Escherichia coli(E. coli) morphology, arrangement, Cultural Characteristics, Diagnosis

Escherichia coli also termed E. coli, which is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus Escherichia.

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This article writter by MN Editors on September 26, 2021

Microbiology Notes is an educational niche blog related to microbiology (bacteriology, virology, parasitology, mycology, immunology, molecular biology, biochemistry, etc.) and different branches of biology.

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Escherichia coli morphology, arrangement, Cultural Characteristics, Pathogenicity, Diagnosis
Escherichia coli morphology, arrangement, Cultural Characteristics, Pathogenicity, Diagnosis

Scientific classification of Escherichia coli

SpeciesE. coli
Binomial nameEscherichia coli

Escherichia coli

  • Theodor Escherich first discovered E. coli, in 1885 after isolating it from the feces of newborns.
  • Escherichia coli also termed E. coli, which is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus Escherichia.
  • It is usually found in the lower intestine of warm-blooded organisms (endotherms).
  • Most E. coli strains are harmless, however, some serotypes (EPEC, ETEC etc.) are responsible for serious food poisoning in their hosts. They also occasionally cause food contamination incidents that prompt product recalls.
  • The normal microbiota of the gut includes the harmless strains of E. coli. They provide benefits to their host cell by generating vitamin K2, (which helps blood to clot) and preventing colonization of the intestine with pathogenic bacteria, having a mutualistic relationship.
  • In the environment, they are mainly found within fecal matter. In the fresh fecal matter they grow massively under aerobic conditions for 3 days, but its numbers decrease slowly afterward.
  • Cells can survive outside of the body for a limited amount of time, which makes them potential indicator organisms to test environmental samples for fecal contamination.
Scanning electron micrograph of an E. coli colony.
Scanning electron micrograph of an E. coli colony.| Source:

E. coli Habitat

  • The availability of the nutrients within the intestine of host organisms is the main factor on which the niche of E. coli depends.
  • The gastrointestinal (GI) tract of humans and many other warm-blooded animals is the primary habitat of E. coli.
  • They can be found in the mucus or the epithelium on the wall of the intestine. Commonly they are found in the colon of the large intestine.
  • They can form a mutual relationship with its host.
  • They constitute about 0.1% to 1% of GI tract bacteria.
  • They are facultative aerobes.
  • They are also found in human feces.
  • At the outside of the intestinal tract/outside of a host body, they are able to survive only for a few hours.
  • Outside of the host body, they are mainly found in faecally contaminated environments such as water or mud or sediments.
  • If E. coli comes in contact with raw vegetables, it has the potential to attach itself to the leaves of the vegetable.
  • They are also found at a higher temperature, such as on the edge of hot springs.
  • They are found on ground meats due to slaughterhouse processing.

E.coli Morphology and Arrangement

  • E.coli is a gram-negative (-ve) bacteria.
  • These are straight, rod shaped (bacillus) bacterium.
  • They are arranged singly or in pairs.
  • Their size is about 1–3 µm × 0.4–0.7 µm (micrometer).
  • They are motile due to the presence of peritrichous flagella. Some strains of E. coli are non-motile.
  • It is a non–sporing bacteria.
  • Some of them may be fimbriated. The fimbriae are of type 1 (hemagglutinating & mannose-sensitive) and are present in both motile and non-motile strains.
  • It has a polysaccharide capsule which can be easily demonstrated by using India ink preparation, appearing as a clear halo in a dark background.
  • The cell wall is thin with only 1 or 2 layers of peptidoglycan.
  • It is a facultative anaerobe.
  • They can grow over a wide range of temperatures from 15-45°C.
E.coli Morphology and Arrangement
E.coli Morphology and Arrangement

Antigenic Structure of E.coli

Heat Stable Lipopolysaccharide (LPS) is the major cell wall antigen of E. coli. It contains 4 antigens such as H, O, K and F.

  • H or Flagellar Antigen: These are Heat and alcohol labile protein. Mainly found on the flagella. They are Genus specific; Present as monophasic; 75 ‘H’ antigens have been recognized.
  • O or Somatic Antigen: These are heat stable, resistant to boiling up to 2 hrs. 30 minutes. It is found on the surface of the outer membrane. An integral part of the cell wall. 173 ‘O’ antigens have been recognized.
  • K or Capsular Antigen: These are Heat labile, acidic polysaccharide antigen present in the envelope. On Boiling removes the K antigen. They can Inhibit the phagocytosis. 103 ‘K’ antigens have been recognized
  • F or Fimbrial Antigen: These are the Heat labile proteins, present in the fimbriae. K88, K99 antigens. 

Cultural Characteristics of E. coli

  • Escherichia coli or E. coli can grow on ordinary media like Nutrient Agar medium (NAM).
  • Commonly the NAM & MacConkey Agar medium is used for the cultivation of Escherichia coli in the Laboratory. 
  • The optimum temperature required for most of the E.coli strains is 37°C. 
  • E. coli can survive at 4.5– 9.5 pH but the optimum pH is 7.0.
  • Escherichia coli (E. coli) is an aerobic bacterium which means it can grow best in the presence of oxygen and it is also a Facultative anaerobic organism which means it can also grow in a low oxygen environment.

 The following cultural media is used to grow E. coli.

  • Nutrient Agar (NA): The E. coli colony on Nutrient agar media appears large, circular, low convex, grayish, white, moist, smooth, and opaque. There are two forms such as Smooth (S) form and Rough (R) form. The Smooth forms of E. coli are emulsifiable in saline. The smooth to rough variation (S-R variation) occurs due to repeated subculture.
  • Blood Agar (BA): The Colonies of E. coli are big, circular, gray and moist. Beta (β) hemolytic colonies are formed. 
  • MacConkey Agar (MAC): The  E. coli Colonies are circular, moist, smooth and of entire margin; appear flat and pink. These are lactose fermenting colonies.
  • Mueller Hinton Agar (MHA): The  E. coli Colonies are pale straw colored.
  • Eosin Methylene Blue (EMB) Agar: Green Metallic sheen colonies are formed.
  • m-ENDO Agar: The  E. coli Colonies are green metallic sheen. Metabolize lactose with the production of aldehyde and acid.
  • Violet Red Bile Agar (VRBA): The colonies are red  (pink to red). Bluish fluorescence is seen around colonies under UV.
  • Cystine Lactose Electrolyte-Deficient (CLED) Agar: They give lactose positive yellow colonies.
  • Liquid Media: They exhibit homogenous turbid growth within 12-18 hours.  R form agglutinates spontaneously, forming sediment on the bottom of the test tubes. After prolonged incubation (>72 hrs), pellicles are formed on the surface of liquid media. Heavy deposits are formed which disperses on shaking.
cultural Characteristics of E. coli
cultural Characteristics of E. coli

Culture characteristics of E. coli

Cultural CharacteristicsNutrient Agar Medium (NAM)Eosin Methylene Blue (EMB) Agar mediumMacConkey Agar mediumBlood Agar Medium
Size1-3 mm2-3 mm2-3 mm1-3 mm
SurfaceSmooth (fresh isolation) ; Rough (repeated subculture) ; mucoid (capsulated strains)Smooth (fresh isolation) ; Rough (repeated subculture) ; mucoid (capsulated strains)Smooth (fresh isolation) ; Rough (repeated subculture) ; mucoid (capsulated strains)Smooth (fresh isolation) ; Rough (repeated subculture) ; mucoid (capsulated strains)
ColorGreyish whiteGreen metallic sheenPinkGreyish white
StructureTranslucent –OpaqueOpaqueOpaqueTranslucent –Opaque
Hemolysis—–—–—–β-Hemolysis (in some strains)
EmulsifiabilitySmooth form – Easily emulsifiable; Rough forms – Autoagglutinable, hence do not emulsify easilySmooth form – Easily emulsifiable; Rough forms – Autoagglutinable, hence do not emulsify easilySmooth form – Easily emulsifiable; Rough forms – Autoagglutinable, hence do not emulsify easilySmooth form – Easily emulsifiable; Rough forms – Autoagglutinable, hence do not emulsify easily
E. coli on sheep blood agar.
E. coli on sheep blood agar.| Source:

Toxin of E. coli

Except endotoxin associated with O antigen, some E. coli strains produce two types of exotoxin such as enterotoxin and haemolysin.


  • Enterotoxins cause diarrhea, these are of two types such as heat labile (LT); heat stable (ST).
  • The LT is similar to cholera enterotoxin which is similar antigenically and in its mechanism of action. It acts by stimulating the adenyl cyclase—cyclic adenosine monophosphate (cAMP) system to produce fluid accumulation in the intestinal lumen.
  • ST stimulates fluid secretion into the gut by the mediation of cyclic guanosine monophosphate (cGMP) resulting in dehydration.


  • E. coli produced 3 types of hemolysins which are not related to pathogenesis.
  • E. coli produces a part of normal intestinal flora of man and animals and the commensal strains belong to several O groups. 
  • There are many strains of E. coli which include commensal strains as well as strains with virulence determinants that cause a wide variety of infections of all age groups of men and animals.

Clinical infections of E. coli

The virulent form of E. coli found in the gut (enteritis) and of extra-intestinal sites (urinary tract infection, wound infection). The pathogenic form of E. coli is responsible for these following infections;

  1. Urinary tract infection (UTI)
  2. Septic infections of wound
  3. Diarrhoea
  4. Dysentery
  5. Septicaemia
  6. Pneumonia
  7. Neonatal meningitis
  8. Abscess in various organs.

There are four groups of E. coli which are responsible for diarrhoea in infants, children and adults are such as Enteropathogenic E. coli (EPEC); Enterotoxigenic E. coli (ETEC); Enteroinvasive E. coli (EIEC); Enterohaemorrhagic E. coli (EHEC).

Enteropathogenic E. coli (EPEC)

  • EPEC causes infantile diarrhoea.
  • They infect by adhering to the intestinal mucosa, and then cause the loss of microvilli and prevent the entry of bacteria into the mucosa.
  • EPEC also produce a shigella-like toxin.

Enterotoxigenic E. coli (ETEC)

  • The enterotoxins are now known to produce diarrhoea in children with dehydration, traveller’s diarrhoea in adults, and sometimes cholera infantum similar to cholera.
  • ETEC also possesses colonisation factors (pili, K antigen) to enhance their virulence.

Enteroinvasive E. coli (EIEC)

  • They do not produce enterotoxin but invade the intestinal mucosa like dysentery bacilli. 
  • Responsible for kerato-conjunctivitis on installation into the eyes of guinea pig (Sereny test) which is a diagnostic method for EIEC.
  • Another diagnostic method is their invasion of HeLa cells in tissue culture.
  • EIEC is a late lactose fermenter and may be anaerogenic.
  • They have an antigenic relationship with shigella.

Enterohaemorrhagic E. coli (EHEC)

  • EHEC has been very recently identified and is found to cause colitis with marked haemorrhage and absence of fever, producing Verotoxin (Cytotoxin) which affects the Vero cells in tissue culture.

Laboratory Diagnosis of Escherichia Coli


  • To detect the EPEC, fresh diarrhoeal stool is plated directly on blood agar and MacConkey agar medium. 
  • After overnight incubation, E. coli colonies are emulsified in saline on a slide and tested by agglutination with polyvalent and monovalent O antiserum against entero-pathogenic serotypes and further identified by biochemical tests.
  • Enzyme linked immuno-sorbent assay (ELISA) test is simplest and used to detect LT of ETEC. 
  • LT and cholera entero-toxin are antigenically similar. Sereney test is the only method available recently to demonstrate EIEC.

Urinary Tract Infection

  • Most of the urine specimens are collected from adult patients by the clean-catch midstream technique.
  • The detection of bacteria can be done microscopically by using Gram staining of uncentrifuged urine specimens, Gram staining of centrifuged specimens, or direct observation of bacteria in urine specimens.
  • During the staining procedure the E coli appears as a non-spore-forming, Gram-negative rod-shaped bacterium.
  • During the semi-quantitative method the routine urine cultures should be plated using calibrated loops.
  • Only use blood agar and MacConkey’s agar for routine cultures.
  • The culture must be incubated overnight at 35°C–37°C in ambient air before being read.

Other Test/ Reactions

  • E. coli typically produces positive test results for indole, lysine decarboxylase, lactose, and mannitol fermentation and produces gas from glucose.
  • An isolate from urine can be quickly identified as E. coli by its hemolysis on blood agar, typical colonial morphology with an iridescent “sheen” on differential media such as EMB agar, and a positive spot indole test result.
  • More than 90% of E. coli isolates are positive for β-glucuronidase using the substrate 4-methylumbelliferyl-β-glucuronide (MUG).

Treatment of E. coli infections

  • Different antibacterial medicines can be used such as sulfonamides, ampicillin, cephalosporins, fluoroquinolones, and aminoglycosides.
  • E. coli meningitis needs antibiotics, like as third-generation cephalosporins (eg, ceftriaxone).
  • Respiratory support, adequate oxygenation, and antibiotics, such as third-generation cephalosporins or fluoroquinolones are required for E. coli pneumonia.
  • In case of diarrheal disease the patient should drink plenty of fluids to avoid dehydration and to get as much rest as possible. Avoid dairy products, these may induce temporary lactose intolerance, and therefore make diarrhea worse.

Prevention and Control of E. coli infections

  • It is universally suggested that attention be observed in regard to food and drink in areas where environmental hygiene is inadequate and that early and brief treatment (eg, with ciprofloxacin or trimethoprim-sulfamethoxazole) be substituted for prophylaxis.
  • We can control E. coli infections by handwashing, rigorous asepsis, sterilization of equipment, disinfection, restraint in intravenous therapy, and strict precautions in keeping the urinary tract sterile (ie, closed drainage).

Medical Importance of E. Coli

  • E. coli is used to produce insulin vis adopting the genetic engineering technique.
  • In intestine, it Produces certain vitamins.
  • It is used as a parameter to determine the fecal contamination of drinking water.
  • In bacterial genetics, it is used for the plasmid study.


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