Biosecurity practices: Facility cleaning and disinfection

Whether the issue is preventing disease or controlling an outbreak, the most important concept in biosecurity is facility cleaning and disinfection. All equipment should be cleaned and disinfected before and after use to ensure biosecurity.

Whether the issue is preventing disease or controlling an outbreak, the most important concept in biosecurity is facility cleaning and disinfection. Manure and organics removal are paramount, as many disease-causing organisms may be harbored in “dirt”. Additionally, effectiveness of disinfectants may be reduced by contamination with organic materials.

Effective cleaning is total cleaning. All equipment should be cleaned and disinfected before and after use to ensure biosecurity. Whenever possible, and particularly when a disease outbreak has occurred, an “all in, all out” system of animal movement should be employed.

A Process for Total Cleaning

  • Remove organic matter and manure:
  • Sweep top to bottom
  • Clean light fixtures, ceilings, all fans and heaters, louvers, lights and light bulbs, walls, feeders, doors and floors.
  • Scrape, scrub and clean all equipment completely
  • Remove all dirt, debris and manure


  • Disinfect ceiling, walls, curtains, slats, louvers, feeders, waterers, equipment, fencing, doors and floor.
  • Always clean and disinfect with products at the recommended dose; increasing doses of products will not improve efficacy.
  • All sprays should be applied at a minimum of 200 PSI ( range 200-600 PSI).

Work routine:

  • Cleaning personnel should use a systematic cleaning and disinfecting technique.
  • Start at the back of a building and work forward.
  • Start high and work low: ceiling, walls, floor.

Sanitizing the Water Supply

Don’t forget the water supply in your cleaning procedures!

  • Use medicators in line to apply disinfection.
  • Using an appropriate product, run the water through the system until disinfectant can be smelled at the last bleed out.
  • Allow water system disinfectant to remain in the system for at least 24 hours

Disinfectant Choices

A disinfectant should kill bacteria, viruses and fungus on contact. Remember that some harmful bacteria can protect themselves from harm by forming spores. Be sure to consider whether the disease you are trying to prevent or eliminate can form spores. Will the disinfectant you use kill spores?

Disinfectants are more effective with warmer application temperatures. Each 8 degree F drop below 65 degrees will reduce the effectiveness of most disinfectants by 50%. Pressure spray at 200-300 PSI for best effect.

Disinfectant Types

Halogens: iodine and chlorine

  • neutralized by organic matter
  • sunlight/UV decreases efficacy
  • effective in hard water

Cresylic acid

  • very effective against all infective agents
  • works on viruses and bacteria
  • good residual action
  • strong odor

Phenolic Acid

  • you get what you pay for
  • effective disinfectant
  • strong odor

Quaternary Ammonium Compounds

  • inactivated by organic matter
  • inactivated by hard water


  • good for cleaning
  • poor as disinfectants

General precautions for cleaners and disinfectants

Mixing of agents a BAD idea. Chemical reactions can occur that either neutralize products and make them less effective and/or produce toxic byproducts. Be safe - Read the label and follow all safety precautions. Remember, disinfectants are poisons.

In addition to being poisons, many of the compounds discussed above have the potential to cause serious harm to careless users. Read the MSDS (Materials Safety Data Sheets – these must be provided by the manufacturer, although sometimes you need to request them). Follow the product safety precautions listed on the MSDS. Maintain all OSHA labeling and standards.

Restarting a System After Cleanup and Disinfection

Don’t let all your hard work go to waste by letting malfunctioning equipment stress newly arrived animals! Remember that a vigorous, watery cleaning to eliminate infectious agents is potentially destructive to mechanical and electrical components.

  • Run all equipment
  • Check feeders and feed storage
  • Feed storage should be off the ground
  • Check air temperature
  • Make sure all electric circuits operate properly
  • Fix all light sockets and replace necessary light bulbs
  • Determine adequacy of lighting system
  • Check and adjust all clocks
  • Culture facility premises
  • Culture foot baths
  • Run all motors
  • Check all chains, pulleys and belts for correct tension and workability
  • Check all thermostats, humidity indicators and thermometers
  • Check all water lines for leaks and patency
  • Culture water
  • Discuss the importance of restart procedures with employees and any others involved
  • Document, document, document


Scott R.R. Haskell

Scott R.R. Haskell
4 articles

Director and a Professor at the Veterinary Technology Program at Yuba College.

Prior to this position Dr. Haskell has taught and/or done livestock disease research at the University of Minnesota, the University of Maine, University of Illinois, and the University of California. He is the primary editor of the recently published livestock disease textbook: Five Minute Veterinary Consult: Ruminant (2009-Wiley-Blackwell Publishing). Additionally he has worked extensively with international development projects in India, Bangladesh, Egypt, Moldavia, the Ukraine, Belarus, Romania, Guatemala, Mexico, and Haiti.

Dr. Haskell holds the BS, DVM, MPVM and PhD degrees from the University of California, Davis. He was a Visiting Scholar at the University of California, San Diego with research emphasis in microbial ecology. His professional specializations include pre-harvest food safety, biosecurity, concentrated animal feeding operations (CAFO’s), food safety antibiotic residue issues, HACCP, zoonotic disease transmission of E. coli O157:H7 and the environmental effects of manure microbial pathogen loading. 

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