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   » » Wiki: Yersinia Pestis
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Yersinia pestis (formerly pestis) is a Gram-negative, nonmotile, rod-shaped, bacteria, with no spores. It is a facultative anaerobic organism that can infect humans via the Oriental rat flea.

(2019). 9780838585290, McGraw Hill.
It causes the disease plague, which takes three main forms: , septicemic and . Https://www.cdc.gov/plague/< /ref> All three forms were responsible for a number of high-mortality throughout human history, including: the sixth century's Plague of Justinian; the , which accounted for the death of at least one-third of the population between 1347 and 1353; the Great Plague of London of 1665 which was ended in 1666 by the Great Fire of London; and the Third Pandemic, sometimes referred to as the Modern Plague, which began in the late nineteenth century in China and spread by rats on steamboats, claiming close to 10,000,000 lives.
(2019). 9780826328717, University of New Mexico Press. .
These plagues likely originated in and were transmitted west via trade routes. Recent research indicates that the pathogen may have been the cause of what is described as the Neolithic Decline, when European populations declined significantly.Zhang, Sarah, " An Ancient Case of the Plague Could Rewrite History", The Atlantic, December 6, 2018 This would push the date to much earlier and might be indicative of an origin in Europe rather than Eurasia.

Y. pestis was discovered in 1894 by , a / and from the Pasteur Institute, during an epidemic of the plague in . Yersin was a member of the school of thought. Kitasato Shibasaburō, a -trained bacteriologist who practised , was also engaged at the time in finding the causative agent of the plague. However, Yersin actually linked plague with Y. pestis. Named Pasteurella pestis in the past, the organism was renamed Yersinia pestis in 1944.

Every year, thousands of cases of the plague are still reported to the World Health Organization, although with proper treatment, the for victims is now much better. A five- to six-fold increase in cases occurred in Asia during the time of the , possibly due to the disruption of ecosystems and closer proximity between people and animals. The plague is now commonly found in sub-Saharan Africa and Madagascar, areas which now account for over 95% of reported cases. The plague also has a detrimental effect on nonhuman mammals.CDC, "The Plague", Centers for Disease Control and Prevention, Oct. 2017 In the United States, mammals such as the black-tailed prairie dog and the endangered black-footed ferret are under threat.


General characteristics
Y. pestis is a nonmotile, stick-shaped, facultative anaerobic bacterium with bipolar staining (giving it a appearance) that produces an antiphagocytic slime layer.
(1996). 9780963117212, Univ. of Texas Medical Branch. .
Similar to other species, it tests negative for , lactose fermentation, and .
(2019). 9780387254999, Springer.
The closest relative is the gastrointestinal pathogen Yersinia pseudotuberculosis, and more distantly Yersinia enterocolitica.


Genome
The complete sequence is available for two of the three subspecies of Y. pestis: strain KIM (of biovar Y. p. medievalis), and strain CO92 (of biovar Y. p. orientalis, obtained from a clinical isolate in the United States). As of 2006, the genomic sequence of a strain of biovar Antiqua has been recently completed. Similar to the other pathogenic strains, signs exist of loss of function mutations. The of strain KIM is 4,600,755 base pairs long; the chromosome of strain CO92 is 4,653,728 base pairs long. Like Y. pseudotuberculosis and Y. enterocolitica, Y. pestis is host to the pCD1. It also hosts two other plasmids, pPCP1 (also called pPla or pPst) and pMT1 (also called pFra) that are not carried by the other Yersinia species. pFra codes for a that is important for the ability of Y. pestis to be transmitted by fleas. pPla codes for a , Pla, that activates in human hosts and is a very important for pneumonic plague. Together, these plasmids, and a pathogenicity island called HPI, encode several proteins that cause the pathogenesis, for which Y. pestis is famous. Among other things, these virulence factors are required for bacterial adhesion and injection of proteins into the host cell, invasion of bacteria in the host cell (via a type-III secretion system), and acquisition and binding of iron harvested from red blood cells (by ). Y. pestis is thought to be descended from Y. pseudotuberculosis, differing only in the presence of specific virulence plasmids.

A comprehensive and comparative analysis of Y. pestis strain KIM was performed in 2006. The analysis focused on the transition to a growth condition mimicking growth in host cells.


Small noncoding RNA
Numerous bacterial small noncoding RNAs have been identified to play regulatory functions. Some can regulate the virulence genes. Some 63 novel putative sRNAs were identified through deep sequencing of the Y. pestis sRNA-ome. Among them was Yersinia-specific (also present in Y. pseudotuberculosis and Y. enterocolitica) Ysr141 ( Yersinia small RNA 141). Ysr141 sRNA was shown to regulate the synthesis of the type III secretion system (T3SS) effector protein YopJ. The Yop-Ysc T3SS is a critical component of virulence for Yersinia species. Many novel sRNAs were identified from Y. pestis grown in vitro and in the infected lungs of mice suggesting they play role in bacterial physiology or pathogenesis. Among them sR035 predicted to pair with SD region and transcription initiation site of a thermo-sensitive regulator ymoA, and sR084 predicted to pair with fur, ferric uptake regulator.


Pathogenesis and immunity
In the urban and sylvatic (forest) cycles of Y. pestis, most of the spreading occurs between rodents and fleas. In the sylvatic cycle, the rodent is wild, but in the urban cycle, the rodent is primarily the . In addition, Y. pestis can spread from the urban environment and back. Transmission to humans is usually through the bite of infected fleas. If the disease has progressed to the pneumonic form, humans can spread the bacterium to others by coughing, vomiting and possibly sneezing.


In reservoir hosts
Several species of rodents serve as the main reservoir for Y. pestis in the environment. In the , the natural reservoir is believed to be principally the . In the western United States, several species of are thought to maintain Y. pestis. However, the expected disease dynamics have not been found in any rodent. Several species of rodents are known to have a variable resistance, which could lead to an asymptomatic carrier status. Evidence indicates fleas from other mammals have a role in human plague outbreaks.

The lack of knowledge of the dynamics of plague in mammal species is also true among susceptible rodents such as the black-tailed prairie dog ( Cynomys ludovicianus), in which plague can cause colony collapse, resulting in a massive effect on prairie food webs. However, the transmission dynamics within prairie dogs do not follow the dynamics of blocked fleas; carcasses, unblocked fleas, or another vector could possibly be important, instead.

In other regions of the world, the reservoir of the infection is not clearly identified, which complicates prevention and early-warning programs. One such example was seen in a 2003 outbreak in . The domestic house cat is susceptible to plague. Their symptoms are similar to those experienced by humans. Cats infected with plague can infect people through bites, scratches, coughs, or sneezes.


Vector
The transmission of Y. pestis by fleas is well characterized. Initial acquisition of Y. pestis by the vector occurs during feeding on an infected animal. Several proteins then contribute to the maintenance of the bacteria in the flea digestive tract, among them the hemin storage system and Yersinia toxin (Ymt). Although Ymt is highly toxic to rodents and was once thought to be produced to ensure reinfection of new hosts, it is important for the survival of Y. pestis in fleas.

The hemin storage system plays an important role in the transmission of Y. pestis back to a mammalian host. While in the insect vector, proteins encoded by hemin storage system genetic loci induce formation in the , a valve connecting the to the . Aggregation in the biofilm inhibits feeding, as a mass of clotted blood and bacteria forms (referred to as "Bacot's block"). Transmission of Y. pestis occurs during the futile attempts of the flea to feed. Ingested blood is pumped into the esophagus, where it dislodges bacteria lodged in the proventriculus and is regurgitated back into the host circulatory system.


In humans and other susceptible hosts
due to Y. pestis infection of mammalian hosts is due to several factors, including an ability of these bacteria to suppress and avoid normal responses such as and production. Flea bites allow for the bacteria to pass the skin barrier. Y. pestis expresses a activator that is an important virulence factor for pneumonic plague and that might degrade on blood clots to facilitate systematic invasion. Many of the bacteria's are antiphagocytic in nature. Two important antiphagocytic , named F1 (fraction 1) and V or , are both important for . These antigens are produced by the bacterium at normal human body temperature. Furthermore, Y. pestis survives and produces F1 and V antigens while it is residing within white blood cells such as , but not in . Natural or induced immunity is achieved by the production of specific against F1 and V antigens; antibodies against F1 and V induce phagocytosis by neutrophils.

In addition, the type-III secretion system (T3SS) allows Y. pestis to inject proteins into macrophages and other immune cells. These T3SS-injected proteins, called Yersinia outer proteins (Yops), include Yop B/D, which form pores in the host cell membrane and have been linked to . The YopO, , YopM, YopT, YopJ, and YopE are injected into the of host cells by T3SS into the pore created in part by YopB and YopD. The injected Yops limit phagocytosis and cell signaling pathways important in the innate immune system, as discussed below. In addition, some Y. pestis strains are capable of interfering with immune signaling (e.g., by preventing the release of some ).

Y. pestis inside , where it is able to avoid destruction by cells of the such as . The ability of Y. pestis to inhibit phagocytosis allows it to grow in lymph nodes and cause . YopH is a protein tyrosine phosphatase that contributes to the ability of Y. pestis to evade immune system cells. In macrophages, YopH has been shown to dephosphorylate p130Cas, ( binding protein) SKAP-HOM and Pyk, a homologous to FAK. YopH also binds the p85 subunit of phosphoinositide 3-kinase, the Gab1, the Gab2 adapter proteins, and the Vav guanine nucleotide exchange factor.

YopE functions as a GTPase-activating protein for members of the Rho family of GTPases such as RAC1. YopT is a cysteine protease that inhibits by removing the , which is important for localizing the protein to the . YopE and YopT has been proposed to function to limit YopB/D-induced cytolysis. This might limit the function of YopB/D to create the pores used for Yop insertion into host cells and prevent YopB/D-induced rupture of host cells and release of cell contents that would attract and stimulate immune system responses.

YopJ is an acetyltransferase that binds to a conserved of MAPK kinases. YopJ acetylates MAPK kinases at and that are normally phosphorylated during activation of the MAP kinase cascade. YopJ is activated in eukaryotic cells by interaction with target cell (IP6). This disruption of host cell protein kinase activity causes of macrophages, and this is proposed to be important for the establishment of infection and for evasion of the host immune response. YopO is a protein kinase also known as Yersinia protein kinase A (YpkA). YopO is a potent inducer of human macrophage apoptosis.

Depending on which form of the plague with which the individual becomes infected, the plague develops a different illness; however, the plague overall affects the host cell’s ability to communicate with the immune system, hindering the body to bring phagocytic cells to the area of infection.

Y. pestis is a versatile killer. In addition to rodents and humans, it is known to have killed dogs, cats, camels, chickens, and pigs.

(2019). 9780007150694, Fourth Estate.


Immunity
A -inactivated once was available in the for adults at high risk of contracting the plague until removal from the market by the Food and Drug Administration. It was of limited effectiveness and could cause severe . Experiments with genetic engineering of a vaccine based on F1 and V antigens are underway and show promise. However, bacteria lacking antigen F1 are still virulent, and the V antigens are sufficiently variable such that vaccines composed of these antigens may not be fully protective. The United States Army Medical Research Institute of Infectious Diseases has found that an experimental F1/V antigen-based vaccine protects crab-eating macaques, but fails to protect . A systematic review by the Cochrane Collaboration found no studies of sufficient quality to make any statement on the efficacy of the vaccine.


Isolation and identification
In 1894, two bacteriologists, Alexandre Yersin of and Kitasato Shibasaburō of , independently isolated in the bacterium responsible for the Third Pandemic. Though both investigators reported their findings, a series of confusing and contradictory statements by Kitasato eventually led to the acceptance of Yersin as the primary discoverer of the organism. Yersin named it Pasteurella pestis in honor of the Pasteur Institute, where he worked. In 1967, it was moved to a new genus and renamed Yersinia pestis in his honor. Yersin also noted that rats were affected by plague not only during plague epidemics, but also often preceding such epidemics in humans and that plague was regarded by many locals as a disease of rats; villagers in and asserted that, when large numbers of rats were found dead, plague outbreaks soon followed.

In 1898, French scientist Paul-Louis Simond (who had also come to China to battle the Third Pandemic) established the rat-flea vector that drives the disease. He had noted that persons who became ill did not have to be in close contact with each other to acquire the disease. In Yunnan, China, inhabitants would flee from their homes as soon as they saw dead rats, and on the island of (), residents considered the handling of dead rats heightened the risks of developing plague. These observations led him to suspect that the flea might be an intermediary factor in the transmission of plague, since people acquired plague only if they were in contact with recently dead rats, that had died less than 24 hours before. In a now classic experiment, Simond demonstrated how a healthy rat died of plague, after infected fleas had jumped to it, from a rat which had recently died of the plague. The outbreak spread to Chinatown, San Francisco from 1900 to 1904 and then to Oakland and the East Bay from 1907 to 1909. It has been present in the rodents of western North America ever since, as fear of the consequences of the outbreak on trade caused authorities to hide the dead of the Chinatown residents long enough for the disease to be passed to widespread species of native rodents in outlying areas.Chase, M. (2004). The Barbary Plague: The Black Death in Victorian San Francisco. Random House Trade Paperbacks.


Ancient DNA evidence
In 2018, the emergence and spread of the pathogen during the Neolithic Decline (as far back as 6,000 years ago) was published.Rascovan, Nicolas, et al, Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline, Cell, December 6, 2018, A site in Sweden was the source of the DNA evidence and trade networks were proposed as the likely avenue of spread rather than migrations of populations.

DNA evidence published in 2015 indicates Y. pestis infected humans 5,000 years ago in Eurasia, This article contains quotations from this source, which is available under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. but genetic changes that made it highly virulent did not occur until about 4,000 years ago. This article contains quotations from this source, which is available under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. The highly virulent version capable of transmission by fleas through rodents, humans, and other mammals was found in two individuals associated with the from the in Russia from around 3,800 years ago and an individual from , Armenia from around 2,900 years ago. This indicates that there were at least two lineages of Y. pestis circulating during the Bronze Age in Eurasia. The Y. pestis bacterium has a relatively large number of non-functioning genes and three "ungainly" plasmids suggesting a recent origin less than 20,000 years ago.

Three main strains are recognised: Antiqua, which caused a plague pandemic in the sixth century; Medievalis, which caused the Black Death and subsequent epidemics during the second pandemic wave; and Orientalis, which is responsible for current plague outbreaks.

Plague causes a blockage in the of the flea by forming a . The biofilm formation is induced by the ingestion of blood. The presence of a biofilm seems likely to be required for stable infection of the flea. It has been suggested that a  – Ypφ – may have been responsible for increasing the virulence of this organism.


Recent events
In 2008, the plague was commonly found in sub-Saharan Africa and Madagascar, areas which accounted for over 95% of the reported cases.

In September 2009, the death of Malcolm Casadaban, a molecular genetics professor at the University of Chicago, was linked to his work on a weakened laboratory strain of Y. pestis. was hypothesised to be a predisposing factor in Casadaban's death from this attenuated strain used for research.

In 2012, researchers in Germany collected samples of Y. pestis from gravesites with a view to reconstructing the DNA of the bacterium. In 2015, Cell published results from a study of ancient graves. of Y. pestis were detected in archaeological samples of the teeth of seven Bronze Age individuals, in the culture in Siberia, the Corded Ware culture in Estonia, the Sintashta culture in Russia, the in Poland, and the Andronovo culture in Siberia.

On June 8, 2015 in Larimer County, CO, a fatality was confirmed by the CDC as listed on the RSOE EDIS – Emergency and Disaster Information Service.

On September 8, 2016, the Y. pestis bacterium was identified from in teeth found at a building site in . The human remains were found to be victims of the Great Plague of London, which lasted from 1665 to 1666.

On January 15, 2018, researchers at the University of Oslo and the University of Ferrara suggested that humans and their parasites were the biggest carriers of the plague.


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