The general term for a microorganism that causes disease is a pathogen. Pathogens include certain bacteria, viruses, fungi, protozoa, and other infectious agents that can invade a host and produce disease.
The word comes from Greek roots meaning “disease-producing.” A pathogen may harm the body directly, such as by destroying cells, or indirectly, such as by releasing toxins or provoking an damaging immune response. Whether infection leads to illness can depend on the organism’s virulence, the amount that enters the body, and the host’s immune defenses.
“Virus,” “bacterium,” and “parasite” are narrower terms, which is why they are not the best general answer. A virus is one type of pathogen, and some bacteria are pathogenic while others are harmless or beneficial. Parasite usually describes an organism that lives in or on a host and benefits at the host’s expense, but not every use of the word is interchangeable with pathogen.
Pathogens are also distinguished from normal microbiota: many microorganisms live harmlessly on or inside humans, while others can cause disease when they reach the wrong tissue or when immunity is weakened.