Enterobacteriaceae

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Enterobacteriaceae
Citrobacter freundii.jpg
Citrobacter freundii , one member of the family
Scientific classification OOjs UI icon edit-ltr.svg
Domain: Bacteria
Phylum: Pseudomonadota
Class: Gammaproteobacteria
Order: Enterobacterales
Family: Enterobacteriaceae
Rahn, 1937
Genera [1]

See text

Enterobacteriaceae is a large family of Gram-negative bacteria. It includes over 30 genera and more than 100 species. Its classification above the level of family is still a subject of debate, but one classification places it in the order Enterobacterales of the class Gammaproteobacteria in the phylum Pseudomonadota. [2] [3] [4] [5] In 2016, the description and members of this family were emended based on comparative genomic analyses by Adeolu et al. [6]

Contents

Enterobacteriaceae includes, along with many harmless symbionts, many of the more familiar pathogens, such as Salmonella , Escherichia coli , Klebsiella , and Shigella . Other disease-causing bacteria in this family include Enterobacter and Citrobacter . Members of the Enterobacteriaceae can be trivially referred to as enterobacteria or "enteric bacteria", [7] as several members live in the intestines of animals. In fact, the etymology of the family is enterobacterium with the suffix to designate a family (aceae)—not after the genus Enterobacter (which would be "Enterobacteraceae")—and the type genus is Escherichia .

Morphology

Members of the Enterobacteriaceae are bacilli (rod-shaped), and are typically 1–5 μm in length. They typically appear as medium to large-sized grey colonies on blood agar, although some can express pigments.

Most have many flagella used to move about, but a few genera are nonmotile. Most members of Enterobacteriaceae have peritrichous, type I fimbriae involved in the adhesion of the bacterial cells to their hosts. [8]

They are not spore-forming.

Metabolism

Like other Pseudomonadota, Enterobacteriaceae have Gram-negative stains, [9] and they are facultative anaerobes, fermenting sugars to produce lactic acid and various other end products. Most also reduce nitrate to nitrite, although exceptions exist. Unlike most similar bacteria, Enterobacteriaceae generally lack cytochrome c oxidase, there are exceptions.

Catalase reactions vary among Enterobacteriaceae.

Ecology

Many members of this family are normal members of the gut microbiota in humans and other animals, [10] while others are found in water or soil, or are parasites on a variety of different animals and plants. [11] [12]

Model organisms and medical relevance

Escherichia coli is one of the most important model organisms, and its genetics and biochemistry have been closely studied.

Some enterobacteria are important pathogens, e.g. Salmonella, or Shigella e.g. because they produce endotoxins. Endotoxins reside in the cell wall and are released when the cell dies and the cell wall disintegrates. Some members of the Enterobacteriaceae produce endotoxins that, when released into the bloodstream following cell lysis, cause a systemic inflammatory and vasodilatory response. The most severe form of this is known as endotoxic shock, which can be rapidly fatal.

Historical systematics and taxonomy

Enterobacteriaceae was originally the sole family under the order 'Enterobacteriales'. The family contained a large array of biochemically distinct species with different ecological niches, which made biochemical descriptions difficult. [13] [14] The original classification of species to this family and order was largely based on 16S rRNA genome sequence analyses, which is known to have low discriminatory power and the results of which changes depends on the algorithm and organism information used. Despite this, the analyses still exhibited polyphyletic branching, indicating the presence of distinct subgroups within the family. [15]

In 2016, the order 'Enterobacteriales' was renamed to Enterobacterales, and divided into 7 new families, including the emended Enterobacteriaceae family. [6] This emendation restricted the family to include only those genera directly related to the type genus, which included most of the enteric species under the order. This classification was proposed based on the construction of several robust phylogenetic trees using conserved genome sequences, 16S rRNA sequences and multilocus sequence analyses. Molecular markers, specifically conserved signature indels, specific to this family were identified as evidence supporting the division independent of phylogenetic trees.

In 2017, a subsequent study using comparative phylogenomic analyses identified the presence of 6 subfamily level clades within the family Enterobacteriaceae, namely the “Escherichia clade”, “Klebsiella clade”, “Enterobacter clade”, “Kosakonia clade”, “Cronobacter clade”, “Cedecea clade” and a “Enterobacteriaceae incertae sedis clade” containing species whose taxonomic placement within the family is unclear. [16] However, this division was not officially proposed as the subfamily rank is generally not used.

Molecular signatures

Analyses of genome sequences from Enterobacteriaceae species identified 21 conserved signature indels (CSIs) that are uniquely present in this family in the proteins NADH:ubiquinone oxidoreductase (subunit M), twitching motility protein PilT, 2,3-dihydroxybenzoate-AMP ligase, ATP/GTP-binding protein, multifunctional fatty acid oxidation complex (subunit alpha), S-formylglutathione hydrolase, aspartate-semialdehyde dehydrogenase, epimerase, membrane protein, formate dehydrogenylase (subunit 7), glutathione S-transferase, major facilitator superfamily transporter, phosphoglucosamine mutase, glycosyl hydrolase 1 family protein, 23S rrna [uracil(1939)-C(5)]-methyltransferase, co-chaperone HscB, N-acetylmuramoyl-L-alanine amidase, sulfate ABC transporter ATP-binding protein CysA, and LPS assembly protein LptD. [6] These CSIs provide a molecular means of distinguishing Enterobacteriaceae from other families within the order Enterobacterales and other bacteria.

Genera

Validly published genera

The following genera have been validly published, thus they have "Standing in Nomenclature". The year the genus was proposed is listed in parentheses after the genus name.

Candidatus genera

Proposed genera

The following genera have been effectively, but not validly, published, thus they do not have "Standing in Nomenclature". The year the genus was proposed is listed in parentheses after the genus name.

Identification

To identify different genera of Enterobacteriaceae, a microbiologist may run a series of tests in the lab. These include: [17]

In a clinical setting, three species make up 80 to 95% of all isolates identified. These are Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis. However, Proteus mirabilis is now considered a part of the Morganellaceae, a sister clade within the Enterobacterales.

Antibiotic resistance

Several Enterobacteriaceae strains have been isolated which are resistant to antibiotics including carbapenems, which are often claimed as "the last line of antibiotic defense" against resistant organisms. For instance, some Klebsiella pneumoniae strains are carbapenem resistant. [18] Various carbapenemases genes (blaOXA-48, blaKPC and blaNDM-1, blaVIM and blaIMP) have been identified in carbapenem resistant Enterobacteriaceae including Escherichia coli and Klebsiella pneumoniae. [19]

Related Research Articles

<span class="mw-page-title-main">Beta-lactamase</span> Class of enzymes

Beta-lactamases (β-lactamases) are enzymes produced by bacteria that provide multi-resistance to beta-lactam antibiotics such as penicillins, cephalosporins, cephamycins, monobactams and carbapenems (ertapenem), although carbapenems are relatively resistant to beta-lactamase. Beta-lactamase provides antibiotic resistance by breaking the antibiotics' structure. These antibiotics all have a common element in their molecular structure: a four-atom ring known as a beta-lactam (β-lactam) ring. Through hydrolysis, the enzyme lactamase breaks the β-lactam ring open, deactivating the molecule's antibacterial properties.

<span class="mw-page-title-main">Gram-negative bacteria</span> Group of bacteria that do not retain the Gram stain used in bacterial differentiation

Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. Their defining characteristic is their cell envelope, which consists of a thin peptidoglycan cell wall sandwiched between an inner (cytoplasmic) membrane and an outer membrane. These bacteria are found in all environments that support life on Earth.

<i>Klebsiella pneumoniae</i> Species of bacterium

Klebsiella pneumoniae is a Gram-negative, non-motile, encapsulated, lactose-fermenting, facultative anaerobic, rod-shaped bacterium. It appears as a mucoid lactose fermenter on MacConkey agar.

<span class="mw-page-title-main">Chlamydiota</span> Phylum of bacteria

The Chlamydiota are a bacterial phylum and class whose members are remarkably diverse, including pathogens of humans and animals, symbionts of ubiquitous protozoa, and marine sediment forms not yet well understood. All of the Chlamydiota that humans have known about for many decades are obligate intracellular bacteria; in 2020 many additional Chlamydiota were discovered in ocean-floor environments, and it is not yet known whether they all have hosts. Historically it was believed that all Chlamydiota had a peptidoglycan-free cell wall, but studies in the 2010s demonstrated a detectable presence of peptidoglycan, as well as other important proteins.

<span class="mw-page-title-main">Enterobacterales</span> Order of gram-negative bacteria

Enterobacterales is an order of Gram-negative, non-spore forming, facultatively anaerobic, rod-shaped bacteria with the class Gammaproteobacteria. The type genus of this order is Enterobacter.

<span class="mw-page-title-main">Coliform bacteria</span> Group of bacterial species

Coliform bacteria are defined as either motile or non-motile Gram-negative non-spore forming bacilli that possess β-galactosidase to produce acids and gases under their optimal growth temperature of 35–37 °C. They can be aerobes or facultative aerobes, and are a commonly used indicator of low sanitary quality of foods, milk, and water. Coliforms can be found in the aquatic environment, in soil and on vegetation; they are universally present in large numbers in the feces of warm-blooded animals as they are known to inhabit the gastrointestinal system. While coliform bacteria are not normally causes of serious illness, they are easy to culture, and their presence is used to infer that other pathogenic organisms of fecal origin may be present in a sample, or that said sample is not safe to consume. Such pathogens include disease-causing bacteria, viruses, or protozoa and many multicellular parasites. Every drinking water source must be tested for the presence of these total coliform bacteria.

<i>Escherichia</i> Genus of bacteria

Escherichia is a genus of Gram-negative, non-spore-forming, facultatively anaerobic, rod-shaped bacteria from the family Enterobacteriaceae. In those species which are inhabitants of the gastrointestinal tracts of warm-blooded animals, Escherichia species provide a portion of the microbially derived vitamin K for their host. A number of the species of Escherichia are pathogenic. The genus is named after Theodor Escherich, the discoverer of Escherichia coli. Escherichia are facultative aerobes, with both aerobic and anaerobic growth, and an optimum temperature of 37 °C. Escherichia are usually motile by flagella, produce gas from fermentable carbohydrates, and do not decarboxylate lysine or hydrolyze arginine. Species include E. albertii, E. fergusonii, E. hermannii, E. ruysiae, E. marmotae and most notably, the model organism and clinically relevant E. coli. Formerly, Shimwellia blattae and Pseudescherichia vulneris were also classified in this genus.

<i>Enterobacter</i> Genus of bacteria

Enterobacter is a genus of common Gram-negative, facultatively anaerobic, rod-shaped, non-spore-forming bacteria of the family Enterobacteriaceae. Cultures are found in soil, water, sewage, feces and gut environments. It is the type genus of the order Enterobacterales. Several strains of these bacteria are pathogenic and cause opportunistic infections in immunocompromised hosts and in those who are on mechanical ventilation. The urinary and respiratory tracts are the most common sites of infection. The genus Enterobacter is a member of the coliform group of bacteria. It does not belong to the fecal coliforms group of bacteria, unlike Escherichia coli, because it is incapable of growth at 44.5 °C in the presence of bile salts. Some of them show quorum sensing properties.

<span class="mw-page-title-main">Carbapenem</span> Class of highly effective antibiotic agents

Carbapenems are a class of very effective antibiotic agents most commonly used for treatment of severe bacterial infections. This class of antibiotics is usually reserved for known or suspected multidrug-resistant (MDR) bacterial infections. Similar to penicillins and cephalosporins, carbapenems are members of the beta-lactam antibiotics drug class, which kill bacteria by binding to penicillin-binding proteins, thus inhibiting bacterial cell wall synthesis. However, these agents individually exhibit a broader spectrum of activity compared to most cephalosporins and penicillins. Furthermore, carbapenems are typically unaffected by emerging antibiotic resistance, even to other beta-lactams.

<span class="mw-page-title-main">Viable but nonculturable</span>

Viable but nonculturable (VBNC) bacteria refers as to bacteria that are in a state of very low metabolic activity and do not divide, but are alive and have the ability to become culturable once resuscitated.

<span class="mw-page-title-main">New Delhi metallo-beta-lactamase 1</span> Enzyme

NDM-1 is an enzyme that makes bacteria resistant to a broad range of beta-lactam antibiotics. These include the antibiotics of the carbapenem family, which are a mainstay for the treatment of antibiotic-resistant bacterial infections. The gene for NDM-1 is one member of a large gene family that encodes beta-lactamase enzymes called carbapenemases. Bacteria that produce carbapenemases are often referred to in the news media as "superbugs" because infections caused by them are difficult to treat. Such bacteria are usually sensitive only to polymyxins and tigecycline.

Carbapenem-resistant Enterobacteriaceae (CRE) or carbapenemase-producing Enterobacteriaceae (CPE) are Gram-negative bacteria 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. The resistance can vary from moderate to severe. Enterobacteriaceae are common commensals and infectious agents. Experts fear CRE as the new "superbug". The bacteria can kill up to half of patients who get bloodstream infections. Tom Frieden, former head of the Centers for Disease Control and Prevention has referred to CRE as "nightmare bacteria". Examples of enzymes found in certain types of CRE are KPC and NDM. KPC and NDM are enzymes that break down carbapenems and make them ineffective. Both of these enzymes, as well as the enzyme VIM have also been reported in Pseudomonas.

<span class="mw-page-title-main">Yersiniaceae</span> Family of bacteria

The Yersiniaceae are a family of Gram-negative bacteria that includes some familiar pathogens. For example, the type genus Yersinia includes Yersinia pestis, the causative agent of plague. This family is a member of the order Enterobacterales in the class Gammaproteobacteria of the phylum Pseudomonadota.

Escherichia virus CC31, formerly known as Enterobacter virus CC31, is a dsDNA bacteriophage of the subfamily Tevenvirinae responsible for infecting the bacteria family of Enterobacteriaceae. It is one of two discovered viruses of the genus Karamvirus, diverging away from the previously discovered T4virus, as a clonal complex (CC). CC31 was first isolated from Escherichia coli B strain S/6/4 and is primarily associated with Escherichia, even though is named after Enterobacter.

<i>Phytobacter</i> Genus of bacteria

Phytobacter is a genus of Gram-negative bacteria emerging from the grouping of isolates previously assigned to various genera of the family Enterobacteriaceae. This genus was first established on the basis of nitrogen fixing isolates from wild rice in China, but also includes a number of isolates obtained during a 2013 multi-state sepsis outbreak in Brazil and, retrospectively, several clinical strains isolated in the 1970s in the United States that are still available in culture collections, which originally were grouped into Brenner's Biotype XII of the Erwinia herbicola-Enterobacter agglomerans-Complex (EEC). Standard biochemical evaluation panels are lacking Phytobacter spp. from their database, thus often leading to misidentifications with other Enterobacterales species, especially Pantoea agglomerans. Clinical isolates of the species have been identified as an important source of extended-spectrum β-lactamase and carbapenem-resistance genes, which are usually mediated by genetic mobile elements. Strong protection of co-infecting sensitive bacteria has also been reported. Bacteria belonging to this genus are not pigmented, chemoorganotrophic and able to fix nitrogen. They are lactose fermenting, cytochrome-oxidase negative and catalase positive. Glucose is fermented with the production of gas. Colonies growing on MacConkey agar (MAC) are circular, convex and smooth with non-entire margins and a usually elevated center. Three species are currently validly included in the genus Phytobacter, which is still included within the Kosakonia clade in the lately reviewed family of Enterobacteriaceae. The incorporation of a fourth species, Phytobacter massiliensis, has recently been proposed via the unification of the genera Metakosakonia and Phytobacter.

<span class="mw-page-title-main">Erwiniaceae</span> Family of bacteria

The Erwiniaceae are a family of Gram-negative bacteria which includes a number of plant pathogens and insect endosymbionts. This family is a member of the order Enterobacterales in the class Gammaproteobacteria of the phylum Pseudomonadota. The type genus of this family is Erwinia.

The Pectobacteriaceae are a family of Gram-negative bacteria which largely consist of plant pathogens. This family is a member of the order Enterobacterales in the class Gammaproteobacteria of the phylum Pseudomonadota. The type species of this family is Pectobacterium.

The Hafniaceae are a family of Gram-negative bacteria. This family is a member of the order Enterobacterales in the class Gammaproteobacteria of the phylum Pseudomonadota. Genera in this family include the type genus Hafnia, along with Edwardsiella and Obesumbacterium.

<span class="mw-page-title-main">Morganellaceae</span> Family of bacteria

The Morganellaceae are a family of Gram-negative bacteria that include some important human pathogens formerly classified as Enterobacteriaceae. This family is a member of the order Enterobacterales in the class Gammaproteobacteria of the phylum Pseudomonadota. Genera in this family include the type genus Morganella, along with Arsenophonus, Cosenzaea, Moellerella, Photorhabdus, Proteus, Providencia and Xenorhabdus.

The Budviciaceae are a family of Gram-negative bacteria. This family is a member of the order Enterobacterales in the class Gammaproteobacteria of the phylum Pseudomonadota. The type genus of this family is Budvicia.

References

  1. ↑ "List of genera included in families - Enterobacteriaceae". List of Prokaryotic Names with Standing in Nomenclature. Retrieved 26 June 2016.
  2. ↑ Don J. Brenner; Noel R. Krieg; James T. Staley (July 26, 2005) [1984 (Williams & Wilkins)]. George M. Garrity (ed.). The Gammaproteobacteria. Bergey's Manual of Systematic Bacteriology. Vol. 2B (2nd ed.). New York: Springer. p. 1108. ISBN   978-0-387-24144-9. British Library no. GBA561951.
  3. ↑ Zipcodezoo site Enterobacteriales Archived 2014-04-27 at the Wayback Machine accessed 9 Mar 2013
  4. ↑ NCBI Enterobacteriales accessed 9 Mar 2013
  5. ↑ Taxonomicon Enterobacteriales accessed 9 Mar 2013
  6. 1 2 3 Adeolu, M; Alnajar, S; Naushad, S; S Gupta, R (December 2016). "Genome-based phylogeny and taxonomy of the 'Enterobacteriales': proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov". International Journal of Systematic and Evolutionary Microbiology . 66 (12): 5575–5599. doi: 10.1099/ijsem.0.001485 . PMID   27620848.
  7. ↑ Corkery, Liz (2020-02-12). "Enteric Bacteria | Safety Services". safetyservices.ucdavis.edu. Retrieved 2023-11-07.
  8. ↑ Edwards, P.R.; Ewing, W.H. (1972). Identification of Enterobacteriaceae. Burgess Publishing Company. ISBN   978-0-8087-0516-1.
  9. ↑ "Dorlands Medical Dictionary:Enterobacteriaceae". Archived from the original on 2009-08-28.
  10. ↑ Ferreira da Silva, Miguel; Vaz-Moreira, Ivone; Gonzalez-Pajuelo, Maria; Nunes, Olga C.; Manaia, Célia M. (2007). "Antimicrobial resistance patterns in Enterobacteriaceae isolated from an urban wastewater treatment plant". FEMS Microbiology Ecology. Oxford University Press (OUP). 60 (1): 166–176. doi: 10.1111/j.1574-6941.2006.00268.x . ISSN   0168-6496. PMID   17250754.
  11. ↑ Kleeberger, A.; Braatz, R.; Busse, M. (1980). "Zur Taxonomie und Okologie der Enterobakterien in Milch" [Taxonomy and ecology of Enterobacteriaceae in milk.]. Milchwissenschaft (in German). 35 (8): 457–460.
  12. ↑ Wang, Zhiying; Hu, Huifeng; Zhu, Tongbo; Zheng, Jinshui; Gänzle, Michael G.; Simpson, David J. (31 August 2021). Rodríguez-Verdugo, Alejandra (ed.). "Ecology and Function of the Transmissible Locus of Stress Tolerance in Escherichia coli and Plant-Associated Enterobacteriaceae". mSystems. American Society for Microbiology. 6 (4): e0037821. doi:10.1128/msystems.00378-21. ISSN   2379-5077. PMC   8407380 . PMID   34402641.
  13. ↑ Brenner, Don J.; Krieg, Noel R.; Staley, James T.; Garrity, George M.; Boone, David R.; De Vos, Paul; Goodfellow, Michael; Rainey, Fred A.; Schleifer, Karl-Heinz, eds. (2005). Bergey's Manual® of Systematic Bacteriology. doi:10.1007/0-387-28022-7. ISBN   978-0-387-24144-9.
  14. ↑ Octavia, Sophie; Lan, Ruiting (2014), "The Family Enterobacteriaceae", The Prokaryotes, Berlin, Heidelberg: Springer Berlin Heidelberg, pp. 225–286, doi:10.1007/978-3-642-38922-1_167, ISBN   978-3-642-38921-4 , retrieved 2021-06-02
  15. ↑ Francino, M. Pilar; Santos, Scott R.; Ochman, Howard (2006), "Phylogenetic Relationships of Bacteria with Special Reference to Endosymbionts and Enteric Species", The Prokaryotes, New York, NY: Springer New York, pp. 41–59, doi:10.1007/0-387-30746-x_2, ISBN   978-0-387-25496-8 , retrieved 2021-06-02
  16. ↑ Alnajar, Seema; Gupta, Radhey S. (October 2017). "Phylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family". Infection, Genetics and Evolution. 54: 108–127. doi:10.1016/j.meegid.2017.06.024. ISSN   1567-7257. PMID   28658607.
  17. ↑ MacFaddin, Jean F. Biochemical Tests for Identification of Medical Bacteria. Williams & Wilkins, 1980, p 441.
  18. ↑ "Klebsiella pneumoniae in Healthcare Settings - HAI". CDC. 17 May 2019. Retrieved 6 April 2022. Increasingly, Klebsiella bacteria have developed antimicrobial resistance, most recently to the class of antibiotics known as carbapenems.
  19. ↑ Ghaith, Doaa M.; Mohamed, Zeinat K.; Farahat, Mohamed G.; Aboulkasem Shahin, Walaa; Mohamed, Hadeel O. (March 2019). "Colonization of intestinal microbiota with carbapenemase-producing Enterobacteriaceae in paediatric intensive care units in Cairo, Egypt". Arab Journal of Gastroenterology. 20 (1): 19–22. doi:10.1016/j.ajg.2019.01.002. PMID   30733176. S2CID   73444389.
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