The Flies Have It

Viruses, bacteria, and parasites…oh my! Learn about the most common infectious diseases carried by flies and how you can protect your horse from those threats. 

By Barb Crabbe, DVM

Flies are annoying, but they’re much more than a nuisance to your horse. They can cause career-ending—even life-threatening—diseases and other ailments. (Photo by Shelley Paulson)

Have you ever been enjoying a ride, when out of nowhere a bot fly appears? She’s determined to lay her eggs on your horse’s legs, and your horse is just as determined to avoid the pest. He pins his ears and takes off running. You’re just along for the ride as he tries to evade the fly. 

Flies may annoy your horse with their buzzing and biting, but that’s not all they do; in fact, flies carry some of the deadliest diseases out there and can pose a serious health threat to all the horses in your barn. 

Think of a fly like a tiny commercial jet, loaded with potentially dangerous passengers. They pick up those passengers from the environment or other horses, then deposit them on your horse’s skin or directly into his bloodstream. Your role is to understand the most common infectious organisms carried by flies, including a variety of viruses, bacteria, and parasites. I’ll cover that here, as well as share the diseases they can cause, what signs to watch for, and what steps you can take to protect your horse. Then, I’ll outline a four-step strategy to keep flies away. 

Viral Threats

Viruses are often the deadliest fly-borne diseases—in part because flies inject the virus directly into your horse’s bloodstream through a bite. Here are the most common viral threats to your horse’s health.

Virus #1: Equine Infectious Anemia

Transmitted by: Biting flies, such as horse flies and deer flies. Equine infectious anemia (EIA) can also be transmitted through virus-contaminated needles or surgical equipment. 

What it looks like: Within two to three weeks of being bitten, your horse can develop a very high fever (as high as 108 degrees F), severe anemia, weakness, and swollen legs. In severe cases, this virus can lead to sudden death.  →

The consequences: Once your horse is infected with this virus, he’s infected for life, resulting in intermittent episodes of fever, anemia, and swollen legs. In many cases he’ll become an inapparent carrier—meaning he carries the virus with no sign of disease. EIA is detected by the Coggin’s test that’s required for transport across state lines or for participation in many shows and events. Because the signs of this disease are non-specific, many horses never get diagnosed; instead they’re identified as carriers by a positive result on a routine Coggin’s test. 

What to do: Prevent it at all costs! EIA is one of the scariest diseases of all. If your horse survives the initial onset, you may not even know there’s anything amiss.  But if your horse has a positive Coggin’s test, laws require he either be euthanized or kept in isolation from other horses for the rest of his life. Risk of EIA is a pretty compelling reason to keep flies at bay. 

Virus #2: Vesicular Stomatitis

Transmitted by: Black flies, sand flies, and midges. Vesicular Stomatitis (VS) can also be spread by direct exposure to saliva or fluid released from blisters (see below). The virus can be shed in these secretions for as long as a week after they appear. 

What it looks like: Signs of vesicular stomatitis are likely to appear two to eight days after exposure, beginning with a fever. Over the course of approximately two weeks, your horse may develop blisters on his tongue, gums, or nose that can lead to drooling, frothing at the mouth, and a reluctance to eat. Blisters may also appear on the coronary bands or on a mare’s teats. These blisters will eventually rupture, and the resulting sores can take as long as two months to heal. In severe cases, sores developing on the coronary bands can cause the hoof to slough away. 

The consequences: Vesicular Stomatitis is a reportable disease; if your horse contracts it, he may be under mandatory quarantine for 14 days or more. All susceptible species (such as cows and pigs) on your property may also be quarantined. This can have a significant impact on competitions and travel across state lines. VS can be transmitted to humans, too. 

What to do: Treatment primarily involves keeping your horse as comfortable as possible by providing soft feeds and administering medications for pain. If your horse becomes dehydrated, he may require other supportive care, such as intravenous fluids. Antibiotics might be recommended if your horse develops a secondary bacterial infection. Heed mandatory quarantine recommendations if your horse is diagnosed. Protect him from VS by paying attention to notifications that cases have been identified in your area, avoiding any contact with potentially affected horses, and controlling flies. 

A good fly spray, applied regularly, can help ward off threats posed by flies, including viruses, bacterium, and parasites. Outsmart fly spray from NRHA Corporate Partner SmartPak Equine is nontoxic and also repels ticks and mosquitoes. (Photo Courtesy of SmartPak Equine)

Bacterial Threats

In contrast to viruses that are injected directly into your horse’s bloodstream via a bite, bacterial threats can hitch a ride on flies that walk through pus or discharge from a sick horse or in a contaminated area. The carrier fly then transfers that bacteria to infect another horse. These diseases are most likely characterized by abscesses—large pockets of pus (bacteria and white blood cells) that form on various parts of your horse’s body. 

Bacterial Threat #1: Strangles

Transmitted by: The bacteria that carries strangles (streptococcus equi) is present in the discharge that’s released from abscesses, meaning it can be spread by almost any fly, as well as via contact with contaminated equipment, clothing, or even people. 

What it looks like: When a fly carries the strangles bacterium to your horse, it takes three to 14 days to identify the signs. Initially, your horse will have a fever, followed by a nasal discharge that makes it easy to mistake a strangles infection for a simple “cold” in the early stages. After several days, your horse may have swelling between his lower jaws as the lymph node abscesses typical of this disease develop. These abscesses can become quite large and may eventually drain large quantities of pus. 

The consequences: In most cases, the disease will run its course within a period of two to three weeks. Complications can occur, however, including abscess formation deeper within your horse’s body (called bastard strangles) or a severe reaction of the immune system (called purpura hemorrhagica) that can be life-threatening. The biggest complicating factor is that an infected horse can become an asymptomatic carrier once recovered. Carrier horses can shed bacteria and infect other horses, leading to intermittent outbreaks in facilities where they reside. 

What to do: It’s controversial whether or not to treat a strangles infection with antibiotics. Most experts agree that if an infection is identified early, antibiotics should be given. However, once abscesses begin to develop, it’s generally best to withhold antibiotics and allow the abscesses to mature and drain. A strangles diagnosis can be easily confirmed with a bacterial culture of the draining pus. Talk to your vet about whether a vaccination against strangles should be a part of your preventive health care plan. Take steps to control spread by isolating your sick horse, minimizing contamination of the stable, and controlling flies. 

Bacterial Threat #2: Pigeon Fever 

Transmitted by: Similar to strangles, the bacterium that causes pigeon fever (corynebacterium pseudotuberculosis) is shed in pus that oozes from ruptured abscesses, so it can be spread by almost any fly that touches the pus, as well as through contact with contaminated equipment or handlers.  

What it looks like: Pigeon fever typically begins when a fly carrying this organism feeds on your horse’s belly or chest. You’ll first notice small swellings that eventually become large abscesses. This disease gets its name from the large abscesses that often develop on the horse’s chest, giving the appearance of a “pigeon breast.” If these abscesses don’t open and drain on their own, your vet will lance and flush them to help speed along your horse’s recovery. Your horse may also have a low-grade fever for several days.

The consequences: Complete recovery from this disease within a period of several weeks is likely, unless complications, such as internal abscesses, develop. In some cases, abscesses along tracts in your horse’s legs can cause more serious and lingering disease. 

What to do: Similar to strangles, antibiotic treatment for pigeon fever is controversial and usually only recommended either very early in the disease or after abscesses have ruptured and drained. Call your vet if your horse shows signs of pigeon fever, and, like strangles, confirm a diagnosis with a culture of the draining pus. Control spread by minimizing contamination of the environment with draining pus. And, once again, control those flies. 

Protective fly masks and sheets, like the Crusader Mask and Econo Fly Sheet from Cashel Company, a sister brand of NRHA Corporate Partner Classic Equine, can help protect even the most fly-sensitive horses. (Photo Courtesy of Cashel Company)

Parasitic Threats

The spread of most parasites is similar to the spread of bacteria—flies pick up the organism from the environment and deposit it in some location on the horse’s body. 

Parasitic Threat #1: Habronema 

Transmitted by: Habronema, also known as summer sores and stomach worms, are transmitted to horses when house, face, or stable flies pick up larvae from manure and deposit it near the horse’s mouth. The horse ingests the larvae, which mature into adults in the horse’s stomach and eventually lay eggs that are passed in manure. In some cases, flies deposit larvae on wounds or other open sores on the horse’s body. 

What it looks like: The habronema parasite causes minimal damage during its normal life cycle as it passes  through the horse’s digestive tract. However, when it’s deposited on wounds or open sores, it can cause intense itching, exuberant granulation tissue (proud flesh), and sores that don’t heal (summer sores). A typical summer sore has yellowish, grainy material on its surface. 

The consequences: Summer sores can be extremely difficult or even impossible to heal. In some cases, they may require aggressive treatment, including surgery.

What to do: In addition to controlling flies, a deworming program that includes medications effective against the habronema worm can reduce the number of eggs passed in the manure. Recognizing and treating sores immediately increases the chances that they’ll heal. Call your vet right away if you suspect your horse has a summer sore. 

Parasitic Threat #2: Onchocerca

Transmitted by: These tiny threadworm larvae are most commonly transmitted to the horse when midges (also known as culicoides gnats) feed. Larvae migrate through the tissues, and adults take up residence in various ligaments (including the large nuchal ligament that runs along the neck) depending on their species.  

What it looks like: Your horse will develop pea-sized lumps that are scabby and extremely itchy. Often these lesions will appear on your horse’s belly, although they can show up anywhere on his body. 

The consequences: Onchocerca parasites have been associated with blindness if larvae migrate to the eyes and die, which causes extreme inflammation. Some reports indicate they can also cause lameness if adults take up residence in tendons and ligaments of the legs, although this association isn’t completely proven. 

What to do: The onchocerca parasite can be very difficult to eradicate. Use of a thorough deworming program that includes ivermectin or moxidectin may be recommended. Most important is controlling the midges that transmit the larvae.

Bye-Bye Fly Checklist

Use this four-layer prevention plan to help you say goodbye to flies.

Layer 1: Control the environment

If there’s nothing to attract them, flies won’t come. Make your environment less inviting using the following strategies.

  1. Keep stalls, paddocks, and pastures clean. Flies like filth and manure. By keeping stable areas clean, they’re less likely to congregate.
  2. Manage your manure. Compost your manure pile, or have it hauled away. Avoid spreading manure on pastures. 
  3. Eliminate standing water. Wet, mucky ponds are a perfect breeding ground for many flies. Provide sufficient drainage to prevent water from accumulating in low-lying areas. 
  4. Provide adequate ventilation. Flies prefer stagnant air, where they can lounge around without a worry. A well-ventilated barn with fans running in summer months will make your horse’s home much less popular with flies. This is especially important for culicoides gnats.

Layer 2: Limit the Population 

No matter how hard you try to make your environment uninviting, flies are likely to show up anyway. Control their numbers by hitting where it hurts—in the larval stage. 

  1. Use feed-through fly control. These products pass through your horse’s digestive system unabsorbed and inhibit development of fly larvae in manure. (Read more about feed-through options here).
  2. Place fly predators on the manure pile. Small wasps consume fly larvae to help minimize numbers of flies that mature. 
  3. Use fly traps. When placed in strategic locations around your barn, these will trap and kill large numbers of adult flies that manage to emerge in spite of your other efforts. 

Layer 3: Repel

You’ve destroyed their home and attacked their young—yet flies still show up. Even after flies have invaded to your barn, there’s more you can do to keep them away from your horse. 

  1. Use fly spray. Apply it regularly to make your horse less attractive to pests.
  2. Apply gels or roll-on repellants. Use these around your horse’s eyes to keep flies away from this particularly inviting area to prevent conjunctivitis. 
  3. Use ointments on his belly. These protect this sensitive area—especially important if your horse shows signs of fly-bite dermatitis.

Layer 4: Protect

Flies are hardy critters, and sometimes the only way to prevent them from attacking your horse is with a physical barrier to keep them off his skin. 

  1. Employ a fly mask. This will prohibit access to your horse’s eyes. 
  2. Use a fly sheet. This will protect his body from bites. Look for one with a wide belly panel to protect his sensitive underside. 
  3. Consider fly bandages. These limit access to his lower legs, which can alleviate stomping that may lead to soreness.


Dr. Barb Crabbe

Dr. Barb Crabbe is a graduate of UC Davis School of Veterinary Medicine and completed an internship in large animal medicine and surgery at Washington State University. Crabbe is a private equine practitioner and owner of Pacific Crest Sporthorse in Oregon City, Oregon. She’d like to thank Ryan Ferris DVM, MS, Dipl. ACT of Summit Equine in Newberg, Oregon, for assistance with preparation of this article.