The Limitations of Fecal Egg Counts

As concerns grew over emerging parasite resistance to existing deworming drugs, owners were increasingly advised to make deworming decisions based on the results of fecal egg   counts (FEC). While this approach has merit, it’s not foolproof.

Strongyle egg

To be accurate, a sample for parasite eggs should be taken from the rectum or from the   center of a freshly passed pile of manure. A simple technique is to grasp a fecal ball with a gloved hand then turn the glove inside out when you remove it, trapping the sample inside. This should then be placed into a small sealed container and examined immediately or kept cold until it is tested. Samples sent through the mail or allowed to sit around at room temperatures or warmer are not reliable because eggs can hatch. Hatched larvae are not detected by egg flotation techniques.

Egg counts of small strongyles, currently the major intestinal parasite in horses, show a seasonal pattern in temperate areas that have a clear winter and summer.  There is a sharp rise in spring and a smaller secondary peak mid summer, followed by precipitous drops. FECs in late fall and into winter do not reflect the parasite burden of adults or arrested encysted tissue forms.

Large strongyles (“bloodworms”) have the potential to produce even more extensive damage to the horse than the small strongyles. Intensive deworming had all but eliminated them but they are starting to re-emerge now with less frequent treatments. Like small strongyles, the eggs may hatch if manure is not handled properly.

Onchocerca are parasites that live in the nuchal ligament of the neck.  Their larvae can cause intense itching, allergic reactions and midline dermatitis.  They do not have eggs in the feces so cannot be detected with an FEC.

Similarly, bot fly larvae cause erosions in the stomach but never leave eggs in the manure so are undetectable. Tapeworms break off egg packed segments of their bodies into the manure rather than having eggs mixed throughout. It’s sometimes possible to detect tapeworms on a FEC but you have to get really lucky.

Pinworms cause an agonizing itch in the anal area that can drive a horse to rub their tail raw. The eggs are laid on the skin in this area, not in the manure.

Another problem is that the FEC only detects egg-laying adults. By the time you see eggs from roundworms and strongyles, the damage to the intestinal tract, liver and lungs from migrating larvae has already been done. Strongyloides larvae infect foals by migrating to the dam’s udder and getting into the milk. Their migration in the foal damages tissues and is often the cause of “foal heat diarrhea”. The FEC is more a tool for herd health and  monitoring eggs in the environment than it is for monitoring individual health.

Many people deworm once or twice a year using a combination of ivermectin or moxidectin with praziquantel.  This combination gets the bots and tapeworms which do not show up on FEC.  FEC may be checked once or twice a year. For healthy adults with strong intestinal immune systems in a stable, low exposure environment, this can work well.  However, there are many potential scenarios where it won’t be enough, including:

  • Very young or very old horses with poor immunity
  • Mares immediately after foaling
  • High exposure environments at home or horses that travel and may have high exposure
  • Pinwoms
  • Threadworm larvae reactions

Looks for issues such as colic, “pot belly”, weight loss or failure to gain, poor hair coat and slow shedding which can indicate intestinal parasite problems.  Finally, fear of causing dewormer resistance is often behind reluctance to treat the horse but the #1 cause of resistance is underdosing.  If your horse may need deworming, do it and make sure the dose is adequate for weight.

Eleanor Kellon, VMD

About Dr. Kellon

Graduate of University of Pennsylvania Veterinary School. Owner of Equine Nutritional Solutions,, industry and private nutritional consultations, online nutritional courses. Staff Veterinary Expert at Uckele Health and Nutrition .
This entry was posted in Equine Nutrition. Bookmark the permalink.

4 Responses to The Limitations of Fecal Egg Counts

  1. H.B.T. says:

    What is best for Onchocerca ?


  2. Carol Bush says:

    Is the Panacur power pack still wotking or is the 3 dose ivermectin better. Should it be done annually or not?


    • Dr. Kellon says:

      Resistance to fenbendazole in Panacur is now pretty widespread, even with larvicidal dosing. If the horse isn’t being exposed to high levels and doesn’t show high FEC, regular dose deworming is adequate. If there’s any question, do a follow up FEC in 45 days and if positive do two more ivermectin 3 weeks apart.


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