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Four steps to effective cleaning and disinfecting

Cleaning and disinfecting are critical parts of all biosecurity programs. The goal is not to completely sterilize the environment, but rather to decrease the pathogen load significantly to a point where disease transmission does not occur. There are many important steps to any cleaning and disinfecting process. Those steps and some important concepts will be identified here. 

Cleaning and disinfecting are critical parts of all biosecurity programs. The goal is not to completely sterilize the environment, but rather to decrease the pathogen load significantly to a point where disease transmission does not occur.

There are many important steps to any cleaning and disinfecting process. Those steps and some important concepts will be identified here.

Cleaning and disinfecting are included in the National Pork Board's Pork Quality Assurance Plus and the Trucker Quality Assurance programs.

Cleaning and disinfecting

To maximize the effectiveness of cleaning and disinfecting, focus on these four steps:

1. Cleaning. The first step is to remove all organic material. This is best achieved using a broom, shovel or scraper. Remove as much solids as possible to minimize the use of water in the next step.

In a farrowing house, this step is easy to do (except for emptying the sow feeders). On the other hand, when cleaning a semi trailer, the removal of wood chips or other bedding material takes significant time. Time spent properly doing this step will decrease the overall time of the process.

2. Washing. This step is the most time-consuming of the entire process, but it is also the most important. When done correctly, washing will remove 99.99% of the microorganisms in the environment.

The objective here is to remove all remaining organic matter (manure, feed, urine, etc). This is usually done with a high-pressure washer. There are two important numbers to look at when comparing equipment: pressure (pounds per square inch = psi) and how much water is being moved (gallons per minute = gpm). To calculate the effective cleaning units (or ecu), multiply the psi by the gpm (ecu = psi × gpm).

For example, a machine that delivers 4 gpm of water at 2,000 psi is considered to have 8,000 ecu (2,000 × 4.0 = 8,000), which would be comparable to a 2,500-psi machine delivering 3.2 gpm (2,500 × 3.2 = 8,000).

However, using too high of pressure, more than 3,000 psi, can cause problems. This rate of pressure can cause damage to surfaces or even cause organic matter to be displaced at high speeds, which can be dangerous to personnel.

As a general rule, 9,000 ecu are usually needed to strip paint off a wall.

The speed of cleaning will be dependent on the volume of water used. A psi of more than 2,000 is usually sufficient to do the job. A 4-gpm machine will remove manure twice as fast as a 2-gpm unit.

Besides having a good power washer, there are several other steps to facilitate this washing process.

  • Soaking — Soaking surfaces before washing will cut down on the amount of time needed to do a more complete job. Soaking can be achieved by placing a sprinkler system in the rooms to be washed. When soaking a trailer, you may want to just wet the entire trailer first with a moderate amount of water, then start thorough washing at one end while other surfaces have more time to soak.

  • Detergents — Another excellent way to maximize cleaning and minimize time spent on the chore is to use special detergents to help break down manure and other organic matter. This is the equivalent of using soap to wash your hands. You can wash your hands with plain water, but it is much quicker to use soap.

    Detergents are products used to reduce surface tension and suspend particles to facilitate cleaning. They can be acidic (good for protein removal) or alkaline (good for fats). Some commercial products contain both types.

    Many operations forget the value of detergents, mainly because of the added expense. In reality, most products are worth the investment not only because they cut down on labor, but also because they maximize the cleaning process and can break down bacterial biofilms (slime), which can harbor bacteria.

  • Hot water — Hot water can also speed up the washing process. The one disadvantage of hot water is that it can produce steam and hamper visibility, particularly in winter. The goal is to have the water hot enough to facilitate cleaning without putting employees at risk. You will not be able to have the water hot enough to kill bacteria or viruses, as these high temperatures would cause skin burns. Studies have shown that the money used to heat the water will be saved in reduced labor.

3. Disinfecting — This is a critical step in the cleaning process that requires some use of science. Unless surfaces are completely cleaned (none-to-minimal organic matter), disinfection will not be effective.

Disinfectants are defined as chemicals used to control, prevent or destroy microbes on inanimate objects or surfaces. Most disinfectants are inactivated when they come in contact with organic material. There is no disinfectant that will work for all situations.

Traditionally, disinfectants are selected based on preferences or price rather than on specific objectives. All disinfectants used in the United States must be approved by the Environmental Protection Agency. So it is very important to read the labels.

Disinfectant class characteristics

The following will summarize the general characteristics of each of the different classes of disinfectants.

Acids (acetic acid, citric acid) — Acids are used to precipitate proteins. They can be caustic and toxic if they reach high concentrations in the air. Their activity is dependent on the pH of the substances they come in contact with. They have limited use in most swine cleaning and disinfecting programs.

Alcohols (ethanol, isopropanol) — Alcohols denature (break down) proteins and are non-corrosive. They are highly flammable and need to be in concentrations of 70-90% to be effective.

Aldehydes (formaldehyde, glutaraldehyde) — These chemicals are non-corrosive and denature proteins. Formaldehyde is carcinogenic, but glutaraldehyde is considered much safer for humans and animals. Glutaraldehyde can be slightly effective in the presence of some organic material.

Alkalis (lye, ammonium hydroxide) — Alkalis saponify (make into soap) fats in enveloped organisms. Activity increases with temperature. They are very corrosive.

Biguanides (chlorhexidine) — Biguanides alter cell membrane permeability. They are easily inactivated by detergents and hard or alkaline water. They are toxic to fish, but relatively nonirritating to tissues.

Halogens (chlorine or iodine compounds) — Halogens denature proteins but loose potency with time, organic matter, sunlight and some metals. Bleach (sodium hypochlorite) is probably one of the cheapest and most common disinfectants used. Iodine compounds can be irritating to skin at higher concentrations. Both iodine and chlorine are readily inactivated by organic material.

Oxidizing agents (hydrogen peroxide, peracitic acid) — Oxidizing agents denature proteins and lipids, are moderately corrosive and can be irritating at higher concentrations.

Phenols — Phenols denature proteins and change cell membrane permeability. They have a milky or cloudy appearance when added to water. They are usually not effective against non-enveloped viruses, but are effective in the presence of organic matter, and are therefore good options for foot baths; they have residual activity.

Quaternary ammonium compounds (quats) — Quats also denature proteins and change cell membrane permeability. They are usually not effective against non-enveloped viruses, are toxic to fish and inactivated by organic matter, detergents and hard water.

These general characteristic are helpful in understanding the differences between products. Product labels should always be read to better understand the specific characteristics or effectiveness of a particular product, which may be different than the general characteristics we have described here.

Know target organism

One other important part of the disinfection process is to know your target organism. As a rule of thumb, different classes of disinfectants are more likely to be effective against a particular type of pathogen. Bacteria can be grouped into gram-positive or gram-negative bacteria based on the ability of the organism to pick up special staining. These staining characteristics relate to properties of their cell wall, and therefore can be used to decide which type of products may work best for the different groups of bacteria.

Table 1 identifies some of the common bacteria of interest in swine operations as either gram-positive or negative. In regards to viruses and disinfection, classification is based on whether they have an envelope or not. Generally, non-enveloped viruses tend to be hardier, survive longer periods in the environment and require special disinfectants to be effective.

Table 2 helps organize some of the common swine viruses into categories as well as identify them as either being a DNA (deoxyribonucleic acid) or RNA (ribonucleic acid) virus. Although from the perspective of cleaning and disinfecting this characteristic is not relevant, it is important from the overall perspective of biosecurity. RNA viruses tend to mutate often, and therefore are more difficult to control through vaccination compared to DNA viruses. The porcine reproductive and respiratory syndrome virus is an example of an enveloped RNA virus. This means that it should be relatively easy to disinfect (envelope) and it mutates often (RNA).

On the other hand, porcine circovirus Type 2 virus is a DNA virus (low mutation rate) and does not have an envelope (hard to disinfect).

The Center for Food Security and Public Health at Iowa State University has free resources on their websites on disinfectants at: Table 3 lists the general characteristics of the different classes of disinfectants. Tables 1 and 2 can be used to select the target pathogen. Then refer to Table 3 to decide what class of disinfectants you want to use.

For example, if PRRS is your target pathogen (enveloped virus), then you would know as a general rule that the aldehyde class of disinfectants would be a better choice than phenolics or quats. Companies may add specific pathogens to their labels if they have done laboratory testing (standard test established by EPA) to demonstrate effectiveness of their product against that particular pathogen. The three tables serve as general guidelines; fully read the specific labels for all products to be sure they are effective against your target pathogens.

Generally, differences in pathogen strain don't change the organism's susceptibility to a particular disinfectant. A good example of this is the novel H1N1 influenza strain. The Centers for Disease Control and Prevention recommend that any product labeled effective against influenza (avian, swine or human) viruses could be used to disinfect surfaces.

There is also no evidence that swine pathogens develop any type of resistance to a particular class of disinfectants, as is the case for some bacteria and antibiotics. Therefore, rotating disinfectants is not necessary unless rotated to broaden the scope of target pathogens.

Another key element of the disinfection process is contact time. In general, most disinfectants need at least 10 minutes of contact time to be effective. Read the label to make sure proper contact time is provided.

Inadvertently, farrowing processing crews are probably the biggest violators of this rule. For effective disinfection of processing equipment, each operation should have two or three different sets of equipment, so that while one set is being used, the other sets are having plenty of contact time for the disinfectant to do its job.

Many of today's disinfectants are labeled for use in foaming equipment. Foaming has two great advantages. First, it allows one to visualize where the product has been applied, assuring a more even and complete application. Second, it dramatically increases contact time of the disinfectants with the different surfaces, especially vertical surfaces (walls, dividers, etc.). Both of these advantages are worth the investment.

Another way to apply disinfectants is to use a fogger. Historically, fumigation was used as a means to vaporize disinfectants into gases. Due to personnel concerns, fumigation is not used on a routine basis; instead, foggers are used.

Fogging usually involves aerosolizing the disinfectant in a very fine mist. The objective is to make sure that the disinfectant reaches all surfaces in a room. This is of particular interest when objects are brought into a building that cannot be disinfected manually.

A special room is built that has some type of rack or wire mesh table to allow all materials to be placed above the floor so disinfectant can reach all surfaces of the objects. The objects are placed in the room, and the fogger is filled with an approved disinfectant and turned on. The doors to the room are closed and the disinfectant mist is allowed to run for about five minutes.

Then, all materials are rotated and the fogger is allowed to run another five minutes or so. The fogger is turned off and the room sits idle for 2-3 hours to allow plenty of time for the disinfectant to come in contact with the desired objects.

4. Drying time. One of the challenges with most cleaning and disinfection programs is allowing ample time for extended drying. The purpose of this downtime/drying time is so that all moisture can evaporate from the building and all its surfaces.

Water is critical for the survival of all living organisms, including viruses and bacteria. Research in the poultry industry has shown that a 48-hour downtime can dramatically reduce the clostridial environmental contamination compared to 24 hours.

Ideally, downtime in the farrowing room would be 48 to 72 hours after cleaning and disinfection. Often, that's impossible due to pig flow and limited space. To maximize drying time, consider these options:

  • Allow farrowing rooms to dry overnight before moving sows into the room. Turn on the room heaters to maximize drying.

  • If overnight is not possible, then try to use scrapers to remove all puddles of water as a means to speed up the drying process before moving sows into the room.

  • Two or three times a year, plan enough time for the rooms to completely dry in order to break disease cycles before moving animals in. This is especially helpful when dealing with significant health problems in the farrowing house.

  • Remember, this is not an all-or-none effect. Small intervention steps add up to a more productive system.

Drying is especially critical for livestock trailers, which have been implicated as a major risk for disease transmission. This is usually not the fault of the driver, but rather due to the high-risk areas these vehicles travel to and from. Trailers usually end up in areas where animals are concentrated, and therefore the potential to pick up new disease pathogens dramatically increases.

Today's new trailers have been designed with better insight into higher biosecurity demands. Many of our high-health herds are using thermally assisted drying and decontamination (TADD) systems. In these systems, trailers are washed and disinfected, then placed in a bay to add heat as the final pathogen removal step. The success of these systems is greatly increased because of this drying process.

These systems are being designed so that critical areas of the trailers can reach at least 142°F for at least 10 minutes. Some in the field would prefer reaching 160-165°F for 10 minutes to maximize pathogen kill, but these higher temperatures increase the cost of operation and may shorten the life expectancy of some trailer equipment.

Monitor cleaning, disinfecting

In the swine industry, while cleaning and disinfecting is considered a highly valuable job, too often it is left to the person with the least experience. Everyone understands the importance of it, but no one wants to do this job all of the time.

Having the least experienced person in charge of power washing can be a problem if they are not trained properly. All employees need to understand the importance of this job; take the time to explain to new employees why every step is critical to the success of the entire operation.

The following steps can help monitor the effectiveness of your operation's cleaning and disinfecting program:

  • Visual inspection — Periodically, all managers should visually check each of the cleaning and disinfecting steps described above. The goal is to look for overall cleanliness. Especially with new employees, careful evaluation after each step is completed will help them better understand your expectations. The word “clean” is subjective and may have different meaning/degrees to different people. Remember, just because a room or trailer looks “clean” doesn't mean it is pathogen-free.

  • Quantitative evaluation — This usually involves swabs or Sterile Replicate Organism Detection and Counting (RODAC) plates. Many veterinarians offer this service. Through a process of standardizing test surface areas, actual bacterial counts can be done for the different test areas. The actual type of organism grown is not of concern, but rather the quantity of organisms grown. Plates and/or swabs need to be taken to a laboratory and allowed to incubate for 48 hours, so results are not readily available.

Cleaning and disinfecting programs can be difficult to evaluate. Many times the program's success is based on controlling clinical diseases. If there are scours problems in farrowing, then pay more attention to cleaning and disinfection. But this method can't detect subclinical diseases, which can affect performance and ultimately profitability.

Cleaning, disinfecting costs

When evaluating the costs of different programs, one must consider all parts of the process, including labor. As noted, detergents add direct costs to all cleaning programs, but labor savings must also be considered. These savings are not only in reduced time to complete the process, but also in improved morale of employees, who now have an easier job to do. The benefits of a cleaner room are difficult to quantify, but definitely offer positives.

Probably the easiest part to calculate is the cost of the disinfectant. Make sure you are comparing apples to apples. Based on the target pathogen, read the product label and determine the lowest dilution (highest concentration) needed. Calculate prices based on 1 gal. of final solution.

For example, product A might seem more expensive because it costs $82.50/gal. compared to product B, which costs $53.60/gal. According to the label, when targeting PRRS, product A is used at a rate of½ oz./gal. of water compared to product B, which is used at 1 oz./gal. of water. So, ½ oz. of product A will cost $0.32 ($82.50 / 128 oz. in a gallon / ½ oz. application rate = $82.50 / 256 = $0.32, while 1 oz. of product B will cost $0.42 ($53.60 / 128 oz. in a gallon / 1 oz. ap- plication rate = $53.60 / 128 = $0.32). Therefore, product A is about 24% cheaper than product B.


The objective of a cleaning and disinfecting program is not to completely sterilize the environment, but rather decrease the pathogen load significantly so that infection does not occur. Science needs to be applied to the entire process and all steps of the process have a purpose. Each step of the process is dependent on the successful completion of the previous steps.

Employees need to be trained to better understand the importance of the cleaning and disinfecting process as well as understanding that the selection of disinfectant should be based on target organism(s). Visual inspection of a cleaned room helps make sure most of the pathogens in the room have been removed, but does not indicate the room is sterile (pathogen-free).

Using the information in this article, your operation should be able to implement a successful cleaning and disinfecting program that should be an integral part of your overall biosecurity program.

Table 1 - Bacterial Grouping
Gram-Positive Bacteria Gram-Negative Bacteria
Staphylococcus (Greasy Pig) Bordetella
Streptococcus (Strep) Escherichia coli (E. coli)
Clostridium* Haemophilus parasuis (Parasuis)
Erysipelothrix (Erysipelas) Pasteurella multocida
Salmonella Brachyspira (Dysentery)
*Spore former and therefore difficult to kill
Table 2. Viral Grouping of Some Common Swine Pathogens
Enveloped 2 Non-Enveloped 3
DNA 4  
African Swine Fever (ASF) 1 Porcine Circovirus Type 2 (PCV2)
Pseudorabies (PRV)* Parvovirus
RNA 5  
Porcine Reproductive and Respiratory Syndrome (PRRS) Foot-and-Mouth Disease (FMD) 1
Transmissible Gastroenteritis (TGE) Rotavirus
Classical Swine Fever (CSF) 1 Swine Vesicular Disease (SVD) 1
Japanese Encephalitis1
Swine Influenza Virus (SIV)
Vesicular Stomatitis (VS)
1 Foreign animal disease
2 Enveloped viruses: more susceptible to environmental inactivation including disinfectants
3 Non-enveloped viruses: more resistant to disinfectants and environmental inactivation
4 DNA viruses: genetically low mutation rates
5 RNA viruses: genetically higher mutation rates
*PRV has been eradicated from the U.S. domestic swine population.
Table 3. Characteristics of Selected Disinfectants
Disinfectant Category Alcohols Aldehydes Biguanides Halogens: Hypochlorites Halogens: Iodine Compounds Oxidizing Agents Phenols Quaternary Ammonium Compounds (QAC)
Sample Trade Names Ethyl alcohol Isopropyl alcohol Formaldehyde Glutaraldehyde Chlorhexidine Nolvasan Virosan Bleach Betadyne Providone Hydrogen peroxide, Peracetic acid, Virkon S, Oxy-Sept 333 One-Stroke EnvironPheno-Tek IITek-Trol RoccalDiQuatD-256
Mechanism of Action
  • Precipitates proteins

  • Denatures lipids acids

  • Denatures proteins

  • Alkylates nucleic acids

  • Alters membrane permeability

  • Denatures proteins

  • Denatures proteins

  • Denatures proteins and lipids

  • Denatures proteins

  • Alters cell wall permeability

  • Denatures proteins

  • Binds phospholipids ofcell membrane

  • Fast acting

  • Leaves no residue

  • Broad spectrum

  • Broad spectrum

  • Broad spectrum

  • Short contact time

  • Inexpensive

  • Stable in storage

  • Relatively safe

  • Broad spectrum

  • Good efficacy with organic material

  • Non-corrosive

  • Stable in storage

  • Stable in storage

  • Non-irritating to skin

  • Effective at high temperatures and high pH (9-10)

  • Rapid evaporation

  • Flammable

  • Carcinogenic

  • Mucous membranes and tissue irritation

  • Only use in well ventilated areas

  • Only functions in limited pH range (5-7)

  • Toxic to fish (environmental concern)

  • Inactivated by sunlight

  • Requires frequent application

  • Corrodes metals

  • Mucous membrane and tissue irritation

  • Inactivated by QACs

  • Requires frequent application

  • Corrosive

  • Stains clothes and treated surfaces

  • Damaging to some metals

  • Can cause skin and eye irritation

Precautions Flammable Carcinogenic Never mix with acids; toxic chlorine gas will be released May be toxic to animals, especially cats and pigs
Vegetative Bacteria Effective Effective Effective Effective Effective Effective Effective YES — Gram Positive Limited — Gram Negative
Mycobacteria Effective Effective Variable Effective Limited Effective Variable Variable
Enveloped Viruses Effective Effective Limited Effective Effective Effective Effective Variable
Non-enveloped Viruses Variable Effective Limited Effective Limited Effective Variable Not Effective
Spores Not Effective Effective Not Effective Variable Limited Variable Not Effective Not Effective
Fungi Effective Effective Limited Effective Effective Variable Variable Variable
Efficacy with Organic Matter Reduced Reduced ? Rapidly reduced Rapidly reduced Variable Effective Inactivated
Efficacy with Hard Water ? Reduced ? Effective ? ? Effective Inactivated
Efficacy with Soap/Detergents ? Reduced Inactivated Inactivated Effective ? Effective Inactivated
Disclaimer: The use of trade names does not in any way signify endorsement of a particular product. For additional product names, please consult the most recent Compendium of Veterinary Products.
References: Linton AH, Hugo WB, Russel AD. Disinfection in Veterinary and Farm Practice. 1987. Blackwell Scientific Publications; Oxford, England; Quinn PJ, Markey BK. Disinfection and Disease Prevention in Veterinary Medicine, In: Block SS, ed., Disinfection, Sterilization and Preservation. 5th edition. 2001. Lippincott, Williams and Wilkins: Philadelphia.
For more information, see the “Disinfection 101” document at
? Information not found
Source: The Center for Food Security & Public Health, Iowa State University