Cleaning and Disinfecting

Cleaning and disinfection of people, equipment, animals and material entering a farm are important for protecting animal health. Routine farm operations such as feeding, milking, animal handling, medical treatments, contact with vehicles and equipment, interactions with service providers and outside visitors, are all possible contact points for the transfer of diseases and pests. Entry and exit routes from buildings and a property have the potential to bring and take away disease-causing organisms.

Some form of cleaning and disinfection should be done before people and their clothing, equipment, supplies, and larger items such as vehicles and heavy equipment cross from dirty or low risk (the farm perimeter) to clean or higher risk areas (animal housing, animal transport vehicles, feed, water and other items that come into close contact with livestock).

Establish a controlled access zone, which is a transitional space with reduced contamination between the farm perimeter and where livestock are housed. A farm may want to require that all organic material be cleaned from boots, clothing, equipment and vehicles before entering this area. Personnel may be required to shower and wear clean outerwear prior to arrival, or clean and disinfect footwear and wear site-specific outerwear prior to entering the buffer area. A Line of Separation dividing dirty from clean may serve as a convenient location to reduce, remove, inactivate, eliminate, or destroy disease-causing organisms prior to crossing into livestock areas.

Basic Cleaning and Disinfection Considerations

Sanitation practices of cleaning and disinfection are intended to stop the transmission of infectious agents. It involves inactivating or destroying disease-causing microorganisms on the farm premises, equipment, vehicles and personnel.

  • Cleaning - removes germs, dirt and impurities from surfaces or objects. Cleaning works by using soap (or detergent) and water to physically remove germs from surfaces. This process does not necessarily kill germs, but by removing them, it lowers their numbers and the risk of spreading infection. Areas that are determined to be a low risk for disease transmission may only require cleaning.
  • Sanitizing - lowers the number of germs on surfaces or objects to a safe level, depending on the requirements. This process works by either cleaning or disinfecting surfaces or objects to lower the risk of spreading infection.
  • Disinfecting - kills germs on surfaces or objects. Disinfecting works by using physical or chemical agents to kill germs on surfaces or objects. This process does not necessarily clean dirty surfaces or remove germs, but by killing germs on a surface after cleaning, it can further lower the risk of spreading infection.
  • Sterilization - kills all forms of microbial life. Steam under pressure, dry heat and liquid chemicals are used in this process.

The life span of infectious agents/disease-causing microorganisms varies. Many viruses and bacteria have short life spans outside of a host, from hours to days. However, others can live a long time with the right environmental conditions for them (anthrax, foot and mouth disease). Removing organic material such as dirt, feed and manure is the first step in the sanitation process, no matter if you are cleaning boots, floors, buckets, water troughs, equipment or vehicles.

Other Factors Affecting Cleaning and Disinfection Success

Sanitation should be a part of your every day biosecurity procedures. Cleaning and disinfecting does not have to be complicated or get in the way of work to be done. Sanitation is part of that work. This website offers resources to help you build a biosecurity plan for your livestock operation. Sanitation is an important part of the plan, for the prevention of diseases in your herd, and to know what to do when diseases are present.

The general order for the sanitation process is:

  1. Dry clean (remove solids)
  2. Wet wash
  3. Rinse
  4. Dry
  5. Disinfect

Cleaning and Disinfection Steps

  • Surface Type

    Porous, uneven, cracked, or pitted surfaces, especially wooden surfaces and earthen floors, are difficult to disinfect. Some chemical disinfectants may also be incompatible with or corrosive to certain materials or surface types (e.g., metal, rubber, plastic). Due to the construction and presence of uneven surfaces on equipment, equipment cleaning and disinfection procedures can be difficult. Heat may be a more effective method for inactivating the virus on these surfaces.

  • pH

    The activity of some disinfectants is also affected by pH because it changes the degree of ionization of a chemical disinfectant, thereby impacting its effectiveness. For example, the effectiveness of phenols, acids, and hypochlorites are decreased as pH increases; in contrast, quaternary ammonium compounds have greatest efficacy as pH increases.

  • Water Quality

    The water quality used when diluting and applying detergents and disinfectants is important. Water hardness can inactivate or reduce the effectiveness of certain disinfectants (e.g., quaternary ammonium compounds). Be sure to consider any standing water or other water sources (e.g., rainfall) present that may immediately dilute the disinfectant during application.

  • Temperature

    Some disinfectants are less effective or ineffective at low temperatures (e.g., cold weather conditions). Additionally, disinfectant solutions may freeze outdoors under low temperature conditions. When possible, buildings and equipment should be heated to approximately 68℉ (20℃) when applying disinfectants. Elevated temperatures can aid in microorganism destruction; however, higher temperatures can also accelerate decomposition or evaporation of a disinfectant, thereby reducing the necessary contact time and efficacy. Excessive heat may also damage items being disinfected.

  • Weather

    Inclement weather conditions (e.g., cold, rain, wind) may also make these procedures difficult.

Line of Separation

A Line of Separation (LOS) or the clean/dirty line is an important part of both sanitation and traffic control in any biosecurity plan and procedures. It is a line, physical or imagined, that separates the clean from the dirty. The LOS could be a line or a barrier such as a bench to cross that separates areas. It is site-specific and may be set up at the farm level (the farm perimeter), the barn level, or somewhere in between.

Line of Separation diagram

Example of a Danish Entry Set Up for Crossing the Line of Separation. Outside entry is from the left side.

Cleaning is done before disinfecting. Cleaning can remove up to 90 percent of infectious agents. It improves the effectiveness of disinfectants.

Dry Cleaning - remove contamination such as soil, manure, bedding and feed.

  • Moisten the area to control dust.
  • Air blowers should not be used because of the risk of infectious agent spread.

Washing - the most overlooked step.

  • Use of detergents - a detergent disperses and removes organic materials from surfaces.
  • Washing reduces infectious agents and removes oil, grease, and body fluids such as blood.
  • Shut off, remove or cover electrical equipment before washing.
  • High pressure water is very effective but avoid using it if you know that a highly infectious or zoonotic disease is present.
  • Warm to hot water should be used.
  • Scrubbing may be necessary.
  • Steam is effective for cracks, crevices and pipework.

Rinsing - rinse with cold water at low pressure.

  • Surfaces should be inspected to make sure there is no beading water.

Drying - surfaces should be allowed to dry completely,  overnight if possible

  • Fans can be helpful in drying.

Source: Center for Food Security and Public Health presentation, Cleaning and Disinfection Overview, at

Clean and sanitize before crossing the line of separation. Exclude vehicles from crossing the line of separation. For carcass and manure disposal, keep disposal service vehicles outside the line of separation.

Whether you’re part of a large commercial enterprise or keep farm animals as a hobby, using a line of separation will protect animal health. Determining where the line of separation is will help with siting sanitation stations as well. More about setting up a Line of Separation can be found in the Traffic Control section of this site.

Disinfection Selection and Use

Tips for how to choose and use disinfectants, with a chart listing their characteristics.