Pathogenicity refers to the ability of an organism to cause disease (ie, harm the host). This ability represents a genetic component of the pathogen and the overt damage done to the host is a property of the host-pathogen interactions. Commensals and opportunistic pathogens lack this inherent ability to cause disease. However, disease is not an inevitable outcome of the host-pathogen interaction and, furthermore, pathogens can express a wide range of virulence.

Virulence, a term often used interchangeably with pathogenicity, refers to the degree of pathology caused by the organism. The extent of the virulence is usually correlated with the ability of the pathogen to multiply within the host and may be affected by other factors (ie, conditional). In summary, an organism (species or strain) is defined as being pathogenic (or not), and depending upon conditions, may exhibit different levels of virulence.

Infectious diseases are caused by pathogens, which include bacteria, fungi, protozoa, worms, viruses, and even infectious proteins called prions. They rely entirely on subverting the machinery of the host cell to produce their proteins and to replicate their genomes.

A variety of microorganisms can cause disease. Pathogenic organisms are of five main types: viruses, bacteria, fungi, protozoa, and worms.

Types of pathogenesis include microbial infection, inflammation, malignancy and tissue breakdown. For example, bacterial pathogenesis is the mechanism by which bacteria cause infectious illness. Most diseases are caused by multiple processes.

Bacterial pathogens use common regulatory mechanisms, such as alternative sigma factors and two component signal transduction systems, to control the expression of their virulence genes in response to environmental conditions encountered during infection of the human host, including changes in temperature, pH, osmotic pressure etc.

It is common to speak of an entire species of bacteria as pathogenic when it is identified as the cause of a disease (cf. Koch's postulates). However, the modern view is that pathogenicity depends on the microbial ecosystem as a whole. A bacterium may participate in opportunistic infections in immunocompromised hosts, acquire virulence factors by plasmid infection, become transferred to a different site within the host, or respond to changes in the overall numbers of other bacteria present. For example, infection of mesenteric lymph glands of mice with Yersinia can clear the way for continuing infection of these sites by Lactobacillus, possibly by a mechanism of "immunological scarring".

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.[citation needed]. 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.

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