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Sanitation in the Animal Shelter

Lila Miller, D.V.M., Sr. Director, Animal Sciences ASPCA


Sanitation in the Animal Shelter

Whenever there is an outbreak of disease in the shelter, it is tempting to call the veterinarian to begin immediately reassessing programs of vaccination and disease testing. However, one of the first things the veterinarian and management should evaluate is the cleaning procedure. Poor sanitation is frequently overlooked as one of the main contributing factors to the spread of disease. It is not enough to perform a cursory study that establishes that bleach is being used or that the shelter is cleaned every day. Staff should be observed mixing and applying disinfectants and cleaning cages to make certain it is being done properly whenever an outbreak occurs.

It is virtually impossible to kill all disease causing agents in a shelter. Some organisms are highly resistant to disinfectants, and some areas of poorly designed shelters may be inaccessible or too porous to effectively disinfect. Disease causing spores may be caught up in the ventilation system or residing in carpeted areas of administrative offices. Attention must be paid to all the elements that may cause a sanitation protocol to fail. Detection of these problems enables management to devise methods of proper cleaning and disinfecting that offset the shelter’s shortcomings. It cannot be stressed enough how important it is to at least reduce the number of organisms in the facility.

In shelters where staffing shortages or overcrowding occurs, it is tempting to take short cuts when cleaning. This should be avoided. Either more staff should be employed, fewer animals taken in (in shelters that have control over admissions) or more time devoted to cleaning. If staff is cleaning multiple areas, they should clean in areas with healthy animals first, and sick or otherwise unadoptable animals last. The use of disposable gloves, gowns or aprons and footbaths outside each room is advised especially whenever there is a disease problem. Overcrowding makes cleaning much more difficult, yet even more critical to perform properly. At the very least, as a general rule, animals should be kept in the same cage whenever possible.

It should be borne in mind that cleaning and disinfecting are two different procedures. Cleaning must precede disinfecting in order for disinfecting to be effective. Cleaning involves the removal of dirt and organic debris, but does not actually kill disease-causing organisms. Disinfecting kills the organisms, but is only effective if the surface is clean and the appropriate disinfectant that will kill the specific disease organism is properly applied. Fortunately for shelters, in most cases it is not necessary to identify the specific disease-causing agent for sanitizing purposes because disinfectants like bleach will kill most organisms (proper identification of the disease may be necessary for effective treatment and other preventative measures such as vaccination).


  1. The first step involves removing the animal and any mats, platforms, paper, bedding, bowls, toys, litter pans, etc., from the cage. The cage cannot be cleaned properly if the animal remains in it.
  2. All organic debris and fecal material should be physically removed from the cage.
  3. Hot water and soap should be used to actually clean the cage. If hot water is not used, cleaning will generally not be effective.
  4. Mops and high pressure hosing systems may actually help spread disease organisms and should be avoided or used with caution.
  5. The entire cage should be cleaned, including the top, bars, glass fronts, walls, etc.
  6. Food and water bowls, and litter boxes should also be cleaned.
  7. In order to prevent the spread of disease, cleaning and disinfecting equipment should not be moved from one room to another.


  1. The disinfectant must be mixed and applied according to the manufacturer’s instructions. Mixing different disinfectants together can actually be dangerous.
  2. The disinfectant must be allowed to stay in contact with all the surfaces to be disinfected for the specified length of time or it will not kill the disease organism. This step is frequently overlooked, and a false sense of security results that the disinfectant is working.
  3. The area should be rinsed thoroughly after the appropriate contact time.
  4. The area should be dried before the animal is returned to the cage
  5. Bowls and litter boxes must be disinfected before their return to the cage. Keep the bowls and litter boxes with the same animal for the duration of their stay in the shelter.
  6. Toys should be disinfected if possible or discarded. They should not be shared.
  7. Transport cages, disinfecting equipment and communal animal gathering spaces, as well as hallways and lobbies in animal traffic areas must also be cleaned and disinfected to maintain a sanitary and odor-free environment.

The two most commonly used disinfectants in shelters are bleach (sodium hypochlorite) and quaternary ammonium (quats) products. Although labeled to kill parvo and calici virus, quats have been shown to be less than effective in killing these disease agents. Bleach diluted 1:32 with water has consistently been found to yield better results and is the recommended disinfectant for both routine use or use during a disease outbreak. If not diluted properly however, it may be an irritant to delicate mucus membranes or cages. No odor should be detected when bleach is diluted properly.

The minimization of disease spread requires a team effort that involves the consideration of many different factors, proper sanitation being just one of them. The minimization of disease spread requires a team effort that involves the consideration of many different factors, proper sanitation being just one of them. All staff should be properly instructed in cleaning procedures, and periodic reevaluations of those procedures conducted, especially in shelters with high population densities, high staff turnover or when staff training is informal.

© 2003 ASPCA

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424 East 92nd Street
New York, NY 10128-6804

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