Coccidia & Cryptosporidiosis

These two protozoans can be acquired different than most parasites. Not only infected food and water are a source, the environment itself can be the cause due to the buildup in the enclosure.
Coccidia and Crypto are potentially fatal parasites and prove why proper isolation of new geckos for 4-5 months and an advanced fecal specifically for these parasites is so important, especially when you have many geckos it could affect.

Coccidia

As explained above, this parasite can be contracted many ways including the environment.
Symptoms vary from diarrhea to more severe cases including severe diarrhea, anorexia, lethargy eventually leading to death if untreated.
Fecal tests can detect this and if diagnosed, in time can be treated unlike crypto with Albon® as prescribed by your vet.
Hygiene is extremely critical. If possible, have 2 disinfected enclosures and change the gecko into each newly disinfected enclosure with only paper towel substrate, clean water dish and a hide spot (with, of course, the necessary heat)

Cryptosporidiosis

FACTS: Cryptosporidia was first reported in 1977 by Brownstein. Snakes and lizards only reptiles that the parasite will cause disease, however, it affects and is found in animals as well. Cryptosporidium is found in mice and even sometimes found in tap water.
HUMANS: Claimed parasite to cause disease in humans, however, it is most commonly seen to affect patients but limited to mostly gastrointestinal symptoms that last about 30 days.
REPTILES: Healthy specimens who are exposed may be affected my mild diarrhea for 2-4 weeks or no symptoms at all. Affected animals can become carriers that shed the protozoal agent for up to a year or longer. Obviously an affected animal should be COMPLETELY isolated from the rest - meaning another room. Caution of careful hygiene should never be neglected after contact with the animal, use antibacterial soap, rinse and dry well and change clothing if animal is in physical contact before handling any others.
CONTRACTED BY: Exposure to sporulated oocysts in water, food and the surrounding environment, meaning it could be airborne covering all areas of the terrarium.
LESIONS AND OTHER ADVANCED SYMPTOMS: Snakes - stomach wall; Lizards - intestinal wall. Both symptoms lead to vomiting. Some other signs include anorexia, listlessness, depression. Since there is no known cure yet, death is likely although the animals could linger for months or years.
DIAGNOSIS: Crypto is difficult to diagnose due to the small size of the oocysts. Author of the book mentions a fast-acid stain (carbol-fuchsin and brilliant green dye) in which the oocysts appear as small red organelles on a green background. Fresh feces are pretty much mandatory, regurgitated food or a biopsy may be needed. Sometimes it may not be diagnosed until autopsy.

Other preventive measures can besides proper quarantine is to feed pre-frozen mice and give reverse osmosis purified water or properly filtered water to your gecko.

Further, it has been highly recommended by vets at this present time to either use rubber gloves or disinfect your hands after handling infected animals and their environment with a 10% ammonia solution, that is the only solution to actually kill the parasite.

I personally suggest that if you own other animals, isolate crypto infected animals completely away from others and refrain from handling other animals the same day after handling and cleaning after infected animals.