"Escherichia coli" redirects here. For the protozoan parasite, see Entamoeba coli.
For the 2011 E.coli outbreak, see 2011 E. coli O104:H4 outbreak. For a specific strain, see Escherichia coli (disambiguation). For Escherichia coli in molecular biology, see Escherichia coli (molecular biology).
| Escherichia coli | |
|---|---|
 |
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| Scientific classification | |
| Domain: | Bacteria |
| Phylum: | Proteobacteria |
| Class: | Gammaproteobacteria |
| Order: | Enterobacteriales |
| Family: | Enterobacteriaceae |
| Genus: | Escherichia |
| Species: | E. coli |
| Binomial name | |
| Escherichia coli (Migula 1895) Castellani and Chalmers 1919 |
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| Synonyms | |
| Bacillus coli communis Escherich 1885 | |
E. coli and related bacteria constitute about 0.1% of gut flora, and fecal-oral transmission is the major route through which pathogenic strains of the bacterium cause disease. Cells are able to survive outside the body for a limited amount of time, which makes them ideal indicator organisms to test environmental samples for fecal contamination.. There is, however, a growing body of research that has examined environmentally persistent E. coli which can survive for extended periods of time outside of the host . The bacterium can also be grown easily and inexpensively in a laboratory setting, and has been intensively investigated for over 60 years. E. coli is the most widely studied prokaryotic model organism, and an important species in the fields of biotechnology and microbiology, where it has served as the host organism for the majority of work with recombinant DNA.
History
The genera Escherichia and Salmonella diverged around 102 million years ago (credibility interval: 57–176 mya), which coincides with the divergence of their hosts: the former being found in mammals and the latter in birds and reptiles. This was followed by a split of the escherichian ancestor into five species (E. albertii, Escherichia coli, E. fergusonii, E. hermannii and E. vulneris. The last E. coli ancestor split between 20 and 30 mya.In 1885, Theodor Escherich, a German pediatrician, first discovered this species in the feces of healthy individuals and called it Bacterium coli commune due to the fact it is found in the colon and early classifications of Prokaryotes placed these in a handful of genera based on their shape and motility (at that time Ernst Haeckel's classification of Bacteria in the kingdom Monera was in place Bacterium coli was the type species of the now invalid genus Bacterium when it was revealed that the former type species ("Bacterium triloculare") was missing. Following a revision of Bacteria it was reclassified as Bacillus coli by Migula in 1895 and later reclassified in the newly created genus Escherichia, named after its original discoverer.
The genus belongs in a group of bacteria informally known as "coliforms", and is a member of the Enterobacteriaceae family ("the enterics") of the Gammaproteobacteria
Biology and biochemistry
Optimal growth of E. coli occurs at 37°C (98.6°F) but some laboratory strains can multiply at temperatures of up to 49°C (120.2°F) Growth can be driven by aerobic or anaerobic respiration, using a large variety of redox pairs, including the oxidation of pyruvic acid, formic acid, hydrogen and amino acids, and the reduction of substrates such as oxygen, nitrate, dimethyl sulfoxide and trimethylamine N-oxide.
Strains that possess flagella are motile. The flagella have a peritrichous arrangement.
E. coli and related bacteria possess the ability to transfer DNA via bacterial conjugation, transduction or transformation, which allows genetic material to spread horizontally through an existing population. This process led to the spread of the gene encoding shiga toxin from Shigella to E. coli O157:H7, carried by a bacteriophage.
Diversity
Escherichia coli encompasses an enormous population of bacteria that exhibit a very high degree of both genetic and phenotypic diversity. Genome sequencing of a large number of isolates of E. coli and related bacteria shows that a taxonomic reclassification would be desirable. However, this has not been done, largely due to its medical importance and Escherichia coli remains one of the most diverse bacterial species: only 20% of the genome is common to all strains. In fact, from the evolutionary point of view, the members of genus Shigella (dysenteriae, flexneri, boydii, sonnei) should be classified as E. coli strains, a phenomenon termed taxa in disguise. Similarly, other strains of E. coli (e.g. the K-12 strain commonly used in recombinant DNA work) are sufficiently different that they would merit reclassification.A strain is a sub-group within the species that has unique characteristics that distinguish it from other strains. These differences are often detectable only at the molecular level; however, they may result in changes to the physiology or lifecycle of the bacterium. For example, a strain may gain pathogenic capacity, the ability to use a unique carbon source, the ability to take upon a particular ecological niche or the ability to resist antimicrobial agents. Different strains of E. coli are often host-specific, making it possible to determine the source of fecal contamination in environmental samples. For example, knowing which E. coli strains are present in a water sample allows researchers to make assumptions about whether the contamination originated from a human, another mammal or a bird.
Serotypes
Main article: Pathogenic Escherichia coli#Serotypes
A common subdivision system of Escherichia coli, but not based on evolutionary relatedness, is by serotype, which is based on major surface antigens (O antigen: part of lipopolysaccharide layer; H: flagellin; K antigen: capsule), e.g. O157:H7) (NB: K-12, the common laboratory strain is not a serotype.)Genome plasticity
Like all lifeforms, new strains of Escherichia coli evolve through the natural biological processes of mutation, gene duplication and horizontal gene transfer, in particular 18% of the genome of the laboratory strain MG1655 was horizontally acquired since the divergence from Salmonella. In microbiology, all strains of E. coli derive from E. coli K-12 or E. coli B strains. Some strains develop traits that can be harmful to a host animal. These virulent strains typically cause a bout of diarrhea that is unpleasant in healthy adults and is often lethal to children in the developing world. More virulent strains, such as O157:H7 cause serious illness or death in the elderly, the very young or the immunocompromised.Neotype strain
Escherichia coli is the type species of the genus (Escherichia) and in turn Escherichia is the type species of the family Enterobacteriaceae, where it should be noted that the family name does not stem from the genus Enterobacter + "i" (sic.) + "aceae", but from "enterobacterium" + "aceae" (enterobacterium being not a genus, but an alternative trivial name to enteric bacterium).The original strain described by Escherich is believed to be lost, consequently a new type strain (neotype) was chosen as a representative: the neotype strain is ATCC 11775, also known as NCTC 9001, which is pathogenic to chickens and has a O1:K1:H7 serotype.However, in most studies either O157:H7 or K-12 MG1655 or K-12 W3110 are used as a representative E.coli.
Recent events
One such E. coli strain, Escherichia coli O104:H4, has been the subject of a bacterial outbreak that began in Germany in May 2011. Certain strains of Escherichia coli are a major cause of foodborne illness. The outbreak started when several people in Germany were infected with enterohemorrhagic E. coli (EHEC) bacteria, leading to hemolytic-uremic syndrome (HUS), a medical emergency that requires urgent treatment. On 30 June 2011 announced the German Bundesinstitut für Risikobewertung (BfR) (Federal Institute for Risk Assessment, a federal, fully legal entity under public law of the Federal Republic of Germany, an institute within the German Federal Ministry of Food, Agriculture and Consumer Protection), that seeds of fenugreek from Egypt were likely the cause of the EHEC outbreak.
Phylogeny of Escherichia coli strains
Escherichia coli is a species. A large number of strains belonging to this species have been isolated and characterised. In addition to serotype (vide supra), they can be classified according to their phylogeny, ie. the inferred evolutionary history, as shown below where the species is divided into six groups.The link between phylogenetic distance ("relatedness") and pathology is small, e.g. the O157:H7 serotype strains, which form a clade ("an exclusive group") — group E below — are all enterohaerogic strains (EHEC), but not all EHEC strains are closely related. In fact, four different species of Shigella are nested among E. coli strains (vide supra), while Escherichia albertii and Escherichia fergusonii are outside of this group. All commonly used research strains of E. coli' belong to group A and are derived mainly from Clifton's K-12 strain (λ⁺ F⁺; O16) and to a lesser degree from d'Herelle's "Bacillus coli" strain (B strain)(O7).
Genomes
The first complete DNA sequence of an E. coli genome (laboratory strain K-12 derivative MG1655) was published in 1997. It was found to be a circular DNA molecule 4.6 million base pairs in length, containing 4288 annotated protein-coding genes (organized into 2584 operons), seven ribosomal RNA (rRNA) operons, and 86 transfer RNA (tRNA) genes. Despite having been the subject of intensive genetic analysis for approximately 40 years, a large number of these genes were previously unknown. The coding density was found to be very high, with a mean distance between genes of only 118 base pairs. The genome was observed to contain a significant number of transposable genetic elements, repeat elements, cryptic prophages, and bacteriophage remnants.Today, over 60 complete genomic sequences of Escherichia and Shigella species are available. Comparison of these sequences shows a remarkable amount of diversity; only about 20% of each genome represents sequences that are present in every one of the isolates, while approximately 80% of each genome can vary among isolates. Each individual genome contains between 4,000 and 5,500 genes, but the total number of different genes among all of the sequenced E. coli strains (the pan-genome) exceeds 16,000. This very large variety of component genes has been interpreted to mean that two-thirds of the E. coli pan-genome originated in other species and arrived through the process of horizontal gene transfer.