Pathogen


In biology, a pathogen, in the oldest and broadest sense, is any organism, agent or micro-organism 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 pathogen is used to describe an infectious microorganism or agent, such as a virus, bacterium, protozoan, prion, viroid, or fungus. Small animals, such as helminths and insects, can also cause or transmit disease. However, these animals are usually referred to as parasites rather than pathogens. The scientific study of microscopic organisms, including microscopic pathogenic organisms, is called microbiology, while parasitology refers to 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. Not all diseases are caused by pathogens, such as black lung from exposure to the pollutant coal dust, genetic disorders like sickle cell disease, and autoimmune diseases like lupus.

Pathogenicity

Pathogenicity is the potential disease-causing capacity of pathogens, involving a combination of infectivity and virulence. 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 vectors like mosquitos and ticks. 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 microbial toxins 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 eukaryotes 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 prokaryotes 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 gut microbiome that support digestion, a small percentage are pathogenic and cause infectious diseases. Bacterial virulence factors include adherence factors to attach to host cells, invasion factors supporting entry into host cells, capsules to prevent opsonization and phagocytosis, toxins, and siderophores to acquire iron.
The bacterial disease tuberculosis, primarily caused by Mycobacterium tuberculosis, has one of the highest disease burdens, killing 1.6 million people in 2021, mostly in Africa and Southeast Asia. Bacterial pneumonia is primarily caused by Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, and Haemophilus influenzae. Foodborne illnesses typically involve Campylobacter, Clostridium perfringens, Escherichia coli, Listeria monocytogenes, and Salmonella. Other infectious diseases caused by pathogenic bacteria include tetanus, typhoid fever, diphtheria, 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. Typical fungal spores are 4.7 μm long or smaller.

Prions

s are misfolded proteins that transmit their abnormal folding pattern to other copies of the protein without using nucleic acids. 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 herbivorous animals. 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 diseases like Creutzfeldt–Jakob disease, variant Creutzfeldt–Jakob disease, Gerstmann–Sträussler–Scheinker syndrome, fatal familial insomnia, 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 virusoids 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, the Baltimore classification separates viruses by seven classes of mRNA production:
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, Acanthamoeba keratitis, and primary amoebic meningoencephalitis.
Parasitic worms 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. Helminthiasis is the generalized term for parasitic worm infections, which typically involve roundworms, tapeworms, and flatworms.

Pathogen hosts

Bacteria

While bacteria are typically viewed as pathogens, they serve as hosts to bacteriophage viruses. 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 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 pathogens 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.
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.