In biology, a pathogen (Greek: πάθος pathos "suffering, passion" and -γενής -genēs "producer of") or a germ in the oldest and broadest sense is anything that can produce disease; the term came into use in the 1880s. Typically the term is used to describe an infectious agent such as a virus, bacterium, protozoa, prion, a fungus, or other micro-organism. The scientific study of pathogens is called Pathology.
There are several substrates including pathways where the 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.
Pathogenicity is the potential disease-causing capacity of pathogens. Pathogenicity is related to virulence in meaning, but some authorities have come to distinguish it as a qualitative term, whereas the latter is quantitative. By this standard, an organism may be said to be pathogenic or non-pathogenic in a particular context, but not "more pathogenic" than another. Such comparisons are described instead in terms of relative virulence. Pathogenicity is also distinct from the transmissibility of the virus, which quantifies the risk of infection.
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.
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.
The vast majority of bacteria, which typically range between 1 and 5 micrometers in length, are harmless or beneficial to humans. However, a relatively small list of pathogenic bacteria can cause infectious diseases. One of the bacterial diseases with the highest disease burden is tuberculosis, caused by the bacterium Mycobacterium tuberculosis, which kills about 2 million people a year, mostly in sub-Saharan Africa. Pathogenic bacteria contribute to other globally significant 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 leprosy.
Bacteria can often be killed by antibiotics, which are usually designed to destroy the cell wall. This expels the pathogen's DNA, making it incapable of producing proteins and causing the bacteria to die. A class of bacteria without cell walls is mycoplasma (a cause of lung infections). A class of bacteria which must live within other cells (obligate intracellular parasitic) is chlamydia (genus), the world leader in causing sexually transmitted infection (STI).
Pathogenic viruses are diseases mainly of the families of: Adenoviridae, Picornaviridae, Herpesviridae, Hepadnaviridae, Flaviviridae, Retroviridae, Orthomyxoviridae, Paramyxoviridae, Papovaviridae, Polyomavirus, Rhabdoviridae, Togaviridae. Viruses typically range between 20 and 300 nanometers in length.
Fungi comprise a eukaryotic kingdom of microbes that are usually saprophytes (consume dead organisms) 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 micrometers 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.
Examples of algae acting as a mammalian pathogen are known as well, notably the disease protothecosis. Protothecosis is a disease found in dogs, cats, cattle, and humans caused by a type of green alga known as prototheca that lacks chlorophyll.
Bacteria are usually treated with antibiotics while viruses are treated with antiviral compounds. Eukaryotic pathogens are typically not susceptible to antibiotics and thus need specific drugs. Infection with many pathogens can be prevented by immunization. A small amount of pathogens are used in vaccines to make immunity stay alert and strengthen defense on the insides to prepare for a larger quantity of the virus ever getting inside. Hygiene is critical for the prevention of infection by pathogens.
Many pathogens are capable of sexual interaction. Among pathogenic bacteria sexual interaction occurs between cells of the same species by the process of natural genetic transformation. Transformation involves the transfer of DNA from a donor cell to a recipient cell and the integration of the donor DNA into the recipient genome by recombination. Examples of bacterial pathogens capable of natural transformation are Helicobacter pylori, Haemophilus influenzae, Legionella pneumophila, Neisseria gonorrhoeae and Streptococcus pneumoniae.
Eukaryotic pathogens are often capable of sexual interaction by a process involving meiosis and syngamy. Meiosis involves the intimate pairing of homologous chromosomes and recombination between them. Examples of eukaryotic pathogens capable of sex include the protozoan parasites Plasmodium falciparum, Toxoplasma gondii, Trypanosoma brucei, Giardia intestinalis, and the fungi Aspergillus fumigatus, Candida albicans and Cryptococcus neoformans.
Viruses may also undergo sexual interaction when two or more viral genomes enter the same host cell. This process involves pairing of homologous genomes and recombination between them by a process referred to as multiplicity reactivation. Examples of viruses that undergo this process are herpes simplex virus, human immunodeficiency virus, and vaccinia virus.
The sexual processes in bacteria, microbial eukaryotes and viruses all involve recombination between homologous genomes that appears to facilitate the repair of genome damages inflicted on the genome of the pathogens by the defenses of their respective target hosts.