Small coccidia


Coccidia are microscopic parasites that disrupt intestinal function. Although they can be diagnosed on fecal examination, they are not worms. Instead, they are single celled organisms known as protists. Protists are obligate intracellular parasites — they must complete part of their life cycle in the cells of a host organism. Coccidia are widespread organisms that affect not only alpacas, but almost every group of animals from fish, to reptiles, to birds, to mammals. They are ubiquitous in the environment, and naturally infect most animals to some degree. Problems arise when their numbers exceed the ability of their host to carry them without suffering negative consequences.

There are numerous coccidia of veterinary significance, including Eimeria, Cryptosporidium, Plasmodium, and Toxoplasma. The following species of Eimeria coccidia have been identified in New World camelids: Eimeria alpacae, Eimeria lamae, Eimeria punoensis, Eimeria peruviana, Eimeria ivitaensis, and Eimeria macusaniensis [Duzynski, et al., 1998a]. The first four species are typically grouped together as “small coccidia.” Little information is available on E. ivitaensis, although this is apparently another large coccidian. It is unclear whether this coccidian has been found in camelids living in North America. The large coccidian Eimeria macusaniensis, commonly known as E. mac or “big Mac,” will be dealt with separately, as will Cryptosporidium.


Coccidia are present in the environment as oocysts, roughly equivalent to the egg stage of other parasites. The oocysts are usually passed from the host in the feces, and this is the form by which almost all coccidia are known and identified. Oocysts do not become infective unless environmental conditions are appropriate, at which point sporocysts containing sporozoites develop. The encapsulated oocyst is then referred to as a sporulated oocyst, and it can persist in the environment in this stage for years.

Once a sporulated oocyst is ingested by a host, the covering of the oocyst is broken down either by mechanical or chemical activity in the host’s gut. After release, the sporozoites seek out and penetrate epithelial cells lining the gut. Inside the host’s cells, the sporozoites begin to multiply asexually into merozoites. The proliferation of merozoites eventually bursts the host cell, and the released merozoites begin seeking out new cells in which to begin the process of multiplication again.

Each species of coccidian is believed to have a specific number of asexual replication cycles that it completes. The final generation of sporozoites again seek out new host cells, but instead of making more sporozoites by fission, they develop into two types of gamonts: large, sessile macrogamonts (analogous to eggs) and smaller microgametocytes, which produce motile microgametes (analogous to sperm). When a macro- and microgamete fuse, a protective wall develops around the resulting zygote, which pushes free of the host cell and is excreted in the feces [Duzynski, et al., 1998b].

The prepatent period, the time between ingestion of a sporulated oocyst and passing oocysts in the feces, varies from species to species of coccidia. The prepatent period for the two most common small coccidia in alpacas are ten days for E. punoensis and 16–18 for E. alpacae [Foreyt, 1992].


Oocysts are known to sporulate more quickly at higher temperatures than lower, within the range of 50°F to 122°F. Unsporulated oocysts do not survive outside of these temperature extremes, although sporulated oocysts can. Oocysts require moisture, oxygen and shade to sporulate. Direct exposure to sunlight will kill unsporulated oocysts [Duzynski, et al., 1998b]. Once sporulated, oocysts remain infective for anywhere from several weeks to several years in the natural environment, depending on the species.

In essence, coccidia thrive in damp, dark locations at moderate temperatures — accumulated dung and bedding that do not dry out are a haven for coccidia growth. You can limit your animals’ chances at (re)infection in several ways. Good manure management is important: remove manure from animal living areas regularly and consider allowing free range poultry to turn over your manure piles, since exposing the oocysts to sunlight prior to sporulating will kill them.

The better overall health your animals are in, the better able they are to resist infection and mitigate the effects of the parasite. Keeping stocking rates low and removing stressors from your animals’ environment will promote good health and reduce the effects of coccidia. A good plane of nutrition also permits an animal to carry a coccidia load without significant ill effects. Over time, your alpacas will also build immunity to the coccidia to which they have been repeatedly exposed, which is why clinical cases of coccidiosis are usually seen in young alpacas or older animals with compromised immune systems.


Coccidiosis typically causes a clumped or ball stool in mild cases, progressing to diarrhea and weight loss in more severe infestations. The severity of the intestinal upset is related to the numbers of coccidia present, and the damage they cause to the intestinal lining. In very severe infestations, portions of the intestinal lining may be shed, and the damage to the intestinal wall can be permanent, causing continued ill thrift or stunted growth. Coccidiosis is not the only parasite that causes gastrointestinal upset and diarrhea [Cebra, 2003], but it is one of the more common causes.

Coccidiosis can be diagnosed with a fecal flotation. Since a coccidial infection is self-limiting, given that only a certain number of reproductive generations will be produced, animals otherwise in good health with minor numbers of oocysts observed often can be allowed to weather the infection with no need for intervention. This permits the animal to build immunity to the species of coccidia with which it is infected.


Animals with diarrhea, weight loss, or other signs of ill thrift can be treated in two different ways: with a coccidiostat that prevents additional reproduction of the coccidia, or with a coccidiocide, which kills the organisms outright. Coccidiostats include amprolium (Corid), which inhibits thiamine uptake in coccidia; sulfadimethoxine (Albon), which prevents the uptake of folic acid; and sulfamethoxazole/trimethoprim (SMZ-TMP), which also prevents the uptake of folic acid.

Without access to thiamine or folic acid, coccidia are unable to continue reproduction, and the alpaca’s immune system will clear the remaining organisms on its own. Although dosages and protocols vary, most coccidiostats are used on an on-off-on rotation over several weeks. It is important to note that alpacas are very susceptible to thiamine depletion, much more so than other ruminants. Thiamine depletion results in polioencephalomalacia (PEM), characterized by swelling in the brain, which can be fatal. Symptoms include lack of appetite, poor coordination and other neurological signs. High doses of injected thiamine can reverse PEM.

For this reason, if using amprolium to treat coccidiosis, it is recommended that you concurrently administer thiamine subcutaneously every third day during treatment. It may seem counterintuitive to administer thiamine when amprolium works by blocking access to thiamine (the coccidia preferentially uptake the amprolium in place of thiamine). However, the injected thiamine is available to the alpaca’s metabolism, but does not reach the gut where the coccidia are.

Toltrazuril (Baycox) is a relatively new treatment for cocciodiosis. It is a coccidiocide, which kills the intracellular life stages of coccidia. It must be imported from Australia, and is available in this country from Light Livestock Equipment or can be ordered directly from Australian sources. Many farms have reported success with single treatments, while others indicate that two doses several days apart are more effective.

You should consult with your veterinarian to see which medication is recommended for your particular situation. In mild cases of clinical coccidiosis, coccidiostats may be preferred, as they do permit the animal to mount its own immune response to the nonreproductive coccidia. This will reduce the likelihood of future reinfection. In severe cases, where immediate relief from severe infection is required, toltrazuril’s coccidiocide action may be more appropriate. It is important that the alpaca community refrain from overusing toltrazuril, in order to maintain its effectiveness for the future. Proper hygiene and good husbandry to prevent coccidiosis are preferable to chemical intervention.


Cebra, Chris, et al., “Potential Pathogens in Feces from Unweaned Llamas and Alpacas with Diarrhea,” Journal of the American Veterinary Medical Association, 223(12), 2003, pp. 1806-1808

Duzynski, D.W. et al., “The Coccidia of Camelidae,” 1998a, NSF‑PEET DEB 9521687, available as an on-line reference at

Duzynski, D.W. et al., “Biology of the Eimeriidae,” available as an on-line reference at

Foreyt, W.J. and John Lagerquist, “Experimental Infections of Eimeria alpacae and Eimeria punoensis in Llamas (Lama glama),” Journal of Parasitology, 1992, 78(5), pp. 906-909

Palacios, C. A., et al., “Eimeria macusaniensis and Eimeria ivitaensis co-infection in fatal cases of diarrhoea in young alpacas (Lama pacos) in Peru,” Vet Rec., 158(10), 2006, p. 344