Rosie Lerner of Purdue University Extension reports that gardeners long have used manure from various farm animals to fertilize and enrich their soil. However, recent public awareness of food-borne illnesses has left many gardeners wondering if using manure is safe.
There are a number of pathogens, including E. coli, salmonella and listeria, that can be transferred to humans from animal manure. Some manures also may contain parasites, such as roundworms and tapeworms.
If fresh manure is applied to the garden or compost pile, there is a high risk of causing illness to the gardener, as well as anyone eating fresh produce from that garden. Fresh manure also can be harmful to growing plants, due to being too high in available nitrogen, thus burning roots.

It is safer for both plants and people to apply only composted, rotted manure to an active garden bed. Manure should be composted for a minimum of six months to reduce the risk of contamination.
If fresh manure must be applied, do so during the previous fall so that it has a chance to decompose for as long as possible before the garden will be planted. Do not apply manure to actively growing fruits or vegetables.
Root vegetables and other crops that have their edible portions below ground pose the greatest risk of transmission, since they have the most contact with potentially contaminated soil. Vegetables, such as carrots, radishes, sweet potatoes, Irish potatoes, turnips, parsnips, onions and beets should be thoroughly washed and/or peeled to decrease risk.
Leafy vegetables, such as lettuce, spinach, cabbage, chard and other greens, where the edible portion is in contact with soil, and especially crinkly leaves that catch soil particles, are also at high risk for contamination.
Some fruits also may be in contact with the soil, such as tomatoes that are not staked or caged, and strawberries. Thorough washing and removing outer leaves from heads of lettuce and cabbage will reduce risk. Thorough cooking is the only way to eliminate the risk completely.
Manure from pigs, dogs and cats should not be used at all in gardens or compost because they may contain parasites that can infect humans.