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A pathogen (Greek: πάθος pathos “suffering, passion” and γενής genēs “producer of”) or infectious agent (colloquially known as a germ) is a microorganism—in the widest sense, such as a virus, bacterium, prion, or fungus—that causes disease in its host. The host may be an animal (including humans), a plant, or even another microorganism.
There are several substrates including pathways whereby pathogens can invade a host. The principal pathways have different episodic time frames, but soil contamination has the longest or most persistent potential for harboring a pathogen. Diseases caused by organisms in humans are known as pathogenic diseases. Some of the diseases that a pathogen can cause are smallpox, influenza, mumps, measles, chickenpox, ebola, and rubella.
Not all pathogens are necessarily undesirable to humans. In entomology, pathogens are one of the "Three P's" (predators, pathogens and parasitoids) that serve as natural or introduced biological controls to suppress arthropod pest populations.
Pathogenic viruses are mainly those of the families of: Adenoviridae, bacteria Picornaviridae, Herpesviridae, Hepadnaviridae, Flaviviridae, Retroviridae, Orthomyxoviridae, Paramyxoviridae, Papovaviridae, Polyomavirus, Rhabdoviridae, Togaviridae. Viruses typically range between 20-300 nanometers in length. 
Although the vast majority of bacteria are harmless or beneficial, a few pathogenic bacteria can cause infectious diseases. Bacteria can often be killed by antibiotics because the cell wall in the outside is destroyed, expelling the DNA out of the body of the pathogen, therefore making the pathogen incapable of producing proteins and dies. They typically range between 1 and 5 micrometers in length.
Fungi comprise a eukaryotic kingdom of microbes that are usually saprophytes but can cause diseases in humans, animals and plants. Fungi are the most common cause of diseases in crops and other plants. The typical fungal spore size is 1-40 micrometer in length.
According to the prion theory, prions are infectious pathogens that do not contain nucleic acids. These abnormally-folded proteins are found characteristically in some diseases such as scrapie, bovine spongiform encephalopathy (mad cow disease) and Creutzfeldt–Jakob disease. Although prions fail to meet the requirements laid out by Koch's postulates, the hypothesis of prions as a new class of pathogen led Stanley B. Prusiner to receive the Nobel Prize in Physiology or Medicine in 1997.
Animal pathogens are disease-causing agents of wild and domestic animal species, at times including humans.
Virulence (the tendency of a pathogen to cause damage to a host's fitness) evolves when that pathogen can spread from a diseased host, despite that host being very debilitated. Horizontal transmission occurs between hosts of the same species, in contrast to vertical transmission, which tends to evolve symbiosis (after a period of high morbidity and mortality in the population) by linking the pathogen's evolutionary success to the evolutionary success of the host organism.
Evolutionary medicine has found that under horizontal transmission, the host population might never develop tolerance to the pathogen.
Transmission of pathogens occurs through many different routes, including airborne, direct or indirect contact, sexual contact, through blood, breast milk, or other body fluids, and through the fecal-oral route.