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Escherichia coli is a type of bacteria that lives in many places in the environment, including the gastrointestinal system of humans and warm-blooded animals, where it is part of the gut microbiota. Some strains of E. coli can be administered as probiotics and are known to have a positive effect on host health. However, some strains can be pathogenic, causing intestinal and extraintestinal infections in humans as well as animals. E. coli is hence a bacterium with a wide range of different natural types of strains, each with its own set of features. Because of its unique qualities, such as simplicity of handling, availability of the entire genome sequence, and capacity to grow in both aerobic and anaerobic conditions, E. coli is also a popular bacterium for laboratory research and biotechnology. So, E. coli is considered to be the utmost widely utilized microbe in the field of recombinant DNA technology, and it is used in a wide range of industrial and medical applications.
Department of Studies and Research in Microbiology, PG Centre, Mangalore University, Karnataka, India
B.S. Gunashree
Department of Studies and Research in Microbiology, PG Centre, Mangalore University, Karnataka, India
*Address all correspondence to: microbasava@gmail.com
1. Introduction
The bacteria Escherichia coli was discovered by German pediatrician Theodor Escherich (1857–1911), who isolated it from babies' feces in 1885 [1]. E. coli is a gram-negative, non-sporulating, rod-shaped, facultative anaerobic, and coliform bacterium pertaining to the genus Escherichia that commonly inhabits the environment, foods, and warm-blooded animals' lower gut [2]. In the domains of biotechnology and microbiology, it is the most widely studied prokaryotic model organism. It can live for long periods of time in feces, soil, and water, and is frequently used as a water contamination indicator organism. For 2–3 days, the bacterium multiplies rapidly in fresh feces under aerobic circumstances, but its numbers gradually fall after that. E. coli is gram-negative, straight, rod-shaped, non-sporing, non-acid fast, and bacilli that exist in single and pairs. Cells are typically rod-shaped, with 1–3 μm × 0.4–0.7 μm (micrometer) in size around 1 μm long, 0.35 μm wide, and 0.6–0.7 μm in volume [3]. It is motile due to peritrichous flagellar arrangement, and very few strains are non-motile. The optimal growth of E. coli occurs at 37°C (98°F) but some laboratory strains can multiply at temperatures of up to 49°C (120.2°F). It takes as little as 20 min to reproduce in favorable conditions [4]. Fimbriated strains exist both as motile and non-motile. A polysaccharide capsule has been discovered in some E. coli strains isolated from extraintestinal infections. The E. coli capsules can be clearly seen using negative staining procedures, which produce a bright halo over a dark backdrop. They have a thin cell wall with only one or two layers of peptidoglycan [5] as shown in Figure 1.
Figure 1.
Structure of E. coli [6].
It colonizes a newborn’s gastrointestinal (GI) tract within hours after birth and even helps to keep our digestive tract healthy. Several strains of E. coli have been identified as good and effective probiotics and are currently employed in pharmaceuticals. It truly is a facultative anaerobic chemoorganotroph capable of both respiratory and fermentative metabolism [7]. Although most strains of E. coli are safe, some serotypes can induce diarrhea when consumed through contaminated food or drink, while others might cause urinary tract infections (UTIs), anemia, and respiratory or kidney infections [8]. However, certain strains have developed into pathogenic E. coli by using plasmids, transposons, bacteriophages, and/or pathogenicity islands to acquire virulence factors [9]. Serogroups, pathogenicity mechanisms, clinical signs, and virulence factors can all be used to classify the pathogenic strain of E. coli [10].
The bacterium can be grown easily and inexpensively in a laboratory setting under appropriate conditions. It takes as little as 20 min to reproduce and has been intensively investigated for over 60 years [11]. E. coli is the most widely studied prokaryotic model organism and an important species in the field of biotechnology and microbiology, where it serves as the host organism for recombinant DNA and experimental workhorse for DNA manipulation and protein production [12].
Escherichia coli can live on a wide variety of substrates. The availability of nutrients within the intestine of host species determines E. coli niche. The (GI) tract of humans and many other warm-blooded animals is the principal niche for E. coli. It cycles between two major habitats-warm-blooded animal intestines and the environment (water, sediment, and soil), which is considerably different in terms of physical conditions, the range, and quantity of nutrients availability. E. coli form a mutual relationship with its host. E. coli in the colon synthesizes K and B complex vitamins and protects the GI tract against colonization with pathogenic microbes, while the host offers an ecological niche and nutrients. E. coli is the most common type of facultative anaerobes in the intestine, accounting for around 0.1% of the gut microbiota [13]. E. coli can also be found in hotter conditions, such as on the edge of hot springs and on-ground meats due to slaughterhouse processing [14].
E. coli is classified into 150–200 serotypes or serogroups based on 3 antigens, somatic (O) or cell wall antigen, capsular (K) antigen, and flagellar (H) antigen. Seventy five types of the H or flagellar antigen and 173 types of O or somatic antigens 103 types of the K or capsular antigens have been recognized [16] (Figure 2).
E. coli cells may grow on a solid or in a liquid growth medium under laboratory conditions. It may be grown in a basic minimum of media, which includes glucose as a carbon and energy source, ammonium salts as a nitrogen source, other salts, and trace elements [18]. As E. coli have simple nutritional requirements it can be easily cultured on a common medium, such as Nutrient agar, Mac Conkey agar, and EMB agar [19].
E. coli can grow at temperatures ranging from 10°C to 40°C, although the optimum temperature for most strains is 37°C (98.6°F), however, some laboratory strains can proliferate at temperatures as high as 49°C (120.2°F) [20]. E. coli can survive at 4.5–9.5 pH but the maximum growth is observed at 7.0, i.e., neutral pH. Also, the pH requirements vary with the strains of E. coli; [21]. The cultural characteristics of E. coli are presented in Table 1.
E. coli, on NAM, forms large, thick, greyish white, moist, smooth, opaque, or translucent discs like colonies as shown in Figure 3. The smooth forms (S) of colonies seen in fresh isolation are easily emulsifiable in saline. The rough forms (R) of colonies seen in older cultures, with dull surfaces often auto-agglutinable in saline. S-R variation occurs as a result of repeated subcultures and is associated with the loss of surface antigens and usually of virulence [24].
Figure 3.
Growth of E. coli on nutrient agar [23].
5.2 Blood agar
Some of the strains show beta hemolysis, especially those that are isolated from the pathologic conditions, whereas those which are isolated from normal persons may or may not show hemolysis on blood agar [25, 26] shown in Figure 4.
Figure 4.
A. A non-hemolytic E. coli strain on blood agar [25]. B. A beta-hemolytic E. coli strain on blood agar [26].
5.3 Mac Conkey agar
The colonies are pink in color due to lactose fermentation, which is important for distinguishing E. coli from other bacteria in the specimen, particularly gram-positive bacteria and Salmonella species, which are non–lactose fermenters and produce colorless colonies on MacConkey agar media [27] shown in Figure 5.
Figure 5.
Colonies of E. coli on MacConkey agar plate are pink to dark pink, [27].
5.4 E. coli on Mueller Hinton agar
Starch is added to absorb any toxic metabolites produced and starch hydrolysis yields dextrose, which serves as a source of energy. The use of a suitable medium for testing the susceptibility of microorganisms to sulfonamides and trimethoprim [28] is shown in Figure 6.
Figure 6.
E. coli on Mueller Hinton Agar (MHA) tested for susceptibility for five different types of antibiotics [29].
5.5 Eosin methylene blue agar
The colonies of E. coli grow with a green metallic sheen, which is due to the metachromatic property of dyes (eosin and methylene blue in the ratio of 6:1) and the lactose fermenting property of E. coli, which changes the pH of the medium to acidic. Hence, making the medium more selective for E. coli makes the identification much more easier [30] as shown in Figure 7.
Figure 7.
E. coli on EMB agar showing green metallic sheen colonies [30].
5.6 E. coli on m-ENDO agar
Coliforms appear as red colonies with a metallic green sheen. In E. coli, this reaction is so intense that the fuchsin crystallizes out giving the colonies a metallic green sheen. The selective agents contained in the medium, sodium deoxycholate and sodium lauryl sulfate help to inhibit non-coliforms metabolize lactose with the production of aldehyde and acid [31] shown in Figure 8.
Figure 8.
E. coli on ENDO agar with green metallic sheen colonies [31].
5.7 E. coli on violet red bile agar
Violet red bile agar (VRBA) is a selective medium used to detect and enumerate lactose-fermenting coliform. Lactose-fermenting microorganisms produce pink to red colonies that are generally surrounded by a reddish zone of precipitated bile. Bluish fluorescence is seen around colonies under UV [32] as shown in Figure 9.
Figure 9.
VRBA agar, A: E. coli, pinkish red with bile precipitate B: Salmonella gallinarium, fair to good growth; colorless colonies [32].
5.8 E. coli on cystine lactose electrolyte-deficient agar
It promotes the growth and enumeration of UTIs however due to a shortage of electrolytes; it prevents excessive swarming of Proteus species. On cystine lactose electrolyte-deficient (CLED) agar, lactose fermenters form yellow colonies, while non-lactose fermenters form blue colonies [33] as shown in Figure 10.
Figure 10.
Growth of E. coli on cysteine lactose electrolyte-deficient agar, [34].
Within 12–18 h, they demonstrate homogeneous murky development because of the increasing quantity of bacteria, the broth gets hazy. Pellicles grow on the surface of a liquid medium after a long period of incubation (>72 h). Heavy deposits occur, which disperse when shaken [19] as seen in Figure 11.
Figure 11.
Growth of E. coli on LB liquid medium. (Photo: M. Basavaraju.)
The majority of E. coli strains in the colon are not harmful, however pathogenic E. coli isolates cause intestinal or extraintestinal infections, depending on the array of virulence-associated genes that they harbor. The intestinal pathogenic E. coli (IPEC) strains are divided and classified into several pathotypes (Table 2). Diseases associated with various intestinal pathogenic E. coli pathotypes in animals are as shown in Table 3. E. coli is linked also to a number of extraintestinal diseases and is the most prevalent cause of cholecystitis, bacteremia, cholangitis, UTI, traveler's diarrhea, and septicemia as well as neonatal meningitis, etc., [37]. Most infections, with the exception of infant meningitis and gastroenteritis, are endogenous, like E. coli from the patient's normal microbiota, cause infection when the patient's defenses are impaired, e.g., through trauma or immune suppression [38]. In order to cause disease E. coli to possess several different types of virulence factors: fimbrial and fimbrial adhesins, capsules, toxins (exotoxins, hemolysins, and enterotoxins), iron up-take systems, etc., [39]. Important ExPEC virulence-associated genes, their encoded proteins, function, and connection to different ExPEC pathotypes are given in Table 4 [41].
Category
Clinical manifestations
Susceptible population
Virulence factors
Diagnostic
Treatment
ETEC (enteropathogenic E. coli)
Watery stool (without blood or inflammatory cells) leading to dehydration, headache, fever, nausea and vomiting
Children 0–5 years of age and adults traveling to developing countries.
ST, LT, CFs
Culture, detection of ST (STa, STb) and LT, CFAs using ELISA and PCR-based methods.
Self-limited, responsive to oral rehydration therapy (low response in children <2 years). Antimicrobial therapy on individual cases
EPEC (enteropathogenic E. coli)
Secretory and persistent diarrhea, anorexia, low fever, and rapid wasting
Children 0–2 years of age, occasionally adults
pEAF, BFP, LEE and Nle effectors
Culture, adherence patterns (LA LAL, etc.), serotyping, PCR-based methods.
Self-limited, responsive to oral rehydration therapy. Antimicrobial therapy on individual cases.
People of all ages in developing and industrialized countries, HIV-infected adults
EAST Pet Pic ShET-1 Aap AAF/II
Culture, adherence pattern (stacked-brick pattern), pAA DNA probe, multiplex and real-time PCR assays.
Self-limited, responsive to oral rehydration therapy. Antimicrobial therapy on individual cases
STEC/VTE/EHEC (a hybrid Pathotypes)
Mild uncomplicated diarrhea to hemorrhagic colitis with severe abdominal pain and bloody diarrhea.
During the summer, it's the most common, and the incidence is higher in children under the age of five.
Stx 1 and 2 verotoxins (VT)
Shiga toxins rather and A/E cytopathology.
To drink plenty of fluids to prevent dehydration and blood transfusions and kidney dialysis.
EIEC (enteroinvasive E. coli)
Invade and destroy the colonic epithelium, producing a disease characterized initially by watery diarrhea.
A small percentage of patients develop dysenteric illness, which includes fever, stomach pains, and blood and leukocytes in stool specimens.
Inv plasmid, Chromosome, pInv genes
Human stool samples from patients with signs and symptoms of GI infection
Fluoroquinolones, such as ciprofloxacin, macrolides, such as azithromycin, and rifaximin, are antibiotics used to treat non-STEC diarrheagenic E. coli.
DAEC (diffusely adherent E. coli)
Watery diarrhea
Involved in diarrhea in children but not in adults.
Adhesins
Afa/Dr adhesins
multiplex PCR for DEP genes
AIEC (adherent-invasive E. coli)
Type 1 fimbriae, cellular invasion
Associated with Crohn disease.
Persistent intestinal inflammation.
None
Bacteria with antibacterial compounds or with phage therapy, probiotics, or anti-adhesive molecules.
Antibiotic resistance genes have been generated in many gram-negative bacteria and E. coli is not an exception. These bacteria evolved different mechanisms that confer resistance to anti-biotics. E. coli can produce extended-spectrum beta-lactamase (ESBL) that makes the bacteria resistant to beta lactams (e.g., cephalosporins, monobactams, etc.). Carbapenemase-producing E. coli strains, on the other hand, have genes that confer carbapenem resistance (e.g., imipenem, ertapenem, and meropenem). ESBL producing E. coli are a rapidly evolving group of β-lactamases, produced by certain types of bacteria where E. coli are the major ones. These enzymes can break down the active ingredients by cleaving the beta-lactam ring of penicillin’s and cephalosporin antibiotics, resulting in the inactivation of these drugs, there are at least 200 different types of ESBL enzymes, increasingly isolated as causes of complicated UTIs and remain an important cause of failure of therapy with cephalosporin’s and have serious infection control consequences. ESBL producing Enterobacteriaceae have been responsible for numerous outbreaks of infection throughout the globe and pose challenging infection control issues [42]. These organisms are associated with multidrug resistance causing a high rate of mortality and treatment failure [43].
MUG is an acronym for 4-methylumbelliferyl-β-d-glucuronide, most strains of E. coli (97%) produce the enzyme β-d-glucuronidase hence, the detection of this enzyme is commonly employed in laboratories to identify and differentiate such organisms [44]. β-d-glucuronidase is an enzyme that hydrolyzes the beta-d-glucopyranoside-uronic derivatives to aglycons and d-glucuronic acid. In about 97% of E. coli strains, the enzyme-glucuronidase is present [45].
According to older phylogenetic studies, the E. coli strains were classified into four main phylogenetic groups: A, B1, B2, and D. However, recent studies showed that there are more phylogenetic groups seven (A, B1, B2, C, D, E, and F) belong to E. coli sensu stricto, whereas the eighth is represented by cryptic Clade I. Apart from clade I, also clades II, III, IV, and V are known to exist [46]. The majority of strains that cause extraintestinal infections belong to the phylogenetic group B2, whereas as strains belonging to the phylogenetic groups A and B1 are known to have low extraintestinal pathogenicity potential but beside commensal strains, strains also cause diarrhea (Figure 12). According to Doumith M, et al., E. coli strains belonging to various phylogenetic groups displayed diverse phenotypic and genotypic features thought to support fitness in various ecological settings, resulting in niche preference according to scientific findings [48]. To determine E. coli phylogroups, several approaches have been described. Polymerase chain reaction (PCR)-based tests, multi-locus sequence typing (MLST), ribotyping, and sequencing of the 16S rRNA gene are among them [49]. For the determination of the original four different phylogroups (A, B1, B2, and D), the Clermont triplex PCR phylogroup method was used [50].
Figure 12.
Phylogenetic tree of E. coli strains [47].
However, research has revealed that this method can only confirm 80–85% of all E. coli phylogroups, and in 2013 Clermont et al. [51], proposed a revisited method, the quadruplex PCR, which can be used to classify E. coli in the seven phylogenetic groups and clade I [52]. Clermont et al. [53] also proposed a PCR method for the detection of clades II–V.
11. The E. coli genome and proteome
The full genome of E. coli K12 was published by Science in 1997, making it one of the first species to have its genome completely sequenced. E. coli has a circular DNA molecule with 4288 annotated protein-coding genes (arranged into 2584 operons), 7 ribosomal RNA (rRNA) operons, and 86 transfer RNA (tRNA) (data for the E. coli laboratory strain K-12 derivative MG1655) [8]. However, E. coli core genome (i.e., genes found in all strains) accounts for less than 20% of the pan genome's genes or nearly all (90%) of the genomes, leaving only a tiny fraction of genes found in roughly half of the genomes [54]. The E. coli core genome is estimated to have less than 1500 genes, while it has a huge pan-genome with more than 22,000 genes [55]. According to genomic analysis many of the genes of the pan-genome could be not yet unidentified but crucial virulence factors [56]. There are 27,621 E. coli genome assemblies and annotation sequences available to date and each genome comprises between 4000 and 5500 genes [57]. The E. coli genome as a whole is remarkably ordered in terms of local replication direction and oligonucleotides that may be involved in replication and recombination [58].
The diverse behavior of this species is explained by its enormous genetic and phenotypic diversity. With a mean distance between genes of only 118 base pairs, the coding density was found to be extremely high. A multitude of factors contribute to the higher gene density: a. bacterial genes lack introns throughout the genome, and neighboring genes are fairly near together, i.e., there are no many large non-coding DNA sections between genes. There are several transposable genetic elements, repetitive elements, cryptic prophages, and bacteriophage remnants in the genome and a variety of additional patches with unique compositions, showing genome plasticity due to horizontal gene transfer [58, 59].
E. coli is an excellent model for studying the general characteristics of the bacterial proteome, such as its dynamics under different physiological situations, its dynamic range of expression, and its changes. According to the genomic sequence data of the E. coli K-12 strain, there are 4364 ORFs or ORF fragments in the E. coli K-12 W3110 strain. The E. coli proteome has been used as a standard for evaluating and validating new technologies and methodologies in recent years, including sample prefractionation, protein enrichment, two-dimensional gel electrophoresis (2-DE), protein detection, bio-mass spectrometry (MS), combinatorial assays with n-dimensional chromatography and image analysis. In comparison to the proteomes of other organisms such as plants and animals, the E. coli proteome is much smaller and with less protein modification and hence provides an excellent model for various research needs. The usage of the E. coli proteome as a model is further boosted by the existence of public databases such as SWISS-PROT (http://www.expasy.ch/ch2d/) and NCBI (http://www.ncbi.nlm.nih.gov/), which contain rich information on proteins and corresponding genes of E. coli and the existence of the E. coli SWISS-2DPAGE maps, which are based on a large amount of biochemical and biological data [60].
12. E. coli as a model organism
Escherichia coli is a well-known prokaryotic bacterium that is widely used as a model organism for a variety of research due to its adaptability. E. coli is more understood than other living species because of its minimal dietary requirements, rapid growth rate, and, most critically, well-established genetics [61]. E. coli cells divide once every 20–30 min on average, allowing them to adapt to their surroundings quickly. It also promotes the growth of numerous bacterial viruses (bacteriophages), allowing researchers to examine the structure and pathogenicity of viruses in greater detail. It is a good model organism for molecular genetics because of its ability to grow quickly on low-cost media and the availability of molecular tools to perform genetic modifications [62].
Recent research on “wild” E. coli, for example, has revealed a lot about the bacterial existence in the environment, its variety and genetic development, and its function in the human microbiome and diseases [7]. Vaccine development, bioremediation, biofuel generation, and immobilized enzymes have all exploited modified E. coli cells [61]. Furthermore, because E. coli reproduce primarily asexually, alterations to the genome are preserved, and the effects exhibited in these mutants are repeatable. Because of these characteristics, E. coli is an excellent model organism for molecular genetics and microbiology research, as well as modern biological engineering [62].
13. What discoveries were made using E. coli as a model organism
Several key inventions in the field of molecular biology, including molecular genetics, were achieved using E. coli as a model organism. This includes an understanding of the genetic code, the mechanisms of DNA replication, the discovery of the genetic operon systems, and the creation of a genetically modified organism. Many proteins previously thought difficult or impossible to be expressed in E. coli in folded form have been successfully expressed in E. coli. The process of conjugation was discovered in E. coli in 1946 by Joshua Lederberg and Edward L. Tatum [63]. The availability of DNA sequence information coupled with vast biochemical and physiological data makes E. coli the organism of choice not only for virologists, biochemists, and molecular biologists but for all researchers of biology [8]. The most prominent discoveries made with E. coli are presented in Table 5.
Year
Nobel-worthy discoveries
Discoverer
1958
Bacterial sex and other methods through which bacteria can transfer DNA
Joshua Lederberg
1959
The process by which life duplicates its genetic code is known as DNA replication
Arthur Kornberg
1965
Gene regulation, how genes are turned on or off
Ellis Englesberg
1968
The genetic code, the language in which our DNA is written.
Nirenberg and Matthaei'
1969
Viral replication is the process by which viruses reproduce within cells.
Max Knoll
1978
Restriction enzymes, also known as "molecular scissors," that enable scientists to cut DNA
Werner, Nathans, and Smith
1980
Recombinant DNA was used to make the first genetically modified DNA
Paul Berg
1982
The first licensed drug produced using recombinant DNA technology was human insulin
Developed by Genentech and licensed as well as marketed by Eli Lilly
1989
Additional uses for RNA such as an enzyme have been revealed
Sidney Altman and Thomas R. Cech
1997
Found ATP, the energy molecule synthesis is the process by which cells keep life going
Paul Boyer and John Walker
1999
Found that protein signal sequences are one way by which cells organize themselves
Günter Blobel
2008
Scientists employed green fluorescent protein as a marker to track cell components
Roger Y. Tsien, Osamu Shimomura, and Martin Chalfie
2009
Bacteria make computers look like pocket calculators; Biologists have created a living computer from E. coli bacteria that can solve complex mathematical problems
A team of US scientists DOI: 10.1186/1754-1611-3-11
E. coli is a truly resourceful microorganism possessing many facets. It is known for its fast-growing rate in chemically defined media and its adaptability, for ease of handling. So, E. coli is the most studied and well-understood organism on the planet. It’s been widely used in research, employed as a model organism to investigate biological processing protein engineering, genetic research, and used in biotechnology, its versatility continues to open up new avenues for future investigations.
References
1.Feng P, Weagant S, Grant M. Enumeration of Escherichia coli and the Coliform Bacteria. Bacteriological Analytical Manual. 8th ed. USA: FDA/Center for Food Safety & Applied Nutrition; 2007
3.Facts about E. coli: Dimensions as discussed in bacteria: Diversity of structure of bacteria. Britannica 2015:06-25. Available from: https://www.britannica.com/science/ bacteria/The-cell-envelope
4.Bacteria. Microbiology online. Archived from the original on 27 February 2014. Available from: https://web.archive.org/web/20140227212658/ DOI: 10.1128/AAMCol.1-2011
5.Köhler CD, Dobrindt U. What defines extra intestinal pathogenic Escherichia coli? International Journal of Medical Microbiology. 2011;301:642-664
6.Enger ED, Ross FC. Concepts in Biology. 10th ed. New York, USA: McGraw-Hill; 2003. Available from: http://hyperphysics.phy-astr.gsu.edu/hbase/Biology/ecoli.html
7.Blount ZD. The unexhausted potential of E. coli. eLife. 2015;25(4):e05826. DOI: 10.7554/eLife.05826
8.FAQ: E.coli: Good, Bad, & Deadly—NCBI Bookshelf; Retrieved 07 June 2021 from https://www.ncbi.nlm.nih.gov/books/NBK562895. DOI: 10.1128/AAMCol.1-2011
10.Sarowska J, Futoma-Koloch B, Jama-Kmiecik A, et al. Virulence factors, prevalence and potential transmission of extra intestinal pathogenic Escherichia coli isolated from different. Gut Pathogens. 2019;11:10
11.Bacteria. Microbiologyonline. Archived from the original on 27 February 2014; Retrieved: 27 February 2014. Available from: https://web.archive.org/web/20140227212658/http://www.microbiologyonline.org.uk/about-microbiology/introducing-microbes/bacteria
12.Idalia VN, Bernardo F. Escherichia coli as a model organism and its application in biotechnology. In: Samie A, editor. Escherichia coli. Recent advances on physiology, pathogenesis and biotechnological applications. London: Intech Open; 2017. DOI: 10.5772/67306
13.Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al. Diversity of the human intestinal microbial flora. Science. 2005;308(5728):1635-1638
14.Li H, Gänzle M. Some like it hot: Heat resistance of Escherichia coli in food. Frontiers in Microbiology. 2016;7:1763
15.Escherichia coli (Migula, 1895) Castellani & Chalmers, 1919 in Döring M (2022). English Wikipedia - Species Pages. Wikimedia Foundation. Checklist dataset. DOI: 10.15468/c3kkgh. Available from: https://www.gbif.org/species/113662963
16.Van Dijk WC, Verbrugh HA, Tol ME, Peters R, Verhoef J. Role of Escherichia coli K capsular antigens during complement activation, C3 fixation, and opsonization. Infection and Immunity. 1979;25(2):603-609. DOI: 10.1128/iai.25.2.603-609
18.Elbing KL, Brent R. Recipes and tools for culture of Escherichia coli. Current Protocols in Molecular Biology. 2019;125(1):83. DOI: 10.1002/cpmb.83
19.Bonnet M, Lagier JC, Raoult D, Khelaifia S. Bacterial culture through selective and non-selective conditions: The evolution of culture media in clinical microbiology. New Microbes and New Infections. 2019;34:100622
20.Fotadar U, Zaveloff P, Terracio L. Growth of Escherichia coli at elevated temperatures. Journal of Basic Microbiology. 2005;45(5):403-404
22.Silva RM, Toledo RF, Trabulsi LR. Biochemical and cultural characteristics of invasive Escherichia coli. Journal of Clinical Microbiology. 1980;11(5):441-444
23.Patond A, Narang R. A low cost ingenious approach for ultraviolet decontamination of N95 filtering face-piece respirators to deal with dwindling supply during the COVID-19 pandemic. Journal of Mahatma Gandhi Institute of Medical Sciences. 2020;25:80-85
24.Surinder K. Textbook of Microbiology, Enterobacteriaceae: Escherichia, Klebsiella, Proteus and Other Genera. New Delhi, India: Jaypee Brothers Medical Publishers (P) Ltd; 2012. Available from: https://www.jaypeedigital.com/book/9789350255100/chapter/ch36
25.Association of Public Health Laboratories. STEC Work Group..; Centers for Disease Control and Prevention (U.S.); Guidance for public health laboratories: Isolation and characterization of Shiga toxin-producing Escherichia coli (STEC) from clinical specimens. 2012. Available from: https://stacks.cdc.gov/view/cdc/21592
26.Luppi A. Swine enteric colibacillosis: Diagnosis, therapy and antimicrobial resistance. Porcine Health Management. 2017;3:16. DOI: 10.1186/s40813-017-0063-4
28.Atlas RM, Snyder JW. Handbook of Media for Clinical and Public Health Microbiology. Boca Raton, FL: CRC Press. Taylor & Francis Group; 2014. pp. 324-325
29.Neupane A, Parajuli P, Bastola R, Paudel A. Bacterial etiology of diarrhoeal disease in children and antibiogram of the isolates. Clinical Microbiology. 2017;6:278. DOI: 10.4172/2327-5073.1000278
30.Archana L, Naowarat C. Eosin-methylene blue agar plates protocol. American Society for Microbiology. 2007:29
32.Davidson R, Gambrel L. In: Wehr, Frank, editors. Standard Methods for the Microbiological Examination of Dairy Products. 17th ed. Washington, DC: American Public Health Association; 2004
34.Rahman MS, Garg R, Singh VA, Biswas D. Antibiotic susceptibility profile and extended spectrum β-lactamases production by uropathogenic Escherichia coli from tertiary care hospital of rural settings. International Journal of Medical Sciences. 2018;6(12):4022-4027
37.Clinical and public health microbiology. Clinical Microbiology Procedures Handbook. 4th ed. American Society of Microbiology; 2016. DOI: 10.1128/9781555818814
38.Hemm MR, Weaver J, Storz G. Escherichia coli small proteome. EcoSal Plus. 2020;9(1):10
39.Johnson JR. Virulence factors in Escherichia coli urinary tract infection. Clinical Microbiology Reviews. 1991;4(1):80-128. DOI: 10.1128/CMR.4.1.80
40.Sora VM, Meroni G, Martino PA, Soggiu A, Bonizzi L, Zecconi A. Extra-intestinal pathogenic Escherichia coli: Virulence factors and antibiotic resistance. Pathogens. 2021;10(11):1355
41.HMM A, Martínez LY, Torres AG. Clinical implications of enteroadherent Escherichia coli. Current Gastroenterology Reports. 2012;14(5):386-394. DOI: 10.1007/s11894-012-0277-1
42.Michael LW, Loretta G. Laboratory diagnosis of urinary tract infections in adult patients. Clinical Infectious Diseases. 2004:1150-1158. DOI: 10.1086/383029
43.Gandra S, Tseng KK, Arora A, et al. The mortality burden of multidrug-resistant pathogens in India: A retrospective, observational study. Clinical Infectious Diseases. 2019;69(4):563-570. DOI: 10.1093/cid/ciy955
44.Ley AN, Bowers RJ, Wolfe S. Indoxyl-beta-d-glucuronide, a novel chromogenic reagent for the specific detection and enumeration of Escherichia coli in environmental samples. Canadian Journal of Microbiology. 1988;5:690-693. DOI: 10.1139/m88-115
45.Ananthanarayan P. Textbook of Microbiology. 11th ed. Bengaluru, India: Prithvi Books; 2020
46.Ahumada-Santos YP, Báez-Flores ME, Díaz-Camacho SP, Uribe-Beltrán MJ, Eslava-Campos CA, Parra-Unda JR, et al. Association of phylogenetic distribution and presence of integrons with multidrug resistance in Escherichia coli clinical isolates from children with diarrhoea. Journal of Infection and Public Health. 2020;13:767-772
47.Sims GE, Kim SH. Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs). Proceedings of the National Academy of Sciences of the United States of America. 2011;108(20):8329-8334
48.Katongole P, Kisawuzi DB, Bbosa HK, Kateete DP, Najjuka CF. Phylogenetic groups and antimicrobial susceptibility patterns of uropathogenic Escherichia coli clinical isolates from patients at Mulago National Referral Hospital, Kampala, Uganda. F1000 Research. 2019;8:1828
49.Logue CM, Wannemuehler Y, Nicholson BA, Doetkott C, Barbieri NL, Nolan LK. Comparative analysis of phylogenetic assignment of human and avian ExPEC and faecal commensal E. coli using the Clermont phylogenetic typing methods and its impact on avian pathogenic E. coli classification. Frontiers in Microbiology. 2017;8:2-9
50.Clermont O, Bonacorsi S, Bingen E. Rapid and simple determination of the Escherichia coli phylogenetic group. Applied and Environmental Microbiology. 2000;66(10):4555-4558
51.Clermont O, Christenson JK, Denamur E, Gordon DM. The Clermont Escherichia coli phylo-typing method revisited: Improvement of specificity and detection of new phylo-groups. Environmental Microbiology Reports. 2013;5:58-65
52.Iranpour D, Hassanpour M, Ansari H, Tajbakhsh S, Khamisipour G, Najafi A. Phylogenetic groups of Escherichia coli strains from patients with urinary tract infection in Iran based on the new Clermont phylotyping method. BioMed Research International. 2015;2015:846219. DOI: 10.1155/2015/846219
53.Clermont O, Olier M, Hoede C, Diancourt L, Brisse S, Keroudean M, et al. Animal and human pathogenic Escherichia coli strains share common genetic backgrounds. Infection, Genetics and Evolution. 2011;3:654-662. DOI: 10.1016/j.meegid.2011.02.005
54.Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, et al. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genetics. 2009;5(1). DOI: 10.1371
55.Nanda Kafle G, Seale T, Flint T, Nepal M, Venter SN, Brözel VS. Distribution of diverse Escherichia coli between cattle and pasture. Microbes and Environments. 2017;32:226-233
56.Robins-Browne RM, Holt KE, Ingle DJ, Hocking DM, Yang J, Tauschek M. Are Escherichia coli pathotypes still relevant in the era of whole-genome sequencing. Frontiers in Cellular and Infection Microbiology. 2016;6:141
57.Mueller M, Tainter CR. Escherichia coli. In: StatPearls [Internet]. Treasure Island (FL): Stat Pearls Publishing; 2021
58.Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, et al. The complete genome sequence of Escherichia coli K-12. Science. 1997;277(5331):1453-1462. DOI: 10.1126/science.277.5331.1453
59.Zhaxybayeva O, Doolittle WF. Lateral gene transfer. Current Biology. 2011;21(7):242-246. DOI: 10.1016/j.cub.2011.01.045
60.Weiner JH, Li. Proteome of the Escherichia coli envelope and technological challenges in membrane proteome analysis. Biochimica et Biophysica Acta (BBA)—Biomembranes. 2008;1778-9:1698-1713
61.Muhammad K, Zohra S, Ji Xiu L, Taj I, Taj MH, Wei Y. Escherichia coli as a model organism. International Journal of Engineering Sciences & Research Technology. 2014;3:3-8
62.Vargas MNI, Franco B. Escherichia coli as a model organism and its application in biotechnology. 2017. DOI: 10.5772/67306. Available from: https://www.intechopen.com/chapters/53916
63.Lederberg J, Tatum E. Gene recombination in Escherichia coli. Nature. 1946;158(4016):558. DOI: 10.1038/158558a0
Written By
M. Basavaraju and B.S. Gunashree
Submitted: 23 July 2021Reviewed: 23 May 2022Published: 11 November 2022
Open access peer-reviewed chapter
