Disease Eradication

Decontamination and Disinfection

Proper decontamination and disinfection procedures can help producers minimize the costs associated with animal sickness, mortality, and weight loss, and reduced productivity. Furthermore, costs associated with personal protective gear, disinfection, labor, and carcass disposal can be justified if procedures limit the spread of disease or subsequent contamination of other animals.

Decontamination and disinfection (or cleaning and disinfection as it is commonly called) can be important components of the response and recovery phases during a livestock disease outbreak or disaster. Reducing human exposure to contaminants and pathogens will enable responders to more effectively address the needs of animals during a disaster. It is also important that premises are clean and safe for animals that survive the incident.


Decontamination is the necessary first step in the process to remove harmful substances from people, vehicles, buildings, equipment, land, and animals to prevent or mitigate adverse health affects. It is tmost frequently used on farms in disease outbreaks.

Decontamination of humans involves removal of contaminated clothing, followed by thorough washing and inactivation of the substance (if possible). In emergency situations, decontamination is primarily handled by the hazardous materials team of the fire department.

During an emergency, the agent causing harm to animals may be unknown. Contaminants on animals can easily be transferred to people who are not wearing appropriate Personal Protective Equipment (PPE). Because of the possibility zoonotic pathogens, lay personnel should not touch or approach contaminated animals until cleared to do so by officials.

Once the causative agent of an animal emergency has been identified, one of the first priorities should be to determine if it is hazardous to people. Veterinarians (for animal diseases) and fire department personnel (for hazardous materials) can provide information to assess the threat to humans. The following lists contain factors to be considered once a contaminant has been determined to be hazardous or nonhazardous to humans. Click on each term for more information.

Hazardous to humans

  • If the contaminant is deemed hazardous to public health, food animals may be condemned and not allowed into the food and fiber chain. Special equipment may be needed to safely decontaminate animals, including respirators because of dangerous fumes. Responders should have proper training in the equipment used for decontamination.
  • If water run-off from the decontamination process is unsafe for sewer, septic, and the environment, alternative disposal routes for the contaminated water must be established. Thoroughly washing a 1000 pound horse uses approximately 1200 gallons of water, so the amount of run-off water is significant.
  • Because the water supply may be contaminated (such as during a flood), decontamination should be conducted with potable (drinkable) water. The response will require enough water for decontamination and the future drinking needs of surviving animals.
  • In many instances, decontamination may not be practical or safe, as with topical chemical contamination of a beef cattle herd.

Non-hazardous to humans

  • This could involve a biological agent that is still highly contagious to other animals. If the disease must be reported to regulatory veterinarians, the local veterinarian gets guidance from state and perhaps federal veterinarians regarding decontamination and disinfection.
  • For foreign animal diseases, federal veterinarians have responsibility.
  • Even though an agent is non-hazardous to humans, people can mechanically transmit disease agents to other animals during decontamination. Additionally, animal facilities and equipment must be decontaminated and disinfected to prevent re-contamination of animals.

For non-zoonotic disease outbreaks common to the US, routine decontamination of animals and premises should be performed. Decontamination is a common practice on the farm, particularly when animals have cases of diarrhea or respiratory disease. Wash and wipe clean all discharges using disposable towels to limit disease spread.

Precautions should be taken to avoid carrying infectious agents to other animals on hands, boots, coveralls, pitchforks, or tractor wheels. Veterinarians can advise farmers on proper disease prevention precautions in the midst of a disease outbreak, and USDA and Cooperative Extension Service resource materials are also available.

On large poultry and swine units, personnel routinely take a complete shower and change clothes prior to entering the barn, and follow the same procedure when exiting the barn. This practice minimizes the potential spread of infectious diseases between barns and other animals. While this is not practical for many operations, use of protective clothing, properly maintained foot baths or disposable boots, hand washing, controlling human and animal traffic, and routine disinfection can be an effective response to reduce the impact of an infectious disease outbreak.

During a routine disease outbreak, protective clothing, such as coveralls and disposable gloves and boots, should be changed between animals and/or barns. Hand washing following contact with each sick animal is extremely important, even when disposable gloves are worn. Washrooms should ideally provide a source of warm running water, liquid hand soap, and disposable paper towels with an available waste basket. Avoid touching the faucet with clean hands and consider using a paper towel to turn off the water. Bar soaps should be avoided since they can harbor bacteria between uses; cloth towels used for drying hands can readily spread germs. Bactericidal hand soaps are not necessary since the act of thorough hand washing is adequate.

Alternatively, 62 percent ethyl alcohol hand gels and foams are germicidal if applied to hands free from excessive dirt or other organic matter. Users should be aware that ethyl alcohol preparations are flammable.

After thorough cleaning and decontamination of surfaces (e.g., stalls, equipment, tires) in response to a biological incident, proper disinfection is required. Disinfection is the use of physical or chemical processes to kill or significantly reduce pathogens (viruses, bacteria, fungi, molds, parasites, etc.). An example of a physical process is the use of autoclaves that utilize high heat and pressure to sterilize surgical instruments. An example of a chemical process would be the use of a bleach solution to reduce microbial populations on previously cleaned surfaces.

Decontamination Methods

Procedures used to reduce the level of infectious agents are divided into sterilization, and the application of disinfectants, sanitizers and antiseptics.

Sterilization is a process that kills all microorganisms, including spores, which is usually accomplished by autoclaving (using steam to generate high temperature and pressure). This is commonly done with surgical instruments, but it is not practical or safe for use on the farm.

Sanitizing uses chemical or physical methods to establish surface conditions favorable to health but does not have the killing power of disinfection. Sanitizing table tops and washed eating utensils in restaurants are examples of sanitizing; strong disinfectants are not used, but sanitizing agents reduce contamination to an acceptable level of public health.

Antiseptics are chemicals that inhibit growth or kill microorganisms on living tissue, such as povidone iodine or chlorhexidine applied to umbilical stumps or used to scrub skin where a surgical incision will be made.

Chemical disinfectants are commonly used against biological agents on farms. In order for disinfectants to be effective, surfaces must first be thoroughly cleaned to remove organic matter and biofilms. Organic matter (feces, blood, secretions, dirt, etc.) interferes with the ability of disinfectants to work and can render some chemicals totally useless.

Disinfection is often associated with cleaning stalls where a contagious animal was housed. However, disinfection also applies to livestock trailers, farm vehicles, farm equipment (pitchforks, rakes, shovels, etc.), and clothing people wear when handling infected animals.

No one disinfectant kills all pathogens on all surfaces. Disinfectants are chemicals and must be used in conjunction with manufacturer's directions and with the use of proper PPE.

Never mix disinfectants. Mixing bleach with ammonia can produce highly toxic chlorine gas. Disinfectants labeled for use on farms and equipment should never be used on hands or any living tissue.

Anyone using a disinfectant should thoroughly understand the proper dilution, mixture, application rate, and PPE to be used. Emergency first aid directions (skin, eye, respiratory or ingestion exposure) should also be understood as any effective disinfectant is a potentially hazardous chemical.

Disinfection protocols are highly variable depending on the livestock and facilities involved. In general, the following steps should be performed for proper decontamination (cleaning) and disinfection:

  • Remove all loose objects (water buckets, hay nets, etc.) from the area.
  • Properly dispose of all bedding and other organic material that can be removed.
  • Wet the surfaces with water from top to bottom beginning with surfaces most distant from drains or downward slope.
  • Scrub all surfaces with a detergent and water to remove organic matter (feces, urine, blood, dirt, etc.).
  • Rinse surfaces from top to bottom, starting at the most distant point from the drain or downward slope.
  • Inspect surfaces, corners, drains, and other areas for remaining organic material; a second washing with detergent may be necessary.
  • Squeegee surfaces to remove excessive water.
  • While wearing appropriate PPE, dilute a disinfectant (recommended by the veterinarian) to its proper concentration and apply it to surfaces, following label instructions. Consult the instructions on whether the chemical is to dry on walls or should be rinsed off after a certain amount of time.
  • Clean and disinfect any equipment that is returned to the stall or will be used in the stall.
  • Be aware that walking from an uncleaned area (aisle ways) into a cleaned stall can easily recontaminate that area.

With an ever-expanding list of disinfectants available to animal owners, making an intelligent choice can be difficult. Here are some questions to ask when selecting an appropriate disinfectant:

  • Is the disinfectant approved by the U.S. Environmental Protection Agency?
  • Is the disinfectant labeled for use with the species of animals involved?
  • Is the disinfectant able to kill the pathogens of concern and is it effective in the presence of organic matter? For example, some disinfectants cannot kill rotaviruses but are effective against many other pathogens. Bleach, used in household concentrations, is ineffective in the presence of organic matter.
  • Is the disinfectant useful with the hardness of water on the farm?Do personnel need specialized training or specialized PPE for safe use of the disinfectant?
  • Is the disinfectant corrosive or harmful to the materials to which it will be applied? If so, is the amount of damage acceptable?
  • Is the disinfectant economical to use in farm situations? Is it biodegradable?
  • Are there any local, state, or federal regulations about using the disinfectant (which may be a concern with non-biodegradable products)?

Veterinarians are often knowledgeable about suitable disinfectants, as are infectious disease specialists at universities and physicians. These professionals can provide guidance on products most suitable for a particular situation and answer many of the questions above.

Animal diseases that require PPE often result in animal deaths. Mortality losses are common at low levels in any animal agriculture operation. Producers should have plans in place to accommodate the carcasses resulting from these losses. In an incident involving a natural disaster or CBRNE agent(s), the number of carcasses can quickly exceed the capacity of a routine operation. Carcass disposal is critically important during the response and recovery phases of animal emergency management. During an emergency, some regulations that normally limit carcass disposal options may be waived.

Euthanasia and Mass Depopulation

During an animal health emergency, the euthanasia of large numbers of animals (or mass depopulation) may be necessary. Humane treatment of the animals and use of approved methods are essential for this response activity.

Euthanasia/Mass Depopulation
  • Most commonly used for highly contagious disease outbreaks to minimize the spread of disease.
  • Also used to end the suffering of injured or ill animals following a natural disaster.
Goals of Euthanasia
  • Humane treatment of the animals at all times.
  • Use of an acceptable euthanasia method that is quick, efficient and humane.
  • Minimize negative psychological impact on animal owners and caretakers, responders and the public.
  • Prevent disease spread.
  • Prevent adulterated animal products from entering food chain.
  • Follow guidelines. Method selected should follow current recommendations and guidelines:
    • AVMA Guidelines on Euthanasia
    • OIE Terrestrial Animal Health Code
    • FAD PReP Guidelines: Mass Depopulation and Euthanasia
  • Method selection will depend on:
    • Species and number of animals involved.
    • Level of handling and restraint required.
    • Technical skill of responders.
    • Cost.
    • Potential for chemical residue.
    • Personnel safety.
  • Animal welfare
    • Humane treatment.
    • Quickly render unconscious.
    • Minimize stress and pain.
  • Skilled personnel needed.
  • Public perception.
  • Laws for acceptable methods vary with state.
Euthanasia Methods

Livestock euthanasia diagram

Source: Center for Food Security and Public Health

The following overviews some of the methods for humane euthanasia of animals. Consult appropriate euthanasia guidelines (listed at the end) for specific methods for a particular species.

  • Physical Euthanasia Methods
    • Quick, painless, humane and practical
    • Requires technical skill and highly trained personnel
    • Methods:
      • Captive bolt or gunshot
      • Electrocution
      • ┬áCervical dislocation, decapitation
      • Adjunct physical methods:
        • Exsanguination, pithing
  • Chemical Euthanasia Methods
    • Most often used for pet livestock and companion animal species; usually impractical for mass depopulation of livestock
    • Methods
      • Injectable drugs: barbiturates and barbituric acid derivatives
      • Gas: anesthetic gases, carbon monoxide, carbon dioxide
      • Adjunct chemical methods:
        • Potassium chloride, magnesium salts
  • Manually applied blunt trauma.
  • Injection of any chemical not labeled for use as a euthanasia agent.
  • Injection of air into a vein.
  • Electrocution with a 120 or 220 volt electrical cord.
Confirmation of Death
  • Death must be confirmed on each animal.
  • Parameters:
    • Lack of heartbeat.
    • Lack of respiration/breathing.
    • Lack of corneal reflex (no movement of the eyelid when the cornea/eye surface is touched lightly.
    • Presence of rigor mortis (stiffening of the body after death.
  • A back-up euthanasia method should be ready!
Personnel Performing Euthanasia Activities
  • Training
    • Animal handling and restraint.
    • Approved euthanasia method to be used.
    • Safety issues.
    • Personal protective equipment required.
    • Biosecurity measures to follow.
    • Cleaning and disinfection procedures needed.
  • Safety
    • Be aware of risk of injury based on animal species, size, weight, and temperament.
  • Psychological Impact
    • All parties affected.
    • Responders performing euthanasia.
    • Animal owners/caretakers, families.
    • Community.
    • Compassion fatigue.
    • Post-traumatic stress disorder (PTSD).
    • Counselors and mental health experts should be available.

Carcass Disposal

Even after death, diseased or contaminated animals can pose a threat to animal and human health unless they are properly disposed. Allowing carcasses to decompose naturally in a remote corner of the farm should be avoided due to health, environmental, and legal concerns.

Local, state, and national regulations govern animal disposal procedures. Local ordinances may prevent animal burial. Environmental agencies may issue citations and/or fines to individuals who bury animals near waterways due to potential water contamination. In addition, they may determine burning animal carcasses is not an appropriate method of disposal because of the resulting air pollution and potential disease spread. Producers must consult their local authorities about legal and proper disposal methods; some options will be discussed in this section.

Large numbers of animals can also be involved in disasters that do not involve disease or contamination, such as the Rocky Mountain/Great Plains States blizzards in the winter of 2006/2007. The freezing temperatures and four feet of snow decreased the urgency for immediate carcass disposal. However, a similar death toll in a southern state after a flood in mid-summer would present a much more urgent situation.

If local, state, or federal agencies become involved during an emergency response, they may dictate how carcasses will be handled, especially in disease or contamination situations where the food supply is at risk.

During an agricultural emergency that results in animal deaths, a rapid assessment to determine how many animals are involved (including the total poundage) is needed. The numbers can vary from a few backyard chickens to thousands of swine or cattle. Determining the scope of the disaster can be challenging, especially when it is unknown how many animals might eventually die as the incident progresses.

Whenever possible, carcass disposal on the farm using one of the approved methods to be discussed in this lesson is usually the best way to contain the disease or contamination to one area. A study of a 2002 avian influenza outbreak in North Carolina reported that transportation of diseased chicken carcasses to landfills helped spread the disease.

Specific locations on the farm should be identified for possible disposal sites if the geographic area is suitable. An accurate map of the farm can be critical in determining these sites. Important considerations that may determine whether on-farm carcass disposal is an option include:

  • Proximity to natural water and wells, soil composition, topography, and ability to use large equipment (e.g., sinkholes, inadequate roads).
  • Effects on neighbors (e.g., odor, perception).
  • Weather conditions that affect disposal options (e.g., resulting in frozen ground or flooded soil, which could preclude burial).

If vehicles are used to transport animal carcasses for off-site disposal, consider that:

  • Some pathogens remain viable in soil for extended periods of time.
  • Tire treads are filled with soil and manure on the farm.
  • Tires can effectively spread contaminants to another farm.
  • Rubber tires are porous and difficult to clean.
  • The entire undercarriage of the vehicle may be contaminated.
  • Merely driving a vehicle through a tire bath may not provide effective disinfection.
  • Fluids that spill from the vehicle can also be highly hazardous to animal and public health.
  • Vehicles used for transporting carcasses should have waterproof liners and tight fitting covers to reduce the possible spread of disease or other contaminants.

The first priority for disease outbreaks, especially ones that are highly contagious, is to keep the carcasses on the farm or within the exposed zone for disposal if at all possible. On-farm disposal reduces risk of pathogen spread and decreases the costs for transportation of animal carcasses.

It is always wise to speak with rendering personnel first to determine the cost of disposal and what animals they will not accept. For example, some renderers will not accept animals euthanized with veterinary euthanasia solution. As mentioned on the previous page, renderers have stopped accepting sheep or goat carcasses because of the risk of scrapie. State Departments of Agriculture can assist with locating renderers.

Multiple state and federal agencies inspect and work with rendering plants to ensure compliance with environmental regulations. Rendering plants must also ensure public health and safety. For example, the Food and Drug Administration enforces compliance with BSE regulations for rendered animal products to be used in animal feed.

The thought, smell, and sound of dead animals being burned are unpleasant and can be an emotionally devastating experience for the farm owner and responders. However, if depopulation of animals is deemed necessary, such as in the case of an extremely contagious foreign animal disease outbreak, incineration may be the only viable option.

Several considerations affect the feasibility of incineration as a carcass disposal option:

  • Local, regional, and national regulation.
  • Air pollution and potential pathogen spread.
  • Cost of large amount of fuel to burn animals.
  • Fire hazards.
  • Aesthetic concerns.

While disposal of carcasses on the farm can be a key factor in the management of serious disease outbreaks, when evaluating incineration as an option, geography and weather conditions such as drought, wildfire potential, high winds, rain, etc., also need to be considered.

Incineration can occur outside or in a fixed facility where the burning process is highly contained and out of public view, such as a crematorium. Crematoriums and carcass incinerators that hold larger animals are contained and strictly regulated. Most incineration units kill all pathogens except for prions, which are the cause of diseases such as BSE, CWD, scrapie, etc.

However, contained facility incineration may not be an expedient way to dispose of large numbers of carcasses. The factors associated with the transportation of carcasses must also be taken into consideration (e.g., disease spread, costs, distances) if there is no carcass incinerator on the farm.

Euthanasia Content Source
Center for Food Security and Public Health Just In Time Training. Euthanasia and Mass Depopulation During Animal Health Emergencies. Retrieved from http://www.cfsph.iastate.edu/Emergency-Response/Just-in-Time/15-Euthanasia-HANDOUT.pdf
Disease Eradication Content Source
Extension Disaster Education Network (EDEN). Animal Agrosecurity and Emergency Management. Retrieved from https://campus.extension.org/enrol/index.php?id=166


A livestock disease outbreak can be extremely stressful for a producer, the farm family, staff and others involved in the response.