Pathogen

A pathogen (πάθος pathos, "suffering, passion" and γἰγνομαι (γεν-) gignomai (gen-) "I give birth to") or infectious agent — colloquially, a germ — is a microbe or microorganism such as a virus, bacterium, prion, or fungus that causes disease in its animal or plant host. 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.

The body contains many natural orders of defense 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 flora. However, if the immune system or "good" bacteria is 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. Such cases are called opportunistic infection.

Some pathogens (such as the bacterium Yersinia pestis which may have caused the Black Plague, the Variola virus, and the Malaria protozoa) have been responsible for massive numbers of casualties and have had numerous effects on afflicted groups. Of particular note in modern times is HIV, which is known to have infected several million humans globally, along with the Influenza virus. Today, while many medical advances have been made to safeguard against infection by pathogens, through the use of vaccination, antibiotics, and fungicide, pathogens continue to threaten human life. Social advances such as food safety, hygiene, and water treatment have reduced the threat from some pathogens. Not all pathogens are negative. 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.

Viral
Pathogenic viruses are mainly those of the families of: Adenoviridae, Picornaviridae, Herpesviridae, Hepadnaviridae, Flaviviridae, Retroviridae, Orthomyxoviridae, Paramyxoviridae, Papovaviridae, Polyomavirus, Rhabdoviridae, Togaviridae. Some notable pathogenic viruses cause: smallpox, influenza, mumps, measles, chickenpox, ebola, and rubella. Viruses typically range between 20-300 nanometers in length.

Bacterial
Although the vast majority of bacteria are harmless or beneficial, a few pathogenic bacteria can cause infectious diseases. The most common bacterial disease is tuberculosis, caused by the bacterium Mycobacterium tuberculosis, which affects about 2 million people mostly in sub-Saharan Africa. Pathogenic bacteria contribute to other globally important diseases, such as pneumonia, which can be caused by bacteria such as Streptococcus and Pseudomonas, and foodborne illnesses, which can be caused by bacteria such as Shigella, Campylobacter and Salmonella. Pathogenic bacteria also cause infections such as tetanus, typhoid fever, diphtheria, syphilis and Hansen's disease. Bacteria can often be killed by antibiotics because the cell wall in the outside is destroyed and then the DNA. They typically range between 1-5 micrometers in length.

Fungal
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. Life threatening fungal infections in humans most often occur in immunocompromised patients or vulnerable people with a weakened immune system, although fungi are common problems in the immunocompetent population as the causative agents of skin, nail or yeast infections. Most antibiotics that function on bacterial pathogens cannot be used to treat fungal infections because fungi and their hosts both have eukaryotic cells. Most clinical fungicides belong to the azole group. The typical fungal spore size is 1-40 micrometer in length.

Other parasites
Some eukaryotic organisms, such as protists and helminths, cause disease. One of the best known diseases caused by protists in the genus Plasmodium is malaria. These can range from 3-200 micrometers in length.

Prionic
Prions are infectious pathogens that do not contain nucleic acids. Prions are abnormal proteins whose presence causes some diseases such as scrapie, bovine spongiform encephalopathy (mad cow disease) and Creutzfeldt–Jakob disease. The discovery of prion as a new class of pathogen has lead Stanley B. Prusiner to receive Nobel Prize in Physiology or Medicine in 1997.

Potency
One hypothesis regarding pathogens states that the longer a pathogen can survive outside of the body, the more dangerous it can be to a potential host. For example, the smallpox virus (variola virus) can survive outside the human body for approximately 885 days. It is also one of the most deadly pathogenic viruses, as it kills between 20-50% of the people it infects. The tuberculosis bacterium kills 1 in 5 of the people it infects, but only survives 244 days outside of its host. However, research into the basis of the ability of pathogens to cause disease provides evidence from multiple and diverse species of the existence of pathogenicity or virulence factors, encoded within the pathogens' genetic material, that facilitate microbes to cause disease.

In countries that have higher sanitation standards, pathogens cannot survive for as long outside of the human. This is seen as encouragement to mutations to the pathogen which would make it less deadly, as such mutations would allow the pathogen to survive in the host for longer periods of time.

Transmission
One of the primary pathways by which food or water become contaminated is from the release of untreated sewage into a drinking water supply or onto cropland, with the result that people who eat or drink contaminated sources become infected. In developing countries most sewage is discharged into the environment or on cropland; even in developed countries there are periodic system failures resulting in a sanitary sewer overflow.

Major human pathogens

 * Bacillus anthracis &mdash; the causative agent of anthrax in humans and animals.
 * Clostridium botulinum &mdash; releases the most powerful neurotoxin leading to death from botulism.
 * Mycobacterium tuberculosis &mdash; the causative agent of most cases of tuberculosis
 * Mycobacterium leprae &mdash; the bacterium that causes leprosy (Hansen's disease)
 * Yersinia pestis &mdash; pneumonic, septicemic, and the notorious bubonic plagues (aka "Black Death")
 * Rickettsia prowazekii &mdash; the etiologic agent of typhus fever
 * Bartonella spp.
 * Spanish influenza virus