Escherichia coli microbiology

Escherichia coli microbiology DEFAULT
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Pathogenic E. coli (page 1)

(This chapter has 4 pages)

© Kenneth Todar, PhD

E. coli O157:H7. Phase contrast image of cells immobilized on an agar-coated slide. William Ghiorse, Department of Microbiology, Cornell University, Ithaca, New York. Licensed for use by ASM Microbe Library

Escherichia coli

Theodor Escherich first described E. coli in 1885, as Bacterium coli commune, which he isolated from the feces of newborns. It was later renamed Escherichia coli, and for many years the bacterium was simply considered to be a commensal organism of the large intestine. It was not until 1935 that a strain of E. coli was shown to be the cause of an outbreak of diarrhea among infants.

The GI tract of most warm-blooded animals is colonized by E. coli within  hours or a few days after birth. The bacterium is ingested in foods or water or obtained directly from other individuals handling the infant. The human bowel is usually colonized within 40 hours of birth. E. coli can adhere to the mucus overlying the large intestine. Once established, an E. coli strain may persist for months or years. Resident strains shift over a long period (weeks to months), and more rapidly after enteric infection or antimicrobial chemotherapy that perturbs the normal flora. The basis for these shifts and the ecology of Escherichia coli in the intestine of humans are poorly understood despite the vast amount of information on almost every other aspect of the organism's existence. The entire DNA base sequence of the E. coli genome has been known since 1997.

E. coli is the head of the large bacterial family, Enterobacteriaceae, the enteric bacteria, which are facultatively anaerobic Gram-negative rods that live in the intestinal tracts of animals in health and disease. The Enterobacteriaceae are among the most important bacteria medically. A number of genera within the family are human intestinal pathogens (e.g. Salmonella, Shigella, Yersinia). Several others are normal colonists of the human gastrointestinal tract (e.g. Escherichia, Enterobacter, Klebsiella), but these bacteria, as well, may occasionally be associated with diseases of humans.

Physiologically, E. coli is versatile and well-adapted to its characteristic habitats. It can grow in media with glucose as the sole organic constituent. Wild-type E. coli has no growth factor requirements, and metabolically it can transform glucose into all of the macromolecular components that make up the cell. The bacterium can grow in the presence or absence of O2. Under anaerobic conditions it will grow by means of fermentation, producing characteristic "mixed acids and gas" as end products. However, it can also grow by means of anaerobic respiration, since it is able to utilize NO3, NO2 or fumarate as final electron acceptors for respiratory electron transport processes. In part, this adapts E. coli to its intestinal (anaerobic) and its extraintestinal (aerobic or anaerobic) habitats.

E. coli can respond to environmental signals such as chemicals, pH, temperature, osmolarity, etc., in a number of very remarkable ways considering it is a unicellular organism. For example, it can sense the presence or absence of chemicals and gases in its environment and swim towards or away from them. Or it can stop swimming and grow fimbriae that will specifically attach it to a cell or surface receptor. In response to change in temperature and osmolarity, it can vary the pore diameter of its outer membrane porins to accommodate larger molecules (nutrients) or to exclude inhibitory substances. With its complex mechanisms for regulation of metabolism the bacterium can survey the chemical contents in its environment in advance of synthesizing any enzymes that metabolize these compounds. It does not wastefully produce enzymes for degradation of carbon sources unless they are available, and it does not produce enzymes for synthesis of metabolites if they are available as nutrients in the environment.

E. coli is a consistent inhabitant of the human intestinal tract, and it is the predominant facultative organism in the human GI tract; however, it makes up a very small proportion of the total bacterial content. The anaerobic Bacteroides species in the bowel outnumber E. coli by at least 20:1. however, the regular presence of E. coli in the human intestine and feces has led to tracking the bacterium in nature as an indicator of fecal pollution and water contamination. As such, it is taken to mean that, wherever E. coli is found, there may be fecal contamination by intestinal parasites of humans.

Unstained cells of E. coli viewed by phase microscopy. about 1000X magnification. CDC.

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Escherichia coli

Escherichia coli occurs naturally in the intestines of people and animals. Even though E. coli has a bad name, this bacterium is still very useful to us. In the large intestine, it prevents the uncontrolled growth of harmful bacteria.

Beneficial intestinal bacterium

E. coli is the most well-known intestinal bacterium. In popular terms, E. coli is even known as the ‘poo bacterium’. This is remarkable, as there really aren’t so many of them in your intestines. The reason that it is so well known is mainly due to its role in microbiology. It is used, for example, in the testing of drinking water. Unlike many other gut microbes, E. coli can also survive for a long time outside the body. It is found in places such as water taps, door handles or in water. Therefore, this bacterium is widely used to reveal possible traces of poo in drinking water.


E. coli is generally important for intestinal health. This bacterium occurs in a variety of strains, most of which do not cause disease symptoms. However, some strains can be dangerous. They can occur in raw meat, raw vegetables and unpasteurised milk products.

E. coli as a model species

A harmless type of E. coli has been used in various types of research since 1927. One advantage of E. coli is that it divides rapidly. As a result, scientists can culture many generations in a short period of time. Furthermore, its genome is composed of relatively simple genes, and has been fully mapped. All of which makes this bacterium highly suitable for the purposes of science.

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Clinical, microbiological and epidemiological aspects of Escherichia coli O157 infection


In the last decade infections caused by Escherichia coli O157:H7 and other verocytotoxigenic E. coli (VTEC) have emerged as a major public health concern in North America and in Europe, and increasingly in other areas of the world. Although absolute numbers of infections are low in comparison with other enteric pathogens such as Salmonella or Campylobacter, it is well-recognised that E. coli O157 can produce severe, potentially life-threatening, illness. As a consequence of this awareness, there has been a rapid expansion of our knowledge about these organisms and the diseases which they cause. In this article, the clinical, microbiological and epidemiological features of VTEC O157 infection are reviewed.

Escherichia coli O157, Escherichia coli infection, Epidemiology, Microbiology, Gastrointestinal infection, Food poisoning

1 Introduction

Escherichia coli is a common inhabitant of the gastrointestinal tract of man and other animals, but there are several pathogenic types of E. coli, which cause a variety of human diseases. In the last decade infections caused by E. coli O157 have emerged as an important new zoonosis giving rise to serious public health concern in North America, Europe, and increasingly in other areas of the world. Although the absolute numbers of infections are small in comparison with other enteric pathogens such as Salmonella or Campylobacter, it is well-recognised that E. coli O157 has the potential to produce severe, potentially life-threatening, illness. In this article it is intended to review the clinical features and pathogenesis of infection, to discuss microbiological diagnosis, to consider epidemiological aspects, including the various routes of transmission of the organism, and finally to look at some of the strategies which will be required to reduce or ameliorate the burden of E. coli O157 disease.

E. coli O157 is one of the enterohaemorrhagic group of E. coli (EHEC). As the name suggests the main feature of infection with these organisms is bloody diarrhoea. However they are commonly referred to as verocytotoxigenic E. coli (VTEC) following the observation by Konawalchuk [1] in 1977 that they could produce a toxin which has a direct cytotoxic effect on cultured Vero cells. In 1982 O'Brien and co-workers [2] demonstrated that this verotoxin (VT) was closely homologous to the Shiga toxin of Shigella dysenteriae type I, and the organisms are still commonly referred to in the literature as Shiga-toxin producing E. coli (STEC). However the clinical and public health significance of these organisms was not appreciated until the occurrence of an extensive community outbreak of bloody diarrhoea in 1982 associated with a fast-food restaurant chain in the United States [3]. Around the same time Karmali [4] and colleagues in Toronto, Canada demonstrated that VTEC O157 infection was associated with the development of haemolytic-uraemic syndrome (HUS) in children. It is now recognised that there are more than 100 serogroups of E. coli which may produce verotoxins, and a number of these have been associated with sporadic human infections and outbreaks. However E. coli O157 remains the most important of the VTEC group of organisms, particularly in North America and the United Kingdom.

2 Clinical features and pathogenesis

Infection with E. coli O157 presents with a wide spectrum of clinical manifestations which can significantly include asymptomatic carriage, and this may be important in relation to subsequent secondary spread. Diarrhoea is the most common clinical presentation, with an incubation period of 1–14 days, and is frequently, but not invariably, bloody in nature, commonly accompanied by severe, cramping abdominal pain. Vomiting occurs in about half of patients, but fever is uncommon. The quantity of blood present in faeces may vary from a few streaks only, to a stool which is comprised almost entirely of blood. This severe haemorrhagic colitis (HC) may be life-threatening, particularly at the extremes of age [5,6].

HUS is the most important complication of E. coli O157 infection. This clinical syndrome comprises microangiopathic haemolytic anaemia, thrombocytopaenia and acute renal failure and occurs in approximately 7% of cases 5–10 days after the symptom onset, often as the initial diarrhoeal illness is resolving. VTEC infection is the commonest cause of HUS in North America and Europe, and HUS is the commonest medical cause of acute renal failure in children from these areas [7]. Approximately 5% of HUS patients die in the acute phase of the disease. Pre-school children in particular and the elderly are more likely to develop HUS [5,6], and a proportion of patients develop long term renal sequelae [8]. The clinical features of HUS may be further complicated by the development of neurological and other organ involvement, as seen particularly in adults in whom this may manifest as thrombotic thrombocytopaenic purpura (TTP). Around half of those infected with VTEC O157 require hospitalisation. Although overall mortality, usually as a result of HC and HUS, has been quoted as 3%, this figure varies widely and higher rates are associated with the extremes of age, particularly in the elderly.

Extra-intestinal isolations of VTEC O157 are rare and deep tissue invasion is not a pathogenic feature [5]. However adherence to the underlying intestinal mucosa mediated by the eaeA gene is thought to be important. This interaction produces a typical attaching and effacing lesion [9]. It is thought that other colonisation factors and adhesins play a role in the adherence process [10].

The more severe manifestations of VTEC O157 disease, particularly HUS, are thought to be the result of VT production. There are two distinct toxins, VT1 and VT2, along with a small number of VT variants. VT1 and VT2 share approximately 60% sequence homology. VT1 is structurally and biochemically similar to the Shiga toxin of Shigella dysenteriae, from which it differs by a single amino acid. Strains of VTEC O157 produce either, both or none of the toxins, which are bacteriophage encoded [7]. The verotoxins comprise 5 B (binding) subunits of 8 kDa, and a single active A subunit of 32 kDa. The binding pentamer interacts with a specific surface glycolipid, globotriaosyl ceramide (Gb3), and the toxin is internalised via receptor-mediated endocytosis. Within the cytoplasm, the A subunit catalyses the enzymatic inactivation of 28S RNA within the 60S ribosomal subunit, resulting in inhibition of protein synthesis and cell death [11].

Damage to renal endothelial cells by this process is probably the primary aetiological event in HUS. Swelling of the damaged endothelial cells, hypertrophy of mesangial cells and detachment from the underlying basement membrane narrow the lumina of the glomerular capillaries. Secondary activation of coagulation, with the formation of platelet thrombi and fibrin generation further occlude the narrowed glomerular capillaries and afferent arterioles, and renal injury results from ischaemic glomerular and tubular necrosis. Analogous, although pathologically distinct, processes occur in TTP, the other thrombotic microangiopathy which may occur following VTEC O157 infection. In both HUS and TTP, this process can occasionaly affect other organs including the brain, myocardium and pancreas, with consequent development of encephalopathy, cardiomyopathy and diabetes mellitus [5,11].

Factors determining the severity of outcome of VTEC O157 infection are poorly understood. It is known that Gb3 expression can be upregulated by pro-inflammatory cytokines, and that local production of these mediators within the kidney may be important [12]. Equally there is evidence that expression of P group antigen on peripheral blood cells, which mimics VT receptor structure, may afford some protective effect [13]. Attempts to unravel the precise aetiological roles and interplay of the various cellular and biochemical components involved has been hindered by lack of good animal models. The recent description of a naturally-occurring canine infection caused by VTEC O157, which bears a striking resemblance to the human disease [14] may well be important. The role of additional pathogenicity factors, such as a virulence plasmid-encoded enterohaemolysin EHEC-Hly [15], remains to be elucidated.

3 Microbiology and laboratory diagnosis

VTEC O157 are facultatively anaerobic Gram-negative bacilli; carbon dioxide concentrations in excess of 80% are inhibitory [7]. Most strains are motile and the flagellar antigens account for the predominant serotype designation of O157:H7 [16]. Although non-motile strains have been reported in the wild [17], it is well known that strains may become non-motile on subculture or prolonged storage. H types of E. coli O157 other than H7 have been described, but these are not verocytotoxigenic [16]. Unlike other E. coli, VTEC O157 grow poorly at 44°C and above, and this may be important, as many routine public health microbiology tests for E. coli utilise such temperatures. Although it does not actively multiply, VTEC O157 can survive at refrigerator and freezer temperatures. VTEC O157 are not heat tolerant, and are readily killed by normal cooking and pasteurisation procedures [18].

VTEC O157 are more acid tolerant than other E. coli, and this may be important for survival in fermented meat products, or in non-fermented apple ciders which have been associated with outbreaks in North America. This can be offset by the presence of organic acids, or as has been recently described, by the presence of alcohol, and other preservative agents [19].

In contrast to other E. coli isolates of human origin, most strains of VTEC 0157 do not ferment d-sorbitol within 24 h [20], which led to the development of sorbitol MacConkey agar (SMAC) as a selective screening medium. The majority of organisms of the faecal flora are sorbitol-fermenting and yield pink colonies, whilst non-sorbitol fermenting (NSF) E. coli O157 produce pale, colourless colonies on SMAC. Various modifications of this medium have been developed to increase selectivity, such as the addition of sub-inhibitory concentrations of cefixime to inhibit Proteus and the sugar rhamnose (VTEC O157 are non-rhamnose fermenters) [21]. Clinical laboratories in the UK increasingly employ SMAC supplemented with cefixime and tellurite (CT-SMAC) [22], which further inhibits other NSFs including Plesiomonas, Aeromonas, Morganella and Providencia. Other media, such as MacConkey sorbitol agar with methyl-umbelliferyl glucuronide (MSA-MUG) or MacConkey sorbitol agar with bromo-chloro-indolyl glucuronide (MSA-BCIG), incorporate chromogenic or fluorogenic substrates into the media which exploits the failure of E. coli O157 to produce β-glucuronidase [7]. The high cost of these substrates precludes routine use in most diagnostic laboratories. Occasional sorbitol-fermenting, and indeed β-glucuronidase producing, strains of VTEC O157 have been isolated, particularly in Germany [23,17].

The O157 antigen is detected either by direct agglutination tests [24] or, more commonly, by latex particle agglutination [25]. Suspect colonies are subjected to biochemical tests to confirm species identification, and to distinguish them from other NSFs, e.g. Proteus, Plesiomonas, Aeromonas, Morganella and Providencia[7,16]. Agglutination tests with specific ‘H’ antisera are important in confirmation of identity, as other organisms such as E. hermanii may be NSFs and may agglutinate with some O157 antisera, although such testing is usually performed only at reference centres [7,16]. Full strain characterisation in the reference laboratory will include toxin detection and typing, either by Vero cell assay, or increasingly by hybridisation with specific DNA probes or PCR-based methods [26,27]. Further sub-typing is required to elucidate the epidemiology of infections. A phage typing scheme, initially developed in Canada [28], is routinely used in UK reference centres. Various other typing methodologies have been employed, including biotyping [23], multilocus enzyme electrophoresis [29] and DNA-based methodologies. The latter have included plasmid profiling [30] and PCR-based methods [31,32]. However, pulsed field gel electrophoresis (PFGE) analysis of chromosomal DNA [33] has proved particularly useful and robust.

Considerable effort has been directed towards development of techniques to increase speed and/or sensitivity of detection of these organisms employing a variety of cultural and non-cultural methodologies. There are now a range of commercial enzyme immunoassays for the detection of verotoxins in clinical samples [34] and foodstuffs [35], and similar systems are available for the detection of O157 antigen [36]. Again, DNA-based detection systems, either probe or PCR-based, have been developed and some of these are also available in commercial kit form [7].

Levels of contamination as low as 2 organisms per 25 g have been found in incriminated food and environmental samples, which supports the hypothesis that the infectious dose for VTEC O157 is low [37]. This has provided a further impetus to enhance culture sensitivity, where successful isolation of an organism which can be typed may be crucial for epidemiological or medico-legal purposes. Increased sensitivity of detection may also be useful in some clinical settings. In the acute diarrhoeal phase organisms are present in large numbers in the faeces and are readily isolated by direct culture on SMAC agar. However, Tarr and co-workers [38] have demonstrated that the number of organisms declines rapidly after the first few days. Frequently more severe manifestations of disease, such as HUS may not develop for 7–10 days after onset of symptoms [5,6], at which time diarrhoea may be resolving. Although liquid enrichment media, particularly modified tryptone soya broth or buffered peptone water containing vancomycin, cefsulodin and cefixime, have shown some promise, their value remains to be fully assessed [39].

On the other hand, a number of studies have clearly demonstrated the value of immunomagnetic separation (IMS) for detection of VTEC O157 in a range of clinical [40–42], food [43, 44, 36, 45] and environmental [44] samples. This immunocapture method employs paramagnetic beads coated with polyclonal antibodies against E. coli O157. Beads are added to broth enrichment cultures and then separated, together with bound VTEC O157, in a magnetic field. After removal of the culture supernatant the beads are plated out onto solid media, most commonly CT-SMAC, and the net result is a 10- to 100-fold increase in sensitivity of detection [46].

Serodiagnosis of E. coli O157 infection may be useful in patients who lack other confirmatory evidence of infection. Most commonly antibodies to O157 lipopolysaccharide (LPS) are detected [47] by either ELISA or immunoblot methods. Detection of VT-neutralising antibodies has proven considerably less useful [48]. In addition detection of faecal IgA has shown some promise as a diagnostic test [49].

4 Epidemiology

In most countries were surveillance has been instituted, there has been an increase in the number of VTEC O157 infections reported. In Canada throughout the 1980s an exponential rise in infections was observed to a peak of 8.8 per 100 000 population in 1989 [50]. Between 1982 and 1992 an average of 2–3 outbreaks annually were recorded in the USA [7]. However, between 1992 and 1993 more than 500 laboratory-confirmed cases occurred in association with a very large multi-state outbreak in the western USA linked to consumption of undercooked contaminated hamburgers from a single restaurant chain [51]. As a result of this and other outbreaks surveillance in the USA was enhanced and during 1993–1994, 46 clusters of VTEC O157 infection involving 1300 people were described [7]. The US Centers for Disease Control (CDC) have estimated that E. coli O157 infection probably accounts for at least 20 000 cases of illness and 250 deaths per year in the USA, at a financial cost of between 250 and 500 million dollars [52]. Isolates and outbreaks have been reported from an increasing number of other countries in recent years including Argentina, Australia, Belgium, Denmark, Germany, Italy, Israel, Sweden and South Africa [53, 7, 54]. A huge outbreak centred on Sakai city in Japan in 1996 affected more than 7000 people [55].

In England and Wales, between 1992 and 1996 37 outbreaks of VTEC O157 infection were investigated, involving 381 people, of whom 59 developed HUS, 120 required hospitalisation and 14 died [56]. Throughout the latter part of the 1980s and during the 1990s, partly as a result of enhanced ascertainment, there has been a continuing increase in the number of cases in England and Wales, with a reported rate of infection of 1.29 per 100 000 population in 1996 [54]. However, the highest UK rates of infection are seen in Scotland, where the annual number of cases has risen from 115 (2.2 per 100 000) in 1992 to 506 (9.8 per 100 000) in 1996 [57]. Twenty-five outbreaks are known to have occurred in Scotland between 1990 and 1996 affecting over 700 people [58]. These have included the largest milkborne outbreak of VTEC O157 infection world-wide in West Lothian during 1994 [44](69 laboratory-confirmed cases; 1 death), and Britain's largest outbreak of foodborne illness in Central Scotland in 1996 [59](272 laboratory-confirmed cases; 20 deaths). Differences in rates of infection between Scotland and other parts of the UK, or indeed regional variations observed within Scotland remain to be fully explained [60]. In North America and the UK, there is a characteristic seasonal distribution, with over 60% of cases occurring during the summer and early autumn [54]. The extremes of age, particularly pre-school children are most commonly infected [53,5].

Much of our information on sources and spread of infection with VTEC O157 is derived from outbreaks. There is considerable evidence of food-borne and water-borne transmission, classically associated with ground-beef, but also with other meat products [6, 61, 54, 53], raw milk [62] and milk products such as yoghurt [63], or cheese [60]. Other incriminated foodstuffs have included cured and fermented meat products [64], non-fermented apple cider [65], raw vegetables and salads [54], but in most cases these have either had an animal-derived component (usually bovine) or there has been evidence of environmental contamination via animal by-products, e.g. sewage contamination of pasture lands, or of drinking water supplies [66], particularly in rural communities [67]. In a number of other instances there has been evidence of inadequate cooking [7] or pasteurisation [44] of food(s), or failure of some other process which should otherwise have rendered a protective effect.

Secondary infection is common, and presumably reflects the low infectious dose. This has occurred in a variety of settings including households, hospitals, residential homes for the elderly and day-care facilities, particularly nursery schools [60, 54, 7]. Outbreaks have also been associated with sharing of paddling pools [68], and other communal bathing waters [69]. Thus although infection may initially be acquired from a contaminated foodstuff, subsequent outbreak spread can occur by various routes.

The accumulating evidence is that regardless of the ultimate vehicle of infection, farm animals, in particular bovines, are the major reservoir for human VTEC O157 infection. Human infections have been associated with direct and indirect animal contact on a number of occasions [70, 60, 7], and particular care should be taken with regard to occupational and recreational exposure to animals or their by-products [71]. Veterinary isolations of a range of serotypes of E. coli, some of which are verotoxigenic [7], are not uncommon and may produce enteric symptoms in young animals. However, it appears that although E. coli O157 may be found in the gut of a range of animals, including cattle, sheep, goats and deer, it produces little or no animal disease [7]. Cattle surveys in North America and the UK have consistently shown that around 4% of herds are positive for VTEC O157 at any given time, although there is great variability within herds [7,54]. Carriage in individual animals within a herd appears to be transient and episodic [72].

5 Future prospects

Whether E. coli O157 originated as a result of the acquisition of toxin genes by a previously non-toxigenic strain, or appropriation of suitable colonisation factors for human infection, or a combination of both, is a matter of speculation. However, this is a relatively recently evolved pathogen. In the USA prior to 1982, when the association of this organism with bloody diarrhoea was first described, CDC has no records of any such episodes of unknown origin, suggesting it was not a frequent aetiological agent of HC before that time [7]. In spite of this relatively recent emergence, the organism has already established itself as a major challenge for food safety and public health.

Control of this pathogen presents notable problems. It is present in a small, but significant, percentage of animals, particularly cattle. The ability of the organism to survive in soil for relatively long periods of time [73], and the recent description of carriage in migratory bird populations [54], are further examples of ways in which E. coli O157 persists and circulates in the environment. The low infectious dose ensures that cross-contamination and cross-infection occurs readily and can involve a diverse range of vehicles, including those such as water sources, in which dilutional effects might otherwise provide a protective effect. The spectrum of clinical illness is wide, and may include relatively severe sequelae, for which specific therapy is not available. This combination of low infectious dose and potentially severe disease, coupled with the documented occurrence of laboratory-acquired infection [74,75], has prompted the recent recommendation by the UK Health and Safety Executive (HSE) for re-classification of this organism as a hazard group 3 pathogen.

Our current knowledge and experience of the microbiology and epidemiology of these infections indicates that effective strategies to deal with the problem will have to be aimed at a range of control points. This will include close attention to every stage in production, processing and preparation of foodstuffs from the ‘farm to the fork’, provision of safe drinking water supplies, and measures to contain secondary spread, whether this be within household, nosocomial, day-care or institutional settings.

There is a particular need to increase our knowledge of factors which influence acquisition, carriage, and eradication of the organism in animals. We need to gain a better understanding of what makes an individual more susceptible to develop the most severe clinical manifestations, and how these may be prevented. The significance of prolonged low-level excretion in asymptomatic persons, which is being increasingly documented with the availability of more sensitive detection methods [76], requires clarification. Many of these points were addressed in the report by the working group on verocytotoxin-producing E. coli of the Advisory Committee on the Microbiological Safety of Food (ACMSF) [7], and more recently by the Pennington [77] group. It is hoped that actions arising from these initiatives will help achieve these objectives, and provide a continued stimulus to the multidisciplinary approach, involving veterinarians, microbiologists, clinicians, public health doctors, food scientists, government and industry, which is essential to respond to the growing challenge of VTEC O157.



Advisory Committee on the Microbiological Safety of Food




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Occurrence of attaching and effacing lesions in the small intestine of calves experimentally infected with bovine isolates of Verotoxigenic Escherichia coli


Vet. Rec.









Canine model of HUS


3rd International Symposium and Workshop on Shiga Toxin (Verocytotoxin)-Producing Escherichia coli Infections







Molecular detection of sorbitol fermenting Escherichia coli O157 in patients with haemolytic uraemic syndrome


J. Clin. Microbiol.









Acid tolerance in VTEC


Suppl. SCIEH Weekly Report 97/13








A biotyping scheme for Shiga-like (Vero) cytotoxin-producing Escherichia coli O157 and a list of serological cross-reactions between O157 and other Gram-negative bacteria


Int. J. Med. Microbiol. Virol. Parasitol. Infect. Dis.









Verocytotoxin-producing strains of Escherichia coli from children with haemolytic uraemic syndrome and their detection by specific DNA probes


J. Med. Microbiol.









Clonal relationships among Escherichia coli strains that cause haemorrhagic colitis and infantile diarrhoea


Infect. Immun.









Properties of strains of Escherichia coli belonging to serogroup O157 with special reference to production of Verocytotoxins VT1 and VT2


Epidemiol. Infect.









Identification of Verocytotoxin type 2 variant B subunit genes in Escherichia coli by the polymerase chain reaction and restriction fragment length polymorphism analysis


J. Clin. Microbiol.









Use of digoxigenin-labelled oligonucleotide DNA probes for VT2 and VT2 human variant genes to differentiate Verocytotoxin-producing Escherichia coli strains of serogroup O157


J. Clin. Microbiol.









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Lett. Appl. Microbiol.









Escherichia coli O157:H7 and the haemolytic uraemic syndrome: importance of early cultures in establishing the etiology


J. Infect. Dis.









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PHLS Microbiol. Dig.





Escherichia coli pathogenesis

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Coli microbiology escherichia

Questions and Answers

Some kinds of E. coli cause disease by making a toxin called Shiga toxin. The bacteria that make these toxins are called “Shiga toxin-producing” E. coli, or STEC for short. You might hear these bacteria called verocytotoxic E. coli (VTEC) or enterohemorrhagic E. coli (EHEC); these all refer generally to the same group of bacteria. The strain of Shiga toxin-producing E. coli O104:H4 that caused a large outbreak in Europe in 2011 was frequently referred to as EHEC. The most commonly identified STEC in North America is E. coli O157:H7 (often shortened to E. coli O157 or even just “O157”). When you hear news reports about outbreaks of “E. coli” infections, they are usually talking about E. coli O157.

In addition to E. coli O157, many other kinds (called serogroups) of STEC cause disease. Other E. coli serogroups in the STEC group, including E. coli O145, are sometimes called “non-O157 STECs.” Currently, there are limited public health surveillance data on the occurrence of non-O157 STECs, including STEC O145; many STEC O145 infections may go undiagnosed or unreported.

Compared with STEC O157 infections, identification of non-O157 STEC infections is more complex. First, clinical laboratories must test stool samples for the presence of Shiga toxins. Then, the positive samples must be sent to public health laboratories to look for non-O157 STEC.  Clinical laboratories typically cannot identify non-O157 STEC. Other non-O157 STEC serogroups that often cause illness in people in the United States include O26, O111, and O103. Some types of STEC frequently cause severe disease, including bloody diarrhea and hemolytic uremic syndrome (HUS), which is a type of kidney failure.

E. Coli Bacteria Microbiology

Escherichia coli

"E. coli" redirects here. For the protozoan commensal, see Entamoeba coli. For the grey whale, see Eschrichtius robustus.

This article is about Escherichia coli as a species. For E. coli in medicine, see Pathogenic Escherichia coli. For E. coli in molecular biology, see Escherichia coli (molecular biology).

Gram-negative bacterium

Escherichia coli (),[1][2] also known as E. coli (),[2] is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genusEscherichia that is commonly found in the lower intestine of warm-blooded organisms (endotherms).[3][4] Most E. colistrains are harmless, but some serotypes (EPEC, ETEC etc.) can cause serious food poisoning in their hosts, and are occasionally responsible for food contamination incidents that prompt product recalls.[5][6] The harmless strains are part of the normal microbiota of the gut, and can benefit their hosts by producing vitamin K2,[7] (which helps blood to clot) and preventing colonisation of the intestine with pathogenic bacteria, having a mutualistic relationship.[8][9]E. coli is expelled into the environment within fecal matter. The bacterium grows massively in fresh fecal matter under aerobic conditions for 3 days, but its numbers decline slowly afterwards.[10]

E. coli and other facultative anaerobes constitute about 0.1% of gut microbiota,[11] 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 potential indicator organisms to test environmental samples for fecal contamination.[12][13] A growing body of research, though, has examined environmentally persistent E. coli which can survive for many days and grow outside a host.[14]

The bacterium can be grown and cultured easily and inexpensively in a laboratory setting, and has been intensively investigated for over 60 years. E. coli is a chemoheterotroph whose chemically defined medium must include a source of carbon and energy.[15]E. coli is the most widely studied prokaryoticmodel 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. Under favorable conditions, it takes as little as 20 minutes to reproduce.[16]

Biology and biochemistry[edit]

Model of successive binary fissionin E. coli

Type and morphology[edit]

E. coli is a Gram-negative, facultative anaerobe, nonsporulatingcoliform bacterium.[17] Cells are typically rod-shaped, and are about 2.0 μm long and 0.25–1.0 μm in diameter, with a cell volume of 0.6–0.7 μm3.[18][19][20] Antibiotics can effectively treat E. coli infections outside the digestive tract and most intestinal infections but are not used to treat intestinal infections by one strain of these bacteria.[21] The flagella which allow the bacteria to swim have a peritrichous arrangement.[22] It also attaches and effaces to the microvilli of the intestines via an adhesion molecule known as intimin.[23]


E. coli can live on a wide variety of substrates and uses mixed acid fermentation in anaerobic conditions, producing lactate, succinate, ethanol, acetate, and carbon dioxide. Since many pathways in mixed-acid fermentation produce hydrogen gas, these pathways require the levels of hydrogen to be low, as is the case when E. coli lives together with hydrogen-consuming organisms, such as methanogens or sulphate-reducing bacteria.[24]

In addition, E. coli's metabolism can be rewired to solely use CO2 as the source of carbon for biomass production. In other words, this obligate heterotroph's metabolism can be altered to display autotrophic capabilities by heterologously expressing carbon fixation genes as well as formate dehydrogenase and conducting laboratory evolution experiments. This may be done by using formate to reduce electron carriers and supply the ATP required in anabolic pathways inside of these synthetic autotrophs.[25]

E. coli have three native glycolytic pathways: EMPP, EDP, and OPPP. The EMPP employs ten enzymatic steps to yield two pyruvates, two ATP, and two NADH per glucose molecule while OPPP serves as an oxidation route for NADPH synthesis. Although the EDP is the more thermodynamically favorable of the three pathways, E. coli do not use the EDP for glucose metabolism, relying mainly on the EMPP and the OPPP. The EDP mainly remains inactive except for during growth with gluconate.[26]

Catabolite repression[edit]

When growing in the presence of a mixture of sugars, bacteria will often consume the sugars sequentially through a process known as catabolite repression. By repressing the expression of the genes involved in metabolizing the less preferred sugars, cells will usually first consume the sugar yielding the highest growth rate, followed by the sugar yielding the next highest growth rate, and so on. In doing so the cells ensure that their limited metabolic resources are being used to maximize the rate of growth. The well-used example of this with E. coli involves the growth of the bacterium on glucose and lactose, where E. coli will consume glucose before lactose. Catabolite repression has also been observed in E.coli in the presence of other non-glucose sugars, such as arabinose and xylose, sorbitol, rhamnose, and ribose. In E. coli, glucose catabolite repression is regulated by the phosphotransferase system, a multi-protein phosphorylation cascade that couples glucose uptake and metabolism.[27]

Culture growth[edit]

Optimum growth of E. coli occurs at 37 °C (98.6 °F), but some laboratory strains can multiply at temperatures up to 49 °C (120 °F).[28]E. coli grows in a variety of defined laboratory media, such as lysogeny broth, or any medium that contains glucose, ammonium phosphate monobasic, sodium chloride, magnesium sulfate, potassium phosphate dibasic, and water. 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, fumarate, dimethyl sulfoxide, and trimethylamine N-oxide.[29]E. coli is classified as a facultative anaerobe. It uses oxygen when it is present and available. It can, however, continue to grow in the absence of oxygen using fermentation or anaerobic respiration. The ability to continue growing in the absence of oxygen is an advantage to bacteria because their survival is increased in environments where water predominates.[15]

Redistribution of fluxes between the three primary glucose catabolic pathways: EMPP (red), EDP (blue), and OPPP (orange) via the knockout of pfkA and overexpression of EDP genes (edd and eda).

Cell cycle[edit]

Main article: Cell cycle

The bacterial cell cycle is divided into three stages. The B period occurs between the completion of cell division and the beginning of DNA replication. The C period encompasses the time it takes to replicate the chromosomal DNA. The D period refers to the stage between the conclusion of DNA replication and the end of cell division.[30] The doubling rate of E. coli is higher when more nutrients are available. However, the length of the C and D periods do not change, even when the doubling time becomes less than the sum of the C and D periods. At the fastest growth rates, replication begins before the previous round of replication has completed, resulting in multiple replication forks along the DNA and overlapping cell cycles.[31]

The number of replication forks in fast growing E. coli typically follows 2n (n = 1, 2 or 3). This only happens if replication is initiated simultaneously from all origins of replications, and is referred to as synchronous replication. However, not all cells in a culture replicate synchronously. In this case cells do not have multiples of two replication forks. Replication initiation is then referred to being asynchronous.[32] However, asynchrony can be caused by mutations to for instance DnaA[32] or DnaA initiator-associating protein DiaA.[33]

Genetic adaptation[edit]

E. coli and related bacteria possess the ability to transfer DNA via bacterial conjugation or transduction, which allows genetic material to spread horizontally through an existing population. The process of transduction, which uses the bacterial virus called a bacteriophage,[34] is where the spread of the gene encoding for the Shiga toxin from the Shigella bacteria to E. coli helped produce E. coli O157:H7, the Shiga toxin-producing strain of E. coli.


E. coli encompasses an enormous population of bacteria that exhibit a very high degree of both genetic and phenotypic diversity. Genome sequencing of many 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,[35] and E. coli remains one of the most diverse bacterial species: only 20% of the genes in a typical E. coli genome is shared among all strains.[36]

In fact, from the more constructive point of view, the members of genus Shigella (S. dysenteriae, S. flexneri, S. boydii, and S. sonnei) should be classified as E. coli strains, a phenomenon termed taxa in disguise.[37] 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 subgroup 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.[12][13] 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.

A colony of E. coligrowing


E.coli colonies on agar.
E. colion sheep blood agar.

Main article: Pathogenic Escherichia coli § Serotypes

A common subdivision system of E. 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).[38] It is, however, common to cite only the serogroup, i.e. the O-antigen. At present, about 190 serogroups are known.[39] The common laboratory strain has a mutation that prevents the formation of an O-antigen and is thus not typeable.

Genome plasticity and evolution[edit]

E. coli colonies
E. coligrowing on basic cultivation media.

Like all lifeforms, new strains of E. colievolve 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.[40]E. coli K-12 and E. coli B strains are the most frequently used varieties for laboratory purposes. Some strains develop traits that can be harmful to a host animal. These virulent strains typically cause a bout of diarrhea that is often self-limiting in healthy adults but is frequently lethal to children in the developing world.[41] More virulent strains, such as O157:H7, cause serious illness or death in the elderly, the very young, or the immunocompromised.[41][42]

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.[43] This was followed by a split of an Escherichia ancestor into five species (E. albertii, E. coli, E. fergusonii, E. hermannii, and E. vulneris). The last E. coli ancestor split between 20 and 30 million years ago.[44]

The long-term evolution experiments using E. coli, begun by Richard Lenski in 1988, have allowed direct observation of genome evolution over more than 65,000 generations in the laboratory.[45] For instance, E. coli typically do not have the ability to grow aerobically with citrate as a carbon source, which is used as a diagnostic criterion with which to differentiate E. coli from other, closely, related bacteria such as Salmonella. In this experiment, one population of E. coli unexpectedly evolved the ability to aerobically metabolize citrate, a major evolutionary shift with some hallmarks of microbial speciation.

Scanning electron micrograph of an E. colicolony.

In the microbial world, a relationship of predation can be established similar to that observed in the animal world. Considered, it has been seen that E. coli is the prey of multiple generalist predators, such as Myxococcus xanthus. In this predator-prey relationship, a parallel evolution of both species is observed through genomic and phenotypic modifications, in the case of E. coli the modifications are modified in two aspects involved in their virulence such as mucoid production (excessive production of exoplasmic acid alginate ) and the suppression of the OmpT gene, producing in future generations a better adaptation of one of the species that is counteracted by the evolution of the other, following a co-evolutionary model demonstrated by the Red Queen hypothesis.[46]

Neotype strain[edit]

E. coli is the type species of the genus (Escherichia) and in turn Escherichia is the type genus of the family Enterobacteriaceae, where 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).[47][48]

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 U5/41T,[49] also known under the deposit names DSM 30083,[50]ATCC 11775,[51] and NCTC 9001,[52] which is pathogenic to chickens and has an O1:K1:H7 serotype.[53] However, in most studies, either O157:H7, K-12 MG1655, or K-12 W3110 were used as a representative E. coli. The genome of the type strain has only lately been sequenced.[49]

Phylogeny of E. coli strains[edit]

Ambox current red Americas.svg

This section's factual accuracy may be compromised due to out-of-date information. The reason given is: Cladogram uses an OR extension of Sims & Kim 2011, which is outdated anyways and should be replaced by Meier-Kolthoff et al. 2014 (fig 6).. Relevant discussion may be found on the talk page. Please help update this article to reflect recent events or newly available information.(January 2021)

Many strains belonging to this species have been isolated and characterised. In addition to serotype (vide supra), they can be classified according to their phylogeny, i.e. the inferred evolutionary history, as shown below where the species is divided into six groups.[54][55] Particularly the use of whole genome sequences yields highly supported phylogenies. Based on such data, five subspecies of E. coli were distinguished.[49]

The link between phylogenetic distance ("relatedness") and pathology is small,[49]e.g. the O157:H7 serotype strains, which form a clade ("an exclusive group")—group E below—are all enterohaemorragic 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 E. albertii and E. fergusonii are outside this group. Indeed, all Shigella species were placed within a single subspecies of E. coli in a phylogenomic study that included the type strain,[49] and for this reason an according reclassification is difficult. 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).


An image of E. coliusing early electron microscopy.

The first complete DNA sequence of an E. coligenome (laboratory strain K-12 derivative MG1655) was published in 1997. It is 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 about 40 years, many 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.[56]

More than three hundred complete genomic sequences of Escherichia and Shigella species are known. The genome sequence of the type strain of E. coli was added to this collection before 2014.[49] Comparison of these sequences shows a remarkable amount of diversity; only about 20% of each genome represents sequences present in every one of the isolates, while around 80% of each genome can vary among isolates.[36] 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 pangenome) exceeds 16,000. This very large variety of component genes has been interpreted to mean that two-thirds of the E. colipangenome originated in other species and arrived through the process of horizontal gene transfer.[57]

Gene nomenclature[edit]

Genes in E. coli are usually named in accordance with the uniform nomenclature proposed by Demerec et al.[58] Gene names are 3-letter acronyms that derive from their function (when known) or mutant phenotype and are italicized. When multiple genes have the same acronym, the different genes are designated by a capital later that follows the acronym and is also italicized. For instance, recA is named after its role in homologous recombination plus the letter A. Functionally related genes are named recB, recC, recD etc. The proteins are named by uppercase acronyms, e.g. RecA, RecB, etc. When the genome of E. coli strain K-12 substr. MG1655 was sequenced, all known or predicted protein-coding genes were numbered (more or less) in their order on the genome and abbreviated by b numbers, such as b2819 (= recD). The "b" names were created after Fred Blattner, who led the genome sequence effort.[56] Another numbering system was introduced with the sequence of another E. coli K-12 substrain, W3110, which was sequenced in Japan and hence uses numbers starting by JW... (Japanese W3110), e.g. JW2787 (= recD).[59] Hence, recD = b2819 = JW2787. Note, however, that most databases have their own numbering system, e.g. the EcoGene database[60] uses EG10826 for recD. Finally, ECK numbers are specifically used for alleles in the MG1655 strain of E. coli K-12.[60] Complete lists of genes and their synonyms can be obtained from databases such as EcoGene or Uniprot.



Several studies have investigated the proteome of E. coli. By 2006, 1,627 (38%) of the 4,237 open reading frames (ORFs) had been identified experimentally.[61] The 4,639,221–base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.[56]


The interactome of E. coli has been studied by affinity purification and mass spectrometry (AP/MS) and by analyzing the binary interactions among its proteins.

Protein complexes. A 2006 study purified 4,339 proteins from cultures of strain K-12 and found interacting partners for 2,667 proteins, many of which had unknown functions at the time.[62] A 2009 study found 5,993 interactions between proteins of the same E. coli strain, though these data showed little overlap with those of the 2006 publication.[63]

Binary interactions. Rajagopala et al. (2014) have carried out systematic yeast two-hybrid screens with most E. coli proteins, and found a total of 2,234 protein-protein interactions.[64] This study also integrated genetic interactions and protein structures and mapped 458 interactions within 227 protein complexes.

Normal microbiota[edit]

E. coli belongs to a group of bacteria informally known as coliforms that are found in the gastrointestinal tract of warm-blooded animals.[65]E. coli normally colonizes an infant's gastrointestinal tract within 40 hours of birth, arriving with food or water or from the individuals handling the child. In the bowel, E. coli adheres to the mucus of the large intestine. It is the primary facultative anaerobe of the human gastrointestinal tract.[66] (Facultative anaerobes are organisms that can grow in either the presence or absence of oxygen.) As long as these bacteria do not acquire genetic elements encoding for virulence factors, they remain benign commensals.[67]

Therapeutic use[edit]

Due to the low cost and speed with which it can be grown and modified in laboratory settings, E. coli is a popular expression platform for the production of recombinant proteins used in therapeutics. One advantage to using E. coli over another expression platform is that E. coli naturally does not export many proteins into the periplasm, making it easier to recover a protein of interest without cross-contamination.[68] The E. coli K-12 strains and their derivatives (DH1, DH5α, MG1655, RV308 and W3110) are the strains most widely used by the biotechnology industry.[69] Nonpathogenic E. coli strain Nissle 1917 (EcN), (Mutaflor) and E. coli O83:K24:H31 (Colinfant)[70][71]) are used as probiotic agents in medicine, mainly for the treatment of various gastrointestinal diseases,[72] including inflammatory bowel disease.[73] It is thought that the EcN strain might impede the growth of opportunistic pathogens, including Salmonella and other coliform enteropathogens, through the production of microcin proteins the production of siderophores.[74]

Role in disease[edit]

Main article: Pathogenic Escherichia coli

Most E. coli strains do not cause disease, naturally living in the gut,[75] but virulent strains can cause gastroenteritis, urinary tract infections, neonatal meningitis, hemorrhagic colitis, and Crohn's disease. Common signs and symptoms include severe abdominal cramps, diarrhea, hemorrhagic colitis, vomiting, and sometimes fever. In rarer cases, virulent strains are also responsible for bowel necrosis (tissue death) and perforation without progressing to hemolytic-uremic syndrome, peritonitis, mastitis, sepsis, and Gram-negative pneumonia. Very young children are more susceptible to develop severe illness, such as hemolytic uremic syndrome; however, healthy individuals of all ages are at risk to the severe consequences that may arise as a result of being infected with E. coli.[66][76][77][78]

Some strains of E. coli, for example O157:H7, can produce Shiga toxin (classified as a bioterrorism agent). The Shiga toxin causes inflammatory responses in target cells of the gut, leaving behind lesions which result in the bloody diarrhea that is a symptom of a Shiga toxin-producing E. coli (STEC) infection. This toxin further causes premature destruction of the red blood cells, which then clog the body's filtering system, the kidneys, in some rare cases (usually in children and the elderly) causing hemolytic-uremic syndrome (HUS), which may lead to kidney failure and even death. Signs of hemolytic uremic syndrome include decreased frequency of urination, lethargy, and paleness of cheeks and inside the lower eyelids. In 25% of HUS patients, complications of nervous system occur, which in turn causes strokes. In addition, this strain causes the buildup of fluid (since the kidneys do not work), leading to edema around the lungs, legs, and arms. This increase in fluid buildup especially around the lungs impedes the functioning of the heart, causing an increase in blood pressure.[79][77][78]

Uropathogenic E. coli (UPEC) is one of the main causes of urinary tract infections.[80] It is part of the normal microbiota in the gut and can be introduced in many ways. In particular for females, the direction of wiping after defecation (wiping back to front) can lead to fecal contamination of the urogenital orifices. Anal intercourse can also introduce this bacterium into the male urethra, and in switching from anal to vaginal intercourse, the male can also introduce UPEC to the female urogenital system.

Enterotoxigenic E. coli (ETEC) is the most common cause of traveler's diarrhea, with as many as 840 million cases worldwide in developing countries each year. The bacteria, typically transmitted through contaminated food or drinking water, adheres to the intestinal lining, where it secretes either of two types of enterotoxins, leading to watery diarrhea. The rate and severity of infections are higher among children under the age of five, including as many as 380,000 deaths annually.[81]

In May 2011, one E. coli strain, O104:H4, was the subject of a bacterial outbreak that began in Germany. Certain strains of E. 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. The outbreak did not only concern Germany, but also 15 other countries, including regions in North America.[82] On 30 June 2011, the German Bundesinstitut für Risikobewertung (BfR) (Federal Institute for Risk Assessment, a federal institute within the German Federal Ministry of Food, Agriculture and Consumer Protection) announced that seeds of fenugreek from Egypt were likely the cause of the EHEC outbreak.[83]

Some studies have demonstrated an absence of E.coli in the gut flora of subjects with the metabolic disorder Phenylketonuria. It is hypothesized that the absence of these normal bacterium impairs the production of the key vitamins B2 (riboflavin) and K2 (menaquinone) - vitamins which are implicated in many physiological roles in humans such as cellular and bone metabolism - and so contributes to the disorder.[84]

Carbapenem-resistant E. coli(carbapenemase-producing E. coli) that are resistant to the carbapenem class of antibiotics, considered the drugs of last resort for such infections. They are resistant because they produce an enzyme called a carbapenemase that disables the drug molecule.[85]

Incubation period[edit]

The time between ingesting the STEC bacteria and feeling sick is called the "incubation period". The incubation period is usually 3–4 days after the exposure, but may be as short as 1 day or as long as 10 days. The symptoms often begin slowly with mild belly pain or non-bloody diarrhea that worsens over several days. HUS, if it occurs, develops an average 7 days after the first symptoms, when the diarrhea is improving.[86]


Diagnosis of infectious diarrhea and identification of antimicrobial resistance is performed using a stool culture with subsequent antibiotic sensitivity testing. It requires a minimum of 2 days and maximum of several weeks to culture gastrointestinal pathogens. The sensitivity (true positive) and specificity (true negative) rates for stool culture vary by pathogen, although a number of human pathogens can not be cultured. For culture-positive samples, antimicrobial resistance testing takes an additional 12–24 hours to perform.

Current point of caremolecular diagnostic tests can identify E. coli and antimicrobial resistance in the identified strains much faster than culture and sensitivity testing. Microarray-based platforms can identify specific pathogenic strains of E. coli and E. coli-specific AMR genes in two hours or less with high sensitivity and specificity, but the size of the test panel (i.e., total pathogens and antimicrobial resistance genes) is limited. Newer metagenomics-based infectious disease diagnostic platforms are currently being developed to overcome the various limitations of culture and all currently available molecular diagnostic technologies.


The mainstay of treatment is the assessment of dehydration and replacement of fluid and electrolytes. Administration of antibiotics has been shown to shorten the course of illness and duration of excretion of enterotoxigenic E. coli (ETEC) in adults in endemic areas and in traveller's diarrhea, though the rate of resistance to commonly used antibiotics is increasing and they are generally not recommended.[87] The antibiotic used depends upon susceptibility patterns in the particular geographical region. Currently, the antibiotics of choice are fluoroquinolones or azithromycin, with an emerging role for rifaximin. Oral rifaximin, a semisynthetic rifamycin derivative, is an effective and well-tolerated antibacterial for the management of adults with non-invasive traveller's diarrhea. Rifaximin was significantly more effective than placebo and no less effective than ciprofloxacin in reducing the duration of diarrhea. While rifaximin is effective in patients with E. coli-predominant traveller's diarrhea, it appears ineffective in patients infected with inflammatory or invasive enteropathogens.[88]


ETEC is the type of E. coli that most vaccine development efforts are focused on. Antibodies against the LT and major CFs of ETEC provide protection against LT-producing, ETEC-expressing homologous CFs. Oral inactivated vaccines consisting of toxin antigen and whole cells, i.e. the licensed recombinant cholera B subunit (rCTB)-WC cholera vaccine Dukoral, have been developed. There are currently no licensed vaccines for ETEC, though several are in various stages of development.[89] In different trials, the rCTB-WC cholera vaccine provided high (85–100%) short-term protection. An oral ETEC vaccine candidate consisting of rCTB and formalin inactivated E. coli bacteria expressing major CFs has been shown in clinical trials to be safe, immunogenic, and effective against severe diarrhoea in American travelers but not against ETEC diarrhoea in young children in Egypt. A modified ETEC vaccine consisting of recombinant E. coli strains over-expressing the major CFs and a more LT-like hybrid toxoid called LCTBA, are undergoing clinical testing.[90][91]

Other proven prevention methods for E. coli transmission include handwashing and improved sanitation and drinking water, as transmission occurs through fecal contamination of food and water supplies. Additionally, thoroughly cooking meat and avoiding consumption of raw, unpasteurized beverages, such as juices and milk are other proven methods for preventing E.coli. Lastly, avoid cross-contamination of utensils and work spaces when preparing food.[92]

Model organism in life science research[edit]

Main article: Escherichia coli in molecular biology

Escherichia coli bacterium, 2021, Illustration by David S. Goodsell, RCSB Protein Data Bank
This painting shows a cross-section through an Escherichia coli cell. The characteristic two-membrane cell wall of gram-negative bacteria is shown in green, with many lipopolysaccharide chains extending from the surface and a network of cross-linked peptidoglycan strands between the membranes. The genome of the cell forms a loosely-defined "nucleoid", shown here in yellow, and interacts with many DNA-binding proteins, shown in tan and orange. Large soluble molecules, such as ribosomes (colored in reddish purple), mostly occupy the space around the nucleoid.
Helium ion microscopyimage showing T4 phageinfecting E. coli. Some of the attached phage have contracted tails indicating that they have injected their DNA into the host. The bacterial cells are ~ 0.5 µm wide.[93]

Because of its long history of laboratory culture and ease of manipulation, E. coli plays an important role in modern biological engineering and industrial microbiology.[94] The work of Stanley Norman Cohen and Herbert Boyer in E. coli, using plasmids and restriction enzymes to create recombinant DNA, became a foundation of biotechnology.[95]

E. coli is a very versatile host for the production of heterologousproteins,[96] and various protein expression systems have been developed which allow the production of recombinant proteins in E. coli. Researchers can introduce genes into the microbes using plasmids which permit high level expression of protein, and such protein may be mass-produced in industrial fermentation processes. One of the first useful applications of recombinant DNA technology was the manipulation of E. coli to produce human insulin.[97]

Many proteins previously thought difficult or impossible to be expressed in E. coli in folded form have been successfully expressed in E. coli. For example, proteins with multiple disulphide bonds may be produced in the periplasmic space or in the cytoplasm of mutants rendered sufficiently oxidizing to allow disulphide-bonds to form,[98] while proteins requiring post-translational modification such as glycosylation for stability or function have been expressed using the N-linked glycosylation system of Campylobacter jejuni engineered into E. coli.[99][100][101]

Modified E. coli cells have been used in vaccine development, bioremediation, production of biofuels,[102] lighting, and production of immobilised enzymes.[96][103]

Strain K-12 is a mutant form of E. coli that over-expresses the enzyme Alkaline Phosphatase (ALP).[104] The mutation arises due to a defect in the gene that constantly codes for the enzyme. A gene that is producing a product without any inhibition is said to have constitutive activity. This particular mutant form is used to isolate and purify the aforementioned enzyme.[104]

Strain OP50 of Escherichia coli is used for maintenance of Caenorhabditis elegans cultures.

Strain JM109 is a mutant form of E. coli that is recA and endA deficient. The strain can be utilized for blue/white screening when the cells carry the fertility factor episome.[105] Lack of recA decreases the possibility of unwanted restriction of the DNA of interest and lack of endA inhibit plasmid DNA decomposition. Thus, JM109 is useful for cloning and expression systems.

Model organism[edit]

E. coli is frequently used as a model organism in microbiology studies. Cultivated strains (e.g. E. coli K12) are well-adapted to the laboratory environment, and, unlike wild-type strains, have lost their ability to thrive in the intestine. Many laboratory strains lose their ability to form biofilms.[106][107] These features protect wild-type strains from antibodies and other chemical attacks, but require a large expenditure of energy and material resources. E. coli is often used as a representative microorganism in the research of novel water treatment and sterilisation methods, including photocatalysis. By standard plate count methods, following sequential dilutions, and growth on agar gel plates, the concentration of viable organisms or CFUs (Colony Forming Units), in a known volume of treated water can be evaluated, allowing the comparative assessment of materials performance.[108]

In 1946, Joshua Lederberg and Edward Tatum first described the phenomenon known as bacterial conjugation using E. coli as a model bacterium,[109] and it remains the primary model to study conjugation.[110]E. coli was an integral part of the first experiments to understand phage genetics,[111] and early researchers, such as Seymour Benzer, used E. coli and phage T4 to understand the topography of gene structure.[112] Prior to Benzer's research, it was not known whether the gene was a linear structure, or if it had a branching pattern.[113]

E. coli was one of the first organisms to have its genome sequenced; the complete genome of E. coli K12 was published by Science in 1997[56]

From 2002 to 2010, a team at the Hungarian Academy of Science created a strain of Escherichia coli called MDS42, which is now sold by Scarab Genomics of Madison, WI under the name of "Clean Genome. E.coli",[114] where 15% of the genome of the parental strain (E. coli K-12 MG1655) were removed to aid in molecular biology efficiency, removing IS elements, pseudogenes and phages, resulting in better maintenance of plasmid-encoded toxic genes, which are often inactivated by transposons.[115][116][117] Biochemistry and replication machinery were not altered.

By evaluating the possible combination of nanotechnologies with landscape ecology, complex habitat landscapes can be generated with details at the nanoscale.[118] On such synthetic ecosystems, evolutionary experiments with E. coli have been performed to study the spatial biophysics of adaptation in an island biogeography on-chip.

Studies are also being performed attempting to program E. coli to solve complicated mathematics problems, such as the Hamiltonian path problem.[119]

In other studies, non-pathogenic E. coli has been used as a model microorganism towards understanding the effects of simulated microgravity (on Earth) on the same.[120][121]


In 1885, the German-Austrian pediatrician Theodor Escherich discovered this organism in the feces of healthy individuals. He called it Bacterium coli commune because it is found in the colon. 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).[91][122][123]

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.[124] Following a revision of Bacterium, it was reclassified as Bacillus coli by Migula in 1895[125] and later reclassified in the newly created genus Escherichia, named after its original discoverer.[126]

In 1996, the world's worst to date outbreak of E. coli food poisoning occurred in Wishaw, Scotland, killing 21 people.[127][128] This death toll was exceeded in 2011, when the 2011 Germany E. coli O104:H4 outbreak, linked to organic fenugreek sprouts, killed 53 people.


E. coli has several practical uses besides its use as a vector for genetic experiments and processes. For example, E. coli can be used to generate synthetic propane.[129]

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Pathogenic Escherichia coli

Escherichia coli typically colonizes the gastrointestinal tract of human infants within a few hours after birth. Usually, E. coli and its human host coexist in good health and with mutual benefit for decades. These commensal E. coli strains rarely cause disease except in immunocompromised hosts or where the normal gastrointestinal barriers are breached — as in peritonitis, for example. The niche of commensal E. coli is the mucous layer of the mammalian colon. The bacterium is a highly successful competitor at this crowded site, comprising the most abundant facultative anaerobe of the human intestinal microflora. Despite the enormous body of literature on the genetics and physiology of this species, the mechanisms whereby E. coli assures this auspicious symbiosis in the colon are poorly characterized. One interesting hypothesis suggests that E. coli might exploit its ability to utilize gluconate in the colon more efficiently than other resident species, thereby allowing it to occupy a highly specific metabolic niche1.

However, there are several highly adapted E. coli clones that have acquired specific virulence attributes, which confers an increased ability to adapt to new niches and allows them to cause a broad spectrum of disease. These virulence attributes are frequently encoded on genetic elements that can be mobilized into different strains to create novel combinations of virulence factors, or on genetic elements that might once have been mobile, but have now evolved to become 'locked' into the genome. Only the most successful combinations of virulence factors have persisted to become specific 'PATHOTYPES' of E. coli that are capable of causing disease in healthy individuals. Three general clinical syndromes can result from infection with one of these pathotypes: enteric/diarrhoeal disease, urinary tract infections (UTIs) and sepsis/meningitis. Among the intestinal pathogens there are six well-described categories: enteropathogenic E. coli (EPEC), enterohaemorrhagic E. coli (EHEC), enterotoxigenic E. coli (ETEC), enteroaggregative E. coli (EAEC), enteroinvasive E. coli (EIEC) and diffusely adherent E. coli (DAEC)2 (Fig. 1). UTIs are the most common extraintestinal E. coli infections and are caused by uropathogenic E. coli (UPEC). An increasingly common cause of extraintestinal infections is the pathotype responsible for meningitis and sepsis — meningitis-associated E. coli (MNEC). The E. coli pathotypes implicated in extraintestinal infections have recently been called ExPEC3. EPEC, EHEC and ETEC can also cause disease in animals using many of the same virulence factors that are present in human strains and unique colonization factors that are not found in human strains (Table 1). An additional animal pathotype, known as avian pathogenic E. coli (APEC), causes extraintestinal infections — primarily respiratory infections, pericarditis, and septicaemia of poultry. This review will focus on E. coli strains that are pathogenic for humans.

The six recognized categories of diarrhoeagenic E. coli each have unique features in their interaction with eukaryotic cells. Here, the interaction of each category with a typical target cell is schematically represented. These descriptions are largely the result of in vitro studies and might not completely reflect the phenomena that occurs in infected humans. a | EPEC adhere to small bowel enterocytes, but destroy the normal microvillar architecture, inducing the characteristic attaching and effacing lesion. Cytoskeletal derangements are accompanied by an inflammatory response and diarrhoea. 1. Initial adhesion, 2. Protein translocation by type III secretion, 3. Pedestal formation. b | EHEC also induce the attaching and effacing lesion, but in the colon. The distinguishing feature of EHEC is the elaboration of Shiga toxin (Stx), systemic absorption of which leads to potentially life-threatening complications. c | Similarly, ETEC adhere to small bowel enterocytes and induce watery diarrhoea by the secretion of heat-labile (LT) and/or heat-stable (ST) enterotoxins. d | EAEC adheres to small and large bowel epithelia in a thick biofilm and elaborates secretory enterotoxins and cytotoxins. e | EIEC invades the colonic epithelial cell, lyses the phagosome and moves through the cell by nucleating actin microfilaments. The bacteria might move laterally through the epithelium by direct cell-to-cell spread or might exit and re-enter the baso-lateral plasma membrane. f | DAEC elicits a characteristic signal transduction effect in small bowel enterocytes that manifests as the growth of long finger-like cellular projections, which wrap around the bacteria. AAF, aggregative adherence fimbriae; BFP, bundle-forming pilus; CFA, colonization factor antigen; DAF, decay-accelerating factor; EAST1, enteroaggregative E. coli ST1; LT, heat-labile enterotoxin; ShET1, Shigella enterotoxin 1; ST, heat-stable enterotoxin.

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The various pathotypes of E. coli tend to be clonal groups that are characterized by shared O (lipopolysaccharide, LPS) and H (flagellar) antigens that define SEROGROUPS (O antigen only) or SEROTYPES (O and H antigens)2,4. Pathogenic E. coli strains use a multi-step scheme of pathogenesis that is similar to that used by other mucosal pathogens, which consists of colonization of a mucosal site, evasion of host defences, multiplication and host damage. Most of the pathogenic E. coli strains remain extracellular, but EIEC is a true intracellular pathogen that is capable of invading and replicating within epithelial cells and macrophages. Other E. coli strains might be internalized by epithelial cells at low levels, but do not seem to replicate intracellularly.

Adhesion/colonization. Pathogenic E. coli strains possess specific adherence factors that allow them to colonize sites that E. coli does not normally inhabit, such as the small intestine and the urethra (Table 1). Most frequently these adhesins form distinct morphological structures called fimbriae (also called pili) or fibrillae, which can belong to one of several different classes (Fig. 2). Fimbriae are rod-like structures of 5–10 nm diameter that are distinct from flagella. Fibrillae are 2–4 nm in diameter, and are either long and wiry or curly and flexible5. The Afa adhesins that are produced by many diarrhoeagenic and uropathogenic E. coli are described as afimbrial adhesins, but in fact seem to have a fine fibrillar structure that is difficult to visualize6. Adhesins of pathogenic E. coli can also include outer-membrane proteins, such as intimin of UPEC and EHEC, or other non-fimbrial proteins. Some surface structures trigger signal transduction pathways or cytoskeletal rearrangements that can lead to disease. For example, the members of the Dr family of adhesins that are expressed by DAEC and UPEC bind to the DECAY-ACCELERATING FACTOR (DAF, also known as CD55), which results in activation of phosphatidylinositol 3-kinase (PI-3-kinase) and cell-surface expression of the major histocompatibility complex (MHC) class I-related molecule MICA7. The IcsA protein of EIEC nucleates actin filaments at one pole of the bacterium, which allows it to move within the cytoplasm and into adjacent epithelial cells on a 'tail' of polymerized actin8. Even surface structures that are present on commensal E. coli strains can induce signalling cascades if the organism encounters the appropriate receptor. The LPS of E. coli and other Gram-negative bacteria binds to Toll-like receptor 4 (TLR4), triggering a potent cytokine cascade that can lead to septic shock and death9. Flagellin, the main component of flagella, can bind to TLR5, thereby activating interleukin (IL)-8 expression and an inflammatory response10.

E. coli produce a variety of colonization factors, many of which are hair-like structures of various morphologies called fimbriae (also called pili) or fibrillae. a | Long, straight colonization factor antigen (CFA)/III fimbriae of ETEC (5–7 nm in diameter) protruding peritrichously from the bacterial surface. b | Abundant long, straight CFA/I fimbriae (5–7 nm) of ETEC contrasting with thicker, wavy flagella. c | P pili of UPEC showing the thin (∼3 nm) fibrillar adhesive tip at the end of the pilus (∼10 nm). d | Thin (2–3 nm), flexible, wiry CS3 fibrillar structures produced by ETEC that extend several micrometres from the cell surface. e | Bundle-forming pilus (BFP) of EPEC, a member of the type IV pili family, aggregates laterally to form large rope-like structures (>10 μm long) of variable width. f | Thin (2–5 nm), coiled, highly aggregative curli fibres produced by a variety of pathogenic and non-pathogenic E. coli. Additional characteristics of colonization factors of diarrhoeagenic E. coli have been reviewed elsewhere (see Ref. 5). Panels a,b,df are courtesy of J. Girón. Panel c is reproduced from Ref. 147Nature © Macmillan Magazines Ltd (1992).

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Toxins. More numerous than surface structures that trigger signal transduction pathways are secreted toxins and other effector proteins that affect an astonishing variety of fundamental eukaryotic processes (Table 2). Concentrations of important intracellular messengers, such as cyclic AMP, cyclic GMP and Ca2+, can be increased, which leads to ion secretion by the actions of the heat-labile enterotoxin (LT), heat-stable enterotoxin a (STa) and heat-stable enterotoxin b (STb), respectively — all of which are produced by different strains of ETEC (reviewed in Ref. 11). The Shiga toxin (Stx) of EHEC cleaves ribosomal RNA, thereby disrupting protein synthesis and killing the intoxicated epithelial or endothelial cells12. The cytolethal distending toxin (CDT) has DNaseI activity that ultimately blocks cell division in the G2/M phase of the cell cycle13. Another toxin that blocks cell division in the same phase, called Cif (cycle-inhibiting factor), does not possess DNaseI activity, but might act by inhibition of Cdk1 kinase activity14. The cytotoxic nectrotizing factors (CNF 1 and CNF 2) deaminate a crucial glutamine residue of RhoA, Cdc42 and Rac, thereby locking these important signalling molecules in the 'on' position and leading to marked cytoskeletal alterations, multinucleation with cellular enlargement, and necrosis15. The Map protein of EPEC and EHEC has at least two independent activities — stimulating Cdc42-dependent filopodia formation and targeting mitochondria to disrupt membrane potential in these organelles16.

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The various toxins are transported from the bacterial cytoplasm to the host cells by several mechanisms. LT is a classic A–B subunit toxin that is secreted to the extracellular milieu by a type II secretion system17. Several toxins, such as Sat, Pet and EspC, are called autotransporters because part of these proteins forms a β-barrel pore in the outer membrane that allows the other part of the protein extracellular access18. The SPATEs (serine protease autotransporters of enterobacteriaceae) are a subfamily of serine protease autotransporters that are produced by diarrhoeagenic and uropathogenic E. coli and Shigella strains. EPEC, EHEC and EIEC contain type III secretion systems, which are complex structures of more than 20 proteins forming a 'needle and syringe' apparatus that allows effector proteins, such as Tir and IpaB, to be injected directly into the host cell19. The UPEC haemolysin is the prototype of the type I secretion mechanism that uses TolC for export from the cell20. No type IV secretion systems have been described for pathogenic E. coli, with the exception of the type IV-like systems that are involved in conjugal transfer of some plasmids. By one means or another, pathogenic E. coli have evolved several mechanisms by which they can damage host cells and cause disease.

Pathotypes and pathogenesis

Enteropathogenic E. coli (EPEC). EPEC was the first pathotype of E. coli to be described. Large outbreaks of infant diarrhoea in the United Kingdom led Bray, in 1945, to describe a group of serologically distinct E. coli strains that were isolated from children with diarrhoea but not from healthy children. Although large outbreaks of infant diarrhoea due to EPEC have largely disappeared from industrialized countries, EPEC remains an important cause of potentially fatal infant diarrhoea in developing countries2. For decades, the mechanisms by which EPEC caused diarrhoea were unknown and this pathotype could only be identified on the basis of O:H serotyping. However, since 1979, numerous advances in our understanding of the pathogenesis of EPEC diarrhoea have been made, such that EPEC is now among the best understood of all the pathogenic E. coli.

A characteristic intestinal histopathology is associated with EPEC infections; known as 'attaching and effacing' (A/E), the bacteria intimately attach to intestinal epithelial cells and cause striking cytoskeletal changes, including the accumulation of polymerized actin directly beneath the adherent bacteria. The microvilli of the intestine are effaced and pedestal-like structures on which the bacteria perch frequently rise up from the epithelial cell (Fig. 3). The ability to induce this A/E histopathology is encoded by genes on a 35-kb pathogenicity island (PAI; see below) called the locus of enterocyte effacement (LEE)21. Homologues of LEE are also found in other human and animal pathogens that produce the A/E histopathology, including EHEC, rabbit EPEC (REPEC) and Citrobacter rodentium, which induces colonic hyperplasia in mice. The LEE encodes a 94-kDa outer-membrane protein called intimin, which mediates the intimate attachment of EPEC to epithelial cells22. Intimin not only functions as a ligand for epithelial cell adhesion, but also stimulates mucosal TH1 IMMUNE RESPONSES and intestinal crypt hyperplasia23. Most of the 41 open reading frames of the core LEE PAI encode a type III secretion system and the associated chaperones and effector proteins. One of these effector proteins, known as Tir (translocated intimin receptor), is inserted into the host-cell membrane, where it functions as a receptor for the intimin outer-membrane protein24. This is a fascinating example of a pathogen that provides its own receptor for binding to eukaryotic cells, although additional eukaryotic proteins have also been reported to act as receptors for intimin. A recent study showed that EPEC can disrupt cell polarity, causing basolateral membrane proteins, in particular β1-integrins, to migrate to the apical cell surface where they can bind to intimin25. In addition to β1-integrin, Tir has also been shown to bind to NUCLEOLIN26. In addition to its role as a receptor for intimin, Tir has important signalling functions in epithelial cells. The portion of Tir that is exposed to the cytosol nucleates cytoskeletal proteins, initially binding directly to the adaptor protein Nck, which recruits the amino terminus of Wiskott–Aldrich syndrome protein (N-WASP) and the actin-related protein 2/3 (Arp2/3) complex; recruitment of Arp2/3 results in actin filament nucleation and initiation of the characteristic pedestal complex27 (Fig. 1). Interestingly, the Tir protein of EHEC O157:H7 is not functionally identical to the Tir protein of EPEC O127:H6 because pedestals are formed independently of Nck, which indicates that additional bacterial factors are translocated to trigger actin signalling28. Other cytoskeletal proteins, such as vinculin, cortactin, talin and α-actinin, are also recruited to the pedestal complex29. Formation of the pedestal is a dynamic process whereby the force of actin polymerization can propel the pedestal across the surface of ptK2 epithelial cells30 (see movement of EPEC on ptK2 cells in the Online links). Tir also has a GAP (GTPase-activating protein) motif that has been implicated in the ability of Tir to downregulate filopodia formation16. Another secreted effector protein is EspF, which causes apoptosis31 and induces redistribution of the tight-junction-associated protein occludin, which leads to loss of trans-epithelial electrical resistance32. As noted above, the Map protein affects mitochondrial function and filopodia formation, and additional effectors — for example, EspG and EspH — have recently been described.

The attaching and effacing histopathology results in pedestal-like structures, which rise up from the epithelial cell on which the bacteria perch. Image courtesy of J. Girón.

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Additional EPEC virulence factors that are encoded outside the LEE have also been described. One very large protein of ∼385 kDa called lymphostatin (LifA) inhibits lymphocyte activation33. This protein is also present in strains of EHEC, where it is known as Efa1, and an adhesive property has been attributed to it34. Typical EPEC strains possess a plasmid of 70–100 kb called the EAF (EPEC adherence factor) plasmid35. This plasmid encodes a type IV pilus called the bundle-forming pilus (BFP)36, which mediates interbacterial adherence and possibly adherence to epithelial cells (Fig. 2). It also contains the per locus (plasmid-encoded regulator), the products of which regulate the bfp operon and most of the genes in the LEE by the LEE-encoded regulator (Ler). So-called atypical EPEC contain the LEE but do not contain the EAF plasmid. In industrialized countries, atypical EPEC are more frequently isolated from diarrhoeal cases than are typical EPEC that contain the EAF plasmid, although typical EPEC dominate in developing countries37. Atypical EPEC have also caused large outbreaks of diarrhoeal disease involving both children and adults in industrialized countries.

The model of EPEC pathogenesis is considerably more complex than simple binding to epithelial cells by a single adhesin and secretion of an enterotoxin that induces diarrhoea. The emerging model, several aspects of which are reviewed elsewhere2,38,39,40, indicates that EPEC initially adhere to epithelial cells by an adhesin, the identity of which is not yet clearly established; potential candidates include BFP, the EspA filament, flagella, LifA/Efa1 and intimin (by host-cell receptors). The type III secretion system is then activated and various effector proteins — including Tir, EspF, EspG, EspH and Map — are translocated into the host cell. EPEC binds through the interaction of intimin with Tir inserted in the membrane and numerous cytoskeletal proteins accumulate underneath the attached bacteria. Protein kinase C (PKC), phospholipase Cγ, myosin light-chain kinase and mitogen-activated protein (MAP) kinases are activated, which leads to several downstream effects, including increased permeability due to loosened tight junctions. Nuclear factor (NF)-κB is activated, leading to production of IL-8 and an inflammatory response that involves transmigration of polymorphonuclear leukocytes (PMNs) to the lumenal surface and activation of the adenosine receptor. The galanin-1 receptor is upregulated41, thereby increasing the response of the epithelial cells to the neuropeptide GALANIN, which is an important mediator of intestinal secretion. Some, but not all, typical EPEC strains produce an enterotoxin, EspC, that increases short circuit current in USSING CHAMBERS157. Diarrhoea probably results from multiple mechanisms, including active ion secretion, increased intestinal permeability, intestinal inflammation and loss of absorptive surface area resulting from microvillus effacement.

Enterohaemorrhagic E. coli (EHEC). First recognized as a cause of human disease in 1982, EHEC causes bloody diarrhoea (haemorrhagic colitis), non-bloody diarrhoea and haemolytic uremic syndrome (HUS). The principal reservoir of EHEC is the bovine intestinal tract and initial outbreaks were associated with consumption of undercooked hamburgers. Subsequently, a wide variety of food items have been associated with disease, including sausages, unpasteurized milk, lettuce, cantaloupe melon, apple juice and radish sprouts — the latter were responsible for an outbreak of 8,000 cases in Japan. Facilitated by the extremely low infectious dose required for infection (estimated to be <100 cells), EHEC has also caused numerous outbreaks associated with recreational and municipal drinking water, person-to-person transmission and petting zoo and farm visitations. A recent report indicates potential airborne transmission after exposure to a contaminated building42. EHEC strains of the O157:H7 serotype are the most important EHEC pathogens in North America, the United Kingdom and Japan, but several other serotypes, particularly those of the O26 and O111 serogroups, can also cause disease and are more prominent than O157:H7 in many countries.

The key virulence factor for EHEC is Stx, which is also known as verocytotoxin (VT). Stx consists of five identical B subunits that are responsible for binding the holotoxin to the glycolipid globotriaosylceramide (Gb3) on the target cell surface, and a single A subunit that cleaves ribosomal RNA, causing protein synthesis to cease12. The Stx family contains two subgroups — Stx1 and Stx2 — that share approximately 55% amino acid homology. Stx is produced in the colon and travels by the bloodstream to the kidney, where it damages renal endothelial cells and occludes the microvasculature through a combination of direct toxicity and induction of local cytokine and chemokine production, resulting in renal inflammation (reviewed in Ref. 43). This damage can lead to HUS, which is characterized by haemolytic anaemia, thrombocytopoenia and potentially fatal acute renal failure. Stx also induces apoptosis in intestinal epithelial cells — a process that is regulated by the Bcl-2 family44. Stx was first purified from Shigella dysenteriae, and HUS can also result from infection with this species, although not with other Shigella species or EIEC, which do not produce Stx. Stx also mediates local damage in the colon, which results in bloody diarrhoea, haemorrhagic colitis, necrosis and intestinal perforation.

In addition to Stx, most EHEC strains also contain the LEE pathogenicity island that encodes a type III secretion system and effector proteins that are homologous to those that are produced by EPEC. Animal models have shown the importance of the intimin adhesin in intestinal colonization, and HUS patients develop a strong antibody response to intimin and other LEE-encoded proteins. EHEC O157:H7 is believed to have evolved from LEE-containing O55 EPEC strains that acquired bacteriophage encoding Stx45. Although more than 200 serotypes of E. coli can produce Stx, most of these serotypes do not contain the LEE pathogenicity island and are not associated with human disease. This has led to the use of Shiga toxin-producing E. coli (STEC) or verotoxin-producing E. coli (VTEC) as general terms for any E. coli strain that produces Stx, and the term EHEC is used to denote only the subset of Stx-positive strains that also contain the LEE. However, there are LEE-negative STEC strains that are associated with disease — for example, O103:H21 strains — thereby demonstrating that there are additional virulence factors yet to be characterized. Several other potential adherence factors have been described for O157:H7 and/or non-O157:H7 strains, although the significance of these factors in human disease is not as well established as intimin. One potential adhesin is a large 362-kDa protein (ToxB) encoded on the 93-kb plasmid that is present in O157:H7 and other EHEC strains46. This protein shares sequence similarity with the large Clostridium toxin family, and to the EPEC LifA protein33 and the Efa-1 protein that has been implicated as an adhesin in non-O157:H7 EHEC strains34. This plasmid (pO157)47, also encodes an RTX (repeats in toxin) toxin that is similar to the UPEC haemolysin, a serine protease (EspP), a catalase and the StcE protein. StcE cleaves the C1 esterase inhibitor (C1-INH) of the complement pathway and could potentially contribute to the tissue damage, intestinal oedema and thrombotic abnormalities that are seen in EHEC infections48. The genome sequence of O157:H7 revealed numerous chromosomal islands (see below) that encode additional potential virulence factors. Included among these potential factors are novel fimbriae, iron uptake and utilization systems49, and a urease that is similar to those produced by Klebsiella and other urinary tract pathogens50.

Enterotoxigenic E. coli (ETEC). ETEC causes watery diarrhoea, which can range from mild, self-limiting disease to severe purging disease. The organism is an important cause of childhood diarrhoea in the developing world and is the main cause of diarrhoea in travellers to developing countries2.

ETEC colonizes the surface of the small bowel mucosa and elaborates enterotoxins, which give rise to intestinal secretion. Colonization is mediated by one or more proteinaceous fimbrial or fibrillar colonization factors (CFs), which are designated by CFA (colonization factor antigen), CS (coli surface antigen) or PCF (putative colonization factor) followed by a number. More than 20 antigenically diverse CFs have been characterized, yet epidemiological studies indicate that approximately 75% of human ETEC express either CFA/I, CFA/II or CFA/IV51. Antibodies to CFAs might ameliorate ETEC colonization and disease. ETEC are also an important cause of diarrhoeal disease in animals and these animal strains express fimbrial intestinal colonization factors, such as K88 and K99, which are not found in human ETEC strains.

ETEC enterotoxins belong to one of two groups: the heat-labile enterotoxins (LTs) and the heat-stable enterotoxins (STs). ETEC strains might express only an LT, only an ST, or both LTs and STs. LTs are a class of enterotoxins that are closely related in structure and function to cholera enterotoxin (CT), which is expressed by Vibrio cholerae52. The LT that is found predominantly in human isolates (LT-I; a related protein called LT-II is found in some animal ETEC isolates) has ∼80% amino acid identity with CT and, like CT, consists of a single A subunit and five identical B subunits. The B subunits mediate binding of the holotoxin to the cell surface gangliosides GM1 and GD1b, and the A subunit is responsible for the enzymatic activity of the toxin. LT has ADP-ribosyl transferase activity and transfers an ADP-ribosyl moiety from NAD to the α-subunit of the stimulatory G protein — a regulatory protein of the basolateral membrane that regulates adenylate cyclase. The resulting permanent activation of adenylate cyclase leads to increased levels of intracellular cAMP, activation of cAMP-dependent kinases and the eventual activation of the main chloride channel of epithelial cells — the cystic fibrosis transmembrane conductance regulator (CTFR). The net result of CFTR phosphorylation is increased Cl secretion from secretory crypt cells, which leads to diarrhoea (reviewed in Ref. 11). LT can also stimulate prostaglandin synthesis and stimulate the enteric nervous system; both of these activities can also lead to stimulation of secretion and inhibition of absorption11. LT is also a potent mucosal adjuvant independent of its toxic activity53 and has been incorporated into numerous vaccine candidates containing a variety of antigens, resulting in increased antibody responses to these antigens when they are delivered orally, nasally or even transdermally.

STs are small, single-peptide toxins that include two unrelated classes — STa and STb — which differ in both structure and mechanism of action. Only toxins of the STa class have been associated with human disease2. The mature STa toxin is a ∼2-kDa peptide, which contains 18 or 19 amino acid residues, six of which are cysteines that form three intramolecular disulphide bridges (reviewed in Ref. 11). The main receptor for STa is a membrane-spanning guanylate cyclase; binding of STa to guanylate cyclase stimulates guanylate cyclase activity, leading to increased intracellular cGMP, which, in turn, activates cGMP-dependent and/or cAMP-dependent kinases and, ultimately, increases secretion. Interestingly, intestinal guanylate cyclase is the receptor for an endogenous ligand called guanylin54, which has a similar structure to that of STa. So the ST family seems to represent a case of molecular mimicry. The STb toxin is associated with animal disease and is a 48-amino-acid peptide containing two disulphide bonds (reviewed in Ref. 55). STb can elevate cytosolic Ca2+ concentrations, stimulate the release of prostaglandin E2 and stimulate the release of serotonin, all of which are mechanisms that could lead to increased ion secretion.

ETEC is largely a pathogen of developing countries, and it is well known that these countries typically have a low rate of colon cancer. Pitari et al.56 have reported that STa suppresses colon cancer cell proliferation through a guanylyl cyclase C-mediated signalling cascade. So the high prevalence of ETEC in developing countries might have a protective effect against this important disease, and indicates that infectious diseases might exist in a complex evolutionary balance with their human populations.

Enteroaggregative E. coli (EAEC). EAEC are increasingly recognized as a cause of often persistent diarrhoea in children and adults in both developing and developed countries, and have been identified as the cause of several outbreaks worldwide. At present, EAEC are defined as E. coli that do not secrete LT or ST and that adhere to HEp-2 cells in a pattern known as auto-aggregative, in which bacteria adhere to each other in a 'stacked-brick' configuration2. It is likely that this definition encompasses both pathogenic and non-pathogenic clones, and it remains controversial as to whether all the EAEC have any common factors that contribute to their shared adherence phenotype. Nevertheless, at least a subset of EAEC are proven human pathogens.

The basic strategy of EAEC infection seems to comprise colonization of the intestinal mucosa, probably predominantly that of the colon, followed by secretion of enterotoxins and cytotoxins57. Studies on human intestinal explants indicate that EAEC induces mild, but significant, mucosal damage58 — these effects are most severe in colonic sections. Mild inflammatory changes are observed in animal models59 and evidence indicates that at least some EAEC strains might be capable of limited invasion of the mucosal surface60,61. The most dramatic histopathological finding in infected animal models is the presence of a thick layer of auto-aggregating bacteria adhering loosely to the mucosal surface. EAEC prototype strains adhere to HEp-2 cells and intestinal mucosa by virtue of fimbrial structures known as aggregative adherence fimbriae (AAFs)62,63,64, which are related to the Dr family of adhesins. At least four allelic variants of AAFs exist, but importantly, each is present in only a minority of strains. It should be noted, however, that not all EAEC strains adhere by virtue of AAFs. A recently described protein called dispersin65 forms a loosely associated layer on the surface of EAEC strains and seems to counter the strong aggregating effects of the AAF adhesin, perhaps facilitating spread across the mucosal surface or penetration of the mucous layer. An additional surface structure that is potentially involved in causing inflammation is a novel EAEC flagellin protein that induces IL-8 release66. Release of this cytokine can stimulate neutrophil transmigration across the epithelium, which can itself lead to tissue disruption and fluid secretion.

Several toxins have been described for EAEC. Two such toxins are encoded by the same chromosomal locus on opposite strands. The larger gene encodes an autotransporter protease with mucinase activity called Pic; the opposite strand encodes the oligomeric enterotoxin that is known as Shigella enterotoxin 1 (ShET1), owing to its presence in most strains of Shigella flexneri 2a67,68. The mode of action of ShET1 is not yet understood, but it might contribute to the secretory diarrhoea that accompanies EAEC and Shigella infection. A second enterotoxin that is present in many EAEC strains is enteroaggregative E. coli ST (EAST1), a 38-amino-acid homologue of the ETEC STa toxin69. It is conceivable that EAST1 could contribute to watery diarrhoea in EAST1-positive strains; however, the EAST1 gene (astA) can also be found in many commensal E. coli isolates, and therefore the role of EAST1 in diarrhoea remains an open question70. Many EAEC strains secrete an autotransporter toxin called Pet, which is encoded on the large virulence plasmid in close proximity to the gene encoding the AAF. Pet has enterotoxic activity and can also potentially lead to cytoskeletal changes and epithelial-cell rounding by cleavage of the cytoskeletal protein spectrin71.

Although no single virulence factor has been irrefutably associated with EAEC virulence, epidemiological studies implicate a 'package' of plasmid-borne and chromosomal virulence factors, similar to the virulence factors of other enteric pathogens. Several EAEC virulence factors are regulated by a single transcriptional activator called AggR, which is a member of the AraC family of transcriptional activators64 (J.P.N., unpublished data). One consistent observation from studies involving EAEC epidemiology is the association of the AggR regulon with diarrhoeal disease. Jiang et al. have recently shown that the presence of genes associated with the AggR regulon is predictive of significantly increased concentrations of faecal IL-8 and IL-1 in patients with diarrhoea caused by EAEC72. We suggest that the term 'typical EAEC' should be reserved for strains carrying AggR and at least a subset of AggR-regulated genes (for which the traditional EAEC probe is an adequate marker), and that the term 'atypical EAEC' be used for strains lacking the AggR regulon.

Enteroinvasive E. coli (EIEC). EIEC are biochemically, genetically and pathogenically closely related to Shigella spp. Numerous studies have shown that Shigella and E. coli are taxonomically indistinguishable at the species level73,74, but, owing to the clinical significance of Shigella, a nomenclature distinction is still maintained. The four Shigella species that are responsible for human disease, S. dysenteriae, S. flexneri, Shigella sonnei and Shigella boydii, cause varying degrees of dysentery, which is characterized by fever, abdominal cramps and diarrhoea containing blood and mucous. EIEC might cause an invasive inflammatory colitis, and occasionally dysentery, but in most cases EIEC elicits watery diarrhoea that is indistinguishable from that due to infection by other E. coli pathogens2. EIEC are distinguished from Shigella by a few minor biochemical tests, but these pathotypes share essential virulence factors. EIEC infection is thought to represent an inflammatory colitis, although many patients seem to manifest secretory, small bowel syndrome. The early phase of EIEC/Shigella pathogenesis comprises epithelial cell penetration, followed by lysis of the endocytic vacuole, intracellular multiplication, directional movement through the cytoplasm and extension into adjacent epithelial cells (reviewed in Ref. 75). Movement within the cytoplasm is mediated by nucleation of cellular actin into a 'tail' that extends from one pole of the bacterium. In addition to invasion into and dissemination within epithelial cells, Shigella (and presumably EIEC) also induces apoptosis in infected macrophages76. Genes that are required to effect this complex pathogenetic scheme are present on a large virulence plasmid that is found in EIEC and all Shigella species. The sequence of the 213-kb virulence plasmid of S. flexneri (pWR100) indicates that this plasmid is a mosaic that includes genetic elements that were initially carried by four plasmids77. One-third of the plasmid is composed of insertion sequence (IS) elements, which are undoubtedly important in the evolution of the virulence plasmid. This plasmid encodes a type III secretion system (see below) and a 120-kDa outer-membrane protein called IcsA, which nucleates actin by the binding of N-WASP8,78. The growth of actin micofilaments at only one bacterial pole induces movement of the organism through the epithelial cell cytoplasm. This movement culminates in the formation of cellular protrusions that are engulfed by neighbouring cells, after which the process is repeated. Although EIEC are invasive, dissemination of the organism past the submucosa is rare.

Much of EIEC/Shigella pathogenesis seems to be the result of the multiple effects of its plasmid-borne type III secretion system. This type III secretion system secretes multiple proteins, such as IpaA, IpaB, IpaC and IpgD, which mediate epithelial signalling events, cytoskeletal rearrangements, cellular uptake, lysis of the endocytic vacuole and other actions (reviewed in Refs 79,80). The type III secretion system apparatus, which is encoded by mxi and spa genes, enables the insertion of a pore containing IpaB and IpaC proteins into host cell membranes. In addition to pore formation, IpaB has several functions, such as binding to the signalling protein CD44, thereby triggering cytoskeletal rearrangements and cell entry, and binding to the macrophage caspase 1, resulting in apoptosis and release of IL-1 from macrophages. IpaC induces actin polymerization, which leads to the formation of cell extensions by activating the GTPases Cdc42 and Rac. The actin polymerization activity resides in the carboxy terminus of IpaC, whereas the amino terminus of this protein is involved in lamellipodial extensions. Conversely, IpaA binds to vinculin and induces actin depolymerization, thereby helping to organize the extensions that are induced by IpaC into a structure that enables bacterial entry. The translocated effector protein IpgD is a potent inositol 4-phosphatase that helps to reorganize host-cell morphology by uncoupling the cellular plasma membrane from the actin cytoskeleton, which leads to membrane blebbing81. Although the extensively characterized type III secretion system is essential for the invasiveness characteristic of EIEC and Shigella species, additional virulence factors have been described, including the plasmid-encoded serine protease SepA, the chromosomally encoded aerobactin iron-acquisition system and other secreted proteases that are encoded by genes present on pathogenicity islands (see below).

Diffusely adherent E. coli (DAEC). DAEC are defined by the presence of a characteristic, diffuse pattern of adherence to HEp-2 cell monolayers. DAEC have been implicated as a cause of diarrhoea in several studies, particularly in children >12 months of age2,82. Approximately 75% of DAEC strains produce a fimbrial adhesin called F1845 or a related adhesin (Ref. 83; J.P.N., unpublished observations); F1845 belongs to the Dr family of adhesins, which use DAF, a cell-surface glycosylphosphatidylinositol-anchored protein, which normally protects cells from damage by the complement system, as the receptor84,85,86. DAEC strains induce a cytopathic effect that is characterized by the development of long cellular extensions, which wrap around the adherent bacteria (Fig. 1). This characteristic effect requires binding and clustering of the DAF receptor by Dr fimbriae85. All members of the Dr family (including UPEC as well as the DAEC strain C1845) elicit this effect83. Binding of Dr adhesins is accompanied by the activation of signal transduction cascades, including activation of PI-3 kinase86. Peiffer et al. have reported that infection of an intestinal cell line by strains of DAEC impairs the activities and reduces the abundance of brush-border-associated sucrase-isomaltase and dipeptidylpeptidase IV87. This effect is independent of the DAF-associated pathway described above, and therefore provides a feasible mechanism for DAEC-induced enteric disease and also indicates the presence of virulence factors in DAEC other than Dr adhesins. Tieng et al.7 have proposed that DAEC might induce expression of MICA by intestinal epithelial cells, indicating that DAEC infection could be pro-inflammatory; this effect could potentially be important in the induction of inflammatory bowel diseases.

Uropathogenic E. coli (UPEC). The urinary tract is among the most common sites of bacterial infection and E. coli is by far the most common infecting agent at this site. The subset of E. coli that causes uncomplicated cystitis and acute pyelonephritis is distinct from the commensal E. coli strains that comprise most of the E. coli populating the lower colon of humans. E. coli from a small number of O serogroups (six O groups cause 75% of UTIs) have phenotypes that are epidemiologically associated with cystitis and acute pyelonephritis in the normal urinary tract, which include expression of P fimbriae, haemolysin, aerobactin, serum resistance and encapsulation. Clonal groups and epidemic strains that are associated with UTIs have been identified88,89.

Although many UTI isolates seem to be clonal, there is no single phenotypic profile that causes UTIs. Specific adhesins, including P (Pap), type 1 and other fimbriae (such as F1C, S, M and Dr), seem to aid in colonization90,91. Several toxins are produced, including haemolysin, cytotoxic necrotizing factor and an autotransported protease known as Sat. These virulence factors are found in differing percentages among various subgroups of UPEC92. Uropathogenic strains possess large and small pathogenicity islands containing blocks of genes that are not found in the chromosome of faecal strains. Availability of the genome sequence of E. coli CFT073 (Ref. 93) and efforts by other investigators to identify virulence genes by SIGNATURE-TAGGED MUTAGENESIS94 and other methods have allowed the development of a model of pathogenesis for UPEC (Fig. 4).

The figure shows the different stages of a urinary tract infection. Panels 2, 4, 5 and 11 are courtesy of N. Gunther, A. Jansen, X. Li and D. Auyer (University of Maryland), respectively. CFU, colony-forming units; PMNs, polymorphonuclear leukocytes.

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It is likely that infection begins with the colonization of the bowel with a uropathogenic strain in addition to the commensal flora. This strain, by virtue of factors that are encoded in pathogenicity islands, is capable of infecting an immunocompetent host, as it colonizes the periurethral area and ascends the urethra to the bladder (Fig. 4). Between 4 and 24 hours after infection, the new environment in the bladder selects for the expression of type 1 fimbriae95, which have an important role early in the development of a UTI96. Type 1 fimbriated E. coli attach to mannose moieties of the uroplakin receptors that coat transitional epithelial cells97. Attachment triggers apoptosis and exfoliation; for at least one strain, invasion of the bladder epithelium is accompanied with formation of pod-like bulges on the bladder surface that contain bacteria encased in a polysaccharide-rich matrix surrounded by a shell of uroplakin98. It is argued that invaded epithelial cells containing a tightly packed bacterial 'biofilm' could act as a reservoir for recurrent infection97,98, and indeed, in some cases of recurrent infection, the same serotype is encountered. However, a number of studies have identified different serotypes as being responsible for the recurring infection, an observation that is not consistent with this hypothesis. Iron acquisition and the ability to grow in urine are also crucial for survival.

In strains that cause cystitis, type 1 fimbriae are continually expressed and the infection is confined to the bladder96. In pyelonephritis strains, the invertible element that controls type 1 fimbriae expression turns to the 'off' position and type 1 fimbriae are less well expressed95. It could be argued that this releases the E. coli strain from bladder epithelial cell receptors and allows the organism to ascend through the ureters to the kidneys, where the organism can attach by P fimbriae to digalactoside receptors that are expressed on the kidney epithelium99,100. At this stage, haemolysin could damage the renal epithelium101 and, together with other bacterial products including LPS, an acute inflammatory response recruits PMNs to the site. Haemolysin has also been shown to induce Ca2+ oscillations in renal epithelial cells, resulting in increased production of IL-6 and IL-8 (Ref. 102). Secretion of Sat, a vacuolating cytotoxin, damages glomeruli and is cytopathic for the surrounding epithelium103. In some cases, the barrier that is provided by the one-cell-thick proximal tubules can be breached and bacteria can penetrate the endothelial cell to enter the bloodstream, leading to bacteraemia.

Meningitis/sepsis-associated E. coli (MNEC). This E. coli pathotype is the most common cause of Gram-negative neonatal meningitis, with a case fatality rate of 15–40% and severe neurological defects in many of the survivors104,105. The incidence of infants with early-onset sepsis owing to E. coli infection seems to be increasing, while infection by Gram-positive organisms decreases106. As with E. coli pathotypes that have a well-defined genetic basis for virulence, strains that cause meningitis are represented by only a limited number of O serogroups, and 80% of the strains are of the K1 capsule type. One interesting difference between MNEC and E. coli that cause intestinal or urinary tract infections is that although the latter strains can be readily transmitted by urine or faeces, infection of the central nervous system offers no obvious advantage for the selection and transmission of virulent MNEC strains.

E. coli that cause meningitis are spread haematogenously. Levels of bacteraemia correlate with the development of meningitis107; for example, bacteraemias of >103 colony forming units per ml of blood are significantly more likely to lead to the development of meningitis than in individuals with lower colony forming units per ml in their blood. These bacteria translocate from the blood to the central nervous system without apparent damage to the blood–brain barrier, which indicates a transcytosis process. Electron micrographs imply entry by a zippering mechanism in a process that does not affect transendothelial electrical resistance108. This indicates that the host-cell membrane is not significantly disrupted during entry of the bacterium. Two models for studying MNEC have been developed: a monolayer of brain microvascular endothelial cells109 and an intact animal model using 5-day-old rats110.

As for other E. coli pathotypes, the genomes of these extraintestinal K1 strains have additional genes that are not found in the commensal E. coli K-12 strains. In genomic comparisons, the genome of E. coli RS218, a meningitis-associated strain, was found to have at least 500 kb of additional genes inserted in at least 12 loci compared with E. coli K-12 (Refs 111,112). In addition, strain RS218 harbours a 100-kb plasmid, on which at least one virulence factor has been localized113.

Some insights into the mechanism of pathogenesis of these strains have been obtained. K1 strains use S fimbriae to bind to the lumenal surfaces of brain microvascular endothelium in neonatal rats114. Invasion requires the outer-membrane protein OmpA to bind to the GlcNAcβ1-4GlcNAc epitope of the brain microvascular endothelial cell receptor glycoprotein115. Other membrane proteins — for example, IbeA, IbeB, IbeC and AslA — are also required for invasion (reviewed in Ref. 116). Invasion correlates with microaerobic growth and iron supplementation117. CNF1 is required for invasion113, as is the K1 capsule, which elicits serum resistance and has antiphagocytic properties. In an experimental model, strains that express K1 capsule proteins and those that do not were able to cross the blood–brain barrier, but only the K1-expressing strains survived118. As a consequence of invasion, actin cytoskeletal rearrangement occurs and tyrosine phosphorylation of focal adhesion kinase (FAK) and paxillin is induced119. In addition, a substantial list of in vivo-induced genes, including those that encode iron-acquisition systems, was compiled using in vivo expression technology (IVET) in conjunction with a murine model of septicaemic infection120.

Other potential E. coli pathotypes. Several other potential E. coli pathotypes have been described, but none of these are as well established as the pathotypes described above (Box 1). Among the most intriguing of these potential pathogens are strains of E. coli that are associated with Crohn's Disease, which are known as adherent-invasive E. coli (AIEC)121. No unique genetic sequences have yet been described for AIEC strains, but such strains can invade and replicate within macrophages without inducing host-cell death and can induce the release of high amounts of tumour-necrosis factor (TNF)-α, a characteristic which could lead to the intestinal inflammation that is characteristic of Crohn's Disease. An inflammatory process, together with necrosis of the intestinal epithelium, are characteristics of necrotizing enterocolitis (NEC), an important cause of mortality and long-term morbidity in pre-term infants. The ability of some E. coli strains to transcytose through epithelial cell monolayers has been hypothesized to contribute to NEC122. Necrotoxic E. coli (NTEC) produce either CNF1 or CNF2 and have been associated with disease in both humans and animals123. Strains that are known as cell-detaching E. coli (CDEC) have been isolated from children with diarrhoea and the characteristic ability of these strains to detach cultured epithelial cells from glass or plastic has been associated with the production of haemolysin124. The relationships among the NEC-associated strains, NTEC and CDEC, have not yet been clearly established. The genes encoding CDT are infrequently present in E. coli strains and no significant association with disease has yet been found for this toxin. CDT is usually found in strains that possess other virulence factors, such as CNF, Stx and the LEE. However, recent information indicates that CDT can be encoded by four distinct genetic variants in E. coli and so earlier epidemiological studies using only one or two cdt genes as probes should be re-evaluated125. In at least one strain, the cdt genes are contained on a bacteriophage126, which could account for the presence of this toxin in a number of different E. coli pathotypes.

A poorly characterized subset of E. coli infections outside the gastrointestinal or urinary tract is a group implicated in intra-abdominal infections (IAIs), including abscesses, wounds, appendicitis and peritonitis. The initial microflora at the site of an IAI is polymicrobial, but E. coli and the strictly anaerobic Bacteroides fragilis are often isolated from these abscesses. A recent study indicates that a novel haem-binding protein, known as the 'haemoglobin-binding protease' (Hbp), is significantly associated with E. coli strains isolated from IAIs compared with those E. coli strains isolated from blood, urine or faeces127. Purified Hbp was shown to be capable of delivering haem to B. fragilis, indicating a synergy in abscess formation whereby E. coli provides iron from haem to B. fragilis to overcome iron restrictions imposed by the host. Interestingly, Hbp is identical to Tsh, which is an autotransporter haemagglutinin that is associated with APEC, thereby indicating that this protein can contribute to at least two different infectious diseases — IAIs in humans and respiratory tract infections in poultry127.


Mobile genetic elements. A striking feature of pathogenic E. coli is the association of genes that encode virulence factors with mobile genetic elements (Fig. 5). This was first shown more than 30 years ago with ETEC strains, in which enterotoxic activity was transferred together with a self-transmissible plasmid. In many cases, these 'Ent' plasmids were also shown to encode antibiotic resistance. There are now numerous examples of plasmids that encode crucial virulence factors of pathogenic E. coli, including plasmids in EAEC that encode fimbriae and toxins, plasmids in EIEC/Shigella that encode a type III secretion system and invasion factors, the EPEC EAF plasmid, which encodes BFP, and the pO157 plasmid of EHEC, which encodes accessory toxins. Although many of these plasmids are self-transmissible, some lack conjugation genes and can only be transferred with a conjugative plasmid. For ETEC, the genes that encode both LT and ST are found on plasmids, but some estA genes encoding STa are on transposons that can be inserted into either plasmids or the chromosome. One IS element has been described that contains the astA gene encoding the EAST1 toxin, completely embedded in a large putative transposase gene, the coding sequence of which is on the same strand but in the −1 reading frame relative to astA128.

E. coli virulence factors can be encoded by several mobile genetic elements, including transposons (Tn) (for example, heat stable enterotoxin (ST) of ETEC), plasmids (for example, heat-labile enterotoxin (LT) of ETEC and invasion factors of EIEC), bacteriophage (for example, Shiga toxin of EHEC) and pathogenicity islands (PAIs) — for example, the locus of enterocyte effacement (LEE) of EPEC/EHEC and PAIs I and II of UPEC. Commensal E. coli can also undergo deletions resulting in 'black holes', point mutations or other DNA rearrangements that can contribute to virulence. These additions, deletions and other genetic changes can give rise to pathogenic E. coli forms capable of causing diarrhoea (EPEC, EHEC, EAEC DAEC), dysentery (EIEC), haemolytic uremic syndrome (EHEC), urinary tract infections (UPEC) and meningitis (MNEC). HUS, haemolytic uremic syndrome; UTI, urinary tract infection.

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The main virulence factor of EHEC, Stx, is encoded on a lambda-like bacteriophage; acquisition of this phage was a key step in the evolution of EHEC from EPEC45. The EHEC EDL933 genome sequence contains 18 regions with homology to known bacteriophages, but most seem to be incomplete phage genomes49. Although only the Stx phage seems to be capable of lytic growth and production of infectious particles, these cryptic phage sequences enable the continued evolution of these strains by homologous recombination of phages into different chromosomal sites. The ability to produce Stx can be readily transmitted by transduction of the genes encoding Stx phage to K-12 or commensal E. coli, but this step is probably insufficient to confer virulence because non-O157:H7 E. coli strains containing stx genes without other EHEC virulence factor genes can be readily isolated from commercial meat products. This observation reinforces the concept that a single gene is insufficient to convert commensal E. coli to pathogenic E. coli, and that instead a combination of genes encoding toxins, colonization factors and other functions are required to make E. coli pathogenic.

PAIs are large genomic regions (10–200 kb) that are present in the genomes of pathogenic strains but absent from the genomes of non-pathogenic members of the same or related species (reviewed in Ref. 129). PAIs are typically associated with tRNA genes, have a different G+C content compared with the host DNA and often carry cryptic or functional genes that encode mobility factors, such as integrases, transposases and IS elements. PAIs were first described in pathogenic E. coli and have subsequently been described in several Gram-negative and Gram-positive bacteria. The first PAIs were described in UPEC strain 536, which contains at least four such islands130. The PAI II536 island is 100 kb in size, is inserted at the leuX tRNA gene at minute 97 on the E. coli chromosome and encodes haemolysin and P fimbriae. This island is flanked by 18-bp direct repeats, which facilitate deletion of the entire island at a relatively high frequency.

The first PAI to be described in diarrhoeagenic E. coli was the LEE PAI in EPEC and EHEC21. As described above, the LEE encodes a type III secretion system and other factors that are responsible for the A/E histopathology. In EPEC strain E2348/69 and EHEC strain O157:H7, the LEE is inserted at the selC tRNA gene, which is also the site of insertion of the PAI I536 island of UPEC. The insertion of two different PAIs at the same chromosomal site in EPEC/EHEC and UPEC indicates the presence of 'hot spots' in the E. coli chromosome into which different PAIs can insert and give rise to different E. coli pathotypes. The 35-kb LEE from E2348/69 contains 41 open reading frames that are highly conserved among EPEC and EHEC strains, as well as rabbit and other animal strains of EPEC that produce A/E lesions. In some E. coli strains, the LEE PAI is immediately adjacent to genes that encode other potential virulence factors, such as the efa1/lifA gene, to form a larger PAI of 59.5 kb131. The LEE of one rabbit strain is contained on a ∼85-kb PAI that contains an intact integrase gene and is flanked by direct repeats. This PAI is capable of spontaneous deletion and site-specific integration into the pheU tRNA locus of K-12 (Ref. 131). The prototypic LEE of E2348/69 contains no direct repeats or mobility genes and seems to be incapable of spontaneous deletion or transfer, which indicates that this PAI has evolved to the point that it has lost the genetic elements that were responsible for the initial integration into the chromosome.

PAIs have also been described for EAEC, EIEC/Shigella, MNEC and some ETEC strains (reviewed in Refs 132–134). Some PAIs are unique to individual pathotypes, whereas other PAIs are found in multiple pathotypes. The she (Shi-I) PAI is present in EAEC, where it encodes the ShET1 enterotoxin and the autotransporter toxin Pic. The high pathogenicity island (HPI) was originally described in Yersinia, but is also present in most strains of EAEC, DAEC and UPEC, and in some strains of EIEC, ETEC, EPEC and EHEC, as well as some Klebsiella and Citrobacter strains135. The HPI contains genes that are involved in regulation, biosynthesis and uptake of the siderophore yersiniabactin.

The inverse of PAIs are 'black holes', which refers to the deletion of blocks of genes in commensal or K-12 E. coli that lead to increased virulence. In EIEC/Shigella, lack of the cadA gene, which encodes lysine decarboxylase (LDC) in K-12, enables activity of an enterotoxin which is normally inhibited by the product of the LDC reaction — cadaverine136. In many EIEC strains, the cadC gene that encodes a regulator of cadA is preferentially mutated, which results in the same phenotype137. EIEC/Shigella also have a large number of pseudogenes (see below), which might also comprise functional 'black holes'. Although the genes encoding E. coli virulence factors are usually either present or absent, single-nucleotide polymorphisms (SNPs) that contribute to virulence have been found in the genes that encode the FimH and Dr adhesins138.

Genomic sequences. Prior to the determination of the complete genomic sequence for a pathogenic strain of E. coli it was anticipated that these pathogens differed from K-12 primarily by the presence of a limited number of PAIs, plasmids and phage that encoded specific virulence factors. However, when the first pathotype was sequenced — namely two different strains of EHEC O157:H7 — the extent of lateral gene transfer was found to be far greater than had been anticipated. EHEC strain EDL933 contains nearly 1,400 novel genes scattered throughout 177 discrete regions of DNA greater than 50 bp in size called O-islands; these regions total 1.34 Mb of DNA that is not present in K-12 (Ref. 49). Almost as surprising was the fact that although the two strains shared a 4.1-Mb 'backbone' of common sequences, EDL933 lacked 0.53 Mb of DNA that was present in K-12 in 234 'K-islands' (>50 bp). The absence of a substantial amount of K-12 DNA in other E. coli pathotypes was shown in a recent DNA array study in which up to 10% of E. coli K-12 open reading frames were not detected in several pathogenic and non-pathogenic E. coli strains139.

The striking mosaic structure of EHEC was further shown by the determination of the UPEC genome sequence, which at 5.2 Mb is similar in size to that of EHEC93. UPEC strain CFT073 contains 2,004 genes in 247 islands that are not present in K-12. In contrast to the striking conservation of the core LEE PAI in EPEC and EHEC, substantial differences were seen between the large PAIs of CFT073 and two other well-studied UPEC strains — J96 and 536. The analyses indicated that extraintestinal pathogenic E. coli strains arose independently from multiple clonal lineages. Interestingly, when the predicted proteins from all three strains, K-12, EHEC and UPEC, were compared, only 39.2% of the combined (nonredundant) set of proteins are common to all three strains93.

As noted above, several studies using DNA hybridization, multilocus enzyme electrophoresis and sequencing of a small number of genes indicates that Shigella species clearly fall taxonomically within the E. coli species74. The genome sequence of S. flexneri 2a further supports this grouping and exhibits the backbone and island mosaic structure of the genomes of the E. coli pathogens73. The 4.599-Mb genome size is closer to that of K-12 (4.639 Mb) than to EHEC and UPEC, and the 70.6% of K-12 genes that are found in S. flexneri is of a similar magnitude to the 74.3% of K-12 genes that are found in UPEC CFT073. However, UPEC contains an additional 1,827 proteins that are not found in K-12, whereas S. flexneri contains only 205 proteins that are not found in K-12, thereby indicating that S. flexneri is more similar to K-12 than is UPEC CFT073. The S. flexneri genome is notable for its large number of IS elements — which constitute 6.7% (309.4 kb) of the chromosome — and for the large number (372) of pseudogenes present — which constitute 8.1% of the genome. These pseudogenes arose by several mechanisms, including single-nucleotide insertions or deletions, point mutations and IS-element insertions. Interestingly, phenotypic tests that have traditionally been used to distinguish E. coli from S. flexneri, such as lack of motility, utilization of various carbon sources and the requirement for NAD, are largely the result of pseudogenes. Whether these pseudogenes are advantageous, disadvantageous, or neutral cannot be stated at this time.

Regulation. Consistent with the fact that E. coli virulence factors are typically encoded on 'foreign' DNA that is not contained in commensal E. coli strains, the expression of many virulence factor genes is frequently regulated by transcriptional regulators that are also encoded on pathogenicity islands or plasmids. One such pathogen-specific regulator is the LEE-encoded Ler protein, which positively regulates the EPEC/EHEC genes encoding the type III secretion system that are also found on the LEE140. Another example is the PapB regulator of the pap operon encoded on PAIs in UPEC141. In some instances, a plasmid-encoded regulator can activate transcription of chromosomal genes — for example, regulators such as the regulatory cascade formed by the EPEC plasmid-encoded regulator (Per) that regulates the LEE-encoded regulator, Ler (Fig. 6). Many pathogen-specific regulators belong to the AraC family of transcriptional activators, such as Per (EPEC), AggR (EAEC), VirF (EIEC) and Rns (ETEC).

The attaching and effacing histopathology induced by EPEC and EHEC is encoded by the locus of enterocyte effacement (LEE) pathogenicity island, which contains five major polycistronic operons designated LEE1–5. Expression of the LEE genes is regulated by EPEC-specific regulators (depicted in green) and generic E. coli regulators (depicted in yellow). The first open reading frame of the LEE1 operon encodes the LEE-encoded regulator, Ler, which positively regulates expression of other LEE operons by counteracting the repressive effects of H-NS140,148. Ler also regulates expression of the EspC enterotoxin that is produced by many EPEC strains and potentially other virulence factors. Expression of Ler is itself regulated by several factors, including IHF149, FIS150 and BipA151, and quorum sensing through the QseA regulator152. Quorum sensing also regulates other factors that are potentially involved in virulence, such as flagella, through the QseBC two-component regulator153. In EPEC, but not EHEC, expression of Ler is positively regulated by the products of the per (plasmid-encoded regulator)154 locus, which consists of three open reading frames, perA, perB and perC; PerA (BfpT) also regulates the bfp genes encoding a type IV pilus155. In acidic conditions, the per genes are repressed by GadX, which activates the gadAB genes involved in acid resistance156. This dual action of GadX could prevent premature expression of virulence factors in the stomach while enhancing survival of the organism until it reaches more alkaline conditions in the small intestine where expression of virulence factors is induced. Bip, Ig heavy chain binding protein; FIS, factor for inversion stimulation; IHF, integration host factor.

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Expression of E. coli virulence factors is not solely regulated by pathogen-specific regulators. A common theme among the various E. coli pathotypes is the exploitation of regulators present in commensal E. coli for the regulation of virulence factor genes that are present only in pathogenic E. coli. For example, the stx1 gene encoding Shiga toxin is transcribed from the PR′ promoter that also controls expression of late lambda phage lysis genes, thereby linking toxin expression with a lytic function, which allows release of the toxin142. This linkage leads to induction of transcription of both toxin genes and lysis genes by certain antibiotics, causing increased toxin production, increased release of toxin by lysis and increased death in a mouse model143. Another example is the EPEC Ler, which in addition to being regulated by Per is also regulated by integrative host factor (IHF), factor for inversion stimulation (FIS) and Ig heavy chain binding protein (BipA) — global regulators of housekeeping genes in K-12 (Fig. 6). Another regulatory system present in K-12 that regulates expression of both housekeeping and virulence factor genes is the AI-2/luxS quorum sensing (QS) system. QS is a method of intercellular communication that allows unicellular organisms such as E. coli to behave as multi-cellular organisms. A small autoinducer (AI) molecule is produced by many organisms, including E. coli; AIs can activate the expression of a subset of genes when the microbial population, and therefore the AI concentration, reaches a crucial level. QS regulates the expression of the EPEC and EHEC LEE operons by Ler as well as flagella expression144. As the infectious dose of EHEC (10–100 organisms) is too low to make use of QS, a model has been proposed in which EHEC detect the AI signals that are produced by the large concentration of commensal E. coli and other bacteria present in the large intestine144. In response to this signal, expression of key virulence factors, including the LEE and Stx, is induced, thereby initiating the disease process. This regulatory mechanism can also be activated by mammalian hormones, such as adrenaline and noradrenaline, in an example of regulatory 'cross-talk' between eukaryotic and prokaryotic organisms145.

Regulation of virulence factor expression by physical DNA rearrangements is uncommon in pathogenic E. coli but phase variation is seen with type 1 fimbriae. Transcription of the fim operon that encodes type 1 fimbriae is primarily under the control of an invertible element that contains the promoter responsible for transcription of the main structural subunit. Individual bacterial cells either express the fimbriae over their entire surface or do not express any fimbriae. This phase variation of type 1 fimbriae is controlled at the transcriptional level by the invertible element, which is regulated by the FimB and FimE recombinases146. The inversion seems to be regulated during the course of infection, and the orientation of the element correlates with whether UPEC strains remain localized to the bladder. In cystitis infections most of the strains have the invertible element in the 'on' position and express type 1 fimbriae, whereas when they leave the bladder and ascend to the kidneys to cause pyelonephritis, most of the strains have the element in the 'off' position and do not express type 1 fimbriae95. The regulation of type 1 fimbriae in UPEC is further complicated by cross-talk between two different adhesion operons, whereby PapB, a key regulator of the pap operon, inhibits type 1 phase variation141.


The evolution of pathogenic E. coli that has resulted in formation of distinct pathotypes capable of colonizing the gastrointestinal tract, urinary tract or meninges illustrates how key genetic elements can adapt a strain to distinct host environments. Using E. coli K-12 as a 'base-model', several features can be added (PAIs, plasmids, transposons or phage) or subtracted (black holes or pseudogenes) to modify the base model to adapt to specific environments and to enable these modified strains to cause disease in an immunocompetent human or animal host. This genomic plasticity complicates efforts to categorize the various clusters of pathogenic E. coli strains into sharply delineated pathotypes. The evolutionary process, clearly ongoing, has resulted in a highly versatile species that is capable of colonizing, multiplying in and damaging diverse environments. The host cell activities that are affected by these pathogenic strains of E. coli encompass a broad spectrum of functions, including signal transduction, protein synthesis, mitochondrial function, cytoskeletal function, cell division, ion secretion, transcription and apoptosis. The ability of various E. coli virulence factors to affect such a wide range of cellular functions has led to the use of the various toxins, effectors and cell surface structures as tools to better understand these fundamental eukaryotic processes. Our increased understanding of the mechanisms by which E. coli can cause disease has dramatically changed our perspective of this species that was once dismissed as a harmless commensal of the intestinal tract.

Box 1 | Questions for future research

  • What are the best methods for the diagnosis of intestinal E. coli pathogens so they can be routinely diagnosed in clinical laboratories and their true significance determined?

  • What are the factors that allow commensal E. coli strains to colonize the intestine and survive so successfully in this niche?

  • What is the role of E. coli in Crohn's Disease and possibly other intestinal diseases that were previously considered to be non-infectious in origin?

  • What is the best way to treat and/or prevent enterohaemorrhagic E. coli infection to prevent the most serious outcome — haemolytic uremic syndrome.

  • What are the pathogenetic mechanisms and roles of EAEC and DAEC in enteric disease?

  • What other pathotypes of E. coli are yet to be discovered or yet to evolve?


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