Disinfection Selection and Use

Choosing a disinfectant is a complex process. There is no one best product for all situations. Before deciding on a product to use, answer the questions below to select a disinfectant that best suits your needs. Some disinfectants are effective for routine disinfection at the farm or veterinary clinic level, while others are necessary for outbreak situations.

The health and safety of personnel and animals that may be exposed to disinfectants is always an important consideration.

Physical hazards:

  • Slippery floors
  • High pressure sprays
  • Steam
  • Flames
  • Dust

Biological hazards:

  • Exposure to zoonotic diseases.
  • Cleaning and disinfection in contaminated areas.
  • Sweeping, scraping and blowing actions may disperse disease agents.
  • Inhalation, ingestion and direct contact with disease agents.

Chemical hazards:

  • Exposure to chemical irritants, causing eye, skin or respiratory issues.

Prepare a Sanitation Program

  • Decide who will manage the sanitation process.

    This includes training employees, ordering supplies, frequency (immediately after use, daily, weekly, monthly), and maintaining sanitation stations.

  • What are the disease risks you are concerned about?

    Where on the farm are the risks located? Is there a recurring disease issue that could be controlled by identifying the source(s).

  • Learn how different diseases are transmitted.

    What may be brought in by visitors, arrive with new animals or passed to livestock by wildlife. Is a disease spread by aerosols, ingestion, insects or close contact between animals, and what is needed to break the cycle?

  • What are the conditions under which a sanitation product will be used?

  • What is the type of surface you want to disinfect?

  • Choose the correct product.

    Products that are used for daily sanitation may be different than what you need to use when a disease is already present.

  • Know what the hazards and safety precautions are with the use of sanitation products.

    Personal protective equipment (PPE) will be needed, and the level of protection required, depending on the product. This information can be found in the product's Material Safety Data Sheet (MSDS).

  • Will a quality control process be in place to make sure sanitation is being done correctly?

    Look at boot bottoms, check vehicle tires, create a line of separation, employee compliance with the process, etc.

Other Sanitation Considerations

Most disinfectants won't work if the surface to be disinfected isn't clean before applying the disinfectant.

  • Organic materials such as soil, plant debris (e.g., straw), milk, blood, pus, and manure inactivate some disinfectants or protect germs from the disinfectant's active ingredients.
  • Chlorine-based products are especially subject to this problem.
  • Wash boots, equipment, or housing areas first with water and detergent.
  • Use steam and high-pressure washers to clean porous surfaces.

Disinfectants vary considerably in their activity against the assorted germs—bacteria, viruses, fungi and protozoa—associated with livestock.

  • Plain vinegar (4% acetic acid) will readily kill the foot and mouth disease virus, but is not effective against Mycobacterium avium paratuberculosis (MAP), the cause of Johne's disease.
  • Most commonly used disinfectants are not active against bacterial spores, which are the environmentally hardy life form of the germs that cause tetanus, blackleg, botulism, and anthrax.

It is important to select a disinfectant that will be active across a wide spectrum of germs under the conditions in which it will usually be used.

  • Check the pH (acidity or alkalinity) of your water. Hard water can reduce or destroy the activity of some disinfectants.
  • Use the recommended water temperature for dilution or maintain at the recommended ambient temperature to ensure optimal activity.
  • Know the shelf life of the chemical or the age of the mixture. Some lose activity quickly after being diluted.
  • Record when you mix each solution of disinfectant and refresh regularly. A solution that has been contaminated by organic material like manure, will have decreased effectiveness.
  • Wear protective equipment if indicated. Some chemicals, especially at full strength, may be toxic or cause damage to skin, clothing, or environmental surfaces.

Disinfectants must have sufficient contact time with the surfaces to allow them to kill the germs.  A quick splash of a dirty boot in a footbath will not accomplish anything except to give a false sense of security.

  • The required contact time varies with the product and the germ.
  • Allow sufficient contact time for the disinfectant to do its job.
  • Follow label directions closely and do not mix different classes of disinfectants.

Disinfectants are not to be applied to animals directly, unless labeled for such use.

  • Consult the label to make sure there are no warnings against using them around feeders and in animal quarters.
  • Rinse disinfectants off after the appropriate amount of contact time if animals will have contact with the disinfected surfaces.

Disinfectants vary in their toxicity to the environment.

  • Follow directions for disposal to prevent environmental contamination.
  • Antimicrobial agents used on the environment are regulated as pesticides by the Environmental Protection Agency (EPA).

Characteristics of Selected Disinfectants

This table provides general information for each disinfectant chemical class. Antimicrobial activity may vary with formulation and concentration. Always read and follow the product label for proper preparation and application directions.

+ = effective;   ± = variable or limited activity;  = not effective;  a - slow acting against nonenveloped viruses (e.g., norovirus)

*Disclaimer: The use of trade names serves as examples and does not signify endorsement of a product.

Disinfectant CategoryAlcoholsAlkalisAldehydesOxidizing AgentsPhenolsQuaternary Ammonium Compounds
Halogens: ChlorineHalogens: IodinePeroxygen Compounds
Common Active Ingredientsethanol, isopropanolcalcium hydroxide, sodium carbonate, calcium oxideformaldehyde, glutaraldehyde, ortho-phthalaldehyde,sodium hypochlorite (bleach), calcium hypochlorite, chlorine dioxidepovidone-iodinehydrogen peroxide/ accelerated HP, peracetic acid, potassium peroxymonosulfateortho-phenylphenol, orthobenzylpara-chlorophenolbenzalkonium chloride, alkyldimethyl ammonium chloride
Sample Trade Names*Synergize®Clorox®, Wysiwash®Rescue®, Oxy-Sept 333®, Virkon-S®One-Stroke Environ®, Pheno-Tek II®, Tek-Trol®, Lysol®Roccal-D®, DiQuat®, D-256®
of Action
Precipitates proteins; denatures lipidsAlters pH through hydroxyl ions; fat saponificationDenatures proteins; alkylates nucleic acidsDenatures proteinsDenatures proteinsDenature proteins and lipidsDenatures proteins; disrupts cell wallDenatures proteins; binds phospholipids of cell membrane


and Surface


  • Fast acting
  • Rapid evaporation
  • Leaves no residue
  • Can swell or harden rubber and plastics
  • Slow acting
  • Affected by pH
  • Best at high temps
  • Corrosive to metals
  • Severe skin burns; mucous membrane irritation
  • Environmental hazard
  • Slow acting
  • Affected by pH and temperature
  • Irritation of skin/ mucous membrane
  • Only use in well ventilated areas
  • Pungent odor
  • Noncorrosive
  • Fast acting
  • Affected by pH
  • Frequent application
  • Inactivated by UV radiation
  • Corrodes metals, rubber, fabrics,
  • Mucous membrane irritation
  • Stable in storage
  • Affected by pH
  • Requires frequent application
  • Corrosive
  • Stains clothes and treated surfaces
  • Fast acting
  • May damage some metals (e.g., lead, copper, brass, zinc)
  • Powdered form may cause mucous membrane irritation
  • Low toxicity at lower concentrations
  • Environmentally friendly
  • Can leave residual film on surfaces
  • Can damage rubber, plastic; non-corrosive
  • Stable in storage
  • Irritation to skin and eyes
  • Stable in storage
  • Best at neutral or alkaline pH
  • Effective at high temps
  • High concentrations corrosive to metals
  • Irritation to skin, eyes, and respiratory tract
PrecautionsFlammableVery causticCarcinogenicToxic gas released if mixed with strong acids or ammoniaMay be toxic to animals, especially cats and pigs
Factors Affecting EffectivenessInactivated by organic matterVariableInactivated by organic matter, hard water, soaps and detergentsRapidly inactivated by organic matterRapidly inactivated by organic matterEffective in presence of organic matter, hard water, soaps, and detergentsEffective in presence of organic matter, hard water, soaps, and detergentsInactivated by organic matter, hard water, soaps and anionic detergents
  • Bactericide - kills or inactivates bacteria.
  • Virucide - kills or inactivates viruses.
  • Fungicide - kills or inactivates fungi.
  • Tuberculocidal - kills Mycobacterium tuberculosis, an acid fast bacteria which is generally more difficult to kill than most bacteria.
  • Sporicide - kills all microorganisms including bacterial endospores, a very resistant form of certain microorganisms.

Chart source: The Center for Food Security and Public Health (PDF)

Disinfection Resources

Cleaning and Disinfection Tips

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