Biosecurity: The importance of cleaning and disinfection

By Dr. Pablo Moreno, DVM

Neogen Corporation

Proper cleaning and disinfection of animal facilities is a critical part of any good biosecurity program.

An ideal program will reduce the number of pathogens to levels that are non-pathogenic for the animals housed in the facility. In a healthy animal, low levels of pathogens should have little clinical impact on an animal because of its natural defense mechanisms (both natural and acquired immunity).  However, the level of natural immunity varies with the age and condition of the animal and cannot be fully counted on to protect the animal against illness.

Biosecurity refers to a set plan or procedures for preventing the transmission of diseases into a facility and has numerous facets including proper cleaning and disinfection; preventing disease transmission from other animals (domestic or wild) and those transmitted via pests, humans or equipment; vaccination programs; facility layout; and animal movement.

In order to make it easier to create and adhere to a good biosecurity program, it helps to break it down into its components. In this post, I will focus on cleaning and disinfection as key components of a biosecurity program.

There are questions that should be answered when planning a cleaning and disinfection program:

  1. At what minimum do pathogens need to be kept at to prevent problems for the animals in the facility?
  1. How can we be sure that we are doing a good job when we clean and disinfect the facility?
  2. Do  we have a protocol to routinely evaluate our procedure?

Most of the time,  we assume our program is in compliance with our expectations. This is not because the farmer is not concerned about proper cleaning and disinfection procedures.  Farmers know biosecurity is important but sometimes programs are not completed for various reasons, such as time commitment  and labor cost.

The costs and risks associated with an ineffective biosecurity program and with not monitoring that program’s efficacy can be severe. For example, it often is difficult to see the real cost of a disease or disease outbreak. Disease can affect a farm economically by impacting feed conversion and number of animals sold at a premium. Likewise, the failure to recognize subclinical disease and the continuous effects of subclinical disease on performance may end up being more costly than an overt outbreak throughout a period of time.

Similarly, it is important to remember pathogens are becoming increasingly resistant to our efforts to eradicate them. Given this, it is important to follow the proper rotation of cleaners and disinfectants for each facility.

Lastly, it is important to recognize the source of the disease. For example, did the animals get sick from another animal or were they susceptible to a pathogen that existed on a contaminated surface?

Although each facility has unique needs when it comes to a good biosecurity program, some common threads and techniques should be present in all programs.


Pre-cleaning helps expose as much as of the surface to be cleaned as possible. This way, the chemicals that are going to be applied have a more concentrated effect on the surface.  Additionally,  pre-cleaning removes caked-on organic matter, which may be pulverized and aerosolized when high pressure water is used during the cleaning process. This aerosolization may then spread filth to areas that already have been cleaned.

Initial steps for cleaning facilities

  1. Remove all manure and empty all slurry gutters.
  2. Cut off the electrical supply. This is an important safety precaution.
  3. Disconnect all moveable equipment such as feeders and lamps, and open all inaccessible areas such as channels and fan boxes.
  4. Brush down and sweep out the feed dust and other debris.
  5. Drain and flush out the water system, bowls, nipples, water tanks, etc. and fill with a detergent sterilizer. Leave for two hours, then drain and then refill with water.


The idea of soaking is to soften all the dirt and debris to make the cleaning process easier while saving time and water.

  1. Soak the building completely, using sprinklers or high pressure water and leave for one hour.
  2.  Soak all moveable equipment and clean thoroughly.


The use of detergents facilitates the elimination of organic matter.  An effective cleaning eliminates more than 95 percent of the contamination and allows the disinfectant, which will be applied later, to penetrate more easily.

  1. Apply a cleaner from roof to floor using a foamer and applying with a horizontal movement.
  2. Let it sit for 15 to 30 minutes. This will give the cleaner time to act.
  3. Pressure wash the entire building using hot water or a steam cleaner.
  4. Visually check the building.
  5. Let it dry.  Fast drying of the building (immediately after disinfection) through at least 48 hours, is more efficient than a long downtime.


For a good disinfection, it is essential there is adequate contact time between the disinfectant and the surface.  It also is important farm personnel be prepared, trained and motivated to carry out this job.  All personnel working with disinfectants should be trained to use the correct dilution and adhere to all safety precautions.

  1. Disinfect the entire facility including all equipment and surroundings using a pressure washer or foamer.
  2. It is recommended that a second disinfection using thermo-fogging is performed.  This will ensure all areas of the building are reached including hard-to-reach corners.
  3. Heat and prepare the room for the next group of animals.

Parting thoughts

If a good cleaning and disinfection procedure is followed and the efficacy of the program is constantly monitored, either by using ATP measurement or bacterial enumeration, this will ensure a good cleaning and disinfection protocol. Also, monitoring the procedure on a routine basis will provide farmers with a clear idea when they should rotate disinfectant and cleaner products.

If possible, it is recommended to explore the installation of an automatic soaking system, the use of a detergent before pressure washing and use a foamer for disinfection. This reduces the operation’s cleaning and disinfection costs (mainly saving water and labor time).


 For Neogen’s cleaning and disinfecting products, click here.

For Neogen’s ATP monitoring products, click here.

Comments are closed.