Tuesday, June 15, 2010

Best management practices for pathogen control in manure management systems

Sagar M Goyal
Mindy Spiehs
Published: May 28, 2008
  • Livestock waste contains many microorganisms such as bacteria, viruses, and protozoa. While some are pathogens capable of causing disease in animals and/or humans, many are not harmful.
  • All livestock producers have an important role in limiting pathogen movement from their operation to the environment.
  • The purpose of this bulletin is to provide livestock producers with tools to help control pathogens in their production system.
  • The best management practices (BMPs) addressed in this paper will focus on animal management and housing, dietary modifications, production management, land application of manure, and the chemical and biological treatment of stored manure.
  • Because of the number and variety of pathogens present in livestock waste, adequate control of pathogens may require multiple management interventions to achieve significant reduction of pathogens in a manure management system.

Condensed by Milkproduction.com staff from Minnesota Extension Bulletin M1211 2007

Pathogens and human health

Pathogens can be transmitted to humans directly through contact with animals and animal waste or indirectly through contaminated water or food. Unfortunately, cases of human illness and death caused by exposure to livestock manure have been documented. Water can become contaminated by runoff either from livestock facilities or from excessive land application of manure. Pathogens can contaminate food products during meat and milk processing.

Simply coming into contact with a pathogenic organism does not necessary mean that an individual will become sick. Because it is impossible to know who will come into contact with pathogens from a livestock production area, it is a good management practice to reduce all potential exposures by controlling pathogens in livestock systems.

Some of the most commonly recognized pathogens from livestock include bacteria such as Shiga-toxin producing Escherichia coli (E. coli), Salmonella, Campylobacter, and Yersinia. Most can survive and even multiply in environments outside of the animal such as livestock manure. These bacteria can cause fever, diarrhea, vomiting, nausea, and abdominal pain in humans who are directly or indirectly exposed to contaminated manure.

Protozoa from livestock waste can also cause disease in exposed humans. Giardia and Cryptosporidia are considered to be the two most important waterborne protozoa of livestock origin. These protozoa are important because they are not easily destroyed except by filtration.

Although not as common as bacteria and protozoa, viruses can be present in animal manure. Rotavirus is the most commonly recognized pathogenic virus in animal manure. Viruses can not multiply outside of the animal, but are capable of surviving for long periods of time in the environment depending on environmental conditions. One study found that rotavirus could survive in a manure storage facility for more than six months.[1]

What can producers do to reduce potential contamination of surrounding surface and ground water from their livestock or poultry operations? There are three basic points in the manure management cycle where producers can implement practices to reduce pathogens: (1) in the animal, (2) during manure collection and storage, and (3) during land application of manure. A good pathogen reduction program will include BMPs at each of these three points.

Pathogen reduction - the animal

Animal management and housing

The more pathogens present in an animal, the greater the risk that food or water will be contaminated by its manure. Sick or stressed animals are more likely to shed pathogens in their manure than healthy, comfortable animals. Some animals appear healthy but are “carriers,” meaning they can shed pathogens in their manure when stressed or uncomfortable. Therefore, simple management practices such as vaccinations, adequate access to feed and water, appropriate space allowance, temperature and ventilation control, on-farm sanitation and biosecurity measure, and good animal husbandry practices can be an easy first step for producers to reduce pathogens in manure.

Type of animal housing facility can also influence presence of pathogens. For example, housing pigs so that contact with contaminated feces is minimized will decrease pathogens.[2] This does not seem to be true for cattle in pasture systems. Pasturing cattle does not appear to affect the strains of pathogenic E. coli most commonly associated with severe foodborne illness. Research has shown that there is no difference in the prevalence of E. coli O157:H7 in manure from cattle raised on pasture compared to those raised in confinement.[3]

Fly and vermin control in livestock facilities may reduce the spread and subsequent infection of other animals with pathogenic bacteria. Flies and bird fecal samples from cattle farms have tested positive for E. coli O157.[4] Numerous studies indicate that Salmonella can survive for several days to nine months, on insects, rodents, and surfaces of building materials such as wood, concrete, iron, steel, and brick. [5] Salmonella can survive in rodent feces for up to five months, emphasizing the need for adequate rodent control, and frequent and thorough cleaning of animal facilities.[6]

Producers may not be able to change their housing facility. However, practicing good animal husbandry to reduce animal stress is an easy first step for reducing pathogens in any livestock operation. It is likely that the small economic expense of implementing these BMPs will be recovered with increased animal performance.

Diet modifications

Diet selection can decrease pathogen levels in manure. Fecal shedding can be reduced by additing  antimicrobials to livestock diets.[7] With increased public concern over the routine use of antimicrobials as growth promoters in livestock feeds, especially those similar or identical to those used in human medicine, producers should use antimicrobials only to treat specific diseases rather than adding them routinely.

Organic acids have successfully reduced levels of Campylobacter and Salmonella in poultry diets but results varied in swine. [10,11] Direct-fed microbials have been used to reduce Salmonella and E. coli in swine manure[12,13] and to reduce some pathogenic strains of E. coli in calves,[14,15] feedlot cattle,[16] and sheep.[17] Yeast extracts can reduce E. coli and Salmonella in young pigs and chicks.[18,19]

Abruptly switching cattle from a high-grain diet to a high-quality hay-based diet has been reported to reduce acid-resistant E. coli[20] and E. coli O157:H7.[21] However, due to the complex nature of the cattle digestive systems, this response has been inconsistent. [22-24]

Physical form of feed can affect bacterial levels in manure. Pigs fed finely ground diets (1/16 inch screen) were more likely to test positive for Salmonella compared to pigs fed coarsely ground diets (5/32 inch screen). [25,26] Pigs fed pelleted feed were 3.3 times more likely to test positive for Salmonella compared to growing-finishing pigs fed a meal diet.[26] Therefore, producers wishing to decrease Salmonella in swine manure should feed coarsely ground meal diets instead of finely ground pelleted diets.

The use of dietary modifications can be a relatively simple management tool to use for reduction of pathogen excretion from a livestock operation. It is necessary to determine which pathogens are present and if levels are high enough to justify a dietary modification. Because results have been inconsistent, producers need to consider the economical and performance impacts of a diet change and any necessary adjustments to management that will result.

Pathogen reduction - manure collection and storage

Production management

Use of vegetative filter strips. Runoff from open feedlots and manured fields can be routed through grass filter strips to remove sediment, nutrients, and bacteria. The effectiveness of vegetative filters at removing pollutants and microorganisms depends upon site characteristics such as slope, amount of runoff, type of wastes, and presence or absence of concentrated flows. Time of year is also important. The vegetative filter strips will be less effective during springtime snowmelt when the filter strips may still be frozen or not actively growing. One study has shown that grass filter strips (15 to 30 feet in length) remove 75 to 91% of fecal coliforms and 68 to 74% of fecal streptococci from runoff obtained from manured plots. [27] Animal confinement areas should have a 66 to 99 foot vegetative filter strip between animals and surface water in order to minimize contamination.[28]

Control runoff and leaching from stockpiled manure.

Some livestock operations need to stockpile manure before land application. If manure must be stockpiled, follow all regulations set by the local regulatory authority. Minnesota rules require that stockpiles be located, constructed, and operated so that manure-contaminated runoff from the site does not discharge into waters of the state. Permanent stockpiles must be placed on a concrete pad or clay base and have at least two feet of separation distance between the base of the stockpile and the seasonal high-water table. Catch basins can be used to prevent runoff from reaching surface water.

Control runoff and leaching from open lots. Catch basins can be used to contain manure-contaminated water from an open lot. The water collected in catch basins can be land-applied or further treated by running through vegetative filter strips.

Install clean-water diversion. Berms and ditches can divert up-slope runoff and roof water away from areas where manure may accumulate. Preventing this excess water from entering the lot or manure stockpile area both reduces pollution potential and keeps these areas drier. Drier facilities can improve animal health, which in turn lowers pathogen levels in manure.

Eliminate or reduce livestock access to streams, rivers, lakes, or ponds. Fencing livestock away from open water improves water quality. Keeping animals away from open water will prevent urination and defecation in the stream. Animal health may also be improved through reduced exposure to water-transmitted diseases and foot rot. Alternative livestock water systems must replace direct, uncontrolled livestock access to streams, ponds, and lakes.

Best management practices to control runoff will prevent pathogens from leaving the livestock operation and potentially contaminating food or water supplies. Most systems are relatively easy to install and partial funding for construction may be available through government agencies.

Biological Treatment of Manure

Anaerobic storage. Anaerobic lagoons are widely used in southern climates for the treatment and temporary storage of manure. Deep pits located beneath animal housing facilities, are also anaerobic storage systems. In an anaerobic system, bacteria are not exposed to oxygen.
Although bacteria can survive anaerobic conditions for long periods of time, most pathogens are reduced within 30 days.[29] Surviving bacteria may be destroyed during land application due to exposure to UV light and drying if the manure is surface applied. However, it is recommended that liquid manure from these systems be injected or immediately incorporated to conserve nitrogen and avoid risk of phosphorus runoff.

Composting.Compost is an organically rich soil amendment produced by the decomposition of organic materials. During the composting process, organic materials such as animal manure and livestock carcasses are broken down by microorganisms. Active composting generates heat, carbon dioxide (CO2) and water vapor. The end product of composting is a dark, earthy-smelling material. During composting, temperatures can reach 150°F. Most pathogens that are harmful to humans can be destroyed at 131°F or higher. The Minnesota Board of Animal Health recommends two heat cycles of greater than 131°F to ensure pathogen destruction. However, there is no evidence that composting destroys prions, the abnormal proteins believed responsible for diseases such as Bovine Spongiform Encephalopathy, Chronic Wasting Disease and Scrapie.

For compost to successfully reach a temperature of 150°F, the compost pile must be monitored carefully. Carbon and nitrogen that must be provided in correct quantities. Incorrect ratios of carbon and nitrogen can cause the compost pile to either over-heat (causing a fire) or remain cold and dormant. Heat must be uniform throughout the compost pile and the composted manure must be turned and mixed regularly so that all manure has sustained exposure to the pathogen-killing temperatures.

Aeration. Aeration involves exposing manure to oxygen and air. Natural aeration involves storing manure in large, shallow (less than 5 ft. depth), storage structures so enough oxygen can naturally reach the bacteria. These types of structures are rare in northern climates. Mechanical aeration involves pumping air into a storage structure. Aeration is especially effective against viruses in cattle and pig slurry.[30,31] The combination of supplemented heat and aeration can further reduce pathogens in manure.[30] Storage at 68°F for two to four days in an aerated system reduced infectious viral load 90%. To get the same reduction at 41°F in a nonaerated system, 300 days were required. The combination of aeration and high temperature (122°F) can destroy Salmonella, E. coli, fecal Streptococci, and Cryptosporidium oocysts in cattle manure in as little as 24 hours. [31] The costly nature and the reduced effectiveness of aeration systems during cold weather make them a poor choice for colder climates.

Anaerobic digesters. Anaerobic digesters have been primarily used for manure stabilization and odor control. They have also been shown to reduce E. coli, Salmonella typhimurium, and Yersinia enterocolitica in the digester slurry. At a digester temperature of 95°F, 90% reduction of these bacteria required less than three days. Anaerobic digestion was not as effective against Listeria monocytogenes and Campylobacter jejuni.[32] Many livestock producers already utilize anaerobic manure treatments in their operation. Farms that generate solid waste can incorporate composting. There is growing interest in the use of anaerobic methane digesters for manure treatment. Higher capital investments are required for aeration or anaerobic digester systems, but benefits beyond pathogen control (odor control and energy generation) may justify the additional cost.

Chemical Treatment of Manure

Chlorine. Chlorine is a method of disinfection commonly used for drinking water.Chlorine is very effective against bacteria but less effective against viruses and protozoa. Unfortunately, the high organic matter found in manure substantially inhibits the effectiveness of chlorine.  Additionally, chemical reactions between chlorine and organic matter produce toxic and carcinogenic by-products.

Lime stabilization. Lime stabilization of animal slurry has been used to reduce odor and pathogens before land application. The advantages include low cost of lime, easy disposal of treated slurry, and reduction in soil acidification. However, there may be some additional costs to consider such as labor to mix and haul the lime.

Ozone. Ozone is a powerful oxidizing agent and very effective at killing bacteria. E. coli counts were reduced by 99.9% and total coliforms decreased 90% after treatment with ozone.[33] However, organic materials found in animal waste interfere with ozonation and therefore a pretreatment such as solids separation would be needed for an effective ozonation process.

Ultraviolet light (UV) irradiation. Ultraviolet light irradiation destroys the DNA and RNA of pathogens. There are no residual compounds present after UV disinfection and the nutrient content of manure is not affected by UV exposure. Viruses are more resistant to UV treatment than bacteria and protozoa.

Pasteurization. Pasteurization of manure requires that a temperature of 158°F be maintained for 30 minutes. This would be cost-prohibitive on most livestock operations unless it occurred during composting or anaerobic digestion.

While effective in reducing pathogen levels in stored manure, most chemical treatments are not economically feasible for small to mid-sized livestock producers. Lime stabilization may be the only chemical treatment that could be implemented economically on small or mid-sized farms. However, larger producers may find chemical treatments such as ozone an attractive alternative to current manure management practices.

Pathogen reduction - land application

Land application is a critical period in manure management. Pathogens from animal waste can threaten humans who are exposed to runoff, have direct contact with manure, or consume contaminated food or water. Application rate and seasonal conditions are important factors contributing to the transfer of pathogens from lands where manure has recently been applied to nearby surface water.

Risk of pathogen transfer to the food chain increases with land-application of fresh manure compared with stored manure because there is no storage or treatment period to decrease pathogen numbers.[34] Typically, bacteria are highly susceptible to UV light and drying that naturally occur following surface application of manure to cropland. Pathogen numbers have been reduced by UV exposure and natural drying of manure on the soil surface. [35] Delaying incorporation for even one week significantly reduced pathogen survival following manure application.[36] Immediate incorporation of manure will increase the total time that manure-borne pathogens remain viable in the soil after application.[36] However, leaving manure on the soil surface increases risk for; pathogen transmittal through flies or vermin, surface runoff and contamination of water sources after heavy rainfall, as well as odor and gas emissions from the field.[36]

Runoff poses the greatest risk for pathogen transfer from manured land to surface waters. Runoff into tile lines or surface fractures in Karst soils can contaminate ground water. Production practices that reduce or eliminate runoff of manure-contaminated water will ultimately reduce pathogen transfer. Calibration of application equipment and application at recommended rates based on crop nutrient needs is critical. Manure application rate is positively correlated with indicator organisms for pathogenic viruses.[37] Higher levels of indicator organisms were found in soils where manure was applied at twice the recommended level compared to soils where manure was not applied.[36] These high levels persisted for 143 days after manure application.[37] Injection or incorporation of manure also decreases runoff potential.[37,38] Avoid application when ground is frozen because this increases the likelihood of manure runoff into nearby waters during spring snow melt. Pathogen survival in manure and soil is enhanced at low temperatures [39], increasing the risk of transport of viable pathogens in surface runoff from winter-applied manure.


The practices described above can aid producers in reducing pathogen transfer from their operations. Producers need to determine which BMPs or combinations of BMPs are economically feasible for their operations.

Some of the BMPs described in this bulletin are easily implemented and economically feasible for livestock operations of all sizes. Best management practices that are consistent with good animal husbandry to reduce animal stress should be implemented on every farm. Livestock operations of all sizes need to control runoff and leaching from stockpiled manure and open lots. Many producers already use biological treatments such as anaerobic storage in deep pits and composting that significantly reduce pathogen survival in manure.

Diet modification, installation of vegetative filter strips, elimination of livestock access to open water, changes in animal housing facilities, and use of lime to treat manure may be economical for some producers and should be evaluated on a case-by-case basis. Other practices such as aeration of stored manure, anaerobic digesters, and use of chemical treatments such as chlorine, ozone, UV light, and pasteurization may not be economically feasible for small to mid-sized producers. Large-scale producers may be better able to utilize this type of BMPs.

Best management practices checklist

Good husbandry practices

___ Vaccinations

___ Adequate access to feed and water

___ Adequate space allowance

___ Appropriate temperature for age of animal

___ Adequate ventilation

___ Biosecurity protocol enforced on farm


___ Animals housed on slotted floors

___ Use of antimicrobials to treat disease only

___ Use of antimicrobials to treat disease only

___ Use of organic acids in diet

___ Use of direct-fed microbials in diet

___ Use of yeast extracts in diet

___ Feeding coarsely ground diet

___ Feeding meal diet

___ Use of vegetative filter strips to treat runoff

___ Runoff and leaching controlled from stockpiled manure

___ Runoff and leaching controlled from open lots

___ Clean water diversions installed around open lots

___ Livestock access to streams, rivers, ponds, and lakes eliminated or reduced

___ Anaerobic lagoon or deep pit used for manure storage or treatment

___ Composting used for manure storage or treatment

___ Aeration used for treatment of stored manure

___ Anaerobic digestion (with or without heating) used for manure treatment

___ Chlorine used for manure treatment

___ Lime stabilization use for manure treatment

___ Ozone used for manure treatment

___ Ultraviolet light used for manure treatment

___ Pasteurization used for manure treatment

___ Equipment calibrated before land application of manure

___ Manure applied at recommended rates for crop nutrient removal

___ Manure injected or incorporated immediately following land application

___ Manure not applied during winter months


Resources for additional information

University of Minnesota Extension Manure Management and Air Quality

Livestock and Poultry Environmental Stewardship

National Livestock and Poultry Environmental Learning Center

Minnesota Pollution Control Agency

Midwest Planning Service

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Condensed by Milkproduction.com staff from Minnesota Extension Bulletin M1211 2007