Bacteriophage


A bacteriophage, also known informally as a phage, is a virus that infects and replicates within bacteria. The term is derived. 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.
Bacteriophages are among the most common and diverse entities in the biosphere. Bacteriophages are ubiquitous viruses, found wherever bacteria exist. It is estimated there are more than 1031 bacteriophages on the planet, more than every living organism on Earth, including bacteria, combined. Viruses are the most abundant biological entity in the water column of the world's oceans, and the second largest component of biomass after prokaryotes, where up to 9 virions per millilitre have been found in microbial mats at the surface, and up to 70% of marine bacteria may be infected by bacteriophages.
Bacteriophages were used from the 1920s as an alternative to antibiotics in the former Soviet Union and Central Europe, as well as in France and Brazil. They are seen as a possible therapy against multi-drug-resistant strains of many bacteria.
Bacteriophages are known to interact with the immune system both indirectly via bacterial expression of phage-encoded proteins and directly by influencing innate immunity and bacterial clearance. Phage–host interactions are becoming increasingly important areas of research.

Classification

Bacterial viruses lack common ancestry and, for that reason, are classified in many unrelated taxa, listed hereafter:
  • In the realm Duplodnaviria, the class Caudoviricetes contains bacterial viruses. Unlike the other taxa listed here, Caudoviricetes does not exclusively contain bacterial viruses; archaeal viruses are also included in the class. Caudoviruses are also called tailed viruses or head-tail viruses, and they are often sorted into three types based on tail morphology: podoviruses, myoviruses, and siphoviruses.
  • In the realm Monodnaviria, the kingdoms Loebvirae and Sangervirae contain bacterial viruses.
  • In the realm Riboviria, the phylum Artimaviricota, the class Vidaverviricetes, the class Leviviricetes, and possibly the families Picobirnaviridae and Partitiviridae contain bacterial viruses.
  • In the realm Singelaviria, the family Matsushitaviridae contains bacterial viruses.
  • In the realm Varidnaviria, the class Ainoaviricetes, the order Vinavirales, and the subphylum Prepoliviricotina contain bacterial viruses.
  • Lastly, the families Obscuriviridae and Plasmaviridae, which are unassigned to higher taxa, are bacterial virus families.
The aforementioned taxa can be visualized as follows, with bacterial virus taxa in bold:
  • Realm: Duplodnaviria
  • * Kingdom: Heunggongvirae
  • ** Phylum: Uroviricota
  • *** Class: Caudoviricetes
  • Realm: Monodnaviria
  • * Kingdom: Loebvirae
  • * Kingdom: Sangervirae
  • Realm: Riboviria
  • * Kingdom: Orthornavirae
  • ** Phylum: Artimaviricota
  • ** Phylum: Duplornaviricota
  • *** Class: Vidaverviricetes
  • ** Phylum: Lenarviricota
  • *** Class: Leviviricetes
  • ** Phylum: Pisuviricota
  • *** Class: Duplopiviricetes
  • **** Order: Durnavirales
  • ***** Family: Picobirnaviridae
  • ***** Family: Partitiviridae
  • Realm: Singelaviria
  • * Kingdom: Helvetiavirae
  • ** Phylum: Dividoviricota
  • *** Class: Laserviricetes
  • **** Order: Halopanivirales
  • ***** Family: Matsushitaviridae
  • Realm: Varidnaviria
  • * Kingdom: Abadenavirae
  • ** Phylum: Produgelaviricota
  • *** Class: Ainoaviricetes
  • *** Class: Belvinaviricetes
  • **** Order: Vinavirales
  • * Kingdom: Bamfordvirae
  • ** Phylum: Preplasmiviricota
  • *** Subphylum: Prepoliviricotina
  • Unassigned taxa: Obscuriviridae and 'Plasmaviridae'''''

    History

In 1896, Ernest Hanbury Hankin reported that something in the waters of the Ganges and Yamuna rivers in India had a marked antibacterial action against cholera and it could pass through a very fine porcelain Chamberland filter. In 1915, British bacteriologist Frederick Twort, superintendent of the Brown Institution of London, discovered a small agent that infected and killed bacteria. He believed the agent must be one of the following:
  1. a stage in the life cycle of the bacteria
  2. an enzyme produced by the bacteria themselves, or
  3. a virus that grew on and destroyed the bacteria
Twort's research was interrupted by the onset of World War I, as well as a shortage of funding and the discoveries of antibiotics.
Independently, French-Canadian microbiologist Félix d'Hérelle, working at the Pasteur Institute in Paris, announced on 3 September 1917 that he had discovered "an invisible, antagonistic microbe of the dysentery bacillus". For d'Hérelle, there was no question as to the nature of his discovery: "In a flash I had understood: what caused my clear spots was in fact an invisible microbe... a virus parasitic on bacteria." D'Hérelle called the virus a bacteriophage, a bacterium-eater. He also recorded a dramatic account of a man suffering from dysentery who was restored to good health by the bacteriophages. It was d'Hérelle who conducted much research into bacteriophages and introduced the concept of phage therapy. In 1919, in Paris, France, d'Hérelle conducted the first clinical application of a bacteriophage, with the first reported use in the United States being in 1922.

Nobel prizes awarded for phage research

In 1969, Max Delbrück, Alfred Hershey, and Salvador Luria were awarded the Nobel Prize in Physiology or Medicine for their discoveries of the replication of viruses and their genetic structure. Specifically the work of Hershey, as contributor to the Hershey–Chase experiment in 1952, provided convincing evidence that DNA, not protein, was the genetic material of life. Delbrück and Luria carried out the Luria–Delbrück experiment which demonstrated statistically that mutations in bacteria occur randomly and thus follow Darwinian rather than Lamarckian principles.
In 2018, George Smith and Gregory Winter were awarded Nobel Prize in Chemistry for the phage display of peptides and antibodies.

Uses

Phage therapy

Phages were discovered to be antibacterial agents and were used in the former Soviet Republic of Georgia during the 1920s and 1930s for treating bacterial infections.
D'Herelle "quickly learned that bacteriophages are found wherever bacteria thrive: in sewers, in rivers that catch waste runoff from pipes, and in the stools of convalescent patients."
They had widespread use, including treatment of soldiers in the Red Army. However, they were abandoned for general use in the West for several reasons:
  • Antibiotics were discovered and marketed widely. They were easier to make, store, and prescribe.
  • Medical trials of phages were carried out, but a basic lack of understanding of phages raised questions about the validity of these trials.
  • Publication of research in the Soviet Union was mainly in the Russian or Georgian languages and for many years was not followed internationally.
  • The Soviet technology was widely discouraged and in some cases illegal due to the red scare.
The use of phages has continued since the end of the Cold War in Russia, Georgia, and elsewhere in Central and Eastern Europe. The first regulated, randomized, double-blind clinical trial was reported in the Journal of Wound Care in June 2009, which evaluated the safety and efficacy of a bacteriophage cocktail to treat infected venous ulcers of the leg in human patients. The FDA approved the study as a Phase I clinical trial. The study's results demonstrated the safety of therapeutic application of bacteriophages, but did not show efficacy. The authors explained that the use of certain chemicals that are part of standard wound care may have interfered with bacteriophage viability. Shortly after that, another controlled clinical trial in Western Europe was reported in the journal Clinical Otolaryngology in August 2009. The study concludes that bacteriophage preparations were safe and effective for treatment of chronic ear infections in humans. Additionally, there have been numerous animal and other experimental clinical trials evaluating the efficacy of bacteriophages for various diseases, such as infected burns and wounds, and cystic fibrosis-associated lung infections, among others. On the other hand, phages of Inoviridae have been shown to complicate biofilms involved in pneumonia and cystic fibrosis and to shelter the bacteria from drugs meant to eradicate disease, thus promoting persistent infection.
Meanwhile, bacteriophage researchers have been developing engineered viruses to overcome antibiotic resistance, and engineering the phage genes responsible for coding enzymes that degrade the biofilm matrix, phage structural proteins, and the enzymes responsible for lysis of the bacterial cell wall. There have been results showing that T4 phages that are small in size and short-tailed can be helpful in detecting E. coli in the human body.
Therapeutic efficacy of a phage cocktail was evaluated in a mouse model with nasal infection of multi-drug-resistant A. baumannii. Mice treated with the phage cocktail showed a 2.3-fold higher survival rate compared to those untreated at seven days post-infection.
In 2017, a 68-year-old diabetic patient with necrotizing pancreatitis complicated by a pseudocyst infected with MDR A. baumannii strains was being treated with a cocktail of Azithromycin, Rifampicin, and Colistin for 4 months without results and overall rapidly declining health.
Because discussion had begun of the clinical futility of further treatment, an Emergency Investigational New Drug was filed as a last effort to at the very least gain valuable medical data from the situation, and approved, so he was subjected to phage therapy using a percutaneously injected cocktail containing nine different phages that had been identified as effective against the primary infection strain by rapid isolation and testing techniques. This proved effective for a very brief period, although the patient remained unresponsive and his health continued to worsen; soon isolates of a strain of A. baumannii were being collected from drainage of the cyst that showed resistance to this cocktail, and a second cocktail which was tested to be effective against this new strain was added, this time by intravenous injection as it had become clear that the infection was more pervasive than originally thought.
Once on the combination of the IV and PC therapy the patient's downward clinical trajectory reversed, and within two days he had awoken from his coma and become responsive. As his immune system began to function he had to be temporarily removed from the cocktail because his fever was spiking to over, but after two days the phage cocktails were re-introduced at levels he was able to tolerate. The original three-antibiotic cocktail was replaced by minocycline after the bacterial strain was found not to be resistant to this and he rapidly regained full lucidity, although he was not discharged from the hospital until roughly 145 days after phage therapy began. Towards the end of the therapy it was discovered that the bacteria had become resistant to both of the original phage cocktails, but they were continued because they seemed to be preventing minocycline resistance from developing in the bacterial samples collected so were having a useful synergistic effect.