Creating a Horse Quarantine

Here are the steps to take when introducing a new horse to your farm, and to reduce disease spread within your herd.

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Creating a Horse Quarantine
While most facilities do not have a separate barn for quarantine, there are still ways to care for a horse while limiting his exposure to other horses. | Anne M. Eberhardt/The Horse

Steps to take when introducing a new horse to your farm, and to reduce disease spread within your resident herd.

There are several instances in which a horse owner might need to isolate a horse from the rest of the herd. One is when you bring a new horse onto a farm; the second is if an animal is sick with a possibly contagious agent. A responsible horse owner should also quarantine a horse that is returning from a hospital stay, a sales barn, or any other environment where the horse might have been exposed to disease agents.

While most facilities do not have a separate barn for quarantine, there are still ways to care for a horse while limiting his exposure to other horses. Plan ahead for this type of scenario because the more prepared you are, the better. As the American Association of Equine Practitioners states in its biosecurity guidelines, “Anything that touches an infected horse or carries secretions or manure from sick horses has the potential to transfer pathogens to other horses.” That means anything from your hand to a water hose to a wheelbarrow.

While you can’t completely prevent germs from spreading and horses from getting sick, simple management steps can minimize these risks. As part of everyday practices, work with your veterinarian to keep horses current on necessary vaccines (see the American Association of Equine Practitioners’ vaccination guidelines  for core vaccination guidelines). Keep your facility clean and try to minimize rodent and insect populations, because they (as well as dogs, cats, and other critters) can all move a disease agent. Also keep your equine herd as closed as possible. If you do have some horses that go on and off the farm, such as competition horses, keep them separate from the ones that do not leave the property. Take show horses’ temperatures daily for a week after returning home from competition as a good management practice and to catch any potential illness early. Avoid turning older horses out with younger ones, because young horses are more susceptible to illness.

Caring for a Quarantined Horse

When animals are kept in the same barn, it’s much harder to keep people and equipment from coming in contact with a sick horse. If you don’t have a separate barn as an isolation facility, a paddock with a shelter and a dedicated water source works well. If you don’t have a separate paddock, set up a portable pen and provide the horse with some type of shelter or windbreak. Josie Traub-Dargatz, DVM, MS, Dipl. ACVIM, professor of equine medicine and epidemiology at Colorado State University, remarks that it’s easier for people to change their routines as well as keep track of possibly contaminated equipment if the horse is in a different area of the farm. She even had a client who used a roomy, well-bedded stock trailer (where the horse could move around and lie down) as a temporary isolation area until arrangements could be made for a more suitable location. The horse was accustomed to and comfortable in the trailer, and after he was moved the trailer was easy to clean and disinfect.

Special Feature: Practical Biosecurity Tips to Protect Your Horses
Special Feature: Practical Biosecurity Tips to Protect Your Horses

If you simply do not have a way to isolate the sick horse on your property, consider taking him to a veterinary clinic with an isolation facility. This is especially recommended if you are dealing with a horse that has both diarrhea and a fever, because it is difficult to contain the large volume of diarrhea passed by an adult horse.

Once you isolate a sick horse, Traub-Dargatz recommends maintaining good communication with all the people involved in horse care on the farm. “If people understand what you are trying to accomplish in isolating the sick horse, they’re more likely to do the right thing,” she states.

If possible, assign one person to care for the sick horse(s), and do not allow that person to handle healthy horses. If this is not feasible, care for the healthy, unexposed animals first, exposed animals next, and sick horses last. Protect yourself via physical barriers such as disposable gloves, plastic booties over your shoes, and barrier clothing (e.g., gowns, plastic aprons, or coveralls). Every time you finish tending to the sick horse, place barrier clothing in a covered container immediately. Wash and dry cloth items between each use, and wash your hands regularly. You can provide footbaths and hand sanitizers at access points, but these must be refreshed and maintained to be effective in preventing disease spread; someone should be assigned this job as well.

Ensure that a sick horse does not cross-contaminate unexposed areas. For instance, this means no communal water. If you use one hose to fill water buckets, make sure it does not touch the side of any bucket and is not submerged in the water. Manure on wheelbarrow or tractor tires can easily be spread throughout the facility. Waste material (e.g., used bedding and leftover feed) from the sick horse should not be spread in the pasture or added to an open-air pile. Designate equipment only for the sick horse, and identify it as such.

Disinfectants can be helpful, but always follow the label directions. Their usefulness also depends on the current climate, as some are ineffective in colder weather. Select one that is safe for use around horses and is effective in the presence of 10% organic matter. For example, organic matter readily inactivates bleach and it should be used only after a thorough cleaning. Strip stalls completely, and remove cobwebs before washing. (Videos on how to properly disinfect an average horse stall: Part 1 (cleaning) and Part 2 (disinfection))

Adding to the Herd

Bringing a new horse into an existing herd is a common way infectious diseases come onto a farm. The Ontario Ministry of Agriculture, Food and Rural Affairs cites three important factors to minimize risk when introducing a new horse:

  1. The protection you have given the resident horses with proper vaccination;
  2. The source of purchased horses, including how they are transported to the farm; and
  3. The method you will use to introduce the new horses to the rest of the herd.

If someone expresses interest in moving a horse to your barn, Nathan Slovis, DVM, Dipl. ACVIM, CHT, internal medicine specialist at Hagyard Equine Medicine Institute in Lexington, Ky., recommends you first send that person a list of your stable rules and protocols. He also emphasizes sending a disease questionnaire that asks the horse owner 10-15 questions, such as, “Where is the horse coming from? Has there been any instance of disease on that farm? Has the horse been ill recently? Does the horse travel a lot to shows? Is the horse coming from a hospital setting?” If you are new to the boarding scene, share the answers with your veterinarian to help determine if this is a higher-risk animal. The answers do not necessarily mean you won’t take the horse; rather, they mean you might wait before allowing the horse to come on the farm or you might accept the horse, but put quarantine protocol into place.

If your farm is strangles-free, you want to keep it that way. Slovis suggests having a strangles polymerase chain reaction test (PCR) or culture performed on a nasopharyngeal wash (a sample of material from the back of the horse’s throat and nasal passages) prior to accepting the horse.

Examine vaccination records closely to find out what the horse has been vaccinated for and when. Slovis stresses that the most important way to protect horses from certain diseases is through proper vaccination, but which vaccines to use are specific to your area and should be discussed with your veterinarian.

Before the horse steps foot on your property, consider vaccinating any horses over 6 months of age that haven’t already received their shots. Make sure you also closely review the new horse’s current health certificate and Coggins (which shows the horse tested negative for equine infectious anemia).

Traub-Dargatz advises keeping new horses isolated for three weeks, if possible. Similar to dealing with a sick horse, work with the isolated horse last each day, and use separate pitchforks, wheelbarrows, buckets, etc. To make isolation equipment easier to distinguish from the rest of the facility’s equipment, Slovis suggests picking bright colors for the quarantined horse, such as a pink lead rope or water bucket. Check the newly arrived horse’s temperature daily–optimally twice a day. Keep an eye out for a cough, eye or nasal discharge, swelling of lymph nodes around the head or neck, skin disease, abnormal scratching, or diarrhea. Call your veterinarian at the first sign of a fever or other problems. While the horse is isolated, give him any vaccinations that your other horses have received. For example, a horse moving from Colorado to Maryland might need to be vaccinated for Potomac horse fever.

If a three-week isolation is simply too long to manage for your facility, Slovis says one week to 10 days is typically long enough to reveal if a horse is going to get sick. The exception is when you add a new broodmare to a group of other mares in foal. In that case he says you should be more conservative and follow the three-week isolation period because the last thing you want is an abortion outbreak.

If you don’t have a separate area to keep the new horse, designate a stall at the end of the barn as your isolation stall. It should be located by an entry so that there is good ventilation and the horse doesn’t have to pass every other animal in the barn on exit and entry. Keep it such that the horse can’t hang his head out and come into contact with other animals and equipment. If possible, leave the stall next to the isolation stall empty. Slovis admits this isn’t the ideal isolation (since disease agents that spread through the air, such as those that cause influenza, can travel up to 150 feet), but typically it is the best scenario when you only have one barn.

Perform a fecal egg count before a new horse is turned out with your herd. That way you can get an idea of parasite load before potentially contaminating your pasture. If the horse has a high egg count, turn him out alone in a small pasture or paddock until treated.

Back to Normal

Once you have navigated the tricky waters of quarantine, how long does it take for bacteria and viruses to die? Again, it depends on the agent. Viruses don’t live well outside the body, but they can survive for several days depending on the temperature and humidity level. Sun is very good at destroying some disease-causing agents. Streptococcus equi, the bacterium that causes strangles, for instance, usually does not live for more than seven to 14 days if exposed to the sun, but it can live longer if it has not. S. equi can survive up to 30 days in water, which is why it is important to keep your waterers clean. Then, unfortunately, some types of Salmonella have been known to live in manure for years.

Take-Home Message

Traub-Dargatz reminds us that it is important to focus not just on the horse but all the people and items that could spread a disease agent around a farm. “The devil is in the details on those kinds of things,” she says. She suggests having an objective pair of eyes, such as those of your veterinarian, take a look at the movement of people and objects around your farm.

A horse with a fever is a red flag that should prompt a call to your veterinarian. Some owners might dismiss a horse with nasal discharge as no big deal, but two to three days into the problem other horses might then be exposed. Better to err on the side of caution, have an isolation plan in place, and move into action at the first sign of trouble. Work with your veterinarian to determine the cause of the disease so you can take a targeted approach to control the problem and care for the sick horse.


Written by:

Stephanie Ruff received a MS in animal science from the University of Kentucky in Lexington. She has worked in various aspects of the horse industry, including Thoroughbred and Arabian racing, for nearly 20 years. More information about her work can be found at She has also published the illustrated children’s story Goats With Coats.

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