They are done by fecal test, there are several to detect them, the most commons are direct wet mount, fecal floatation ( flagellates and static nematode ova) Then there is a gram stain on a fecal sample
Gram negative bacteria is the more common in reptiles, if I have an reptile that is not acting right and a normal fecal test(wet mount or floatation) is clear, I have it check for gram negative bacteria, this detects the bacteria like Salmonella, Proteus, Providentia etc..
Cryptosporidium there is no cure for that I know of, this is not a parasite often found. The more common ones found in reptiles are called Isospora and Eimeria, usually treated well with a sulfa-type drug like Albon (sulfadimethoxine) or one of the tri-meth drugs. A big factor in getting rid of these coccidia are cleaning.... and then clean again. Most reptiles in the wild are not exposed to their feces, like in captivity. Small babies seem far more at risk to have out of control coccidia. Its thought they may not have build up the necessary good bacteria to support a strong immune system and stress easily which sets off a blooming of the oocysts. Another good cause for babies to be well established and not sold too young. Most healthy, well cared for reptiles can deal with coccidia themselves and it is not considered a concern if they have minimal amounts in their feces, some researchers think it may be a normal part of the digestive system. I have seen it reduced to a minimal level with good cleaning practice alone in beardies.
Treating the more common coccidia in reptiles is usually not that hard, although there seems to be a very high resistant strain of coccidia emerging. This is one of the main reasons to try to knock it out or to minimal levels early. Roger Klingenberg has a treatment method that I have found works well to follow, the key is not only the medication and duration, you also have to break the cycle of infection and to do that you have to take their living area down to basics, cleaning daily and avoid things that can introduce it to them again.
Treating water?... I know that Cryptosporidium does show up in city water supplies at time, and they do have a treatment method for it in the water, sorry, I don't know what it is they use. I prefer to just give them distilled water.
If your really interested in reptile health, one of the best books I have found and well worth the cost is Reptile Medicine & Surgery by Dr Douglas R. Mader
