Merck Manual

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Professional Version

Cleaning and Disinfection in Shelter Medicine


Martha Smith-Blackmore

, DVM, Cummings School of Veterinary Medicine, Tufts University

Reviewed/Revised Oct 2021 | Modified Nov 2022

The healthful operation of an animal shelter requires that the facility maintain a sanitary environment. Preventing disease transmission through proper cleaning and disinfection techniques is far easier and more cost-effective than dealing with a disease outbreak. Veterinarians can help animal shelters develop protocols for cleaning and disinfection that are efficient and effective.

Cleaning and disinfection protocols should balance the disease suppression benefits of sanitation processes with the negative impact of overzealous procedures that inflict unnecessary stress on shelter animals and contribute to disease expression. It is appropriate to have separate protocols for cleaning common areas, tidying and cleaning primary enclosures while occupied by the same animal or animals, disinfecting cages between animal occupants, and implementing deep cleaning and disinfection procedures in the case of a disease outbreak.

A primary enclosure may be maintained in a tidy state during the continuous and ongoing occupation by an animal or closed group of animals. Doing so reduces the stress of being removed from the enclosure to be returned to one where the occupant’s familiar scents have been replaced by the smell of cleaning and disinfection. Tidying is also referred to as spot cleaning, the removal and replacement of soiled bedding, the removal of visible debris by scooping feces and gently sweeping up spilled litter or kibble, and the replenishment of food and water. When spot-cleaning the cage, it is appropriate to follow scooping of feces with a focused application of a cleaning solution to remove any residue. When an animal is adopted out or otherwise vacates the primary enclosure, the enclosure must undergo full sanitation.

Sanitation is the process of cleaning the kennel environment to reduce the presence of infectious organisms to below the disease transmission threshold (aiming to eliminate the presence of an “infective dose”). Sanitation is achieved through a four-step process: tidying, washing, disinfecting, and drying. Because sanitation involves the application of chemicals and spraying with hoses, animals must always be removed from enclosures during this process.

Tidying, or dry cleaning, is like spot cleaning, described above, but on a larger scale. All materials are removed from the enclosure, and all debris and organic materials are wiped or swept up. When cleaning an animal shelter, every effort must be made to minimize the creation of dust clouds. That goal can be accomplished by using rubber squeegees instead of brooms and by lowering litter trays deep into the trash receptacle before gently tipping them out. This cleaning step reduces the spread of organic material that supports the persistence of infectious agents.

After all visible materials are removed, washing (scrubbing with detergent) may begin. Washing is best accomplished by applying the detergent with a low-pressure foamer using hot water, and then scrubbing with a bristle brush. The foam applicator assists in application to upright and overhead surfaces. In smaller spaces, where foamers are not appropriate, a squeeze bottle that produces a stream with diluted detergent may be used. Scrubbing with detergent breaks down biofilms that can prevent the penetration of disinfectants. Scrubbing should proceed from top to bottom, with special attention paid to cracks, corners, and cage bars, where debris can accumulate. After scrubbing, the detergent should be rinsed out using a low-pressure hose or wiped out with a water spritz and paper towels. High-pressure rinsing should be avoided because it aerosolizes bacteria and viruses that have not yet been inactivated by disinfectant. Buckets and rags should be avoided because they can be fomites—inanimate objects capable of transferring an infectious agent from one place to another. While cages are being washed, all removed laundry, toys, dishes, and litter pans can also be washed and disinfected. The washing step removes up to 99% of the bacteria present and prepares surfaces for disinfection.

Disinfection involves diluting the disinfectant according to the manufacturer’s label and allowing the disinfectant to stay in contact with the surface for the prescribed amount of time. Disinfectant selection should be based on the infective agents being targeted and the safety of the product for the species housed. Bleach is an inexpensive disinfectant that is effective against bacteria, parvoviruses, and respiratory viruses at a 1:32 dilution (0.5 cup/gallon) and against ringworm spores at a 1:10 dilution (1.5 cups/gallon) with a 10-minute wet exposure period. Limitations with bleach are that it is caustic, corrosive, and a respiratory irritant that must be diluted daily. Other choices for disinfection include quaternary ammonium products, oxidizing agents, biguanides, and phenols. Each of these categories of disinfectants have their own benefits and limitations. Veterinarians should work with animal shelters to tailor disinfectant choice to the most useful, cost-efficient, and effective type for a particular shelter’s setting and population.

Drying should be done if there is any residual moisture after the specified wet disinfection exposure period. Drying must be complete before animals are returned to an enclosure. After the specified disinfection period, air drying may be hastened by the use of paper towels or a squeegee. Fans may blow respiratory irritant fumes around the shelter and are not universally recommended; however, they may be appropriate in some settings. Animals returned to enclosures that are still wet with disinfectant may develop sores on or between their footpads, on the scrotum, on the tongue, or around the mouth. Some disinfectants must be rinsed after the specified disinfection period to be safe for animals to reoccupy the space, so careful disinfectant selection and use is essential.

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