Sanitation—the maintenance of conditions conducive to health—involves bedding change (as appropriate), cleaning, and disinfection. Cleaning removes excessive amounts of dirt and debris, and disinfection reduces or eliminates unacceptable concentrations of microorganisms.

The frequency and intensity of cleaning and disinfection should depend on what is needed to provide a healthy environment for an animal, in accord with its normal behavior and physiologic characteristics. Methods and frequencies of sanitation will vary with many factors, including the type, physical properties, and size of the enclosure; the type, number, size, age, and reproductive status of the animals; the use and type of bedding materials; temperature and relative humidity; the nature of the materials that create the need for sanitation; the normal physiologic and behavioral characteristics of the animals; and the rate of soiling of the surfaces of the enclosure. Some housing systems or experimental protocols might require specific husbandry techniques, such as aseptic handling or modification in the frequency of bedding change.

Agents designed to mask animal odors should not be used in animal housing facilities. They cannot substitute for good sanitation practices or for the provision of adequate ventilation, and they expose animals to volatile compounds that might alter basic physiologic and metabolic processes.

Bedding Change

Soiled bedding should be removed and replaced with fresh materials as often as is necessary to keep the animals clean and dry. The frequency is a matter of professional judgment of animal care personnel based on consultation with the investigator and depends on such factors as the number and size of the animals in the primary enclosure, the size of the enclosure, urinary and fecal output, the appearance and wetness of the bedding, and experimental conditions, such as those of surgery or debilitation, that might limit an animal's movement or access to areas of the cage that have not been soiled with urine and feces. There is no absolute minimal frequency of changing bedding, but it typically varies from daily to weekly. In some instances, frequent bedding changes are contraindicated, such as during some portions of the prepartum or postpartum period, when pheromones are essential for successful reproduction, or when research objectives do not permit changing the bedding.

Cleaning and Disinfection of Primary Enclosures

For pens or runs, frequent flushing with water and periodic use of detergents or disinfectants are usually appropriate to maintain sufficiently clean surfaces. If animal waste is to be removed by flushing, this will need to be done at least once

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