In biology, a pathogen (Greek: πάθος pathos "suffering, passion" and -γενής -genēs "producer of"), in the oldest and broadest sense, is anything that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ.
The term pathogen came into use in the 1880s. Typically, the term is used to describe an infectious microorganism or agent, such as a virus, bacterium, protozoan, prion, viroid, or fungus. Small animals, such as certain kinds of worms and insect larvae, can also produce disease. However, these animals are usually, in common parlance, referred to as parasites rather than pathogens. The scientific study of microscopic, pathogenic organisms is called microbiology, while the study of disease that may include these pathogens is called pathology. Parasitology, meanwhile, is the scientific study of parasites and the organisms that host them.
There are several pathways through which pathogens can invade a host. The principal pathways have different episodic time frames, but soil has the longest or most persistent potential for harboring a pathogen. Diseases in humans that are caused by infectious agents are known as pathogenic diseases, though not all diseases are caused by pathogens. Some diseases, such as Huntington's disease, are caused by inheritance of abnormal genes.
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.
An epidemic (from Greek ἐπί epi "upon or above" and δῆμος demos "people") is the rapid spread of infectious disease to a large number of people in a given population within a short period of time, usually two weeks or less. For example, in meningococcal infections, an attack rate in excess of 15 cases per 100,000 people for two consecutive weeks is considered an epidemic.Epidemics of infectious disease are generally caused by several factors including a change in the ecology of the host population (e.g. increased stress or increase in the density of a vector species), a genetic change in the pathogen reservoir or the introduction of an emerging pathogen to a host population (by movement of pathogen or host). Generally, an epidemic occurs when host immunity to either an established pathogen or newly emerging novel pathogen is suddenly reduced below that found in the endemic equilibrium and the transmission threshold is exceeded.An epidemic may be restricted to one location; however, if it spreads to other countries or continents and affects a substantial number of people, it may be termed a pandemic. The declaration of an epidemic usually requires a good understanding of a baseline rate of incidence; epidemics for certain diseases, such as influenza, are defined as reaching some defined increase in incidence above this baseline. A few cases of a very rare disease may be classified as an epidemic, while many cases of a common disease (such as the common cold) would not.Food microbiology
Food microbiology is the study of the microorganisms that inhibit, create, or contaminate food, including the study of microorganisms causing food spoilage, pathogens that may cause disease especially if food is improperly cooked or stored, those used to produce fermented foods such as cheese, yogurt, bread, beer, and wine, and those with other useful roles such as producing probiotics.Immune system
The immune system is a host defense system comprising many biological structures and processes within an organism that protects against disease. To function properly, an immune system must detect a wide variety of agents, known as pathogens, from viruses to parasitic worms, and distinguish them from the organism's own healthy tissue. In many species, the immune system can be classified into subsystems, such as the innate immune system versus the adaptive immune system, or humoral immunity versus cell-mediated immunity. In humans, the blood–brain barrier, blood–cerebrospinal fluid barrier, and similar fluid–brain barriers separate the peripheral immune system from the neuroimmune system, which protects the brain.
Pathogens can rapidly evolve and adapt, and thereby avoid detection and neutralization by the immune system; however, multiple defense mechanisms have also evolved to recognize and neutralize pathogens. Even simple unicellular organisms such as bacteria possess a rudimentary immune system in the form of enzymes that protect against bacteriophage infections. Other basic immune mechanisms evolved in ancient eukaryotes and remain in their modern descendants, such as plants and invertebrates. These mechanisms include phagocytosis, antimicrobial peptides called defensins, and the complement system. Jawed vertebrates, including humans, have even more sophisticated defense mechanisms, including the ability to adapt over time to recognize specific pathogens more efficiently. Adaptive (or acquired) immunity creates immunological memory after an initial response to a specific pathogen, leading to an enhanced response to subsequent encounters with that same pathogen. This process of acquired immunity is the basis of vaccination.
Disorders of the immune system can result in autoimmune diseases, inflammatory diseases and cancer. Immunodeficiency occurs when the immune system is less active than normal, resulting in recurring and life-threatening infections. In humans, immunodeficiency can either be the result of a genetic disease such as severe combined immunodeficiency, acquired conditions such as HIV/AIDS, or the use of immunosuppressive medication. In contrast, autoimmunity results from a hyperactive immune system attacking normal tissues as if they were foreign organisms. Common autoimmune diseases include Hashimoto's thyroiditis, rheumatoid arthritis, diabetes mellitus type 1, and systemic lupus erythematosus. Immunology covers the study of all aspects of the immune system.Infection
Infection is the invasion of an organism's body tissues by disease-causing agents, their multiplication, and the reaction of host tissues to the infectious agents and the toxins they produce. Infectious disease, also known as transmissible disease or communicable disease, is illness resulting from an infection.
Infections are caused by infectious agents including viruses, viroids, prions, bacteria, nematodes such as parasitic roundworms and pinworms, arthropods such as ticks, mites, fleas, and lice, fungi such as ringworm, and other macroparasites such as tapeworms and other helminths.
Hosts can fight infections using their immune system. Mammalian hosts react to infections with an innate response, often involving inflammation, followed by an adaptive response.Specific medications used to treat infections include antibiotics, antivirals, antifungals, antiprotozoals, and antihelminthics. Infectious diseases resulted in 9.2 million deaths in 2013 (about 17% of all deaths). The branch of medicine that focuses on infections is referred to as infectious disease.Innate immune system
The innate immune system is one of the two main immunity strategies found in vertebrates (the other being the adaptive immune system). The innate immune system is an older evolutionary defense strategy, relatively speaking, and it is the dominant immune system response found in plants, fungi, insects, and primitive multicellular organisms.The major functions of the vertebrate innate immune system include:
Recruiting immune cells to sites of infection through the production of chemical factors, including specialized chemical mediators called cytokines
Activation of the complement cascade to identify bacteria, activate cells, and promote clearance of antibody complexes or dead cells
Identification and removal of foreign substances present in organs, tissues, blood and lymph, by specialized white blood cells
Activation of the adaptive immune system through a process known as antigen presentation
Acting as a physical and chemical barrier to infectious agents; via physical measures like skin or tree bark and chemical measures like clotting factors in blood or sap from a tree, which are released following a contusion or other injury that breaks through the first-line physical barrier (not to be confused with a second-line physical or chemical barrier, such as the blood-brain barrier, which protects the extremely vital and highly sensitive nervous system from pathogens that have already gained access to the host's body).Intracellular parasite
Intracellular parasites are microparasites that are capable of growing and reproducing inside the cells of a host. Some parasites can cause disease.Natural reservoir
In infectious disease ecology and epidemiology, a natural reservoir, also known as a disease reservoir or a reservoir of infection, is the population of organisms or the specific environment in which an infectious pathogen naturally lives and reproduces, or upon which the pathogen primarily depends for its survival. A reservoir is usually a living host of a certain species, such as an animal or a plant, inside of which a pathogen survives, often (though not always) without causing disease for the reservoir itself. By some definitions a reservoir may also be an environment external to an organism, such as a volume of contaminated air or water.Because of the enormous variety of infectious microorganisms capable of causing disease, precise definitions for what constitutes a natural reservoir are numerous, various, and often conflicting. The reservoir concept applies only for pathogens capable of infecting more than one host population and only with respect to a defined target population – the population of organisms in which the pathogen causes disease. The reservoir is any population of organisms (or any environment) which harbors the pathogen and transmits it to the target population. Reservoirs may comprise one or more different species, may be the same or a different species as the target, and, in the broadest sense, may include vector species, which are otherwise distinct from natural reservoirs. Significantly, species considered reservoirs for a given pathogen may not experience symptoms of disease when infected by the pathogen.
Identifying the natural reservoirs of infectious pathogens has proven useful in treating and preventing large outbreaks of disease in humans and domestic animals, especially those diseases for which no vaccine exists. In principle, zoonotic diseases can be controlled by isolating or destroying the pathogen's reservoirs of infection. The mass culling of animals confirmed or suspected as reservoirs for human pathogens, such as birds that harbor avian influenza, has been effective at containing possible epidemics in many parts of the world; for other pathogens, such as the ebolaviruses, the identity of the presumed natural reservoir remains obscure.Opportunistic infection
An opportunistic infection is an infection caused by pathogens (bacteria, viruses, fungi, or protozoa) that take advantage of an opportunity not normally available, such as a host with a weakened immune system, an altered microbiota (such as a disrupted gut microbiota), or breached integumentary barriers. Many of these pathogens do not cause disease in a healthy host that has a normal immune system. However, a compromised immune system, which is seriously debilitated and has lowered resistance to infection, a penetrating injury, or a lack of competition from normal commensals presents an opportunity for the pathogen to infect.PHI-base
The Pathogen-Host Interaction database (PHI-base) contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions. The database was created and is maintained by researchers at Rothamsted Research and external collaborators since 2005. Since April 2017 PHI-base is part of ELIXIR, the European life-science infrastructure for biological information via its ELIXIR-UK node.Pathogen-associated molecular pattern
These molecules can be referred to as small molecular motifs conserved within a class of microbes. They are recognized by toll-like receptors (TLRs) and other pattern recognition receptors (PRRs) in both plants and animals. A vast array of different types of molecules can serve as PAMPs, including glycans and glycoconjugates.
PAMPs activate innate immune responses, protecting the host from infection, by identifying some conserved nonself molecules. Bacterial lipopolysaccharides (LPSs), endotoxins found on the cell membranes of gram-negative bacteria, are considered to be the prototypical class of PAMPs. LPSs are specifically recognised by TLR4, a recognition receptor of the innate immune system. Other PAMPs include bacterial flagellin (recognized by TLR5), lipoteichoic acid from gram-positive bacteria (recognized by TLR2), peptidoglycan (recognized by TLR2), and nucleic acid variants normally associated with viruses, such as double-stranded RNA (dsRNA), recognized by TLR3 or unmethylated CpG motifs, recognized by TLR9. Although the term "PAMP" is relatively new, the concept that molecules derived from microbes must be detected by receptors from multicellular organisms has been held for many decades, and references to an "endotoxin receptor" are found in much of the older literature.Pathogenic bacteria
Pathogenic bacteria are bacteria that can cause disease. This article deals with human pathogenic bacteria. Although most bacteria are harmless or often beneficial, some are pathogenic, with the number of species estimated as fewer than a hundred that are seen to cause infectious diseases in humans. By contrast, several thousand species exist in the human digestive system.
One of the bacterial diseases with the highest disease burden is tuberculosis, caused by Mycobacterium tuberculosis bacteria, which kills about 2 million people a year, 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 leprosy. Pathogenic bacteria are also the cause of high infant mortality rates in developing countries.Koch's postulates are the standard to establish a causative relationship between a microbe and a disease.Pathogenic fungus
Pathogenic fungi are fungi that cause disease in humans or other organisms. Approximately 300 fungi are known to be pathogenic to humans. The study of fungi pathogenic to humans is called "medical mycology". Although fungi are eukaryotic, many pathogenic fungi are microorganisms. The study of fungi and other organisms pathogenic to plants is called plant pathology.Plant pathology
Plant pathology (also phytopathology) is the scientific study of diseases in plants caused by pathogens (infectious organisms) and environmental conditions (physiological factors). Organisms that cause infectious disease include fungi, oomycetes, bacteria, viruses, viroids, virus-like organisms, phytoplasmas, protozoa, nematodes and parasitic plants. Not included are ectoparasites like insects, mites, vertebrate, or other pests that affect plant health by eating of plant tissues. Plant pathology also involves the study of pathogen identification, disease etiology, disease cycles, economic impact, plant disease epidemiology, plant disease resistance, how plant diseases affect humans and animals, pathosystem genetics, and management of plant diseases.Prevalence
Prevalence in epidemiology is the proportion of a particular population found to be affected by a medical condition (typically a disease or a risk factor such as smoking or seat-belt use). It is derived by comparing the number of people found to have the condition with the total number of people studied, and is usually expressed as a fraction, as a percentage, or as the number of cases per 10,000 or 100,000 people. Point prevalence is the proportion of a population that has the condition at a specific point in time. Period prevalence is the proportion of a population that has the condition at some time during a given period (e.g., 12 month prevalence), and includes people who already have the condition at the start of the study period as well as those who acquire it during that period. Lifetime prevalence (LTP) is the proportion of a population that at some point in their life (up to the time of assessment) have experienced the condition.Prevalence estimates are used by epidemiologists, health care providers, government agencies, toxicologists, and insurers.
Prevalence is contrasted with incidence, which is a measure of new cases arising in a population over a given period (month, year, etc.). The difference between prevalence and incidence can be summarized thus: prevalence answers "How many people have this disease right now?" or "How many people have had this disease during this time period?" and incidence answers "How many people per year newly acquire this disease?"Pseudomonas infection
Pseudomonas infection refers to a disease caused by one of the species of the genus Pseudomonas.
"Pseudomonas sp. KUMS3" could be considered as an opportunistic pathogen, which can survive on the fish surface or in water or in the gut and may cause disease when unfavorable conditions develop.P. aeruginosa is an opportunistic human pathogen, most commonly affecting immunocompromised patients, such as those with cystic fibrosis or AIDS. Infection can affect many different parts of the body, but infections typically target the respiratory tract (e.g. patients with CF or those on mechanical ventilation), causing bacterial pneumonia. In a surveillance study between 1986 and 1989, P. aeruginosa was the third leading cause of all nosocomial infections, and specifically the number one leading cause of hospital-acquired pneumonia and third leading cause of hospital-acquired UTI. Treatment of such infections can be difficult due to multiple antibiotic resistance, and in the United States, there was an increase in MDRPA (Multidrug-resistant Pseudomonas aeruginosa) resistant to ceftazidime, ciprofloxacin, and aminoglycosides, from 0.9% in 1994 to 5.6% in 2002.P. oryzihabitans can also be a human pathogen, although infections are rare. It can cause peritonitis, endophthalmitis, septicemia and bacteremia. Similar symptoms although also very rare can be seen by infections of P. luteola.P. plecoglossicida is a fish pathogenic species, causing hemorrhagic ascites in the ayu (Plecoglossus altivelis). P. anguilliseptica is also a fish pathogen.Due to their hemolytic activity, even non-pathogenic species of Pseudomonas can occasionally become a problem in clinical settings, where they have been known to infect blood transfusions.Transmission (medicine)
In medicine, public health, and biology, transmission is the passing of a pathogen causing communicable disease from an infected host individual or group to a particular individual or group, regardless of whether the other individual was previously infected.The term strictly refers to the transmission of microorganisms directly from one individual to another by one or more of the following means:
droplet contact – coughing or sneezing on another individual
direct physical contact – touching an infected individual, including sexual contact
indirect physical contact – usually by touching a contaminated surface, including soil (fomite)
airborne transmission – if the microorganism can remain in the air for long periods
fecal-oral transmission – usually from unwashed hands, contaminated food or water sources due to lack of sanitation and hygiene, an important transmission route in pediatrics, veterinary medicine and developing countries.Transmission can also be indirect, via another organism, either a vector (e.g. a mosquito or fly) or an intermediate host (e.g. tapeworm in pigs can be transmitted to humans who ingest improperly cooked pork). Indirect transmission could involve zoonoses or, more typically, larger pathogens like macroparasites with more complex life cycles. Transmissions can be autochthonous (i.e. between two individuals in the same place) or may involve travel of the microorganism or the affected hosts.Two Steps from Hell
Two Steps from Hell is an American production music company based in Los Angeles, California, founded by Thomas Bergersen and Nick Phoenix in 2006. The company focuses predominantly on movie and trailer music, and has supplied tracks to films such as Interstellar, Harry Potter, Pirates of the Caribbean, and X-Men.Virulence
Virulence is a pathogen's or microbe's ability to infect or damage a host.
In the context of gene for gene systems, often in plants, virulence refers to a pathogen's ability to infect a resistant host. In most other contexts, especially in animal systems, virulence refers to the degree of damage caused by a microbe to its host. The pathogenicity of an organism - its ability to cause disease - is determined by its virulence factors. The noun virulence derives from the adjective virulent. Virulent can describe either disease severity or a pathogen's infectivity. The word virulent derives from the Latin word virulentus, meaning "a poisoned wound" or "full of poison."In ecology, virulence is the host's parasite-induced loss of fitness. Virulence can be understood in terms of proximate causes—those specific traits of the pathogen that help make the host ill—and ultimate causes—the evolutionary pressures that lead to virulent traits occurring in a pathogen strain.