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 organisms, including 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
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.
A pathogen may be described in terms of its ability to produce toxins, enter tissue, colonize, hijack nutrients, and its ability to immunosuppress the host.
Context-dependent pathogenicity
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".
Related concepts
Virulence
Virulence (the tendency of a pathogen to reduce a host's fitness) evolves when a pathogen can spread from a diseased host, despite the host becoming debilitated. Horizontal transmission occurs between hosts of the same species, in contrast to vertical transmission, which tends to evolve toward 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 biology proposes that many pathogens evolve an optimal virulence
at which the fitness gained by increased replication rates is balanced
by trade-offs in reduced transmission, but the exact mechanisms
underlying these relationships remain controversial.
Transmission
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.
Types of pathogens
Algae
Algae are single-celled eukaryotes
that are generally non-pathogenic although pathogenic varieties do
exist. 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
The vast majority of bacteria, which can range between 0.15 and 700 μM in length, are harmless or beneficial to humans. However, a relatively small list of pathogenic bacteria
can cause infectious diseases. Pathogenic bacteria have several ways
that they can cause disease. They can either directly affect the cells
of their host, produce endotoxins that damage the cells of their host,
or cause a strong enough immune response that the host cells are
damaged.
One of the bacterial diseases with the highest disease burden is tuberculosis, caused by the bacterium Mycobacterium tuberculosis, which killed 1.5 million people in 2013, 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.
Fungi
Fungi are eukaryotic organisms that can function as pathogens. There
are approximately 300 known fungi that are pathogenic to humans including Candida albicans, which is the most common cause of thrush, and Cryptococcus neoformans, which can cause a severe form of meningitis. The typical fungal spore size is <4 .7="" be="" but="" in="" larger.="" length="" m="" may="" p="" some="" spores="">
Prions
Prions are misfolded proteins that can transfer their misfolded state
to other normally folded proteins of the same type. They do not contain
any DNA or RNA and cannot replicate other than to convert already
existing normal proteins to the misfolded state. These abnormally folded
proteins are found characteristically in some diseases such as scrapie, bovine spongiform encephalopathy (mad cow disease) and Creutzfeldt–Jakob disease.
Viroids
Not to be coinfused with Virusoid or Virus.
Viroids are the smallest infectious pathogens known. They are composed
solely of a short strand of circular, single-stranded RNA that has no
protein coating. All known viroids are inhabitants of higher plants, and
most cause diseases, whose respective economic importance on humans
vary widely.
Viruses
Viruses are small particles, typically between 20 and 300 nanometers in length,
containing RNA or DNA. Viruses require a host cell to replicate. Some
of the diseases that are caused by viral pathogens include smallpox, influenza, mumps, measles, chickenpox, ebola, HIV, rubella, and COVID-19.
Pathogenic viruses are mainly from the families: Adenoviridae, Coronaviridae, Picornaviridae, Herpesviridae, Hepadnaviridae, Flaviviridae, Retroviridae, Orthomyxoviridae, Paramyxoviridae, Papovaviridae, Polyomavirus, Rhabdoviridae, and Togaviridae. HIV is a notable member of the family Retroviridae which affected 37.9 million people across the world in 2018.
Other parasites
Pathogen hosts
Bacteria
Although bacteria can be pathogens themselves, they can also be infected by pathogens. Bacteriophages
are viruses, also known as phage, that infect bacteria often leading to
the death of the bacteria that was infected. Common bacteriophage
include T7 and Lamda phage. There are bacteriophages that infect every kind of bacteria including both gram-negative and gram-positive. Even pathogenic bacteria that infect other species, including humans, can be infected with a phage.
Plants
Plants can play host to a wide range of pathogen types including viruses, bacteria, fungi, nematodes, and even other plants. Notable plant viruses include the Papaya ringspot virus which has caused millions of dollars of damage to farmers in Hawaii and Southeast Asia, and the Tobacco mosaic virus which caused scientist Martinus Beijerinck to coin the term "virus" in 1898. Bacterial plant pathogens are also a serious problem causing leaf spots, blights, and rots in many plant species. The top two bacterial pathogens for plants are P. syringae and R. solanacearum which cause leaf browning and other issues in potatoes, tomatoes, and bananas.
Fungi
are another major pathogen type for plants. They can cause a wide
variety of issues such as shorter plant height, growths or pits on tree
trunks, root or seed rot, and leaf spots. Common and serious plant fungi include the rice blast fungus, Dutch elm disease, chestnut blight and the black knot and brown rot
diseases of cherries, plums, and peaches. It is estimated that
pathogenic fungi alone cause up to a 65% reduction in crop yield.
Overall, plants have a wide array of pathogens and it has been
estimated that only 3% of the disease caused by plant pathogens can be
managed.
Animals
Animals
often get infected with many of the same or similar pathogens as humans
including prions, viruses, bacteria, and fungi. While wild animals
often get illnesses, the larger danger is for livestock animals. It is
estimated that in rural settings, 90% or more of livestock deaths can be
attributed to pathogens. The prion disease bovine spongiform encephalopathy, commonly known as Mad cow disease, is one of the few prion diseases that affect animals.
Other animal diseases include a variety of immunodeficiency disorders
that are caused by viruses related to the Human immunodeficiency virus
(HIV) including BIV and FIV.
Humans
Humans can be infected with many types of pathogens including prions,
viruses, bacteria, and fungi. Viruses and bacteria that infect humans
can cause symptoms such as sneezing, coughing, fever, vomiting, and even
lead to death. Some of these symptoms are caused by the virus itself,
while others are caused by the immune system of the infected person.
Treatment
Prion
Despite many attempts, to date no therapy has been shown to halt the progression of prion diseases.
Virus
A variety of prevention and treatment options exist for some viral pathogens. Vaccines are one common and effective preventive measure against a variety of viral pathogens.
Vaccines prime the immune system of the host, so that when the
potential host encounters the virus in the wild, the immune system can
defend against infection quickly. Vaccines exist for viruses such as the
measles, mumps, and rubella viruses and the influenza virus. Some viruses such as HIV, dengue, and chikungunya do not have vaccines available.
Treatment of viral infections often involves treating the
symptoms of the infection rather than providing any medication that
affects the viral pathogen itself.
Treating the symptoms of a viral infection gives the host immune system
time to develop antibodies against the viral pathogen which will then
clear the infection. In some cases, treatment against the virus is
necessary. One example of this is HIV where antiretroviral therapy, also known as ART or HAART, is needed to prevent immune cell loss and the progression into AIDS.
Bacteria
Much like viral pathogens, infection by certain bacterial pathogens can be prevented via vaccines. Vaccines against bacterial pathogens include the anthrax vaccine and the pneumococcal vaccine.
Many other bacterial pathogens lack vaccines as a preventive measure,
but infection by these bacteria can often be treated or prevented with antibiotics. Common antibiotics include amoxicillin, ciprofloxacin, and doxycycline.
Each antibiotic has different bacteria that it is effective against and
has different mechanisms to kill that bacteria. For example, doxycycline inhibits the synthesis of new proteins in both gram-negative and gram-positive bacteria which leads to the death of the affected bacteria.
Due in part to over-prescribing antibiotics in circumstances
where they are not needed, some bacterial pathogens have developed
antibiotic resistance and are becoming hard to treat with classical
antibiotics. A genetically distinct strain of Staphylococcus aureus called MRSA
is one example of a bacterial pathogen that is difficult to treat with
common antibiotics. A report released in 2013 by the Center for Disease
Control (CDC) estimated that each year in the United States, at least 2
million people get an antibiotic-resistant bacterial infection, and at
least 23,000 people die from those infections.
Due to their indispensability in Bacteria, essential persistent
DNA methyltransferases are potential targets for the development of
epigenetic inhibitors capable of, for example, enhance the therapeutic
activity of antimicrobials , or decrease a pathogen's virulence.
Fungi
Infection by fungal pathogens is treated with anti-fungal medication. Fungal infections such as athlete's foot, jock itch, and ringworm are infections of the skin and can be treated with topical anti-fungal medications like Clotrimazole. Other common fungal infections include infections by the yeast strain Candida albicans. Candida can cause infections of the mouth or throat, commonly referred to as thrush, or it can cause vaginal infections.
These internal infections can either be treated with anti-fungal creams
or with oral medication. Common anti-fungal drugs for internal
infections include the Echinocandin family of drugs and Fluconazole.
Algae
Algae are commonly not thought of as pathogens, but the genus Prototheca is known to cause disease in humans. Treatment for this kind of infection is currently under investigation and there is no consistency in clinical treatment.
Sexual interactions
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 genomic damage to the pathogens caused by the defenses of their respective target hosts.
