Parasites, bacteria, and viruses offer a significant health concern in all livestock production systems. Because all livestock are housed in groups, pathogens are easily transmitted from one animal to the next. Control of many pathogens is enhanced by housing livestock in concrete and metal buildings, which allows for complete sanitation of the environment. Features such as slatted flooring, which allows feces to drop through the floor and away from the livestock, enhance control of parasites. Intensive housing systems that individually house animals, such as veal calves and sows, also aid in our ability to treat livestock that become infected. Individual treatment of poultry is not practical due to large groupings. When necessary, entire flocks are treated. It is significantly more challenging to control pathogen infestation in extensive systems such as pastures. However, such systems benefit from the extensive conditions because: 1) pathogen load is less because of a greater area of distribution and sunlight kills many pathogens; 2) direct contact is less and thus, fewer pathogens are passed directly to herd mates; and 3) 100% open air flow does not allow airborne pathogens to accumulate and thus decreases the stocks' exposure. Common management practices that help reduce pathogen exposure in extensive systems are rotational movement of dairy calf hutches to clean ground to allow any pathogens to be destroyed, and rotational movement of grazing livestock between pastures.

Housing that requires livestock to spend significant amounts of time on hard flooring can cause both lameness and skin lesions. Lameness is a common reason that sows and dairy cows must be culled from the herd. Wet floors in dairy facilities acerbate this problem because cows that slip may cause serious injury to joints and musculature. Skin lesions in sows mainly occur during lactation when sows lose body weight. Less fat cover allows pressure sores to develop from lying on the floor. These sores then rupture, and once they are established, they are extremely difficult to heal.

The group size in which livestock are kept can also have effects on their health. Some of these reasons are those discussed earlier, relating to pathogen exposure. Other effects on health are due to stress from group competition. Anytime animals are grouped, they will compete for any resource that is limited. In production agriculture, all animals being fed to produce meat or milk are not being limited in feed or water, but limitations can occur due to limited access. Limited access to the feeder or water will cause increased aggression, which in turn will activate the stress response. Broiler breeders and sows are limit-fed and thus, a high degree of aggression can be seen when they are housed in groups. Those animals lying intermediate in the dominance hierarchy tend to be more stressed than either those at the top or bottom.

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