The Difference Between Cystoisospora and Eimeria

Veterinary medicine was built on a foundation of preventive care, including regular diagnostic screening. In general practice, fecal testing is standard in small animals and crucial for patient and public health. While there is often variability in the number and type of parasites present in these samples, one of the more common parasites found, especially in puppies and kittens, is Cystoisospora. However, under the microscope, this particular species is often confused with another protozoal parasite, Eimeria, which is not pathogenic in either species.

Veterinarians need to be able to distinguish between the two to know when and how to treat each patient effectively and efficiently. Let's explore the difference between Cystoisospora and Eimeria, why accurate diagnostics are essential, and how fecal antigen testing can help streamline results significantly.


A Cystoisospora Overview

Most small animal veterinarians have seen puppies and kittens infected with Cystoisospora spp. in their early months of life. It's a common cause of diarrhea with weight loss, dehydration, and in severe cases, vomiting and anorexia. However, if this genus name seems unfamiliar, it was renamed from Isospora, a type of coccidia, once it was discovered that it had an extraintestinal phase.1

One large 2018 study found that the infection rate in U.S. veterinary parasitology diagnostic lab fecal exams was 4.35% (204/4692 samples), mainly from the West and Midwest regions of the country.2 An older study from leading parasitologist Dr. Susan Little reported a similar incidence rate, with the infections most commonly seen in dogs younger than six months.3 This highlights the need for standard and frequent screenings in those first few visits.

Preventing transmission and spread from infected animals is also preferred with Cystoisospora spp. because it has a high tenacity for physical stress.4 It is one of the critical parasites causing contamination in crowded spaces, like shelters and dog runs, and it sporulates quickly in the environment. A sporulated oocyst is infective and resistant to many commonly used disinfectants, often surviving for months in the environment.5 This causes increased risks of outbreaks in litters and communal dog spaces. Additionally, some dogs and cats with Cystoisospora can be asymptomatic but still shed oocysts in their feces, placing other puppies, kittens, adult dogs, and cats at risk of infection.

Cystoisospora spp.: A Deeper Dive

As we look deeper into Cystoisospora spp., let's dig into transmission and tissue site predilection. This is critically important as we differentiate between Cystoisospora and another protozoal parasite, Eimeria. Dogs can ingest either parasite by eating the feces of other animals but only Cystoisospora can cause infections in cats and dogs. This pathogenic species starts as a nonsporulated oocyst and then sporulates in the environment.

Once ingested, it starts to undergo developmental changes and maturation of asexual and sexual stages in the enterocytes or villi of the intestines. When mature stages emerge, the infected cells become lytic, causing significant damage. Another stage of this parasite (the zoites) does not cause clinical disease but hibernates in mesenteric lymph nodes, the liver, and the spleen.

This is in stark contrast to another similar parasite. Eimeria is another genus of protozoan parasites, primarily known for infecting rabbits, birds, rodents and livestock species, such as poultry, cattle, sheep, and goats. However, we often misidentify Cystoisospora for Eimeria in healthy adult dogs. Dogs and cats are not hosts to this "pseudoparasite."

A pseudoparasite is an organism that outwardly looks like a parasite but does not reproduce or harm the host. Although transmission of Eimeria occurs by the same route (oral ingestion), this protozoal species never reaches the two-celled infectious stage of Cystoisospora. Instead of infecting the intestinal tract of the dog or cat, it passes right through in the feces.5

Cystoisospora vs. Eimeria: Why Know the Difference

Although both of these protozoal parasites are orally ingested and can look very similar on standard fecal floats, only one, Cystoisospora, will cause clinical signs in dogs and cats and must be treated. Not only does this create illness in many patients, but it can also be shed in the stool of asymptomatic patients, making early and accurate detection at wellness and illness exams a critical step. In addition, endoparasites like Eimeria often cause a false positive result, raising the alarm and even translating into a prescription for a patient when treatment is not indicated.

While centrifugation using fecal O&P may still be the go-to test for some veterinarians, the above scenario creates significant limitations. However, when fecal antigen testing is combined with microscopic examination of feces for eggs, the test can detect up to five times more intestinal parasite infections than fecal O&P alone.6 Fecal antigen testing does not cross-react with other species of coccidia and allows easy differentiation and increased specificity.

One of the essential aspects of veterinary medicine is preventive care, which involves educating clients about the significance of exams and diagnostic screening tests. By adding fecal antigen testing to the routine, veterinarians can detect parasite infections more accurately and at an earlier stage. This approach can help safeguard the health of patients and their families.


  1. Lappin, MR, et al. Greene's Infectious Diseases of the Dog and Cat (Fifth Edition), 104, 1301-1306 (2021).
  2. Sobotyk, C., Upton, K. E., Lejeune, M., Nolan, T. J., Marsh, A. E., Herrin, B. H., Borst, M. M., Piccione, J., Zajac, A. M., Camp, L. E., Pulaski, C. N., Starkey, L. A., & Verocai, G. G. (2021). Retrospective study of canine endoparasites diagnosed by fecal flotation methods analyzed across veterinary parasitology diagnostic laboratories, United States, 2018. Parasites & Vectors, 14.
  3. Little SE, Johnson EM, Lewis D, Jaklitsch RP, Payton ME, Blagburn BL, et al. Prevalence of intestinal parasites in pet dogs in the United States. Vet Parasitol. 2009;166:144–152.
  4. Murnik, LC., Daugschies, A. & Delling, C. Gastrointestinal parasites in young dogs and risk factors associated with infection. Parasitol Res, 122, 585–596 (2023).
  5. Companion Animal Parasite Council. Accessed 10 May 2024.
  6. Data on file at IDEXX Laboratories, Inc. Westbrook, Maine USA: Aggregate detection of hookworm, roundworm, whipworm, and flea tapeworm infections.
Natalie L. Marks

Dr. Marks is a veterinarian, previous veterinary hospital owner, consultant, media expert, national and international educator, and angel investor with over 20 years experience. She is a passionate communicator within multiple media formats, such as industry magazines and national conferences. She has won many industry awards, including the Dr. Erwin Small First Decade Award, given to the veterinarian who has contributed the most to organized veterinary medicine in his or her first decade of practice. Other notable awards that she has received are Petplan’s nationally recognized Veterinarian of the Year (2012), America’s Favorite Veterinarian by the American Veterinary Medical Foundation (2015), and Nobivac’s Veterinarian of the Year for her work on canine influenza (2017). The views and opinions in this piece are the author's own and do not necessarily reflect the views of either The Vetiverse or IDEXX.

Don’t just keep up. Stay ahead. Sign up for the IDEXX Education Newsletter.

Fill out the form to receive new Vetiverse articles, updates on upcoming live events, and exciting on-demand education content.