Researchers have investigated the infection mechanisms used by bacteria causing severe diarrhea. Strains of Escherichia coli (commonly known as E. coli) bacteria, and bacteria of the genus Yersinia, attach themselves to the wall of the small intestine and use a needle-like apparatus to inject toxins into the tissue. Yet these bacteria usually enter the human body via the mouth -- and you would expect them to be killed off by the strong acid in the stomach, which provides a barrier against infection.

Source: How E. coli passes safely through stomach acid