Sanitation for Disease Prevention in Animal Shelters

two shelter staff clean the kennel floor and walls

Cleaning and disinfecting, also referred to as sanitation, play an important role in keeping individual animals healthy and preventing disease outbreaks. It also protects humans from infectious diseases and helps create a welcoming environment that encourages the public to visit and adopt animals. Sanitation protocols keep staff and volunteers aligned by ensuring appropriate product selection and consistent sanitation procedures.

Sanitation includes both cleaning and disinfecting.

Cleaning is the manual removal of organic material (e.g., feces, urine, mucus) from all surfaces in addition to washing with soap and water to remove grime. Cleaning can manually remove environmental pathogens (e.g., viruses and bacteria).
Disinfecting is the application of a chemical product to inactivate remaining pathogens.
Drying the surface is the final step in the process of sanitation.

Cleaning and Disinfecting Products

There are many factors to consider when choosing products for sanitation procedures, including

Detergent activity
Spectrum of disinfecting activity (e.g., effective against unenveloped viruses)
Storage, dilution, and application requirements
Required contact time for effectiveness
Human and animal safety
Environmental impacts
Cost

The Shelter Disinfection Quick Reference compares the features of several different disinfectants. Some products can be utilized for both the cleaning and disinfecting steps since they have detergent activity. If shelters are trying to save their disinfectant for when it is truly needed, dish detergent can be used for the cleaning step. It is important to note that some commonly used shelter disinfectants do not reliably eliminate certain viruses (e.g., parvovirus, panleukopenia, calicivirus, etc.) despite their label claims.

Proper use of disinfectants is critical for the health and safety of people and animals. Products should be used in accordance with manufacturer recommendations or published guidelines.

Do not:

Mix different types of disinfectants as this may result in flammable or otherwise harmful solutions or gas.
Use products containing phenols (e.g., Lysol) or pine oils, as these chemicals are toxic to many animals, including cats.
Use commercial aerosol sanitizers. These are ineffective and may cause respiratory irritation or toxicity if inhaled.

Properly diluted household bleach is an inexpensive product that has historically been used as a disinfectant in many shelters. When stored, diluted, applied, and rinsed appropriately household bleach can be effective against pathogens of concern in the shelter environment – but it is frequently misused. Other products are available that have less of an impact on the environment, fewer health concerns, greater efficacy in the face of organic material, and shorter contact times. Shelters should consider these products first before selecting bleach for general disinfection purposes, especially as disinfectants such as accelerated hydrogen peroxide products have become less expensive and more widely available even for use in foster homes.

If bleach is used, it is critical that the product be appropriately diluted (made fresh and protected from light), applied to already-cleaned surfaces, and allowed to sit for the full contact time before a thorough rinse and drying of all surfaces. For further information, see Diluting Bleach for Disinfection.

Dilution of Disinfectant

Accurate dilution of disinfectant is important and is achieved by measuring the amount of disinfectant that is added to water. Automatic mixing stations are available for some products. Certain products can be mixed to use at various strengths, depending on the intended effect of the product. For example, accelerated hydrogen peroxide products are used at a higher concentration for populations that are at greater risk for exposure to parvovirus, panleukopenia, and calicivirus and for areas with high traffic (i.e., hallways, exam rooms, treatment areas, etc.). Lower concentrations can often be used for the remainder of the shelter. In some cases, a lower concentration with a longer contact time can achieve the same activity against pathogens of concern.

Equipment

Separate sanitation supplies should be designated for each shelter ward. For both cats and dogs, the following is needed:

Disposable gloves and other personal protective equipment (PPE), as warranted
Detergent and disinfectant products
Garbage bags
Laundry bag/basket

For cats and dogs housed in cages:

Labeled hand-pump sprayer or squirt top bottle
Clean hand towels or paper towels
Dust pan
Small scrub brush
Rolling cart to hold items

For dogs housed in kennels, runs, or real-life rooms:

Hose-end foamer
Scooping tool
Squeegee on handle
Scrub brushes on handle
Dilution test strips for Rescue® (if using)

Order of Sanitation

Cleaning and disinfecting steps must be ordered to most effectively minimize the risk of disease transmission. Staff should clean and care for animals in the following general order:

Healthy puppies and kittens
Healthy adult animals
Unhealthy animals

Transport cages and traps, as well as vehicle compartments, must be sanitized after each use.

Instructions for Staff and Volunteers

Detailed written and verbal instructions regarding the process of cleaning and disinfecting animal enclosures should be shared with staff and volunteers who perform these duties. Personnel should know:

How to accurately dilute disinfectant and when newly diluted product needs to be made (the stability of diluted products varies based on disinfectant used)
What needs to be sanitized
Which products to use and how to use them
What PPE to wear in each ward
Removal of organic material, newspapers, bedding, and other items in kennel

Additionally, it is beneficial to post laminated copies of the instructions in various kennel areas for reminders for new staff and volunteers. Periodically reviewing instructions with personnel as well as observing sanitation procedures is important. This ensures consistency, identifies and corrects deficiencies, and allows for modification of written protocol, as needed.

Sufficient staff or volunteers are needed to complete sanitation tasks promptly each day. It is recommended that a minimum of 9 minutes per animal per day be allocated for routine cleaning of enclosures, but more time may be needed depending on the facility and population of animals cared for. The type of disinfectant used, asl well as the required contact time, must be considered when determining the time needed for deep cleaning of enclosures.

Spot vs. Deep Cleaning

In order to conserve supplies, reduce animal handling and stress, and enhance operational efficiency, spot cleaning is recommended when the same animal continues to be housed in an enclosure. Deep cleaning is used when a different animal is to occupy a vacated kennel or every 2 weeks for longer stay residents.

The following videos demonstrate proper techniques for Spot and Deep Cleaning:

Double compartment enclosures allow for an animal to remain within one compartment while the other is tidied up or sanitized. If a cat needs to be removed from enclosure during spot cleaning or deep cleaning, the cat needs to be placed into a sanitized carrier or one that is dedicated for use by specific cat. It is very important that animals in enclosures do not have contact with cleaning and disinfecting products when they are being used nearby.

The steps for deep cleaning a kennel include:

Use of detergent to clean/scrub organic material on kennel followed with rinse.
Application of disinfectant with appropriate contact time, to be wiped dry or rinsed and then dried according to product instructions.
Complete drying of the enclosure before an animal returns to it.

Some products have both detergent and disinfectant properties; therefore, the same product can be used for both cleaning and disinfection. However, it is necessary to perform both the cleaning and disinfection steps even when using a dual-purpose product, to ensure appropriate sanitation.

Personal Protective Equipment (PPE)

In animal shelters, the hands of people handling animals or cleaning enclosures serve as a fomite, potentially transmitting harmful pathogens from one animal to the next. Additionally, some animals can be shedding viruses or bacteria without currently showing any signs of infectious disease. In an effort to decrease the spread of infectious diseases and protect people from acquiring zoonotic diseases, PPE such as disposable gloves, gowns or smocks, shoe covers, and boots should be worn by those performing sanitation duties. What pieces of PPE are needed will depend on the animal’s level of risk and potential pathogens of concern. Contaminated items should be changed prior to sanitizing the next kennel. In between sanitizing kennels and handling animals who are not currently housed together, personnel should wash and dry hands or don a clean pair of disposable gloves. Hand sanitizer (containing at least 60% alcohol) should also be available and applied to visibly clean hands as needed, but can’t be relied on as the only means of hand hygiene. For more information, visit our Infection Control and Personal Protective Equipment resources.

Food/Water Bowls and Litter Pans

Automatic dishwashers destroy the majority of pathogens but may not destroy unenveloped viruses. When these are a concern, application of a disinfectant to dishes and subsequent rinsing with water is needed. If an automatic dishwasher is absent, bowls should first be thoroughly washed with dish detergent and rinsed with water prior to the application of disinfectant (for appropriate contact time) and subsequent water rinse. Litter boxes should be sanitized in a different location or at a different time than bowls to prevent cross-contamination. Items that have become damaged or scratched items should be discarded as thorough disinfection will not be possible.

Laundry

Organic material (e.g., feces, vomit) should be removed from bedding, blankets, and towels prior to placing items in the washing machine. The washing machine should never be overloaded and ½ cup of household bleach per average load of laundry can be used. Items should be thoroughly dried (in a dryer on high heat whenever possible) following washing.

Outdoor Areas

Feces should ideally be removed immediately from outdoor areas to limit contamination, as it is not possible to disinfect grass, dirt, or gravel surfaces. To decrease this risk, shelters could allow use of such outdoor areas only by adult animals who are fully vaccinated, dewormed, and appear healthy. Standing water should not be present on shelter grounds since wet environments are a source of pathogens.

Resources and Downloads

Last Reviewed January 2024

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Topics: Shelter Medicine , Sanitation , How-To Guides

Type: Job Aid Downloads

a white and black cat sits on the floor in a cat room looking at camera

Job Aid Downloads

Sanitation for Group Cat Rooms

Proper cleaning and disinfection is critical to shelter disease control and should occur on a regular basis in group cat rooms.