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University of Minnesota Extension

BMPs for pathogen control in manure

Livestock manure is a valuable source of crop nutrients, but it can also come with pathogens that may cause livestock and people to become ill. The number and type of pathogens in manure vary based on animal species, feed, and animal health. There are many different types of pathogens in manure, so using multiple best management practices at once will give the best results.

Pathogens can infect humans directly through contact with manure or indirectly through contaminated water and food. Children, the elderly, and those with compromised immune systems are at the highest risk for infection.

Common manure pathogens include bacteria, protozoa, and viruses. These pathogens can cause fever, diarrhea, nausea, abdominal pain, vomiting, and in the worst case scenario, death. Over the years, there have been a number of disease outbreaks from manure exposure in the United States.

Common manure pathogens

Bacteria Protozoa Virus
Campylobacter Cryptosporidium Rotavirus
Escherichia coli (E. coli) Giardia

Disease outbreaks from manure exposure in the U.S.

Source Location Year Pathogen $ of people ill # of people deceased Source of outbreak
California 2006 E. coli 199 3 Spinach contaminated by manure from a nearby cattle farm
Washington County, NY 1999 E. coli 781 2 Manure storage drained into shallow, unchlorinated well at fairgrounds
Springfield, IL 1998 Leptospira 98 0 Swimmers in lake contaminated with manure
Indiana 1996 Cryptosporidium 63 0 Swimmers in lake contaminated with manure

Reducing pathogens

There are three main areas of focus where livestock producers can reduce pathogens:

  1. In the animal

  2. During manure collection and storage

  3. During land application of manure


Chryseis Modderman, Extension educator

Reviewed in 2021

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