A human pathogen is a pathogen (microbe or microorganism such as a virus, bacterium, prion, or fungus) that causes disease in humans.The human physiological defense against common pathogens (such as Pneumocystis) is mainly the responsibility of the immune system with help by some of the body's normal flora and fauna.owever, if the immune system or good microbiota are damaged in any way (such as by chemotherapy, human immunodeficiency virus (HIV), or antibiotics being taken to kill other pathogens), pathogenic bacteria that were being held at bay can proliferate and cause harm to the host.