The main pathogens that are commonly looked for in feces include:
Salmonella and Shigella
Yersinia (this tends to be incubated at 30°C, which is cooler than usual.)
Campylobacter (incubated at 42°C, in a special environment.)
Aeromonas >
Candida (if the person is immunosupressed e.g. cancer treatment.)
E. coli O157 (if blood is visible in the stool sample.)
See also: Intestinal parasite
What test do you need for internal parasites?