Maintaining a clean, disinfected environment is an essential component of equine health management, especially following an infectious illness or quarantine period. Pathogens such as streptococcus equi (strangles), equine herpesvirus-1 (EHV-1), salmonella and rotavirus can persist on surfaces and fomites (inanimate objects that can transmit disease) if environments are not properly cleaned and disinfected. Effective sanitation helps reduce pathogen load, prevent reinfection and limit disease spread to other horses and personnel.

In equine settings, disease control is rooted in reducing environmental contamination.

Organic matter inhibits disinfectants, so detergents and disinfectants are rendered ineffective when manure, bedding, dirt or bodily fluids remain on surfaces, therefore removing all organic matter is the first step. Start at the top and work your way down to the bottom so that you reduce reexposing an area you have already cleaned. It is common for pathogens to aerosolize when washed with high-pressure washers and land on edges or rafters, creating potential for reexposure. Wash your stall or horse trailer down with scrub brushes, rags or low-pressure hoses with soap and warm water, then allow all surfaces to dry thoroughly. Once the surfaces have completely dried, apply an appropriate disinfectant according to the manufacturer’s instructions. It is important to note that bleach mixed at a 1:10 ratio with water is effective at removing most pathogens, but organic material will inactive it. However, using other types of disinfectants (phenols) are still effective when organic matter cannot be completely removed. It is also important to note that while bleach can be used in limited contexts, it is not recommended to use on aluminum horse trailers due to risk of corrosion. Sunlight can also be used to kill or inactive pathogens on other equipment that cannot be cleaned with bleach or other sprays, such as leather or other tack.

Cleaning and Disinfection Protocol

1. Personal protection and preparation

• Wear personal protective equipment. Gloves, boots, coveralls and masks help protect handlers from exposure and prevent pathogen movement.

• Separate your equipment. Use dedicated tools for cleaning infected areas. Avoid using the same implements for clean areas unless sanitized.

2. Remove organic material

• Remove bedding, hay, feed tubs, buckets, mats and debris.

• Sweep and shovel small particles of dirt and manure.

3. Wash surfaces thoroughly

• Apply detergent or mild soap with warm water to all surfaces (walls, floors, gates, dividers).

• Scrubbing from top to bottom ensures dislodging debris and loosening pathogens.

• Start at the top of walls, scrub in overlapping sections and work downward.

• Use a stiff brush for concrete or nonporous finishes.

• For trailer interiors, remove mats and washable accessories for separate cleaning. Rinse trailer interior gently with low-pressure water to avoid aerosolizing pathogens.

4. Rinse and dry

• Rinse with clean water to remove all detergent residue.

• Allow full drying before applying disinfectant. This increases disinfectant efficacy and prevents chemical residues from harming horses.

5. Apply disinfectant

• Follow manufacturer instructions for dilution and contact time.

• Cover all surfaces including walls, floors, dividers, latches, buckets and mats.

• Typical options include:

• Phenolic compounds which are effective even with residual organic matter.

• Bleach (sodium hypochlorite) at a 1:10 dilution can be used but works best when surfaces are fully cleaned first.

• Accelerated hydrogen peroxide products are effective and often less corrosive.

6. Disposal and post-cleaning measures

• Dispose of soiled bedding and manure away from the facility to prevent reinfecting clean areas.

• Clean and disinfect tools (buckets, brushes) used in the process.

Cleaning and disinfection of horse stalls and trailers after an illness or quarantine period can be a cumbersome task, however it is essential to be through to control infectious disease spread in equine populations.