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FULL MARKS | EPQ A* Grade Dissertation [Biology] Example- Renewed Research in Bacteriophage Therapy To Solve the Growing Problem of Antibiotic Resistance$8.23
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FULL MARKS | EPQ A* Grade Dissertation [Biology] Example- Renewed Research in Bacteriophage Therapy To Solve the Growing Problem of Antibiotic Resistance
Complete EPQ essay around 9000 words in length so extremely comprehensive. Titled 'To What Extent Will Renewed Research in Bacteriophage Therapy Solve the Growing Problem of Antibiotic Resistance'. This essay goes into great detail explaining the problem of antibiotic resistance and its history as ...
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‘To What Extent Will Renewed Research into Bacteriophage Therapy
Solve the Growing Problem of Antibiotic Resistance’
Introduction:
As the overuse of antibiotics continues to grow fuelling the selective evolution of pathogenic microbes with
immunity or partial immunity towards to them, the prospect of a return to a “pre-antibiotic era” becomes an
increasingly threatening future. Prevalent organisations such as the WHO and Centre for Disease Control
are calling antibiotic resistance a threat to global health [1][2]. According to a 2016 review on antimicrobial
resistance conducted by the United Kingdom government an estimated 700,000 people currently die every
year from antibiotic resistant infections, if this trend continues there it will grow to 10 million by 2050 -
killing more people than cancer - with a global cost of $100 trillion (USD). These ‘superbugs’ represent one
of the greatest threats of modern times and can have devastating effects; just one of these resistant bacterial
infections, methicillin-resistant staphylococcus aureus (MRSA), accounts for more deaths in the US every
year than emphysema, Parkinson’s Disease, HIV, and Tuberculosis combined [3].
The Problem of Antibiotic Resistance:
In the modern world antibiotics are produced and consumed at an enormous rate. In the United States alone
an estimated 23,000,000 tonnes of antibiotics are used annually, with fifty percent of this figure going to
livestock and agriculture often purely for preventative purposes and circa 7,000,000 tonnes are used as
growth promotants [4]. This gross overuse has had a plethora of adverse affects which include massive
spreading of strains of bacteria resistant to the very antimicrobials used to target them both in agriculture and
in hospitals leading to an increase in nosocomial (hospital acquired) diseases. As such, genes coding for
resistance to common antibiotics like 𝜷 - lactams, aminoglycosides, chloramphenicols and tetracycline are
becoming more common and posing a greater risk to human health particularly in immunocompromised
patients[3].
Traditional antibiotics work by inhibiting cell replication or causing a bacterial cell to die during the process
of replication in order to bring down the number of pathogenic bacterial cells in the body to a level at which
the immune system can deal with them. By outlining precisely how a selection of processes of antimicrobial
inhibition work in two common classes of antibiotics and examining the spread of two of the most prevalent
species of resistant bacteria I will illustrate the mechanisms by which they can be circumvented through
bacterial evolution.
For example, 𝜷 lactam antibiotics (the group which contains penicillin) inhibit cell wall synthesis by binding
to the penicillin-binding proteins (PBPs) found in the cell membrane, this then prevents the formation of
cross-links between the peptidoglycan layers of the cell wall during replication causing the cell to burst due
to osmotic instability (its cell wall is not strong enough to cope with the outward pressure exerted from
inside of the cell) - killing the cell. [5][6]. A second common class of antibiotics are the aminoglycosides.
These work differently from the 𝜷-lactam antibiotics in that they enter the bacterial cell and bind to a part of
the ribosomes (the organelle responsible for protein synthesis). This means that when the bacteria “reads” its
DNA to make a new protein it does so incorrectly and therefore interrupts the production of new proteins -
without which the bacterial cell dies[7].
Random genetic mutation leads to the growth of altered bacteria with more advantageous phenotypes which
allow them to survive in the hostile antibiotic-rich environment they find themselves in. On such example is
the production of specialised enzymes which permanently alter and deactivate the antibiotic compounds,
these enzymes include 𝜷-lactamases and aminnoglycoside-modifying enzymes. Once these develop the
antibiotics used to treat these infections will become severely less effective. Antibiotic resistance can also be
developed through other methods; when a mutated gene that codes for the protein target sites (such as the
PBPs) of these antibiotics develops the shape of these sites is altered to the extent that the intended antibiotic
can no longer bind and therefore no longer inhibit bacterial cell growth or reproduction [8]. One study of
this phenomenon focused on the alteration of the protein-binding-sites in S.aureus. It found that strains of
MRSA (Methicillin-resistant S.aureus) had much higher numbers of the altered PBSs in comparison to
,MSSA strains (methicillin-sensitive S.aureus) and it was this that allowed it to sufficiently biosynthesise its
cell walls in concentrations of 𝜷-lactams which made this act lethal in MSSA[9]. The final form of antibiotic
resistance which I will discuss in this section is that of a reduction in intracellular drug accumulation: many
bacteria have developed methods by which to drastically reduce the volume of antibiotic substance actually
able to pass through their cell membranes. They achieve this in two ways: firstly, they reduce the means of
access that these drugs actually have to enter the cell by diminishing the number of protein channels in the
outer membrane - moreover, they actually develop a type of pump (an efflux pump) that expel the drugs
form the cell at such a rate that the concentration never reaches a point where it becomes toxic to the cell -
unsurprisingly these pumps play a key role in resistance to a spectrum of antibiotics including
aminoglycosides.
I will explore specifically the means by which two members of the ESKAPE pathogens have managed to
adapt and the time scales at which they’ve done so in order to exhibit the challenges faced by the production
of traditional antibiotics. In the case of S. aureus - a normal member of the natural environment of bacteria
found on the skin of humans and animals -penicillin treatment was often sufficient to treat the infection with
it responding positively to the drug. However, excessive use of these antibiotics (penicillin was available
over the counter without prescription in the US for 10 years inevitably leading to the formation of resistant
colonies[10]) led to the first 𝜷-lactamase producing isolates emerging in 1948 - now 65 -85% of all clinical
isolates of S. aureus are resistant to Penicillin, the incidence of this new resistant strain has grown to 80% in
clinical and community infections. It wasn’t until the 1960s that the first emergence of S. aureus resistant to
methicillin was recorded, this too has spread and now accounts for an estimated 25% of all S. aureus isolates
globally [3]. Similarly, K. Pneumoniae developed a variety of 𝜷 -lactamase enzymes capable of disrupting
the function of the group of antibiotics used to treat the most persistent infections - carbapenems. This
presents a serious challenge to the medical community has these strains become more wide spread.
The evolution of the above traits and abilities among others is what has enabled the development of
antibiotic resistance in so many species - most notably among which are the ESKAPE pathogens
(Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii,
Pseudomonas aeruginosa and Enterobacter spp.) - these six common nosocomial infections represent the
dangers of antibiotic resistance, as the efficacy of antibiotics continually diminishes these infections become
more and more difficult to treat and will claim more and more lives [3][8]. There is a direct correlation
between the introduction of new novel classes of antibiotics and the evolution of mechanisms to inhibit them
- particularly clear is the correlation between the usage of 𝜷 - lactams and the diversity of 𝜷 - lactamases
identified which render them inactive over the past 50 years - now with over 1000 currently discovered [10].
Shockingly, as the need for new and alternative antibiotics increases the rate at which they’re being produced
is almost idle. Ever since they were first discovered production of new antibiotics has been relatively steady
and reliable, but the “antibiotic pipeline” has slowed over recent years with a 90% reduction in approval and
implementation of new antibiotics between 1980 and the early 2000s - coupled with a decrease in the
discovery of new and novel classes of antibiotics due a lack of incentive for many companies [11] (due to
the rate at which bacteria evolve resistance to antibiotics [3]) leading them to pursue more profitable and
commercially appealing therapeutic treatments. There are many documented cases where new antibiotic
drugs have been withdrawn in less than a year due to rapid evolution and spread of resistance genes
rendering them ineffective.
Reaching the end of this “antibiotic pipeline” is cause for major concern; as strains of nosocomial pathogens
such as K. pneumoniae are now resistant to carbapenem antibiotics. These antibiotics are often the last resort
due to the negative health effects they can have but have the widest spectrum of antimicrobial efficacy and
so are usually our strongest option. Due to an absence of alternative options for treatment infections with K.
pneumoniae are associated with a 40-50% mortality rate [3].
Speaking in February 2017, Dr Marie-Paule Keiny - assistant director general for health systems and
innovation at the World Health Organisation said “Antibiotic resistance is growing and we are running out
of treatment options. “If we leave it to market forces alone, the new antibiotics we most urgently need are
not going to be developed in time,” [12] she also said “the pipeline is practically dry’ - these comments
came after the WHO announced a list of the 12 highest priority pathogens for which the development of new
antibiotics against are required. Top of the list are the carbapenem resistant bacteria such as Acinetobacter
baumannii.
,One reason for the spread of these resistance genes to be so prevalent and so rapid is the capacity of many
bacteria of lateral gene transfer - this is the process by which genes developed in one species of bacteria can
be passed on to another separate species. This can be via transfer of fragments of a genome from other
bacteria or from a viral genome once it has integrated its DNA with that of a bacteria and is predominantly
achieved via transfer of plasmids (small circular sections of DNA found in bacterial cells which are
independent form the main genome and can be passed between bacteria) . Often these laterally transferred
genes confer antibiotic resistance between completely separate species of bacteria [Sadava et al. 2016. pg
497] [6].
As you can no doubt infer from the evidence I have thus far presented the time when the “miracle drugs”
first discovered by Alexander Flemming less than a century ago that were effective in treating the complete
array of bacterial infections we may have found ourselves afflicted by is set to swiftly and morbidly end
within our lifetimes unless other alternative areas of research into a solution are explored. Moreover, as the
number of nosocomial resistant pathogens spreads the pressure on global economic and healthcare systems
will be enormous and trust in orthodox medicine will be inevitably eroded [8]. Currently, production of new
types antibiotics is at an insufficient pace to protect us from the rapidly approaching future where a routine
surgical procedure or infection will often prove fatal. It is this pressure which I hope will shift the focus
away from the traditional antimicrobial strategies pursued by the western world in the last century and onto
the overlooked practise of bacteriophage therapy.
A Brief Context of Bacteriophage Therapy:
Although this technology has only started to gain traction in Western medicine in only relatively recent years
the practise is actually over 100 years old - this means that rudimentary forms of this practise even predate
the advent of antibiotics.
The ownership of the title of bacteriophages is a hotly contested topic - the first evidence of an unknown
viral-like agent came from the British microbiologist Ernest Hankin in 1896; he noted antibacterial activity
against the bacteria Vibrio cholerae in the Ganges river which he suggested might be helping to reduce the
incidence of cholera in the population living in proximity to the river [13]. Similar findings were reported by
other bacteriologists and microbiologist in the following years - but it wasn’t until 1910 when a french
microbiologist by the name of Felix d’Herelle, while studying a means to control the locust population in
Mexico, observed clear zones of no bacterial growth on agar plates he was incubating and confidently
proposed that they were caused by a viral parasite. He proposed the name ‘bacteriophage’ in 1916. It was
d’Herelle who conducted the first clinical trials of his newly discovered bacteriophages at the Hospital des
Enfants-Malades in Paris in 1917. Sulakvelidze, Alavidze and Morris Jr report that before administering his
phage cocktail to a twelve year old boy afflicted with dysentery d’Herelle and several hospital interns
ingested the cocktail the day before in order to test its safety. The boy began to recover within 24 hours after
only one dose of the treatment. He repeated the trial with three more subjects shortly after with similar
results. [15]
Many other clinical trials were conducted by d’Herelle and other bacteriologists following these and other
promising results - one such example, conducted again by d’Herelle, included the treatment of several
thousand people in India by bacteriophage preparations who were suffering infections of cholera and the
bubonic plague. Indeed, this ushered in the hay-day of bacteriophage therapy in the West with many
companies even beginning commercial production of pre-made bacteriophage cocktails (solutions available
for purchase which contained an assortment of virus which had proven to be hostile to common bacterial
pathogens) - one such company, headed by d’Herelle, advertised five phage cocktails to common diseases
and were marketed by a company which would later become a part of L’Oréal [14].
However, the cocktails produced often proved to be ineffective; Lin et al. suggests that this was due to a
series of mistakes which can be attributed to poor understanding of the nature of phages, he explains that
‘rudimentary purification and storage protocols resulted in low titres of active phage and contamination from
bacterial agents and phages that lacked infectivity for the target bacteria were used for treatment’[3].
This apparent lack of efficacy was a major blow for bacteriophage therapy particularly when pharmaceutical
antibiotics became common place in the 1940s. Moreover, poor scientific method led to a failure to prove
the effectiveness of bacteriophages - the is mainly due to a lack of a control group in a majority of the first
, clinical trials leading to a lack of substantial evidence for the use of bacteriophages in the eyes of the wider
scientific community. In order to deal with the controversy surrounding this new treatment in 1934 a paper
was published for the Council on Pharmacy and Chemistry of the American Medical Association upon its
request - the conclusions of this extremely detailed report, called the Eaton-Bayne-Jones report, were
overwhelmingly against bacteriophage therapy and was the final nail in the coffin for bacteriophage therapy
in the West (but it should be noted that the reasoning for this lack of support is now known to be grossly
inaccurate, for example the report states that D’Herelle’s viruses were more likely simply an enzyme.)
Shortly after, just seven years later a second equally damning report was published. These two negative
reports had an immeasurable impact on the enthusiasm of funding agencies looking to invest in
bacteriophage therapy leading to its abandonment after the introduction of antibiotics.
The reason that these reports were not influenced by and so take into consideration the promising continued
research in the former soviet union and Eastern Europe is because for the most part they were not available
in English or accessible to the international scientific community[15]. Phage therapy continues to be
actively used and researched at several Eastern European institutes notable among which are Eliava Institute
of Bacteriophage and the Institute of Immunology and Experimental Therapy in Poland.
Basic Phage Biology;
The final section of basic understanding required before I can begin to formulate the evaluative sections of
my essay is that of the biology of what phages actually are and how they reproduce. In this section I will
outline these details in simple terms for the purpose of being able to properly explore the differences between
bacteriophage therapy and antibiotics, to understand their pros and cons and to appreciate the findings of
case studies both past and current.
First, the basics: a bacteriophage is simply any virus which interacts with (and often kills) bacterial cells.
They are the most abundant biological organism on the planet by a long way, there are more phages on the
planet than all the other organisms (including bacteria) combined [16]. Current estimates state that there are
10(30) to 10(32) in the world at any one time and that they are responsible for the death of 20-40% of all
surface bacteria in the ocean every single day [3][16][17] making them by far the deadliest biological entity
on the planet. An important distinction is that phages are not alive, think of them as a biological robot - little
more that some genetic information in a protein shell. Sadava et al. {pg 549} describe viruses as “the ‘bark’
on the tree of life: certainly an important component all across the tree, but not quite like the main
branches”. Every bacteriophage has the same basic structure which includes an icosahedral protein head sat
atop a long ‘tail’ with several leg-like fibres - the protein coat around a virus is known as the capsid. Viruses
are totally unable to reproduce by themselves and so seek out specific hosts with the correct markers on their
surface. When a virus encounters its target it injects its genetic information into it through the ‘tail’ and
hacks the machinery of its target cell to produce many new viruses known as virions. Once this happens the
virions produce special lytic enzymes which break through the cell wall of the bacteria causing in to burst.
However, at the point where the virus’ genetic information has been injected into the cell the cycle can go
two different ways depending on the virus and environmental conditions these two options are called ‘the
lytic cycle’ and ‘the lysogenic cycle’. The lytic cycle is the one outlined above, i.e the viral genome causes
the cell’s normal activities to cease and even breaks down the nucleus in order to provide resources for the
production of more viral genomes, the virions then burst out of the cell. The lysogenic cycle involves an
alternative successful strategy evolved by many viruses known as lysogeny, instead of immediately initiating
the lytic cycle the viral genome integrates itself with the bacteria’s genome and becomes a ‘prophage’. It can
they lay dormant and be replicated by the bacteria when in divides, thus it can remain inactive for thousands
of generations or until environmental conditions become unfavourable at which point it starts the lytic cycle
[6].
I am now able to fully explain the advantages and disadvantages of bacteriophages as well as the findings if
many case studies with these processes having been explained.
The Pros and Cons of Bacteriophage Therapy Vs. Antibiotics
As research techniques develop bacteriophages have been seen to exhibit several key advantages over
traditional antibiotics as well as several new promising areas of research derived from their study.
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