Cryptosporidium: acid fast staining is not very sensitive if not heavily infected and much more sensitive tests is often/sometimes used.
"There are several immunologic techniques, including immunofluorescence and enzymed-linked immunoassays, which are commercially availiable in several laboratories. These techniques have sensitivity and specificity approaching 100% for Cryptosporidium parvum....."
Tropical Infection Diseases, Second edition, Edited by Guerrant, Walker and Weller, page 1009,