| Citrobacter rodentium | |
|---|---|
Scientific classification  | |
| Domain: | Bacteria |
| Phylum: | Pseudomonadota |
| Class: | Gammaproteobacteria |
| Order: | Enterobacterales |
| Family: | Enterobacteriaceae |
| Genus: | Citrobacter |
| Species: | C. rodentium |
| Binomial name | |
| Citrobacter rodentium Schauer et al. 1996 | |
Citrobacter rodentium is a Gram-negative species of bacteria first described in 1996. [1] It infects the intestinal tract of rodents.
C. rodentium is an extracellular pathogen of rodents. [1] While its specific structure has not been characterized in detail, several characteristics of this species can be inferred by its classification. As a member of the Enterobacteriaceae family, it is Gram-negative, rod-shaped, and non-spore-forming.
C. rodentium contains a conserved pathogenicity island in its genome, the locus of enterocyte effacement (LEE). [2] The LEE encodes a type III secretion system which is critical to the infection and pathogenicity of C. rodentium. Only one virulence factor has been identified that is specific to C. rodentium: cfc (Colonization factor Citrobacter). cfc encodes the CFC type IV pilus, which has an unknown role, but may be related to multiple aspects of pathogenicity. [2]
An analysis of the C. rodentium genome has shown that prophage insertion has disrupted several of its genes, including the flagella biosynthesis pathways and galactitol metabolism. [3]
Initially thought to be a pathogenic biotype of Citrobacter freundii , Citrobacter rodentium has been classified as its own species using biochemical and genomic evidence. [1]
Whole-genome sequencing of Citrobacter rodentium strain ICC168 revealed a single circular chromosome and four plasmids. [3] It also revealed that C. rodentium shares synteny with Escherichia coli and other members of Enterobacteriaceae . Additionally, the genome contains 17 genomic islands, 10 prophage regions, and 109 insertion elements 4. Phylogenetic analyses suggest that Citrobacter is a polyphyletic genus. [3]
Further genome sequencing of C. rodentium strain EX-33 showed significant similarity to strain ICC168. [4]
C. rodentium has lost the ability to synthesize flagella due to the insertion of prophages in genes encoding elements of the biosynthesis pathway. [4]
C. rodentium is a non-motile, facultative aerobe that lives in the intestinal tract of mice. The indole production test is negative, and it cannot grow on citrate or KCN. It is negative for arginine dihydrolase (meaning it cannot utilize arginine as a carbon and energy source) and is negative for H2S production. Additionally, it does not produce acid from sucrose, docitol, melibiose, or glycerol. [1]
In contrast, C. rodentium was positive for the ornithine decarboxylase test, indicating that it contains the enzyme ornithine decarboxylase. It is also positive for malonate utilization. [1]
C. rodentium varies its metabolism during different phases of infection. [5] Oxygenation of the intestinal epithelium occurs as a result of C. rodentium infection, which allows it to switch from anaerobic respiration to aerobic respiration. This helps this pathogen to outcompete many obligate anaerobes of the host’s microbiome. [5]
C. rodentium is a mouse pathogen and causes attaching/effacing lesions in the intestinal epithelium. [1] Because of its relatedness to E. coli, C. rodentium is used as a model pathogen to study E. coli infection in mice. [2] C. rodentium also possesses Intimin β, which is important to its virulence in mice. [2]
The infection cycle of C. rodentium has been studied in detail and comprises four main phases: the establishment phase (phase 1), the expansion phase (phase 2), the steady-state phase (phase 3), and the clearance phase (phase 4). [5] [6] [7] The immune response has similarly been studied in detail and varies across the phases of infection. Inflammasome activation may be an important aspect of C. rodentium infection. [7]
Enterobacteriaceae is a large family of Gram-negative bacteria. It includes over 30 genera and more than 100 species. Its classification above the level of family is still a subject of debate, but one classification places it in the order Enterobacterales of the class Gammaproteobacteria in the phylum Pseudomonadota. In 2016, the description and members of this family were emended based on comparative genomic analyses by Adeolu et al.
Escherichia coli ( ESH-ə-RIK-ee-ə KOH-ly) is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms. Most E. coli strains are harmless, but some serotypes such as EPEC, and ETEC are pathogenic and can cause serious food poisoning in their hosts, and are occasionally responsible for food contamination incidents that prompt product recalls. Most strains are part of the normal microbiota of the gut and are harmless or even beneficial to humans (although these strains tend to be less studied than the pathogenic ones). For example, some strains of E. coli benefit their hosts by producing vitamin K2 or by preventing the colonization of the intestine by pathogenic bacteria. These mutually beneficial relationships between E. coli and humans are a type of mutualistic biological relationship — where both the humans and the E. coli are benefitting each other. E. coli is expelled into the environment within fecal matter. The bacterium grows massively in fresh fecal matter under aerobic conditions for three days, but its numbers decline slowly afterwards.
Escherichia coli O157:H7 is a serotype of the bacterial species Escherichia coli and is one of the Shiga-like toxin–producing types of E. coli. It is a cause of disease, typically foodborne illness, through consumption of contaminated and raw food, including raw milk and undercooked ground beef. Infection with this type of pathogenic bacteria may lead to hemorrhagic diarrhea, and to kidney failure; these have been reported to cause the deaths of children younger than five years of age, of elderly patients, and of patients whose immune systems are otherwise compromised.
Shiga toxins are a family of related toxins with two major groups, Stx1 and Stx2, expressed by genes considered to be part of the genome of lambdoid prophages. The toxins are named after Kiyoshi Shiga, who first described the bacterial origin of dysentery caused by Shigella dysenteriae. Shiga-like toxin (SLT) is a historical term for similar or identical toxins produced by Escherichia coli. The most common sources for Shiga toxin are the bacteria S. dysenteriae and some serotypes of Escherichia coli (STEC), which includes serotypes O157:H7, and O104:H4.
A prophage is a bacteriophage genome that is integrated into the circular bacterial chromosome or exists as an extrachromosomal plasmid within the bacterial cell. Integration of prophages into the bacterial host is the characteristic step of the lysogenic cycle of temperate phages. Prophages remain latent in the genome through multiple cell divisions until activation by an external factor, such as UV light, leading to production of new phage particles that will lyse the cell and spread. As ubiquitous mobile genetic elements, prophages play important roles in bacterial genetics and evolution, such as in the acquisition of virulence factors.
Pathogenicity islands (PAIs), as termed in 1990, are a distinct class of genomic islands acquired by microorganisms through horizontal gene transfer. Pathogenicity islands are found in both animal and plant pathogens. Additionally, PAIs are found in both gram-positive and gram-negative bacteria. They are transferred through horizontal gene transfer events such as transfer by a plasmid, phage, or conjugative transposon. Therefore, PAIs contribute to microorganisms' ability to evolve.
Coliform bacteria are defined as either motile or non-motile Gram-negative non-spore forming bacilli that possess β-galactosidase to produce acids and gases under their optimal growth temperature of 35–37 °C. They can be aerobes or facultative aerobes, and are a commonly used indicator of low sanitary quality of foods, milk, and water. Coliforms can be found in the aquatic environment, in soil and on vegetation; they are universally present in large numbers in the feces of warm-blooded animals as they are known to inhabit the gastrointestinal system. While coliform bacteria are not normally causes of serious illness, they are easy to culture, and their presence is used to infer that other pathogenic organisms of fecal origin may be present in a sample, or that said sample is not safe to consume. Such pathogens include disease-causing bacteria, viruses, or protozoa and many multicellular parasites.
Escherichia is a genus of Gram-negative, non-spore-forming, facultatively anaerobic, rod-shaped bacteria from the family Enterobacteriaceae. In those species which are inhabitants of the gastrointestinal tracts of warm-blooded animals, Escherichia species provide a portion of the microbially derived vitamin K for their host. A number of the species of Escherichia are pathogenic. The genus is named after Theodor Escherich, the discoverer of Escherichia coli. Escherichia are facultative aerobes, with both aerobic and anaerobic growth, and an optimum temperature of 37 °C. Escherichia are usually motile by flagella, produce gas from fermentable carbohydrates, and do not decarboxylate lysine or hydrolyze arginine. Species include E. albertii, E. fergusonii, E. hermannii, E. ruysiae, E. marmotae and most notably, the model organism and clinically relevant E. coli. Formerly, Shimwellia blattae and Pseudescherichia vulneris were also classified in this genus.
Enterobacter is a genus of common Gram-negative, facultatively anaerobic, rod-shaped, non-spore-forming bacteria of the family Enterobacteriaceae. Cultures are found in soil, water, sewage, feces and gut environments. It is the type genus of the order Enterobacterales. Several strains of these bacteria are pathogenic and cause opportunistic infections in immunocompromised hosts and in those who are on mechanical ventilation. The urinary and respiratory tracts are the most common sites of infection. The genus Enterobacter is a member of the coliform group of bacteria. It does not belong to the fecal coliforms group of bacteria, unlike Escherichia coli, because it is incapable of growth at 44.5 °C in the presence of bile salts. Some of them show quorum sensing properties.
Carbapenems are a class of very effective antibiotic agents most commonly used for treatment of severe bacterial infections. This class of antibiotics is usually reserved for known or suspected multidrug-resistant (MDR) bacterial infections. Similar to penicillins and cephalosporins, carbapenems are members of the beta-lactam antibiotics drug class, which kill bacteria by binding to penicillin-binding proteins, thus inhibiting bacterial cell wall synthesis. However, these agents individually exhibit a broader spectrum of activity compared to most cephalosporins and penicillins. Furthermore, carbapenems are typically unaffected by emerging antibiotic resistance, even to other beta-lactams.
Intimin is a virulence factor (adhesin) of EPEC and EHEC E. coli strains. It is an attaching and effacing (A/E) protein, which with other virulence factors is necessary and responsible for enteropathogenic and enterohaemorrhagic diarrhoea.
Pathogenomics is a field which uses high-throughput screening technology and bioinformatics to study encoded microbe resistance, as well as virulence factors (VFs), which enable a microorganism to infect a host and possibly cause disease. This includes studying genomes of pathogens which cannot be cultured outside of a host. In the past, researchers and medical professionals found it difficult to study and understand pathogenic traits of infectious organisms. With newer technology, pathogen genomes can be identified and sequenced in a much shorter time and at a lower cost, thus improving the ability to diagnose, treat, and even predict and prevent pathogenic infections and disease. It has also allowed researchers to better understand genome evolution events - gene loss, gain, duplication, rearrangement - and how those events impact pathogen resistance and ability to cause disease. This influx of information has created a need for bioinformatics tools and databases to analyze and make the vast amounts of data accessible to researchers, and it has raised ethical questions about the wisdom of reconstructing previously extinct and deadly pathogens in order to better understand virulence.
Citrobacter freundii is a species of facultative anaerobic Gram-negative bacteria of the family Enterobacteriaceae which currently consists of 13 recognized species. These bacteria have a rod shape with a typical length of 1–5 μm. Most C. freundii cells have several flagella used for locomotion, although some non-motile taxa do not. C. freundii is a soil-dwelling microorganism, but can also be found in water, sewage, food, and the intestinal tracts of animals and humans. The genus Citrobacter was discovered in 1932 by Werkman and Gillen. Cultures of C. freundii were isolated and identified in the same year from soil extracts.
Omptins are a family of bacterial proteases. They are aspartate proteases, which cleave peptides with the use of a water molecule. Found in the outer membrane of gram-negative enterobacteria such as Shigella flexneri, Yersinia pestis, Escherichia coli, and Salmonella enterica. Omptins consist of a widely conserved beta barrel spanning the membrane with 5 extracellular loops. These loops are responsible for the various substrate specificities. These proteases rely upon binding of lipopolysaccharide for activity.
Escherichia coli is a gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms (endotherms). Most E. coli strains are harmless, but pathogenic varieties cause serious food poisoning, septic shock, meningitis, or urinary tract infections in humans. Unlike normal flora E. coli, the pathogenic varieties produce toxins and other virulence factors that enable them to reside in parts of the body normally not inhabited by E. coli, and to damage host cells. These pathogenic traits are encoded by virulence genes carried only by the pathogens.
The CTXφ bacteriophage is a filamentous bacteriophage. It is a positive-strand DNA virus with single-stranded DNA (ssDNA).
Escherichia fergusonii is a Gram-negative, rod-shaped species of bacterium. Closely related to the well-known species Escherichia coli, E. fergusonii was first isolated from samples of human blood. The species is named for American microbiologist William W. Ferguson.
Enteroaggregative Escherichia coli are a pathotype of Escherichia coli which cause acute and chronic diarrhea in both the developed and developing world. They may also cause urinary tract infections. EAEC are defined by their "stacked-brick" pattern of adhesion to the human laryngeal epithelial cell line HEp-2. The pathogenesis of EAEC involves the aggregation of and adherence of the bacteria to the intestinal mucosa, where they elaborate enterotoxins and cytotoxins that damage host cells and induce inflammation that results in diarrhea.
Citrobacter sedlakii is a species of Gram-negative bacteria. It has been described as causing human disease, but is generally found as a non-pathogenic organism in human stools.
Helicobacter typhlonius is a Gram-negative bacterium and opportunistic pathogen found in the genus Helicobacter. Only 35 known species are in this genus, which was described in 1982. H. typhlonius has a small number of close relatives, including Helicobacter muridarum, Helicobacter trogontum, and Helicobacter hepaticus, with the latter being the closest relative and much more prevalent.