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A pathogen is an infectious thing, such as a virus, bacteria, fungi or parasite, which causes a disease. This ability is called pathogenicity.
The body has many ways to defend against some of the common pathogens (such as Pneumocystis) in the form of the human immune system and by some "helpful" bacteria present in the human body's normal human flora. However, if the immune system or "good" bacteria is damaged in any way (for example, chemotherapy, HIV, or antibiotics being taken to kill other pathogens), pathogenic bacteria that were being held back can grow and cause harm to the host. Such cases are opportunistic infections.