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Microscope for equine fecal testing for parasites

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Can Equine Fecal Egg Counts Reveal Accurate Parasite Burdens?

Fecal egg counts - derived from fecal flotation tests - are a common method for determining parasite levels in horses, which can then influence how often a particular horse is wormed and what class of wormer to administer. As helpful as this information is - it unfortunately doesn't tell us the whole story. Fecal tests will not identify Pin Worms, Bots or Neck Threadworms. These parasites either do not reside in and/or lay eggs in the digestive tract making it impossible to detect their presence from a fecal sample.

Adult Tapeworms and Ascarids, despite residing in the digestive tract,  can go undetected if adult worms present are not actively shedding eggs at that point in their reproductive cycle. In addition, a fecal egg count cannot reveal evidence of an existing population of Encysted Small Strongyles or Ascarid and Large Strongyle migrating larvae or immature adults within the horse.

Read on to learn about some common equine parasites not revealed by fecal tests, including where they reside and/or reproduce, their life cycle, and why a fecal flotation test is not a be-all end-all detector of potential parasite burdens.
Equine fecal testing for parasites
photo courtesy of
​This blog post has been on my to do list for a long time because I knew it would require considerable time and exploration. It is a labor of love for equines and their guardians. While completing my research, I was both fascinated and disgusted with a frequent out loud “eeeeeeww, that’s gross!"  The purpose is to shed some light on potential parasite burdens either not detectable or highly unlikely to be revealed in a fecal flotation test.

Parasites can wreak havoc on your horse’s health and can be responsible for a host of serious conditions, including:
  • Recurrent or fatal colic
  • Ulcerated and bleeding digestive system
  • Damage to the liver and other internal organs
  • Weight loss
  • Anemia
  • Poor hair coat
  • Pot-bellied appearance
  • Lethargy
  • Damaged and irritated lungs and blood vessel damage

3 Parasites Whose Eggs Are Never Present in Fecal Tests

The following 3 equine parasite eggs will never be present in a fecal flotation test. The eggs are either laid on the horses surface (hair or around the anus) or they don’t reside in the digestive tract. 

1.  Pin Worms (Oxyuris equi) - Pinworm eggs are ingested by the horse, hatching to live in the intestine. The life cycle is approximately 5 months long. Once mature and fertile, female pinworms emerge from the anus at night to lay eggs in a sticky residue on the skin surrounding the horse’s rectum and retreat back inside. A female pinworm can lay up to 60,000 eggs per day; eggs are not passed in the feces.

When the eggs are laid they can cause intense irritation which can lead to tail rubbing, biting and licking of hindquarters may also occur. To test for pinworm eggs, you must use clear tape and adhere it to the perianal area to take a sample. The samples then need to be observed under a microscope to determine if pinworms are present and/or the source of irritation.

2.  Botflies (Oestridae) - Horse bots are flies that resemble small bees and glue their tiny eggs or nits to body hairs of horses which is why eggs will not be present in a fecal flotation test. There are three different species which will deposit eggs on either the fore legs, outside of the legs, the mane, on the flanks, the long hairs beneath the jaws or stuck to hairs on the upper and lower lips.
Eggs of the common horse bot hatch after a 2- to 5-day incubation period. Newly hatched larva enter or come in contact with (depending on where they have been laid) the soft tissue of the lips, gums, or tongue; spending about 3 weeks there. Larvae then migrate to the stomach or small intestine to attach to the lining via sharp mouth hooks. Bots can damage the lining of the stomach or small intestine, interfere with the passage of food or cause other gastrointestinal disorders. They reside there approximately 7 months undetected before maturing and passing out in the feces. The mature larva (which may be visible in feces) then migrate to the soil below the manure and pupate. Depending on the season, they emerge (in 2 weeks to 2 months) as an adult bot fly. The adults are not capable of feeding and their only purpose at this time is to reproduce and lay eggs to continue a new life cycle. 

3.  Neck Threadworms (Onchocerca cervicalis) - Adults reside and reproduce in the horse’s nuchal ligament (extending from the poll to the withers) as a parasitic filarial worm (nematode). This makes it impossible to detect in a fecal flotation test because they never enter or reside in the digestive tract. The only method to confirm their presence is through a biopsy of the nuchal ligament. Adults reproduce and release thousands of microfilariae during the course of its ten year life cycle - yes 10 years! There is no class of wormer to rid your horse of adults. Once adults are present they will live out their life cycle.

Microfilariae (offspring) are released in the blood stream by the adult and reside in the horse’s skin; primarily around the mane, tail, head, shoulders, chest and mid-line of the belly potentially causing intense itching; but that’s not the only place. Microfilariae can also migrate to your horse’s eyes with the potential to cause serious damage. The offspring population can be controlled with an appropriate class of wormer. Once treated, itching typically intensifies due to a reaction of the die off.

The biting insect that serves as the carrier (intermediate host) is the female culicoides fly, commonly known as no-see ums, sand gnats and midges. These insects can cause insect bite hypersensitivity. They ingest the microfilariae by feeding off your horse via blood consumption. Once ingested by the fly, the larvae develop. When the fly bites again, the larvae are injected back into your horse or another host. The deposited larvae enter the bloodstream and come to rest most commonly in the nuchal ligament where they molt and develop into adult worms repeating the life cycle.

4 Parasites Highly Unlikely to be Detected in Fecal Tests

Adult Tapeworms and Ascarids - despite residing in the digestive tract - can be difficult to detect. If the adult worms present are not actively shedding eggs at that point in their reproductive cycle, eggs will not be present. In addition, a fecal egg count will not reveal evidence of the potential population of Encysted Small Strongyles, Ascarid and Large Strongyle migrating larvae or immature adults within the horse.

​1. Tapeworms - Are highly unlikely to be revealed in a fecal flotation because the adult worms may not be actively shedding eggs at that point in their reproductive cycle combined with the fact that their eggs are incredibly minute and dense. There are at least three types of equine tapeworms, the most common in the United States is Anoplocephala Perfoliata. They are pumpkin seed shaped, approximately 1 inch long and a half inch wide attaching to the horse’s intestinal lining via four suckers.

Tapeworms require an intermediate host, the oribatid (forage) mite, to complete their life cycle.  Tapeworm eggs are passed in the manure onto forage where the mites ingest them. The immature tapeworm develops within the mite and is ingested by the grazing horse.  When the horse digests the infested forage mite, the tapeworm is released and within 6-10 weeks develops into an adult that attaches to the horse’s intestine and the life cycle repeats itself. Several studies have measured the reliability of fecal flotation tests. In one such study, nearly 80% of known infected horses had zero tapeworm eggs found in the fecal examination. 

2. Ascarid/Roundworms (Parascaris equorum) -  The largest of horse parasites; females can develop to be the size of a pencil (14” long). Roundworms are most commonly present in young horses. They have the ability to produce hundreds of thousands of eggs per day with a thick shell protecting them from drying and freezing. Once the eggs are passed in manure they become infective in the environment after incubating (transforming into larva) at moderate temperatures for a few weeks. The well protected larva have the potential to remain viable in the environment for a decade or longer. Once ingested, larva emerges from their protective shell in the small intestine invading the gut wall and is then carried to the liver. Once in the liver, the Ascarid larva remains for about one week and molts to the next larval stage. It proceeds from the liver, via the bloodstream to the lungs, where it breaks out of tiny blood vessels and enters the terminal air sacs, migrating up the airways, and eventually up the trachea.   
Ascarid Roundworms - the largest of horse parasites
Ascarid females can develop to be the size of a pencil (14” long)
When the migrating Ascarid larva reaches the back of the throat, it is swallowed and returns to the small intestine to mature and begins to reproduce. Female Ascarids generally start to lay eggs within 10-12 weeks after infection. Migrating larva and immature adults are not detectable in a fecal flotation test.

3. Small Encysted Strongyles (Cyatho-stomes) - There are approximately 40 species of Small Strongyles throughout the United States and the world. ​Eggs are laid in the large intestine by adults and are passed in the horse’s manure. Once the eggs are on the ground they hatch and develop into 3 larval stages if optimal climate conditions are present.

The 3rd stage infective larvae climb onto forage waiting to be ingested. Once ingested, they pass into the large intestine and burrow into the mucosal lining by forming a fibrous capsule around themselves (similar to a cocoon)-ultimately becoming encysted. The larvae can remain encysted in the 3rd stage of development for weeks or even years undetected. The fibrous capsules can cause inflammation and limit the absorption of nutrients by decreasing the surface area of healthy intestinal tissue.

Eventually when they develop to the 4th stage, larva emergence occurs (no one knows what signals the fourth stage of development that results in emergence). During this phenomenon toxins are released from accumulated larval waste products. Once emerged, they mature and reproduce; laying eggs, which can be seen in a fecal flotation test if they are actively shedding. It is impossible to ascertain a Small Encysted Strongyle population.
horse manure

Did You Know?

"Approximately 33% of fecal samples examined by Horsemen’s Laboratory are positive for worm eggs. Over 95% of those positive samples are due to strongyle eggs of which 95% are likely due to Small Strongyles."  
John Byrd, DVM, Horsemen's Laboratory


4. Large Strongyles - The three primary species of large strongyles  are:
  • Strongylus vulgaris
  • Strongylus endentatus
  • Strongylus equinus
The adults live in the large intestine. Mature females produce eggs that are passed out in manure. The eggs develop into infective larvae (protected by a thick sheath) that exist on pasture vegetation or in stalls and can survive up to 31 weeks at lower temperatures. The horse is infected by consuming grass, feed, or water contaminated with infective larvae.

The larvae of large strongyles migrate through various parts of the body. Strongylus vulgaris, the bloodworm, will burrow into and migrate in the walls of the arteries that are the primary blood supplier to the small and large intestines. In approximately 4 months, the larvae move to the lumen of the large intestine, where they mature and can lay several thousand eggs each day, completing the life cycle. The entire life cycle is approximately six to seven months.

Strongylus endentatus and Strongylus equinus have similar life cycles but their larval migration is primarily through the liver. These larvae also return to the large intestines, where they mature into adults. Their life cycle is approximately 8 to 11 months.

A fecal flotation test will not reveal migrating Large Strongyle larvae or immature adults - residing undetected for 4 to 9 months depending on the species.

Take Home Message

  • Fecal flotation tests can certainly be beneficial and are recommended. They can reveal a population of parasites (most commonly small and large strongyles) that are actively laying eggs in the digestive tract. The test results can indicate what class of wormer should be administered.
  • It may not be advisable to administer a broad spectrum class of wormer if a heavy burden is present to avoid overwhelming the body with large die offs of various other parasites not detected. Consult your veterinarian. 
  • There is no single class of wormer that has the ability to be effective against all parasites and/or life stages. Be skeptical of rotational type packages that are marketed. Some of them may not offer protection against all parasites and/or life stages.   
  • Because resistance and effectiveness is a concern, dose according to instructions/body weight
  • Know the safety margins & adverse effects. All chemical wormers have safety margins (the number of doses above the recommended dose that typically will not result in adverse effects). The higher the number, the less risk of adverse reactions from the wormer itself. However, individuals can experience adverse reactions to the die off regardless of the chemical used. We strongly advise researching the safety margin and adverse reactions others have experienced prior to administering any product. There is one such product that can cause swelling of the mouth, lips, and/or tongue, ulcers on the mouth, lips, or tongue, colic like symptoms, colic, seizures, and death.
  • Consult your veterinarian to devise a strategic safe protocol appropriate for your region. Foals, miniature horses, ponies, aged horses and underweight or unhealthy individuals should warrant even greater caution in regards to safety margins and class of wormer administered. 

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Monique Warren, Hay Pillow Founder with the Hay Pillow Slow Feeder product line - standard ground hay pillow, mini hay pillow, hanging hay pillow & horse trailer manger hay pillow

About the Author

Monique Warren invented the Hay Pillow® slow feeder and is the owner of Hay Pillow Inc. ​Warren has been an equine guardian for over forty years and slow-feed advocate for over 10 years. She contributes equine nutrition, digestive and hoof health articles to publications such as Equine Wellness, The Journal, The Naturally Healthy Horse, Natural Horse Magazine, Nicker News, The Horse's Hoof and Miniature Horse World Magazine. Equine nutrition and horses feet are her passions. She resides in Southern California.

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