughout their production cycle. 

These changes are with the intention to provide the birds with highest possible welfare. But often the five freedoms of animal welfare conflict with each other. While providing the birds with a greater ability to express natural behaviours, we have created significant health and production challenges. This is especially seen with cage-free flocks that are housed on slats/litter, lay eggs in nest boxes and have access to the outdoors (free-range). These systems allow greater expression of natural behaviours, but often the birds are challenged with increased disease pressures and higher total flock mortality.

Birds within cages are exposed to a controlled environment that minimizes stress and exposure to infectious pathogens. Typically, manure is removed daily with the aid of belts or stored in a deep pit. This process helps limit the amount of dust within the facility and restricts the interaction of birds with their litter. However, this poses a significant challenge within cage-free production as the birds are in direct contact with their litter and natural behaviours, such as dust bathing, tend to increase the amount of dust stirred up within the barns.

Dust can act as an irritant causing damage to a bird’s respiratory tracts and act as a vector for microbes leading to secondary bacterial infections. To help expel the increased dust within cage-free barns it is suggested that producers increase their ventilation. Additionally, with increased exposure to respiratory pathogens it is recommended to ensure your vaccine programs are providing optimal protection to viral respiratory diseases such as Newcastle and Infectious Bronchitis.

Laying birds with access to their litter increases the risk of parasitic diseases within cage-free systems. Coccidiosis is caused by a protozoan parasite with a fecal to oral mode of transmission.  Naïve birds are exposed to the parasite when they ingest litter without any built-up immunity.

Coccidiosis can trigger other enteric diseases such as necrotic enteritis, which can lead to significant losses within a flock. This disease isn’t a frequent problem in conventional housing as the birds don’t have access to their litter, thus not allowing the protozoa to complete its lifecycle.

To help manage this risk within free-run and free-range systems, it is important to guarantee the birds are properly vaccinated for coccidiosis and have gained adequate immunity to last throughout production. In addition to coccidiosis, the cage-free birds might be exposed to an increased burden of roundworms. This could result in emaciation, diarrhea and unthrifty birds. It is recommended to have a regular deworming program with the use of approved products.

In a caged facility, the pecking order is determined in the initial stages after transfer and tends to be quite stable throughout the production cycle. However, within cage-free environments it is a constant shifting dynamic of birds continually trying to determine their rank in the population. This can lead to significant aggression and feather pecking within the flock.

To help focus their attention away from each other it is suggested to have distractors within the barn. This can be as simple as adding a bail of straw into the scratch area of the barn.

One of the greatest health challenges in cage-free operations is increased mortality related to bacterial infections (most commonly E.coli). These bacterial infections have many different presentations (egg yolk peritonitis, airsacculitis, and pericarditis) and can be the result of several factors. The emphasis within these flocks is for prevention rather than treatment, as no antibiotics licensed in Canada have a zero-day egg withdrawal.

Many of the preventative techniques are focused on limiting the flock’s exposure to virulent bacteria. Managing nest box hygiene is critical to lowering the risk of ascending bacterial infections from the oviduct.

Some practical techniques include thoroughly cleaning and disinfecting the nest pads after every cycle and ensuring birds are not allowed to remain in the nest boxes all day.

Another potential source of increased bacterial contamination is from the water source. It is suggested to have a sanitizer (hydrogen peroxide or chlorine) injected into the water throughout the whole production cycle. It is also common for the development of a stable biofilm to occur within the waterlines, which can act as a continual source of bacterial contamination.

It is recommended to follow a standard water cleaning program after ever production cycle:

  1. Acidify the water to a pH of four (let stand for eight to 24 hours) – this helps to dissolve the mineral complexes in the biofilm and the water line.
  2. Add hydrogen peroxide in a final concentration of 0.8 to three per cent (let stand for 12 to 72 hours) – this step disrupts the organic component of the biofilm.
  3. Add a disinfectant (let stand for 20 to 30 minutes) – this step is to kill any remaining bacteria which have been exposed but not killed by the peroxide.

Another layer of protection that can be added for these flocks is the use of a modified-live E.coli vaccine. The vaccine will help provide broad spectrum protection against, E.coli and help reduce total flock mortality in challenged flocks.

In free-range systems the birds are allowed access to the outside environment and can encounter waterfowl such as ducks and geese. These wild birds can carry diseases such as avian influenza and are, thus, a significant risk to the poultry industry. It is important within free-range housing systems to be aware of surveillance programs and respect times of heightened biosecurity.  

In summary, as the industry continues to move in the direction of cage-free production it will come with real challenges that need to be mitigated and addressed.

Tom Inglis is managing partner and founder of Poultry Health Services, which provides diagnostic and flock health consulting for producers and allied industry. Please send questions for the Ask the Vet column to

Print this page


Stories continue below