Bacteriophages cure bacterial infections

Date:
November 16, 2016
Source:
Helsingin yliopisto (University of Helsinki)
Summary:
Phage therapy may be a solution to treating infections caused by antibiotic-resistant bacteria. Since
2013, researchers have collected bacteriophages to combat antibiotic-resistant bacterial strains,
and hope to start clinical phage therapy trials in the near future.

Phage therapy may be a solution to treating infections caused by antibiotic-resistant bacteria. Since 2013,
researchers at the University of Helsinki in Finland have collected bacteriophages to combat antibiotic-
resistant bacterial strains, and hope to start clinical phage therapy trials in the near future.

"The first targets in the clinical trials of phage therapy could be, for example, wound infections or the
eradication of antibiotic-resistant Escherichia coli bacteria from the intestine. Also acne could be
considered as a target," says Mikael Skurnik, from the University of Helsinki.
Bacteriophages (phages) are viruses that kill bacteria. The most common organisms on the planet, they
control the number of bacteria and maintain ecological balances in nature. Each bacteriophage infects only
a few bacterial species or types, potentially making them real precision-guided 'smart weapons' in the
battle against bacterial infections.
"Unlike antibiotics, phages do not disturb the normal microbiota. And importantly, they can be used
against antibiotic-resistant bacteria," Skurnik adds.
The first double-blind controlled clinical trials with phage therapy have recently been carried out in the
United States, the United Kingdom and Belgium. The trials have concentrated mainly on establishing the
safety of the therapy. No adverse effects have been observed in these trials. The EU has also funded the
PhagoBurn project where the efficacy of phage therapy using phage cocktails to treat burn wounds is
being investigated.
Phage therapy has not been used in patient care in Finland. Now, however, a new phage therapy project
directed by Dr. Skurnik has received an €850,000 grant from the Jane and Aatos Erkko Foundation
(http://www.jaes.fi/en/), which will propel phage therapy towards its first clinical trials in Finland. The trials
could focus on such antibioticresistant bacteria as Escherichia coli in the gut or MRSA on the skin. Acne
could also be targeted.
The isolation and characterisation of phages takes place in the phage therapy laboratory at the University
of Helsinki, where patient isolates will also be tested for phage sensitivity in order to identify appropriate
phages for therapy. Clinical trials will be carried out at the Helsinki University Hospital, and a preparation
line of phage therapy products will be set up in the Hospital pharmacy.
"The phage therapy products need to fulfill the drug quality requirements similar to other drugs," professor
Skurnik reminds.
Phages for use against clinically relevant bacteria have been collected at both the University of Helsinki
and University of Jyväskylä, and presently comprise close to 200 different phages.
"We are also discussing with other European phage scientists how to distribute phages between different
laboratories in Europe. It could be possible if Europe had 2 or 3 central repositories for phages. These
would receive phages from researchers, store and characterise them, and phage therapy laboratories in
different countries could then order phages from the repositories," Skurnik tells.
Phage therapy was started a hundred years ago -- the introdruction of antibiotics suspended its use.
Bacteriophages -- bacteria eaters -- were identified already in 1896 and were studied closely in the 1920s.
At that time, phage therapy was used to treat both animal and human infections -- such as cholera and
bubonic plague -- in India, often with good results.
In Western countries the invention of antibiotics ended scientists' interest in phage therapy for several
decades; however, this was not the case in Eastern Europe, especially in the former Soviet Union. The
Eliava Institute in Tbilisi, Georgia, is still one of the most renowned phage therapy centres in the world. In
the new millennium Western countries have realised the increasing threat of antibiotic resistance and a
new interest in the potential use of phage therapy has emerged.
 How viruses outsmart their host cells
Scientists decipher protein structure after more than fifty years of research
Date: March 6, 2019

Source: Charité - Universitätsmedizin Berlin

Summary:

Viruses depend on host cells for replication, but how does a virus induce its host to transcribe its
own genetic information alongside that of the virus, thus producing daughter viruses? For decades,
researchers have been studying a type of bacteriophage known as 'lambda' to try and find an
answer to this question. Using high-resolution cryo-electron microscopy, a research group has now
successfully deciphered this process.

Viruses depend on host cells for replication, but how does a virus induce its host to transcribe its
own genetic information alongside that of the virus, thus producing daughter viruses? For decades,
researchers have been studying a type of bacteriophage known as 'lambda' to try and find an
answer to this question. Using high-resolution cryo-electron microscopy, a research group from
Charité -- Universitätsmedizin Berlin has now successfully deciphered this process. Their findings
have been published in Molecular Cell.

No host, no viruses. While it is true that viruses are capable of spreading by surviving outside a
host, they need a host for replication. Viruses lack the complex apparatus necessary for the
transcription of genetic information and its subsequent translation into new virus components. This
is why all viruses need access to a host cell's molecular infrastructure. For decades, researchers
have been studying the ways in which viruses successfully exploit host functions. Their efforts have
been focused on 'bacteriophages' -- viruses that rely on bacterial hosts for replication. One of the
most intensively studied and best characterized of these is the 'lambda phage'.
Previous research had shown that the lambda phage introduced its own genetic information into
that of its host, inserting it at a specific site in the host genome. 'RNA polymerase', a protein
complex responsible for transcribing genetic information, would normally stop reading this
information at the end of the bacterial gene and would ignore any viral genes inserted behind it.
The virus uses a trick that prevents the RNA polymerase from terminating the transcription process:
it introduces 'lambda-N' (λN), a tiny protein which attaches itself to the host's RNA polymerase and
forces it to continue transcription of the viral genes. Until now, and despite intensive efforts,
researchers had failed to identify how this tiny protein can achieve such a feat. A Berlin-based team
of researchers has now been able to visualize the 3D structure of the RNA polymerase-λN-complex
using high-resolution imaging, enabling them to provide a detailed explanation of this 'viral
exploitation'.
For their study, researchers from Charité worked with colleagues from Freie Universität Berlin and
the Max Planck Institute for Molecular Genetics. They started by producing the individual
components of this large protein complex separately. After reassembling the components, they
placed the resulting complex in a thin film of water and froze it. Using cryo-electron microscopy, the
researchers took a total of 700,000 images of the protein complex from various angles, using these
to compute its 3D structure. "The nature of this structure told us that the small viral ?N protein
seals together the two halves of the RNA polymerase, thus preventing it from falling apart once it
reaches the stop signal at the end of the bacterial gene," explains one of the study's first authors,
Ferdinand Krupp, who is a doctoral student at Charité's Institute of Medical Physics and Biophysics.
"Because of this, the RNA polymerase continues transcribing even once it reaches the viral genes.
Once all the viral genes have been read, they are then used as a blueprint for making daughter
viruses -- meaning the virus has achieved its objective," says the biophysicist. He adds: "Our data
also explain many of the individual results recorded over five decades of research. Taken together,
these findings may contribute to the development of new antibacterial drugs."
 Infectious bacteria hibernate to evade antibiotics
Date:
September 25, 2018
Source:
Faculty of Science - University of Copenhagen
Summary:
Researchers have discovered a surprising tactic of pathogenic bacteria when being attacked by
antibiotics: hibernation.

University of Copenhagen researchers have discovered a surprising tactic of pathogenic bacteria when
being attacked by antibiotics: hibernation.

Almost all pathogenic bacteria develop a small number of antibiotic-tolerant variants. This means that a
significant fraction of bacteria survive courses of antibiotics.
While it is no secret that pathogenic bacteria are able to develop antibiotic resistant variants, a less well-
appreciated fact is that a small number of bacteria, including some of nature's nastiest pathogens, can
resist antibiotics and escape antibiotic treatments without relying on variants.
How's that? Researchers at the University of Copenhagen now have an answer. They have found examples
of a small portion of pathogenic bacteria hiding out in a dormant, hibernation-like state, until the danger
posed to them by antibiotics passes. When safe, they awaken and resume their regular functions.
"We studied E. coli bacteria from urinary tract infections that had been treated with antibiotics and were
supposedly under control. In time, the bacteria re-awoke and began to spread once again," explains
Professor Kenn Gerdes of the University of Copenhagen's Department of Biology.
The study, led by Professor Gerdes of UCPH, and Boris Macek of the University of Tübingen, has just been
published in the latest edition of the journal Science Signaling.
The bacterium's stop growth mechanism
Antibiotics usually target a bacteria cell's ability to grow, which means that a hibernating bacterium is
exempt from attack.
"A bacterium in hibernation is not resistant. It is temporarily tolerant because it stops growing, which
allows it to survive the effects of an antibiotic," says Professor Gerdes.
Genetically, hibernating bacteria share the same characteristics as other bacteria in a given population,
an E. coli population for example. So, for now, there are no clear rules as to why certain bacteria survive
antibiotics by going dormant while others do not.
The researchers used a new method to study what happens in the disease-causing cells that go dormant
and hide in the body.
Enzyme catalyzes hibernation
The researchers found an enzyme in dormant bacteria that is responsible for catalyzing hibernation, which
allows the bacteria to avoid being attacked.
"The discovery of this enzyme is a good foundation for the future development of a substance capable of
combatting dormant bacteria cells," says Professor Gerdes.
The road ahead will not be easy and will require many years of hard work, expertise and research funding
to develop new antibiotics. For Gerdes, it obvious that Denmark ought to play a leading role in this area of
research.
"The enzyme triggers a 'survival program' that almost all disease-causing bacteria deploy to survive in the
wild and resist antibiotics in the body. Developing an antibiotic that targets this general programme would
be a major advance," he says.
 Bacteria and phages: An endless cycles of evolution
Date:
March 28, 2017
Source:
Science Foundation Ireland (SFI)
Summary:
What drives bacterial strain diversity in the gut? Although there are a number of possible
explanations, a recent opinion piece addresses one potentially important and overlooked aspect of
this unresolved question.

What drives bacterial strain diversity in the gut? Although there are a number of possible explanations, a
recent opinion piece published in Trends in Microbiology by Dr Pauline Scanlan, a Royal Society -- Science
Foundation Ireland Research Fellow at the APC Microbiome Institute, University College Cork, addresses
one potentially important and overlooked aspect of this unresolved question.

The human gut is host to an incredible diversity of microbes collectively known as the gut microbiome. Our
gut microbiomes interact with us, their human hosts, to perform a myriad of crucial functions ranging from
digestion of food to protection against pathogens. Whilst superficially it may seem that the microbes
inhabiting the human gut are stable and broadly similar between individuals, recent advances in
sequencing technology that allow for high-level resolution investigations have shown that our gut
microbiomes are dynamic, capable of rapid evolution and unique to each individual in terms of bacterial
species and strain diversity. This unique inter-individual variation is of crucial importance as we know that
differences in bacterial strain diversity within species can have a range of positive or negative
consequences for the human host -- for example some strains of a given bacteria are harmless whilst
another strain of the same bacterial species could kill you. A classic example of this is different strains of
the gut bacterium Escherichia coli -- E. coli Nissle 1917 is used as a probiotic and E. coli O157:H7 has been
responsible for a number of deadly food-borne pathogen outbreaks. Therefore a better understanding of
what drives bacterial strain diversity is not just fundamental to our understanding of the ecology and
evolution of microbes but is also highly relevant for improvements in human health and disease
prevention.
Scanlan researches microbial evolution and ecology in experimental and natural populations. She is
particularly interested in investigating the processes underpinning strain variation in the gut and in this
opinion piece provides compelling evidence in support of a role for a specific process called antagonistic
coevolution between bacteria and bacteriophages (phages) as a key driver of microbial diversity in the
human gut.
What is antagonistic coevolution between bacteria and phages and why is it relevant to strain diversity
and human health? Phages are viruses that infect bacterial cells by binding to specific receptors on the
cell. Upon infecting a bacterial cell, they essentially hijack their bacterial host to make multiple viral
progeny which they release into the environment. However, bacteria are highly adaptable and can evolve
resistance to phage infection, and this resistance evolution in turn can select for phage novel infectivity
and so on. Over time, this continual selection for resistance and infectivity evolution (coevolution) between
bacteria and phages has been shown to drive microbial diversity in both experimental and natural
microbial communities. Crucially, these changes in microbial diversity may also have a wide range of
functional consequences and ultimately impact on host health. For example, evolving resistance to phages
may increase or decrease bacterial virulence and change how the bacteria interact with their human host
immune system.
"Although research into microbial coevolution in natural populations is very much in its infancy, I hope this
opinion piece will provide a different insight and open up new discussions into how fundamental
evolutionary processes, such as coevolution, could potentially shape microbial diversity and functionality in
the gut and ultimately impact on host health" Scanlan says.
 The cholera bacterium can steal up to 150 genes in one go
Date:
October 7, 2019
Source:
Ecole Polytechnique Fédérale de Lausanne
Summary:
Scientists have discovered that predatory bacteria like the cholera pathogen can steal up to 150
genes in one go from their neighbors. The study sheds light on one of the most fundamental
mechanisms of horizontal gene transfer.

In 2015, EPFL researchers led by Melanie Blokesch published a seminal paper in Science showing that the
bacterium responsible for cholera, Vibrio cholerae, uses a spring-loaded spear to literally stab neighboring
bacteria and steal their DNA. They identified the spear mechanism to be the so-called "type VI secretion
system" or T6SS, also used for interbacterial competition by many other bacteria.

V. cholerae uses its T6SS to compete with other bacteria in its aquatic environment and acquire new
genetic material, which the pathogen absorbs and exchanges against some parts of its own genome. This
mode of "horizontal gene transfer" leads to rapid evolution and pathogen emergence. The pathogen V.
cholerae has caused seven major cholera pandemics since 1817 and, according to current WHO data, still
kills more than 100,000 people each year and infects up to 4 million others, mostly in poor or
underdeveloped countries.
Now, Blokesch's group has discovered the extent of DNA that V. cholerae can steal in a single attack: more
than 150,000 nucleic acid base pairs, or roughly 150 genes in one go (the cholera bacterium carries
around 4,000 genes in total). The researchers calculated this number by sequencing the entire genome of
almost 400 V. cholerae strains before and after stealing DNA from their neighboring bacteria.
Previous studies have tried to establish just how much DNA competent bacteria can absorb and integrate
into their genome by feeding them large quantities of purified DNA. However, this does not reflect the
natural conditions in which the bacteria live and operate, as long stretches of free DNA are scarce in the
environment. V. cholerae's T6SS-mediated DNA stealing, however, allows the bacterium to acquire fresly
released and long DNA fragments. This bacterial behavior is tightly linked to the chitinous surfaces (e.g.
shells) on which the bacterium usually lives in oceans and estuaries.
To address this, the EPFL researchers studied two unrelated ("non-clonal") strains of V. cholerae in co-
cultures on chitin. This allowed them to determine the frequency and extent of DNA exchanges between
the two strains, under more natural conditions.
The study, led by PhD student Noémie Matthey, found that V. cholerae strains that carry a functional and
chitin-inducible T6SS system are much more efficient at transferring DNA than bacteria that don't. The
predatory bacterium acquired large genomic regions from its killed prey -- up to the 150,000 base pairs
mentioned above.
The authors conclude that the environmental "lifestyle" of V. cholerae enables exchange of genetic
material with enough coding capacity that it can significantly accelerate the evolution of the bacterium.
"This finding is very relevant in the context of bacterial evolution," says Blokesch. "It suggests that
environmental bacteria might share a common gene pool, which could render their genomes highly
flexible and the microbes prone to quick adaption.
 New mechanism for Type IV pili retraction in Vibrio cholerae
Date:
January 4, 2017
Source:
The City University of New York
Summary:
Although pathogenic bacteria often rely on a specialized molecular motor to retract their pili, a new
study reveals that a minor pilin protein elicits pilus retraction in the cholera bacterium, Vibrio
cholerae

Type IV pili, essential for many pathogens to cause disease, are hair-like appendages that grow out of and
are retracted back into bacteria cells, enabling them to move and adhere to surfaces. Although pathogenic
bacteria often rely on a specialized molecular motor to retract their pili, a new study in PLOS
Pathogens reveals that a minor pilin protein elicits pilus retraction in the cholera bacterium, Vibrio
cholerae.

Bacteria utilize a number of highly sophisticated molecular tools to colonize their hosts. One of the most
ubiquitous is a complex nanomachine called the Type IV pilus. This nanomachine has as few as 10 to as
many as 30 molecular components, producing exquisitely thin filaments that extend from the bacterial
surface and that can be several times the length of the bacteria itself. These pilus filaments have a
remarkable array of functions that rely on their ability to (i) adhere to many substrates, including host cell
surfaces, pili from nearby bacteria, DNA and bacterial viruses (bacteriophage), and (ii) to depolymerize or
retract, which pulls the bacteria along mucosal surfaces, pulls them close together in protective
aggregates, and can even draw in substrates like DNA and bacteriophage for nutrition and genetic
variation.
In collaboration with researchers from Dartmouth College and Simon Fraser University, Dr. Nicolas Biais,
Assistant Professor of Biology at Brooklyn College, City University of New York (CUNY), developed an assay
in his laboratory that revealed for the first time the V. cholerae Type IV pilus can retract without this
molecular motor, and that retraction is necessary for these pili to function. Instead of a molecular motor, a
small minor pilin protein triggers pilus retraction. "The magnitude of the forces though is much smaller,"
said Dr. Biais. "If Neisseria gonorrhoeae can pull roughly 100,000 times its bodyweight, Vibrio
cholerae barely makes it to 1,000 times of its bodyweight. This is a new mechanism for retraction that will
help understand how other pili and closely related secretion systems can work and potentially help with
the design of novel antibiotics."
"This report [...] demonstrates that the bacterium that causes cholera powers a nanomachine required for
infection differently than other disease causing bacteria," said Dr. Hank Seifert, Professor of Biomedical
Sciences at Feinberg School of Medicine, Northwestern University, who was not involved with the study.
"These findings drastically alter our understanding of how these nanomachines function to provide insights
into the mechanisms allowing cholera and the development of synthetic nanomachines."
Research on how Type IV pili function not only advances our understanding of V. cholerae pathogenesis,
but will also aid in developing future prevention and treatment strategies for cholera.