Coccidiosis is a significant disease for chickens, especially affecting the young chicks. It can be fatal or leave the bird with compromised digestion. There are chick feed mixes that contain a coccidiostat to manage exposure levels and control disease. In an outbreak, coccidiocidal medications are given. Examples are toltrazuril (Baycox) or amprolium. After multiple infections, surviving chickens become resistant to the coccidia.

The most common medications used to treat coccidian infections are in the sulfonamide antibiotic family.

Depending on the pathogen and the condition of the animal, untreated coccidiosis may clear of its own accord, or become severe and damaging, and sometimes cause death.

They are treated with antiprotozoal agents. Recent papers have also proposed the use of viruses to treat infections caused by protozoa.

Protozoan infections are parasitic diseases caused by organisms formerly classified in the Kingdom Protozoa. They include organisms classified in Amoebozoa, Excavata, and Chromalveolata.

Examples include "Entamoeba histolytica", "Plasmodium" (some of which cause malaria), and "Giardia lamblia". "Trypanosoma brucei", transmitted by the tsetse fly and the cause of African sleeping sickness, is another example.

The species traditionally collectively termed "protozoa" are not closely related to each other, and have only superficial similarities (eukaryotic, unicellular, motile, though with exceptions). The terms "protozoa" (and protist) are usually discouraged in the modern biosciences. However, this terminology is still encountered in medicine. This is partially because of the conservative character of medical classification, and partially due to the necessity of making identifications of organisms based upon appearances and not upon DNA.

Protozoan infections in animals may be caused by organisms in the sub-class Coccidia (disease: Coccidiosis) and species in the genus "Besnoitia" (disease: Besnoitiosis).

Several pathogenic protozoans appear to be capable of sexual processes involving meiosis (or at least a modified form of meiosis). Included among these protozoans are "Plasmodium falciparum" (malaria), "Toxoplasma gondii" (toxoplasmosis), "Leishmania" species (leishmaniases), "Trypanosoma brucei" (African sleeping sickness), "Trypanosoma cruzi" (Chagas disease) and "Giardia intestinalis" (giardiasis).

The definitive hosts for these "Taenia" species are canids. The adult tapeworms live in the intestines of animals like dogs, foxes, and coyotes. Intermediate hosts such as rabbits, goats, sheep, horses, cattle and sometimes humans get the disease by inadvertently ingesting tapeworm eggs (gravid proglottids) that have been passed in the feces of an infected canid. This can happen from ingesting food, water or soil that has been contaminated by dog feces. The disease cannot be transmitted from one intermediate host to another, but it is still not a good idea to eat meat that presents with cystic nodules from coenurosis.

Because this disease is highly durable in its equine host, it has proved very difficult to develop a vaccine for it. There are four main drugs on the market that are used to treat the clinical signs of dourine: Suramin, Diminazen, Cymerlarsan, and Quinapyramin. However, none of the listed drugs are a cure and even the individual animals that are treated will experience relapses. Although this disease is not fatal in all cases and spontaneous recovery can occur, the death rate is relatively high and listed at a mortality rate of over fifty percent.

This lack of a cure or vaccine is a definite problem in the equine industry, especially in developing countries where equines are highly valuable for both agriculture and transportation. Dourine is considered an endemic problem in developing countries, where over sixty percent of equines in the world are located. The protocol for this disease, as stated by OIE, currently stands at slaughter of seropositive animals. This is not an economically feasible option for many people who depend on horses for their livelihood. Therefore, it is crucial to continue research in this field and develop a viable vaccine.

Humans are accidental hosts of "Toxocara", yet toxocariasis is seen throughout the world. Most cases of toxocariasis are seen in people under the age of twenty. Seroprevalence is higher in developing countries, but can be considerable in first world countries, as well. In Bali, St. Lucia, Nepal and other countries, seroprevalence is over fifty percent. Previous to 2007, the U.S. seroprevalence was thought to be around 5% in children. However, Won et al. discovered that U.S. seroprevalence is actually 14% for the population at large. In many countries, toxocariasis is considered very rare. Approximately 10,000 clinical cases are seen a year in the U.S., with ten percent being OLM. Permanent vision loss occurs in 700 of these cases.

Young children are at the greatest risk of infection because they play outside and tend to place contaminated objects and dirt in their mouths. Dog ownership is another known risk factor for transmission. There is also a significant correlation between high "Toxocara" antibody titers and epilepsy in children.

Parasitic loads as high as 300 larvae in a single gram of liver have been noted in humans. The “excretory-secretory antigens of larvae… released from their outer epicuticle coat [and]… readily sloughed off when bound by specific antibodies” incite the host’s immune response. The tipping point between development of VLM and OLM is believed to be between 100 and 200 larvae. The lighter infection in OLM is believed to stimulate a lower immune response and allow for migration of a larva into the eye. Larvae are thought to enter the eye through the optic nerve, central retinal artery, short posterior ciliary arteries, soft tissues, or cerebrospinal fluid. Ocular granulomas that form around a larva typically are peripheral in the retina or optic disc.

Visceral larva migrans seems to affect children aged 1–4 more often while ocular larva migrans more frequently affects children aged 7–8. Between 4.6% and 23% of U.S. children have been infected with the dog roundworm egg. This number is much higher in other parts of the world, such as Colombia, where up to 81% of children have been infected.

Actively involving veterinarians and pet owners is important for controlling the transmission of "Toxocara" from pets to humans. A group very actively involved in promoting a reduction of infections in dogs in the United States is the Companion Animal Parasite Council -- CAPC. Since pregnant or lactating dogs and cats and their offspring have the highest, active parasitic load, these animals should be placed on a deworming program. Pet feces should be picked up and disposed of or buried, as they may contain "Toxocara" eggs. Practicing this measure in public areas, such as parks and beaches, is especially essential for decreasing transmission. Up to 20% of soil samples of U.S. playgrounds have found roundworm eggs. Also, sandboxes should be covered when not in use to prevent cats from using them as litter boxes. Hand washing before eating and after playing with pets, as well as after handling dirt will reduce the chances of ingesting "Toxocara" eggs. Washing all fruits and vegetables, keeping pets out of gardens and thoroughly cooking meats can also prevent transmission. Finally, teaching children not to place nonfood items, especially dirt, in their mouths will drastically reduce the chances of infection.

Toxocariasis has been named one of the neglected diseases of U.S. poverty, because of its prevalence in Appalachia, the southern U.S., inner city settings, and minority populations. Unfortunately, there is currently no vaccine available or under development. However, the mitochondrial genomes of both "T. cati" and "T. canis" have recently been sequenced, which could lead to breakthroughs in treatment and prevention.

This disease has no vaccination.

Preventative measures can be taken at community and individual levels. Communities and governments can make sure their water supply remains sanitary and free of dog feces. Communities can control wild dog populations, thus preventing infection of the definitive host. Individuals should wash all fruits and vegetables thoroughly before eating and make sure their dogs are not infected with tapeworm.

MAP is capable of causing Johne's-like symptoms in humans, though difficulty in testing for MAP infection presents a diagnostic hurdle.

Clinical similarities are seen between Johne's disease in ruminants and inflammatory bowel disease in humans, and because of this, some researchers contend the organism is a cause of Crohn's disease. However, epidemiologic studies have provided variable results; in certain studies, the organism (or an immune response directed against it) has been much more frequently found in patients with Crohn's disease than asymptomatic people.

"P. multocida" causes numerous pathological conditions in domestic animals. It often acts with other infectious agents, such as "Chlamydia" and "Mycoplasma" species and viruses. Environmental conditions (transportation, housing deficiency, and bad weather) also play a role.

These diseases are considered caused by "P. multocida", alone or associated with other pathogens:

- Shipping fever in cattle and sheep ("shipping fever" may also be caused by "Mannheimia haemolytica", in the absence of "P. multocida", and "M. haemolytica" serovar A1 is known as the most common cause of the disease. The pathologic condition commonly arises where the causative organism becomes established by secondary infection, following a primary bacterial or viral infection, which may occur after stress, e.g. from handling or transport.)

- Enzootic pneumonia of sheep (and goats, with frequent intervention of "M. haemolytica")

- Fowl cholera (chicken and other domestic poultry and cage birds)

- Enzootic pneumonia and atrophic rhinitis of pigs

- Pasteurellosis of chinchillas

- Pasteurellosis of rabbits

- Pasteurellosis suspected in an epizootic illness of saiga antelope, although other causes are possible.

As the infection is usually transmitted into humans through animal bites, antibiotics usually treat the infection, but medical attention should be sought if the wound is severely swelling. Pasteurellosis is usually treated with high-dose penicillin if severe. Either tetracycline or chloramphenicol provides an alternative in beta-lactam-intolerant patients. However, it is most important to treat the wound.

In laboratory animals, prevention includes a low-stress environment, an adequate amount of nutritional feed, and appropriate sanitation measurements. Because animals likely ingest bacterial spores from contaminated bedding and feed, regular cleaning is a helpful method of prevention. No prevention methods are currently available for wild animal populations.

In an endemic herd, only a minority of the animals develops clinical signs; most animals either eliminate the infection or become asymptomatic carriers. The mortality rate is about 1%, but up to 50% of the animals in the herd can be asymptomatically infected, resulting in losses in production. Once the symptoms appear, paratuberculosis is progressive and affected animals eventually die. The percentage of asymptomatic carriers that develop overt disease is unknown.

"Trypanosoma equiperdum" is one of three known strains from the "Trypanosoma" family; along with "Trypanosoma evansi" and "Trypanosoma brucei". "Trypanosoma equiperdum" has been discovered to be most closely linked to "Trypanosoma evansi", so much so that even observation under microscope is not sufficient to differentiate between the two as their structure is very similar.

Dourine is a unique disease in the sense that it has no known vectors or fomites existing in the natural world, other than members of the equine family, including donkeys, mules, and horses. In a laboratory setting, "Trypanosoma equiperdum" has been manipulated to adapt to and proliferate in other species, such as dogs, rabbits, mice and rats, but this has never been observed to occur naturally and without scientific manipulation. Although this limits spread of the disease because it is restricted to the equine population alone, the organism has developed complex mechanisms over time to better equip itself for prolonged survival in the equine species. This parasite efficiently evades the host animal's immune system through the use of variable surface glycoproteins or VSGs. These VSGs allow the organism to constantly manipulate and change the surface structure of its proteins, which means it is constantly being presented to the immune system as a new foreign organism and this prevents the body from mounting a large enough immune response to eradicate the disease. In this sense, "Trypanosoma equiperdum" is a very efficient organism; it may infect less species than other diseases, but it infects and survives very efficiently within its specified hosts.

Tyzzer’s disease is an acute epizootic bacterial disease found in rodents, rabbits, dogs, cats, birds, pandas, deer, foals, cattle, and other mammals including gerbils. It is caused by the spore-forming bacterium "Clostridium piliforme", formerly known as "Bacillus piliformis". It is an infectious disease characterized by necrotic lesions on the liver, is usually fatal, and is present worldwide. Animals with the disease become infected through oral ingestion of the bacterial spores and usually die within a matter of days. Animals most commonly affected include young, stressed animals in laboratory environments, such as immature rodents and rabbits. Most commonly affected wild animals include muskrats "(Ondatra zibethicus)" and occasionally cottontail rabbits "(Lepus sylvaticus)". Even today, much remains unknown about Tyzzer’s disease, including how and why it occurs.

In humans, it can cause arteritis, keratitis, and periorbital cellulitis. This has previously been thought to be a rare disease with only 28 cases reported in the literature up to 1996. However, keratitis due to Pythium may be more common than previously thought, accounting for a proportion of cases that were due to unidentified pathogens. Although this disease was first reported in 1884 the species infecting humans - "Pythium insidiosum" - was only formally recognised in 1987. Diagnosis can be difficult in part because of a lack of awareness of the disease. It does not appear to be transmissible either animal to animal or animal to human. There appear to be three clades of this organism: one in the Americas, a second from Asia and Australia and a third with isolates from Thailand and the USA. The most probable origin of the organism seems to be in Asia.

Most human cases have been reported in Thailand, although cases have been reported elsewhere. In humans, the four forms of the disease are: subcutaneous, disseminated, ocular, and vascular. The ocular form of the disease is the only one known to infect otherwise healthy humans, and has been associated with contact lens use while swimming in infected water. This is also the rarest form with most cases requiring enucleation of the eye. The other forms of the disease require a pre-existing medical condition, usually associated with thalassemic hemoglobinopathy. Prognosis is poor to guarded and treatments include aggressive surgical resection of infected tissue, with amputation suggested if the infection is limited to a distal limb followed by immunotherapy and chemotherapy. A recently published review lists nine cases of vascular pythiosis with five survivors receiving surgery with free margins and all except one requiring amputation. The same review lists nine cases of ocular pythiosis with five patients requiring enucnleation of the infected eye and four patients requiring a corneal transplant.

In cats, pythioisis is almost always confined to the skin as hairless and edematous lesions. It is usually found on the limbs, perineum, and at the base of the tail. Lesions may also develop in the nasopharynx.

The only animals that have been successfully infected with the disease are rabbits which are used for "in vivo" studies of the disease.

Other animals reported to have contracted pythiosis are bears, jaguars, camels, and birds, although these have only been singular events.

Host tropism is the infection specificity of certain pathogens to particular hosts and host tissues. This type of tropism explains why most pathogens are only capable of infecting a limited range of host organisms.

Researchers can classify pathogenic organisms by the range of species and cell types that they exhibit host tropism for. For instance, pathogens that are able to infect a wide range of hosts and tissues are said to be amphotropic. Ecotropic pathogens, on the other hand, are only capable of infecting a narrow range of hosts and host tissue. Knowledge of a pathogen's host specificity allows professionals in the research and medical industries to model pathogenesis and develop vaccines, medication, and preventative measures to fight against infection. Methods such as cell engineering, direct engineering and assisted evolution of host-adapted pathogens, and genome-wide genetic screens are currently being used by researchers to better understand the host range of a variety of different pathogenic organisms.

Although no specific treatment for acute infection with SuHV1 is available, vaccination can alleviate clinical signs in pigs of certain ages. Typically, mass vaccination of all pigs on the farm with a modified live virus vaccine is recommended. Intranasal vaccination of sows and neonatal piglets one to seven days old, followed by intramuscular (IM) vaccination of all other swine on the premises, helps reduce viral shedding and improve survival. The modified live virus replicates at the site of injection and in regional lymph nodes. Vaccine virus is shed in such low levels, mucous transmission to other animals is minimal. In gene-deleted vaccines, the thymidine kinase gene has also been deleted; thus, the virus cannot infect and replicate in neurons. Breeding herds are recommended to be vaccinated quarterly, and finisher pigs should be vaccinated after levels of maternal antibody decrease. Regular vaccination results in excellent control of the disease. Concurrent antibiotic therapy via feed and IM injection is recommended for controlling secondary bacterial pathogens.

SuHV1 can be used to analyze neural circuits in the central nervous system (CNS). For this purpose the attenuated (less virulent) Bartha SuHV1 strain is commonly used and is employed as a retrograde and anterograde transneuronal tracer. In the retrograde direction, SuHV1-Bartha is transported to a neuronal cell body via its axon, where it is replicated and dispersed throughout the cytoplasm and the dendritic tree. SuHV1-Bartha released at the synapse is able to cross the synapse to infect the axon terminals of synaptically connected neurons, thereby propagating the virus; however, the extent to which non-synaptic transneuronal transport may also occur is uncertain. Using temporal studies and/or genetically engineered strains of SuHV1-Bartha, second, third, and higher order neurons may be identified in the neural network of interest.

Cuterebriasis is a parasitic disease affecting rodents, lagomorphs (hares, rabbits, pikas), felines and canines. The etiologic agent is the larval development of bot flies within the "Cuterebra" or "Trypoderma" genera, which occurs obligatorily in rodents and lagomorphs, respectively. Felines and canines serve as accidental hosts, but research suggests only by "Trypoderma" spp. Entrance into the body by first instar larva occurs via mucous membranes of natural orifices or open wounds as opposed to direct dermic penetration.

The risk factors associated with BPF are not well known. However, it has been suggested that children under 5 years of age are more susceptible to BPF since they lack serum bactericidal activity against the infection. Older children and adults have much higher titers of bactericidal antibodies, which serve as a protective measure. Also children residing in warmer geographic areas have been associated with a higher risk of BPF infection.

Occupations at risk include veterinarians, slaughterhouse workers, farmers, sailors on rivers, sewer maintenance workers, waste disposal facility workers, and people who work on derelict buildings. Slaughterhouse workers can contract the disease through contact with infected blood or body fluids. Rowers, kayakers and canoeists also sometimes contract the disease. It was once mostly work-related but is now often also related to adventure tourism and recreational activities.

Leptospirosis is transmitted by the urine of an infected animal and is contagious as long as the urine is still moist. Although "Leptospira" has been detected in reptiles and birds, only mammals are able to transmit the bacterium to humans and other animals. Rats, mice, and moles are important primary hosts—but a wide range of other mammals including dogs, deer, rabbits, hedgehogs, cows, sheep, swine, raccoons, opossums, skunks, and certain marine mammals carry and transmit the disease as secondary hosts. In Africa, the banded mongoose has been identified as a carrier of the pathogen, likely in addition to other African wildlife hosts. Dogs may lick the urine of an infected animal off the grass or soil, or drink from an infected puddle.

House-bound domestic dogs have contracted leptospirosis, apparently from licking the urine of infected mice in the house. The type of habitats most likely to carry infective bacteria includes muddy riverbanks, ditches, gullies, and muddy livestock rearing areas where there is a regular passage of wild or farm mammals. The incidence of leptospirosis correlates directly with the amount of rainfall, making it seasonal in temperate climates and year-round in tropical climates.

Leptospirosis also transmits via the semen of infected animals.

Humans become infected through contact with water, food, or soil that contains urine from these infected animals. This may happen by swallowing contaminated food or water or through skin contact. The disease is not known to spread between humans, and bacterial dissemination in convalescence is extremely rare in humans. Leptospirosis is common among water-sport enthusiasts in specific areas, as prolonged immersion in water promotes the entry of this bacterium. Surfers and whitewater paddlers are at especially high risk in areas that have been shown to contain these bacteria, and can contract the disease by swallowing contaminated water, splashing contaminated water into their eyes or nose, or exposing open wounds to infected water.