Pathogenesis: Most species are not significant pathogens and cause little or no disease. Certain species, however, are highly pathogenic and cause catarrhalic or haemorrhagic enteritis by severe erosion of the mucosal membranes through cell lysis resulting in profuse watery-to-bloody diarrhoea. Clinical disease is not usually manifest until cumulative tissue damage associated with second or third generation schizogony. Moderately-affected animals may show progressive signs such as poor weight gain or weight loss, weakness and emaciation, while severely-affected individuals may die soon after the appearance of disease. Pathogenicity depends on many factors; such as parasite species, viability, infectivity, virulence, tropism, host age, nutritional status, immunological competence, as well as prevailing environmental conditions (temperature, moisture) and management practices. Young animals are most susceptible to clinical disease, although survivors develop strong specific protective immunity against subsequent infection and disease.

Mode of transmission: Oocysts excreted with host faeces contaminate the external environment, but they must undergo internal sporulation (sporozoite formation) before they become infective. New hosts are infected when they ingest sporulated oocysts contaminating food or water supplies (faecal-oral transmission). Following ingestion, oocysts and sporocysts excyst in the intestines releasing their contained sporozoites which invade host cells to begin merogony. Excystation stimuli include appropriate post-gastric physico-chemical conditions, such as oxygen levels, pH, bile salts, pancreatic enzymes, etc.

Differential diagnosis: Clinical signs usually coincide with parasite patency (patent period = period during which oocysts are produced). Infections are usually diagnosed by the coprological examination of host faeces for coccidial oocysts (concentrated using various sedimentation-flotation techniques). Unstained oocysts are best observed by light microscopy using suboptimal transmitted illumination (condenser wound down to introduce diffraction), phase-contrast or interference-contrast optics. Fresh faecal samples may only contain unsporulated oocysts so differential specific diagnosis may sometime require short-term storage to facilitate sporulation (2% potassium dichromate is often used to suppress microflora during storage, but not for piscine species, and refrigeration can slow the process down if so required for field samples). Researchers have recently used a range of molecular techniques to characterize genetic variation between and within parasite species, but few techniques are suitable for routine diagnostic use.

Treatment and control: Disease progression is usually so rapid that any therapeutic (curative) treatment may simply be too late. For this reason, continuous in-food or in-water medication is often used for prophylactic (preventative) treatment in many intensive animal industries. A wide range of drugs are available, including those with coccidio-static (reversible suppressive) activity or coccidio-cidal (irreversible lethal) activity. The main drug groups include sulfonamides (sulfanilamide, trimethoprim, ethopabate), pyridinoles (clopidol, decoquinate), nitrobenzamides (zoalene), organic arsenicals (roxarsone), nitrofurans (furazolidone, amprolium), quinazolinones (halofuginone), polyether ionophorous antibiotics (monensin, laslocid, salinomycin, narasin), asymmetric (diclazuril) and symmetric (toltrazuril) triazines. Regrettably, there are mounting problems being encountered with drug resistance amongst many coccidian species, especially that against synthetic drugs which tends to persist within parasite populations. Many industries recommend periodic rotation between different drug groups and the use of combination (cocktail) drugs to minimize the occurrence of resistance. Most coccidial infections stimulate the development of strong protective immune responses, albeit transient unless premunitive (short-lived unless parasites persist). There has been considerable success with control through immunoprophylaxis using attenuated or precocious strains of parasites, particularly in the poultry industry. Researchers are now attempting to develop recombinant subcellular vaccines. Outbreaks can generally be controlled by management practices based around improving hygiene, reducing crowding, removing contaminated litter and isolating infected individuals. Chemical disinfection is usually impractical as the oocysts are resistant to many conventional disinfectants.

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