Many microbial pathogens cause acute gastrointestinal disease, the second most common cause of death of children up to 5 years in developing countries . C. parvum belong to this group together with pathogens such as enterotoxigenic E. coli, and V. cholerae. In addition, strains of B. cereus and C. difficile are two common food-borne pathogens causing diarrheal disease . Identifying the causing pathogen is vital in an outbreak when choosing the right disinfection method and theraputic approach to diarrheal disease, as well as to minimize the outbreak itself. For Cryptosporidium this is of particular interest since these infections give similar symptoms as enterotoxigenic E. coli and V. cholerae which are treated using antibiotics (for example, tetracycline and fluoroquinolones). However, nitazoxanide is the only FDA approved anti-parasitic treatment for Cryptosporidium infections . Thus, it is very important to have a robust detection method that can discriminate between pathogens to use the right disinfection approach and to know what pathogen to treat for when a person is infected.