Phage typing

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A culture of bacteria infected by bacteriophages, the "holes" are areas where the bacteria have been killed by the virus. The culture is 10cm in diameter. LambdaPlaques.jpg
A culture of bacteria infected by bacteriophages, the "holes" are areas where the bacteria have been killed by the virus. The culture is 10cm in diameter.

Phage typing is a phenotypic method that uses bacteriophages ("phages" for short) for detecting and identifying single strains of bacteria. [1] Phages are viruses that infect bacteria and may lead to bacterial cell lysis. [2] The bacterial strain is assigned a type based on its lysis pattern. [3] Phage typing was used to trace the source of infectious outbreaks throughout the 1900s, but it has been replaced by genotypic methods such as whole genome sequencing for epidemiological characterization. [1]

Contents

Principle

Phage typing is based on the specific binding of phages to antigens and receptors on the surface of bacteria and the resulting bacterial lysis or lack thereof. [4] The binding process is known as adsorption. [5] Once a phage adsorbs to the surface of a bacteria, it may undergo either the lytic cycle or the lysogenic cycle. [6]

Virulent phages enter the lytic cycle where they replicate and lyse the bacterial cell. [7] Virulent phages can differentiate between different species of bacteria based on their specific lytic action. [8] Lysis will only occur if the virulent phage adsorbs to the bacterial surface, configuring species specificity to phages. [5]

Temperate phages enter the lysogenic cycle and do not immediately lyse the cell. [7] The phage is instead integrated into the bacterial genome as a prophage during lysogenization, which protects the cell from being lysed by phages which are serologically identical or related. [9] Since it is incorporated into the genome, the prophage is also passed down to the bacteria's progenies. [7] The bacterial strain carrying the prophage is known as a lysogenic strain. [9] Lysogenization is strain-specific, so it allows for differentiation among different strains of bacteria within the same species. [10] The prophage may be chemically or physically induced to revert to the lytic pathway. [6]

Method

The bacterial strain to be characterized is cultured on an agar Petri dish and dried. [11] Once dry, a grid or another recognizable pattern is drawn on the base to mark out different regions. [11] Each region is inoculated with a different phage at its routine test dilution and then incubated for 5-48 hours. [11] The susceptible phage regions will display a clearing where the bacteria have been lysed, and this is used in differentiation. [12] The size, morphology, and pattern of the lysed region are important criteria for differentiating bacterial species and strains. [13] They are compared against a standard scheme of lysis patterns to assign a type to the strain. [14]

Routine Test Dilution (RTD)

Routine test dilution (RTD) is typically defined as the lowest phage dilution that still yields lysis of its host. [11] This technique prevents a phenomenon known as "lysis from without", which is bacterial lysis induced by high multiplicity phage adsorption rather than phage replication. [15]

History

The first reported use of bacteriophages to identify bacteria was in 1925 when Sonnenschein used typhoid and paratyphoid phages to diagnose typhoid. [16] In 1934, it was discovered that some strains of Salmonella typhi displayed Vi antigens on the surface. [17] This led to the isolation of Vi phages capable of lysing typhoid bacteria strains but only if they displayed the Vi antigen [18] enabling the differentiation of typhoid species expressing the Vi antigen and those which do not.

In 1938, Craigie and Yen adapted Vi phages by selective propagation and used them at their critical test dilutions to differentiate 11 types of B. typhosus. [19] In 1943, Felix and Callow extended the method to Salmonella paratyphi B. in 1943 and differentiated 12 types with 11 phages. [20] The International Committee for Enteric Phage Typing was established in 1947, and these phage typing methods were soon standardized. [21]

Improvements to the specificity of phage typing schemes were made throughout the next few decades. In 1959, Callow improved her initial scheme to differentiate 34 types of Salmonella typhimurium with 29 phages. [22] In 1977, this was extended to 207 types by Anderson at the Enteric Reference Laboratory in London. [22] Since then, phage typing schemes have been developed for Salmonella typhi, Salmonella paratyphi B., Salmonella typhimurium, Shigella sonnei, Staphylococcus aureus, and Escherichia coli to name a few. [23] [24]

Limitations

Phage typing requires the use of a comprehensive number of phages, so it is typically only used in reference laboratories. [25] It also relies on the interpretation of the individual lysis pattern and comparison to a standard which has led to conflicting results from different laboratories in the past. [26] Furthermore, bacteriophages mutate so reference phages must be maintained. [25]

Phage Isolation

Phages used for phage typing are generally isolated from the native habitats of the host bacterial strain. [27] These may include sewage, feces, soil, and water. [27] Temperate phages may be isolated from the bacterium itself since it is incorporated into the bacterial genome during lysogenization. [27]

Related Research Articles

<span class="mw-page-title-main">Bacteriophage</span> Virus that infects and replicates within bacteria

A bacteriophage, also known informally as a phage, is a duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν, meaning "to devour". Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have structures that are either simple or elaborate. Their genomes may encode as few as four genes and as many as hundreds of genes. Phages replicate within the bacterium following the injection of their genome into its cytoplasm.

<span class="mw-page-title-main">Lambda phage</span> Bacteriophage that infects Escherichia coli

Enterobacteria phage λ is a bacterial virus, or bacteriophage, that infects the bacterial species Escherichia coli. It was discovered by Esther Lederberg in 1950. The wild type of this virus has a temperate life cycle that allows it to either reside within the genome of its host through lysogeny or enter into a lytic phase, during which it kills and lyses the cell to produce offspring. Lambda strains, mutated at specific sites, are unable to lysogenize cells; instead, they grow and enter the lytic cycle after superinfecting an already lysogenized cell.

<i>Salmonella</i> Genus of prokaryotes

Salmonella is a genus of rod-shaped (bacillus) gram-negative bacteria of the family Enterobacteriaceae. The two known species of Salmonella are Salmonella enterica and Salmonella bongori. S. enterica is the type species and is further divided into six subspecies that include over 2,600 serotypes. Salmonella was named after Daniel Elmer Salmon (1850–1914), an American veterinary surgeon.

A lysogen or lysogenic bacterium is a bacterial cell which can produce and transfer the ability to produce a phage. A prophage is either integrated into the host bacteria's chromosome or more rarely exists as a stable plasmid within the host cell. The prophage expresses gene(s) that repress the phage's lytic action, until this repression is disrupted. Currently a variety of studies are being conducted to see whether other genes are active during lysogeny, examples of which include phage-encoded tRNA and virulence genes.

Lysis is the breaking down of the membrane of a cell, often by viral, enzymic, or osmotic mechanisms that compromise its integrity. A fluid containing the contents of lysed cells is called a lysate. In molecular biology, biochemistry, and cell biology laboratories, cell cultures may be subjected to lysis in the process of purifying their components, as in protein purification, DNA extraction, RNA extraction, or in purifying organelles.

<span class="mw-page-title-main">Prophage</span>

A prophage is a bacteriophage genome that is integrated into the circular bacterial chromosome or exists as an extrachromosomal plasmid within the bacterial cell. Integration of prophages into the bacterial host is the characteristic step of the lysogenic cycle of temperate phages. Prophages remain latent in the genome through multiple cell divisions until activation by an external factor, such as UV light, leading to production of new phage particles that will lyse the cell and spread. As ubiquitous mobile genetic elements, prophages play important roles in bacterial genetics and evolution, such as in the acquisition of virulence factors.

<span class="mw-page-title-main">Phage therapy</span> Therapeutic use of bacteriophages to treat bacterial infections

Phage therapy, viral phage therapy, or phagotherapy is the therapeutic use of bacteriophages for the treatment of pathogenic bacterial infections. This therapeutic approach emerged at the beginning of the 20th century but was progressively replaced by the use of antibiotics in most parts of the world after the Second World War. Bacteriophages, known as phages, are a form of virus that attach to bacterial cells and inject their genome into the cell. The bacteria's production of the viral genome interferes with its ability to function, halting the bacterial infection. The bacterial cell causing the infection is unable to reproduce and instead produces additional phages. Phages are very selective in the strains of bacteria they are effective against.

<span class="mw-page-title-main">Transduction (genetics)</span> Transfer process in genetics

Transduction is the process by which foreign DNA is introduced into a cell by a virus or viral vector. An example is the viral transfer of DNA from one bacterium to another and hence an example of horizontal gene transfer. Transduction does not require physical contact between the cell donating the DNA and the cell receiving the DNA, and it is DNase resistant. Transduction is a common tool used by molecular biologists to stably introduce a foreign gene into a host cell's genome.

<span class="mw-page-title-main">Viral plaque</span> Visible structure formed by virus propagation within a cell culture

A viral plaque is a visible structure formed after introducing a viral sample to a cell culture grown on some nutrient medium. The virus will replicate and spread, generating regions of cell destruction known as plaques. For example, Vero cell or other tissue cultures may be used to investigate an influenza virus or coronavirus, while various bacterial cultures would be used for bacteriophages.

In virology, temperate refers to the ability of some bacteriophages to display a lysogenic life cycle. Many temperate phages can integrate their genomes into their host bacterium's chromosome, together becoming a lysogen as the phage genome becomes a prophage. A temperate phage is also able to undergo a productive, typically lytic life cycle, where the prophage is expressed, replicates the phage genome, and produces phage progeny, which then leave the bacterium. With phage the term virulent is often used as an antonym to temperate, but more strictly a virulent phage is one that has lost its ability to display lysogeny through mutation rather than a phage lineage with no genetic potential to ever display lysogeny.

<span class="mw-page-title-main">Lysogenic cycle</span> Process of virus reproduction

Lysogeny, or the lysogenic cycle, is one of two cycles of viral reproduction. Lysogeny is characterized by integration of the bacteriophage nucleic acid into the host bacterium's genome or formation of a circular replicon in the bacterial cytoplasm. In this condition the bacterium continues to live and reproduce normally, while the bacteriophage lies in a dormant state in the host cell. The genetic material of the bacteriophage, called a prophage, can be transmitted to daughter cells at each subsequent cell division, and later events can release it, causing proliferation of new phages via the lytic cycle. Lysogenic cycles can also occur in eukaryotes, although the method of DNA incorporation is not fully understood. For instance the AIDS viruses can either infect humans lytically, or lay dormant (lysogenic) as part of the infected cells' genome, keeping the ability to return to lysis at a later time. The rest of this article is about lysogeny in bacterial hosts.

<span class="mw-page-title-main">T7 phage</span> Species of virus

Bacteriophage T7 is a bacteriophage, a virus that infects bacteria. It infects most strains of Escherichia coli and relies on these hosts to propagate. Bacteriophage T7 has a lytic life cycle, meaning that it destroys the cell it infects. It also possesses several properties that make it an ideal phage for experimentation: its purification and concentration have produced consistent values in chemical analyses; it can be rendered noninfectious by exposure to UV light; and it can be used in phage display to clone RNA binding proteins.

Salmonella virus P22 is a bacteriophage in the Podoviridae family that infects Salmonella typhimurium. Like many phages, it has been used in molecular biology to induce mutations in cultured bacteria and to introduce foreign genetic material. P22 has been used in generalized transduction and is an important tool for investigating Salmonella genetics.

P1 is a temperate bacteriophage that infects Escherichia coli and some other bacteria. When undergoing a lysogenic cycle the phage genome exists as a plasmid in the bacterium unlike other phages that integrate into the host DNA. P1 has an icosahedral head containing the DNA attached to a contractile tail with six tail fibers. The P1 phage has gained research interest because it can be used to transfer DNA from one bacterial cell to another in a process known as transduction. As it replicates during its lytic cycle it captures fragments of the host chromosome. If the resulting viral particles are used to infect a different host the captured DNA fragments can be integrated into the new host's genome. This method of in vivo genetic engineering was widely used for many years and is still used today, though to a lesser extent. P1 can also be used to create the P1-derived artificial chromosome cloning vector which can carry relatively large fragments of DNA. P1 encodes a site-specific recombinase, Cre, that is widely used to carry out cell-specific or time-specific DNA recombination by flanking the target DNA with loxP sites.

<span class="mw-page-title-main">Bacteriophage P2</span> Species of virus

Bacteriophage P2, scientific name Escherichia virus P2, is a temperate phage that infects E. coli. It is a tailed virus with a contractile sheath and is thus classified in the genus Peduovirus, subfamily Peduovirinae, family Myoviridae within order Caudovirales. This genus of viruses includes many P2-like phages as well as the satellite phage P4.

Bacteriophage T12 is a bacteriophage that infects Streptococcus pyogenes bacteria. It is a proposed species of the family Siphoviridae in the order Caudovirales also known as tailed viruses. It converts a harmless strain of bacteria into a virulent strain. It carries the speA gene which codes for erythrogenic toxin A. speA is also known as streptococcal pyogenic exotoxin A, scarlet fever toxin A, or even scarlatinal toxin. Note that the name of the gene "speA" is italicized; the name of the toxin "speA" is not italicized. Erythrogenic toxin A converts a harmless, non-virulent strain of Streptococcus pyogenes to a virulent strain through lysogeny, a life cycle which is characterized by the ability of the genome to become a part of the host cell and be stably maintained there for generations. Phages with a lysogenic life cycle are also called temperate phages. Bacteriophage T12, proposed member of family Siphoviridae including related speA-carrying bacteriophages, is also a prototypic phage for all the speA-carrying phages of Streptococcus pyogenes, meaning that its genome is the prototype for the genomes of all such phages of S. pyogenes. It is the main suspect as the cause of scarlet fever, an infectious disease that affects small children.

The Phage 21 S Family is a member of the Holin Superfamily II.

<span class="mw-page-title-main">Kill the Winner hypothesis</span>

The "Kill the Winner" hypothesis (KtW) is an ecological model of population growth involving prokaryotes, viruses and protozoans that links trophic interactions to biogeochemistry. The model is related to the Lotka–Volterra equations. It assumes that prokaryotes adopt one of two strategies when competing for limited resources: priority is either given to population growth ("winners") or survival ("defenders"). As "winners" become more abundant and active in their environment, their contact with host-specific viruses increases, making them more susceptible to viral infection and lysis. Thus, viruses moderate the population size of "winners" and allow multiple species to coexist. Current understanding of KtW primarily stems from studies of lytic viruses and their host populations.

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.

Arbitrium is a viral peptide produced by bacteriophages to communicate with each other and decide host cell fate. It is six amino acids(aa) long, and so is also referred to as a hexapeptide. It is produced when a phage infects a bacterial host. and signals to other phages that the host has been infected.

References

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  14. ↑ Baggesen DL, Sørensen G, Nielsen EM, Wegener HC (2010). "Phage typing of Salmonella Typhimurium - is it still a useful tool for surveillance and outbreak investigation?". Eurosurveillance . 15 (4): 19471. doi: 10.2807/ese.15.04.19471-en . PMID   20122382.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  15. ↑ Abedon, Stephen T (2011). "Lysis from without". Bacteriophage. 1 (1): 46–49. doi:10.4161/bact.1.1.13980. ISSN   2159-7073. PMC   3109453 . PMID   21687534.
  16. ↑ Brandis, Henning (1957), Kikuth, W.; Meyer, K. F.; Nauck, E. G.; Pappenheimer, A. M. (eds.), "Die Anwendung von Phagen in der bakteriologischen Diagnostik mit besonderer Berücksichtigung der Typisierung von Typhus- und Paratyphus B-Bakterien sowie Staphylokokken", Ergebnisse der Mikrobiologie, Immunitätsforschung und experimentellen Therapie: Fortsetzung der Ergebnisse der Hygiene, Bakteriologie, Immunitätsforschung und experimentellen Therapie (in German), Berlin, Heidelberg: Springer, pp. 96–159, doi:10.1007/978-3-662-25832-3_3, ISBN   978-3-662-25832-3 , retrieved 2021-11-15
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  20. ↑ Felix, A.; Callow, B. R. (1943-07-31). "Typing of Paratyphoid B Bacilli by Vi Bacteriophage". British Medical Journal. 2 (4308): 127–130. doi:10.1136/bmj.2.4308.127. ISSN   0007-1447. PMC   2284669 . PMID   20784954.
  21. ↑ "International Federation for Enteric Phage Typing | UIA Yearbook Profile | Union of International Associations". uia.org. Retrieved 2021-11-15.
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  24. ↑ Gershman, M.; Merrill, Cynthia E.; Hunter, Jacqueline (1981-12-01). "Phage Typing Set for Differentiating Escherichia coli". Journal of Dairy Science. 64 (12): 2392–2400. doi: 10.3168/jds.S0022-0302(81)82862-7 . ISSN   0022-0302. PMID   7042781.
  25. 1 2 "Phage Typing Method: Principle, Procedure, Results • Microbe Online". Microbe Online. 2020-03-05. Retrieved 2021-11-20.
  26. ↑ Baggesen DL, Sørensen G, Nielsen EM, Wegener HC (2010). "Phage typing of Salmonella Typhimurium - is it still a useful tool for surveillance and outbreak investigation?". Eurosurveillance . 15 (4): 19471. doi: 10.2807/ese.15.04.19471-en . PMID   20122382.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  27. 1 2 3 "Encyclopedia of Virology | ScienceDirect". www.sciencedirect.com. Retrieved 2021-11-15.
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