Pathogen

A pathogen or infectious agent is a biological agent that causes disease or illness to its host. The term is most often used for agents that disrupt the normal physiology of a multicellular animal or plant. However, pathogens can infect unicellular organisms from all of the biological kingdoms. The term pathogen is derived from the Greek παθογένεια, "that which produces suffering." There are several substrates and pathways where by 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 defenses 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 infections.

Some pathogens (such as the bacterium Yersinia pestis, which may have caused the Black Plague, and the Variola and Malaria viruses) 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 Severe Acute Respiratory Syndrome (SARS) and 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.

Types of pathogens
Below is a listing of different types of notable pathogens as categorized by their structural characteristics, and some of their known effects on infected hosts.

Transmission of pathogens
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 as of 2007; even in developed countries there are periodic system failures resulting in a sanitary sewer overflow. This is the typical mode of transmission for the infectious agents of (at least):
 * Cholera
 * Hepatitis A
 * Polio
 * Rotavirus

Transmission to vascular plants
In the case of terrestrial vascular plants, pathogenic infection can occur by contact with foliage, and also from root uptake of soil pathogens. The latter pathway explains why some plant families such as orchids are more disease resistant, since they rely upon fungal hyphae to supply nutrients rather than root structures, which have larger radii for conveying certain pathogens.