In biology, a pathogen (, "suffering", "passion" and -γενής, "producer of"), in the oldest and broadest sense, is any organism or agent 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.
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. Not all diseases are caused by pathogens, such as black lung from exposure to the pollutant coal dust, like sickle cell disease, and autoimmune diseases like lupus.
Pathogenicity
Pathogenicity is the potential disease-causing capacity of pathogens, involving a combination of
infectivity (pathogen's ability to infect hosts) and
virulence (severity of host disease). Koch's postulates are used to establish causal relationships between microbial pathogens and diseases. Whereas
meningitis can be caused by a variety of bacterial, viral, fungal, and parasitic pathogens,
cholera is only caused by some strains of
Vibrio cholerae. Additionally, some pathogens may only cause disease in hosts with an
immunodeficiency. These opportunistic infections often involve hospital-acquired infections among patients already combating another condition.
Infectivity involves pathogen transmission through direct contact with the bodily fluids or airborne droplets of infected hosts, indirect contact involving contaminated areas/items, or transfer by living Disease vector like and . The basic reproduction number of an infection is the expected number of subsequent cases it is likely to cause through transmission.
Virulence involves pathogens extracting host nutrients for their survival, evading host immune systems by producing and causing immunosuppression. Optimal virulence describes a theorized equilibrium between a pathogen spreading to additional hosts to parasitize resources, while lowering their virulence to keep hosts living for vertical transmission to their offspring.
Types
Algae
Algae include single-celled
that are generally non-pathogenic. Green algae from the genus
Prototheca lack chlorophyll and are known to cause the disease
protothecosis in humans, dogs, cats, and cattle, typically involving the soil-associated species
Prototheca wickerhamii.
Bacteria
Bacteria are single-celled
that range in size from 0.15 and 700 μM.
While the vast majority are either harmless or beneficial to their hosts, such as members of the
Human microbiome that support digestion, a small percentage are pathogenic and cause infectious diseases. Bacterial
include adherence factors to attach to host cells, invasion factors supporting entry into host cells, capsules to prevent
Opsonin and
phagocytosis, toxins, and
to acquire iron.
The bacterial disease tuberculosis, primarily caused by Mycobacterium tuberculosis, has one of the highest , killing 1.6 million people in 2021, mostly in Africa and Southeast Asia.
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
Candidiasis, and
Cryptococcus neoformans, which can cause a severe form of
meningitis.
Typical fungal spores are 4.7 μm long or smaller.
Prions
are misfolded proteins that transmit their abnormal folding pattern to other copies of the protein without using
. Besides obtaining prions from others, these misfolded proteins arise from genetic differences, either due to family history or sporadic mutations.
Plants uptake prions from contaminated soil and transport them into their stem and leaves, potentially transmitting the prions to
Herbivore.
Additionally, wood, rocks, plastic, glass, cement, stainless steel, and aluminum have been shown binding, retaining, and releasing prions, showcasing that the proteins resist environmental degradation.
Prions are best known for causing transmissible spongiform encephalopathy (TSE) diseases like Creutzfeldt–Jakob disease (CJD), variant Creutzfeldt–Jakob disease (vCJD), Gerstmann–Sträussler–Scheinker syndrome (GSS), Fatal insomnia (FFI), and kuru in humans.
While prions are typically viewed as pathogens that cause protein amyloid fibers to accumulate into neurodegenerative plaques, Susan Lindquist led research showing that yeast use prions to pass on evolutionarily beneficial traits.
Viroids
Not to be confused with
or viruses, viroids are the smallest known infectious pathogens. Viroids are small single-stranded, circular RNA that are only known to cause plant diseases, such as the potato spindle tuber viroid that affects various agricultural crops. Viroid RNA is not protected by a protein coat, and it does not encode any proteins, only acting as a
ribozyme to catalyze other biochemical reactions.
Viruses
Viruses are generally between 20–200 nm in diameter.
For survival and replication, viruses inject their genome into host cells, insert those genes into the host genome, and hijack the host's machinery to produce hundreds of new viruses until the cell bursts open to release them for additional infections. The
lytic cycle describes this active state of rapidly killing hosts, while the
lysogenic cycle describes potentially hundreds of years of dormancy while integrated in the host genome.
Alongside the taxonomy organized by the International Committee on Taxonomy of Viruses (ICTV), the Baltimore classification separates viruses by seven classes of
Messenger RNA production:
-
I: dsDNA viruses (e.g., Adenoviridae, Herpesviridae, and Poxviridae) cause Herpes simplex, chickenpox, and smallpox
-
II: ssDNA viruses (+ strand or "sense") DNA (e.g., Parvoviridae) include parvovirus B19
-
III: dsRNA viruses (e.g., Reoviridae) include
-
IV: (+)ssRNA viruses (+ strand or sense) RNA (e.g., , , and Alphavirus) cause COVID-19, dengue fever, Hepatitis A, Hepatitis C, rubella, and yellow fever
-
V: (−)ssRNA viruses (− strand or antisense) RNA (e.g., Orthomyxoviridae and Rhabdoviridae) cause ebola, influenza, measles, mumps, and rabies
-
VI: ssRNA-RT viruses (+ strand or sense) RNA with DNA intermediate in life-cycle (e.g., ) cause HIV/AIDS
-
VII: dsDNA-RT viruses DNA with RNA intermediate in life-cycle (e.g., Hepadnaviridae) cause Hepatitis B
Other parasites
Protozoans are single-celled eukaryotes that feed on microorganisms and organic tissues. Many protozoans act as pathogenic parasites to cause diseases like
malaria,
amoebiasis,
giardiasis,
toxoplasmosis, cryptosporidiosis,
trichomoniasis,
Chagas disease,
leishmaniasis, African trypanosomiasis (sleeping sickness),
Acanthamoeba keratitis, and
Naegleriasis (naegleriasis).
(helminths) are macroparasites that can be seen by the naked eye. Worms live and feed in their living host, acquiring nutrients and shelter in the digestive tract or bloodstream of their host. They also manipulate the host's immune system by secreting immunomodulatory products which allows them to live in their host for years.
Pathogen hosts
Bacteria
While bacteria are typically viewed as pathogens, they serve as hosts to
bacteriophage viruses (commonly known as phages). The bacteriophage life cycle involves the viruses injecting their genome into bacterial cells, inserting those genes into the bacterial genome, and hijacking the bacteria's machinery to produce hundreds of new phages until the cell bursts open to release them for additional infections. Typically, bacteriophages are only capable of infecting a specific species or strain.
Streptococcus pyogenes uses a Cas9 nuclease to cleave foreign DNA matching the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) associated with bacteriophages, removing the viral genes to avoid infection. This mechanism has been modified for artificial CRISPR gene editing.
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 pathology cause leaf spots, blight, and rot in many plant species.
The most common bacterial pathogens for plants are
Pseudomonas syringae and
Ralstonia solanacearum, which cause leaf browning and other issues in potatoes, tomatoes, and bananas.
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.
Animal transmissible spongiform encephalopathy (TSEs) involving prions include bovine spongiform encephalopathy (mad cow disease), chronic wasting disease,
scrapie, transmissible mink encephalopathy, feline spongiform encephalopathy, and ungulate spongiform encephalopathy.
Other animal diseases include a variety of immunodeficiency disorders caused by viruses related to human immunodeficiency virus (HIV), such as BIV and FIV.
Humans
Humans can be infected with many types of pathogens, including prions, viruses, bacteria, and fungi, causing symptoms like sneezing, coughing, fever, vomiting, and potentially lethal organ failure. While some symptoms are caused by the pathogenic infection, others are caused by the immune system's efforts to kill the pathogen, such as feverishly high body temperatures meant to denature pathogenic cells.
Treatment
Prions
Despite many attempts, no therapy has been shown to halt the progression of
prion diseases.
Viruses
A variety of prevention and treatment options exist for some viral pathogens.
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 designed against viruses include annual influenza vaccines and the two-dose
MMR vaccine against
measles,
mumps, and
rubella.
Vaccines are not available against the viruses responsible for HIV/AIDS,
Dengue virus, and
chikungunya.
Treatment of viral infections often involves treating the symptoms of the infection, rather than providing medication to combat the viral pathogen itself.
Bacteria
Much like viral pathogens, infection by certain bacterial pathogens can be prevented via vaccines.
Vaccines against bacterial pathogens include the
Anthrax vaccines and pneumococcal vaccine. Many other bacterial pathogens lack vaccines as a preventive measure, but infection by these bacteria can often be treated or prevented with
. 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 makes it a broad-spectrum antibiotic capable of killing most bacterial species.
Due to misuse of antibiotics, such as prematurely ended prescriptions exposing bacteria to evolutionary pressure under sublethal doses, some bacterial pathogens have developed antibiotic resistance.
Due to their indispensability in combating bacteria, new antibiotics are required for medical care. One target for new antimicrobial medications involves inhibiting DNA methyltransferases, as these proteins control the levels of expression for other genes, such as those encoding virulence factors.
Fungi
Infection by fungal pathogens is treated with anti-fungal medication. Athlete's foot,
Tinea cruris, and
Dermatophytosis are fungal skin infections that are treated with topical anti-fungal medications like
clotrimazole.
Infections involving the yeast species
Candida albicans cause
Candidiasis and vaginal yeast 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
While algae are commonly not thought of as pathogens, the genus
Prototheca causes disease in humans
. Treatment for
protothecosis 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 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 through genetic recombination. The bacterial pathogens
Helicobacter pylori,
Haemophilus influenzae,
Legionella pneumophila,
Neisseria gonorrhoeae, and
Streptococcus pneumoniae frequently undergo transformation to modify their genome for additional traits and evasion of host immune cells.
Eukaryote pathogens are often capable of sexual interaction by a process involving meiosis and Fertilisation. 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 lamblia, and the fungi Aspergillus fumigatus, Candida albicans and Cryptococcus neoformans.
Viruses may also undergo sexual interaction when two or more viral enter the same host cell. This process involves pairing of homologous genomes and recombination between them by a process referred to as multiplicity reactivation. The herpes simplex virus, HIV, and vaccinia virus undergo this form of sexual interaction.
These processes of sexual recombination between homologous genomes supports DNA repair to genetic damage caused by environmental stressors and host immune systems.
See also
External links
