Danyal Chaudry

11-1-16
Annotated Source List
Andersson, D. (2004, May 5-7). The ways in which bacteria resist antibiotics. WHO: The Global
Threat of Antibiotic Resistance, 1-5. Retrieved from
http://archives.who.int/prioritymeds/report/append/bacteria.pdf

Summary: This scholarly journal article by the World Health Organization details the biology of
how bacteria resist antibiotics. There are four main principles of antibiotic resistance, two of
which are phenotypically defined (efflux pump, cell wall resistance); and two of which are
genotypically defined (antibiotic degrading enzymes, antibiotic altering enzymes). Some forms
of bacterial resistance can be genotypically defined, meaning that bacteria have the genes able to
resist antibiotics. This would mean that bacteria would either have antibiotic degrading enzymes
or antibiotic altering enzymes. Antibiotic degrading enzymes inactivate the antibiotics by
destroying them chemically when they enter the bacteria. Antibiotic altering enzymes alter the
structure of the antibiotic. They stick to the antibiotic after it has entered the bacteria, preventing
it from binding to anything, thus preventing significant harm to the bacteria by the antibiotic.
Resistance traits in bacteria that can be phenotypically defined are the efflux pump, and the cell
wall resistance. The efflux pump is a physical trait of resistance because no chemical reactions
are required, it just pumps out any harmful antibiotics that enter the bacteria, rendering them
harmless. The cell wall trait is also physical because it stops any antibiotics from even entering
the cell, let alone harm the bacteria. The bacteria just plainly keeps out any harmful antibiotics in
this manner. The plasmid in the center of the bacteria contains the genes to resist bacteria in all
manners, and is the genetic information or DNA that the bacteria uses to develop resistance.
Application to Research: This journal was very helpful in helping understand the majors ways in
how antibiotics resist antibiotics. This journal goes in-depth in how bacteria resist antibiotics,
and what it means for the future in a short journal or executive summary.
Antibacterial Products May Actually Promote Antibiotic Resistance. (2016). Retrieved from
Gale Opposing viewpoints in Context database. (Accession No. EJ3010972215)

Summary: This database article details that triclosan is causing antibiotic resistance in the
general public It is saying that it is a major trigger, as it improve the pumps in bacteria. These
pumps are designed to push harmful substances out of the bacteria, and triclosan is triggering
these pumps to work more vigorously. With these pumps working more vigorously, they are also
now able to push out antibiotics. This makes the bacteria antibiotic resistant, posing a problem. A
very big issue is that triclosan is found almost everywhere in everyday life. From hand sanitizers
and soaps to yoga mats and the like, triclosan is used in almost every product we use and it could
be a major cause to the antibiotic resistance swarm that is weeping bacteria. There are already
some antibiotic resistant bacteria, but this could contribute to even more of them, and antibiotic
resistant pathogens could be responsible for more deaths than cancer by 2050. There is not much
that is being done so far to limit the use of triclosan in everyday home products, as most of the
focus is currently being directed upon new antibiotics and eliminating the use of antibiotics in
our food supply. But consumers are urged to be smart and use smart in relation to their everyday
products. The best solution so far is for the private industry to resolve its own issues, and this can
be done by the push of triclosan free water bottles, yoga mats, etc. Consumers are also urged to
only use alcohol-based hand sanitizer and soaps, and that washing hands regularly is the the best
defense.
Application to Research: This article has shown me another side of antibiotic resistance, and how
everyday home products containing triclosan can cause it. This might not be very important in
the end, but is good for awareness purposes.

Barker, K. F. (1999, August). Antibiotic resistance: a current perspective. Retrieved from PMC
database. (Accession No. 48(2): 109124)

Summary: This scholarly journal article details antibiotic resistance procedures in testing and the
like. In the UK, the most common antibiotic resistance susceptibility test is the disc diffusion
test. The disc diffusion test is employed by evenly coating the surface of an agar plate with
bacterial isolate, and a filter paper disc with antibiotic applied to the plate. After incubation,
circular zone of inhibition of growth appears around the disc as a result of diffusion of antibiotic
into the agar and inhibition of growth of the isolate. The zone size is compared with control
isolates, and results are observed as sensitive, intermediate, or resistant. It is difficult to
determine the MIC (minimum inhibitory concentration). The MIC is the lowest concentration of
antibiotic that will visibly inhibit the growth of bacteria after the appropriate incubation period.
The mechanisms of antibiotic resistance fall into five categories: enzymatic modification or
destruction of the antibiotic, reduced antibiotic uptake into the bacterium, increased efflux of
antibiotic from the bacterium, alteration or production of a new target site, over-expression of the
drug target. The DNA for these resistance mechanisms are acquired by genetic mutations or gene
transfer between microorganisms. There are three solutions to antibiotic resistance: reduce
antibiotic consumption and preserve existing agents, develop new antibiotics, or develop
therapeutic strategies for infection that do not involve antibiotics.
Application to Research: This article explains many procedures that are involved in antibiotic
resistance, the mechanisms, and possible solutions.
Carter, R. R., Sun, J., & Jump, R. L.P. (2016). A Survey and Analysis of the American Publics
Perceptions and Knowledge About Antibiotic Resistance. Oxford Journals, 2-15.
http://dx.doi.org/10.1093/ofid/ofw112

Summary: This scholarly journal article details the American publics knowledge and level of
concern for antibiotic resistance and the severity of antibiotic resistance. It says that while the
American people are aware that antibiotic misuse contributes to antibiotic resistance, many do
not consider this an important problem. 70% of respondents in the survey disagreed of responded
neutrally that antibiotic resistance was a major problem in American hospitals.Most respondents
were not very well versed in antibiotic resistance, and 89% of respondents said that people could
develop an immunity to antibiotics. They did know some information about antibiotics, as less
than 10% of them thought that antibiotics were appropriate to treat fatigue, headache, moodiness,
and anxiety. The sampling was done at random, and the questions that were asked were proper
scientific poll questions. So this was a credible, scientific poll.With valid results, the turnout of
this poll is very worrying. Antibiotic resistance is one of the biggest problems of the modern day
world, and threatens to throw us back into the dark ages of medicine. Soon, if not remedied, a
minor cut or scratch may become lethal. With the threat of infection and disease by bacteria that
we have no idea how to fight off, millions in the future will die as a result. And with this dark
cloud looming overhead, most people disagree that antibiotic resistance is even a problem, or are
not even aware of it at all.
Application to Research: This can help with my research on the side of awareness and making
sure that people know what is going on. It helps me see how little people know about antibiotic
resistance, and how much of a serious issue it has become. It is huge, and people should know
about it.
CDC: 1 in 3 Antibiotic Prescriptions Unnecessary. (2016, May 3). CDC Press Release.
Retrieved from SIRS Knowledge Source database.

Summary: According to a study published in the Journal of the American Medical Association
released by the CDC and other medical organizations and experts, showed that one-third of all
antibiotic prescriptions in the US were unnecessary. The study analysed doctor's offices and the
like, and found that most of these unnecessary prescriptions were for respiratory conditions
caused by viruses. Antibiotics are lifesaving drugs, and if we continue down the road of
inappropriate use well lose the most powerful too l we have to fight life-threatening infections,
said CDC Director Tom Frieden, M.D., M.P.H. In March of 2015, the White House released a
plan to combat antibiotic resistance (CARB), it says that the goal is to cut all unnecessary
prescriptions by half by 2020. That means that to meet the CARB goal, all unnecessary
prescriptions need to be cut to fifteen percent from thirty percent by 2020. To accomplish this,
the CDC plans to improve the training and education of health care professionals, create new
initiatives of when and how to issue prescriptions effectively setting guidelines, and create a
dialogue between the patient and the doctor of which antibiotics work, infections, medical
history, etc. Congress has acknowledged the importance of fighting antibiotic resistance, and has
given the CDC $160 million during fiscal 2016 to create initiatives to fight it. With the money,
the CDC plans to accelerate outbreak prevention and detection in every state, enhance tracking
of antibiotic use, support innovative research, inform providers and the general public, and
improve antibiotic use by supporting programs at the local level.
Application to Research: This is a great find because it shows what the CDC has produced in
terms of data, and has shown me what the government in general is doing. It also lead me to the
63-page CARB pdf document from the White House, which I plan to incorporate later. I also
found a very cool infographic as well!
Chang, L. (2016, December 17). We might be closer than ever to using CRISPR to cure diseases.
Retrieved December 31, 2016, from Digital Trends website:
http://www.digitaltrends.com/health-fitness/crispr-improvement/

Summary: This website article details how CRISPR gene editing can be used to help cure
disease, which will be a huge leap for the scientific community. Scientists at Western University
have discovered that by adding a new engineered enzyme, the gene editing tool of CRISPR has
improved, making it more specific and efficient. CRISPR has already proven to be very helpful
against diseases like cystic fibrosis and leukemia. But, cutting the gene is not enough to cure a
disease on its own. When CRISPR cuts a gene, the gene usually grows back, as when it cuts the
gene of a specific pathogen. This leads to an endless and futile cycle. But with this new
discovery, it enables CRISPR to keep that gene from growing back, making permanent and
lasting changes to that specific gene. The new enzyme is called TevCas9, which cuts the DNA in
two places, as compared to one. With the gene cut in two places, it makes it much more difficult
for it to repair itself, creating lasting changes in the DNA. Now when pathogens are altered by
CRISPR, they will stay as they are, meaning that our ability now to help the human race by
editing genes has become very useful. This has serious benefits, as it will be able to tackle and
solve some of the biggest health problems that we face today, and could potentially be our saving
grace.
Application to Research: This article applies to the research as it details the most legitimate
weapon that we have against the coming threat we have against antibiotic resistance, and the
progress that is being done to make it better.

Christensen, J. (2015, November 15). Pediatricians want farmers to use fewer antibiotics. CNN.
Retrieved from SIRS Knowledge Source database.

Summary: This database article entails how a major US health organization is releasing the
statement that less antibiotics need to be used in our food supply. The American Academy of
Pediatrics is calling it a significant public health threat, and is calling for the end of
irresponsible use of antibiotics in our food supply. This comes after reports of resistance in
bacteria to antibiotics, creating apocalyptic visions of the future where even a scrape could be
fatal. They say that the cause of major resistance in bacteria is the overuse and misuse of
antibiotics. Physicians say that they are also to be at blame, but they are working to fix things on
their side. They are saying that they need to be sure that government agencies can also help in
ridding the system of the overuse of antibiotics. In 2012, 80% of all antimicrobial agents sold
were used in animals, and 60% are the same antibiotics that are used in humans, posing a huge
problem of antimicrobial resistance. Just as vaccines are practice grounds for our body to get
ready to fight bacteria. Our antibiotics are a practice ground for bacteria to be able to learn to
resist antibiotics. If they get too good at resistance, then doctors will no longer be able to use
these antibiotics to stop bacterial infections and there will be fatal consequences. The argument
for antibiotics in livestock is that livestock will not be able to survive without it, and the meat
will be corrupted with microbial agents. But the agricultural industry keeps these animals in very
cramped, tight, and unhygienic conditions, making it necessary for the use of antibiotics.
Because after all, your burger has to cost $1. According to the article, some farmers administer
antibiotics only for precaution, or to help the animals grow, not solely because they are sick.
Seeing this, the use of antibiotics can be greatly curbed and theoretically be completely stopped
if proper farming practice were put into place. A professional in the field by the name of Paulson
advises to only buy meat that is antibiotic free, and let the market take care of itself.
Application to Research: This article is very useful because it keeps me up to date on the current
events of my topic, and what major health organizations have to say about it. It is very useful
because it also details farming practices used by farmers, and it shows that most antibiotic
resistance is not from human use, but from the use of it in animals. This would explain how a
resistance to colistin has cropped up in China, where this drug was being administered in pigs.
This piece will find a great place in my paper.

Clokie, M. R., Millard, A. D., Letarov, A. V., & Heaphy, S. (2011). Phages in nature. PMC, 1(1),
31-45. http://dx.doi.org/10.4161/bact.1.1.14942

Summary: This scholarly journal article details bacteriophages in nature, their modern history,
how they work, etc. It also provides three case studies through which to see phages doing their
job in nature. The article describes a bacteriophage as a virus that infects a bacterium.
Bacteriophages are the most abundant organisms in the biosphere, and are used by scientists to
do horizontal gene transfer and study the evolution of bacteria, as sources of diagnostic and
genetic tools and as novel therapeutic agents. When early Earth was first formed, two forms of
life first arose that dueled with each other and helped to make early Earth a friendlier place by
creating the atmosphere, etc. These early forms of life were viruses and bacteria, and have been
here for countless millions of years. Bacteriophages were first discovered in 1915 by William
Twort, and in 1917 by Felix d'Herelle realized that they had the potential to kill bacteria.
Bacteriophages, like any organism, has specific life cycles. The two life cycles of natural
bacteriophages are the lytic, lysogenic life cycles. In the lytic life cycle, phages infect and rapidly
kill their infected host cells, this changes bacterial population dynamics, leading to bacterial
evolution via generalized transduction.. This explains how bacteriophages have been the
driving forces of bacterial evolutions throughout the history of our planet. The lysogenic life
cycle is when phages integrate into their hosts genome, or exist as plasmids within their hosts
cell. This form of life cycle can be stable for thousands of years. After infecting a bacteria,
phages can undergo a latency period, in which they lie dormant in the cell. This can be observed
with the animal herpes virus, in which it lies dormant and stops producing virions for a certain
time period. Phages are extremely abundant, the most abundant life form in the biosphere. But a
mechanism is needed to measure their diversity, and therefore phage abundance, and viral
metagenomics is used to do this. Viral metagenomics where the total viral component from a
particular environment is collected and sequenced.. But this proves to sometimes be unreliable
and not worth the effort. But phages are definitely worth the effort in doing future research on.
Application to Research: This article is very helpful in detailing the occurrence of bacteriophages
in the natural world, and how they function. This article would serve as a foundation for the
proposal of bacteriophages as a legitimate option for therapeutic use.
Colarusso, L. (2016, February 19). To Fight Superbugs, Scientists Are Turning Toward
Antibodies; With antibiotics showing diminishing efficacy, it might be time to admit it:
Bacteria have won the arms race. Newsweek. Retrieved from Gale Power Search
database. (Accession No. GALE|A443025968)
Summary: In this database article, it says that last November, a strain of bacteria was
discovered in China that was resistant to the most potent antibiotic, Colistin. This is thought to be
due to years and years of dumping drugs and antibiotics into the feed of the animals, pigs
especially. The Chinese researchers had also discovered the existence of a bacterial gene known
as mcr-1. This gene creates resistance to antibiotics, and can be easily spread from bacteria to
bacteria, even across special lines, to create resistance to bacteria. Dr. Yohe Doi is an expert on
antimicrobial resistance who assisted researches in China, and has been worried about the rise of
antibiotic resistance due to the overuse of antibiotics in agriculture and medicine for years.
"What's really different this time," says Doi, "is how quickly and easily this gene can transmit
from one type of E. coli to another." For much of the 20th century, humans have relied mainly on
antibiotics, disregarding other treatments such as boosting immune response, etc. "The bottom
line is that the bacteria now develop resistance to anti-infectious agents faster than we can
develop the anti-infectious agents," says Dr. Jean-Laurent Casanova, a professor at Rockefeller
University. Scientists are now focusing on harnessing the human immune system to fight these
antibiotic resistant bacteria. Namely, the scientists are trying to use antibodies to combat the
bacteria. By using antibodies, it will become virtually impossible for the bacteria to evolve and
mutate, as the antibodies help white blood cells and trigger complement systems. Antibiotics
only kill the bug, but antibodies also help clean the body of the toxins produced by the bacteria.
Mcr-1 gene is suggesting the need for immunotherapy.
Application to Research: This article mentions the mcr-1 gene, gives an overview of the topic of
antibiotic resistance, and is full of information on the topic. It also presents a new idea of
fighting it called immunotherapy, and provides support and quotations from some of the biggest
firms and institutions.

Crabtree, J. (2016, December 28). Antibiotic resistance: The story that wont go
away. Retrieved December 31, 2016, from CNBC website: http://www.cnbc.com/
2016/12/28/antibiotic-resistance-the-story-that-wont-go-away.html
Summary: This website article details antibiotic resistance and the issue that it poses to the
modern world. Antibiotic resistant bacteria have and are becoming a constantly more feared
phenomenon to the modern medical world. As the World Health Organization said in a 2014
report, it "threatens the achievements of modern medicine." The Review on Antimicrobial
Resistance commissioned by the U.K. states that "by 2050, 10 million lives a year and a
cumulative $100 trillion of economic output are at risk due to the rise of drug resistant
infections." Last September, the United Nations issued a declaration that it would fight antibiotic
resistance, which was only the fourth time that a health risk was treated with such gravity at a
United Nations meeting. This puts antibiotic resistance on par with HIV and ebola. Innovators
and scientists are finding new ways to attack this problem, such as using smart medical dressings
and the like. According to other scientists, new and creative methods are being delved into and
expanded upon such as the use of predatory bacteria, etc. It has become a major issue, and many
different facets of industry are beginning to get involved in it. For example, the financial industry
is getting involved by giving funds, and drug companies are creating new topical treatments, etc.
Many solutions exist, but it will take research in a new field to be able to find any solutions.
Application to Research: This help my research by padding the knowledge that I already know of
this issue, and it lead to some runoff research. Such as the use of smart medical dressings and
predatory bacteria.

D. Nelson, personal communication, Jan. 5, 2017

Summary: During this interview, the subjects of concern regarding antibiotic resistance,
bacteriophages, CRISPR gene editing, possible solutions for antibiotic resistance, etc. It was
discussed that antibiotics are sought after that have a broader range due to profitability,
versatility, and convenience. These broad spectrum antibiotics are are given in excess, and are
thus misused leading to bacterial resistance. Solutions were also discussed, such as
bacteriophages and proper diagnostic and procedural diagnostics. Bacteriophages are small
viruses that infect the bacterial cell and bust its cell walls, killing it. Bacteriophages used to be
sold by a major US drug company in Eli Lilly before the antibiotic era. They were abandoned,
and are now being looked to to provide the solution to antibiotic resistance. Bacteriophages also
need very accurate diagnostics, because they are very specific in which bacteria they attack.
Bacteriophages use needs to be partnered with better diagnostics, but bacteriophages might only
be half of the solution. CRISPR gene editing is also a large part of the possible solution, as it
could change the DNA of bacteria as we know it. But, the CRISPR DNA needs to be transported
into the bacteria somehow, and bacteriophages can fill that role of transferring the CRISPR DNA
into the bacteria.
Application to Research: This interview provides a source from a professional on the topic, of
how solutions to the antibiotic resistance problem can be solved from historical, scientific, and
economical perspectives.

Healy, M. (2016, July 12). Deadly Medical Disaster Slowly Unfolds. Los Angeles Times.
Retrieved from SIRS Knowledge Source database.
Summary: In the above database article by the Los Angeles Times, it details that scientists
working in the Walter Reed Army Institute of Research have identified a strain of E.coli from a
49-year-old woman in Pennsylvania containing the mcr-1 gene. This gene makes the bacteria
impervious to even the the toughest of antibiotics, colistin. The article entails that the gene is
present on a plasmid, which is a small loop of DNA that can travel and attach to other organisms,
making them antibiotic resistant as well. Colistin was the strongest antibiotic scientists had, and
even that doesnt work anymore. Antibiotics are losing their overall effectiveness, the golden age
of antibiotics is coming to a close. As this happens, common ailments will begin to become fatal,
and people will die. The first antibiotic, penicillin, was discovered in 1928 by Alexander
Fleming. Since then, over 100 antibiotic compounds have been introduced. Scientists have been
finding that as they administer these drugs, bacteria begin to develop a resistance to them. This
follows Charles Darwins theory of natural selection. This problem has only been exacerbated by
the administering of antibiotics to livestock, providing bacteria more opportunities to develop
resistance to these antibiotics. Millions of people are infected by these superbugs per year, and
thousands of them die per year. Colistin is toxic to the human kidney, but is now becoming the
last hope for many people, but even colistin is being overwhelmed now. The complete
obsolecense of antibiotics wont happen soon, but this is a big warning to prepare for the fall of
antibiotics and to discover new ways to deal with these pathogens.
Application to Research: This article is very well written and contains lots of new and very
useful information that I could use. It is very reliable, and has lead me on to research more topics
in the scope of my question like colistin. This article will prove to be a very useful source.

Kline, K. E. (2016, September 16). Investigation of First Identified mcr-1 Gene in an Isolate
from a U.S. Patient Pennsylvania, 2016. Retrieved October 23, 2016, from CDC.gov
Summary: This article details the emergence of a gene called mcr-1. This gene is a gene that is
found on plasmids. Plasmids are small loops of DNA that can pass easily from one bacteria to
the other. They can pass from strain to strain, and even from bacterial species to species. This
means that the gene for antibiotic resistance can spread very easily, and that will pose a huge
problem for us going forward. The article says that there has been a discovery of the mcr-1 gene
in a Pennsylvania woman who was admitted to a hospital for a urinary tract infection. She was
found to have a strain of E. coli that was resistant to a last-stand antibiotic known as colistin.
This article details who was in high risk of contracting this bacteria, and who had a low risk of it.
Screening was done on all of these people, and none were found to have contracted the gene, or
any harmful bacteria that had the gene. These findings suggest that the risk for transmission
from a colonized patient to otherwise healthy persons, including persons with substantial
exposure to the patient, might be relatively low. No antibiotics were given to the woman who
had originally contracted the bacteria, and it went away months later after a routine swabbing
found that she was negative for the bacteria. The report then concludes that any finding of said
bacteria be immediately reported and investigated, and all necessary precautions be taken as soon
as possible.
Application to Research: This article show a real world institution and their report on the mcr-1
gene and related bacterium. It is a peek into the real world urgency of staying on top of
colistin resistant bacteria.
Kurzgesagt- In a Nutshell (Producer). (2016). Genetic Engineering Will Change Everything
Forever CRISPR [Video file]. Retrieved from https://www.youtube.com/watch ?v=jAh/
jPd4uNFY

Summary: This youtube video details how our future could be changed and most likely will be
affected by a gene editing process known as CRISPR. It first describes that humans have been
using genetic modification for thousands of years by selectively breeding plants and animals. It
runs through a brief history of human tinkering with genetic code. When humans discovered
DNA, everything changed. Scientists realized that they could now alter any being alive by
simply altering the genetic code. But until recently, gene editing was expensive, complicated,
and took a long time to do. This changed with the introduction of CRISPR (Clustered Regularly
Interspaced Short Palindromic Repeats). CRISPR reduced the price of genetic engineering by
99%, it only takes weeks to conduct experiments, and anyone with labs can do it. The video then
goes on to explain how CRISPR works by explaining the long held rivalry between bacteria and
viruses. It says that bacteriophages are viruses that hunt bacteria. They destroy bacteria by
inserting their own genetic code into bacteria, and taking them over to use as factories. Bacteria
mostly fail in resisting phage attacks, but if they do survive, they can activate their most
powerful anti-virus weapon. They save a part of the code of the virus in a DNA archive called
CRISPR. When the virus attacks again, the bacteria makes an RNA copy from the DNA. It then
arms a protein with this RNA copy, a protein called CAS9. The protein scans the bacteria, and
compares it to every bit of DNA from the archive. When it finds a perfect match, it cuts out the
viral DNA, making it useless; therefore protecting the bacteria from attack. It is extremely
precise and accurate, like a DNA surgeon. When scientists found that the CRISPR system is
programmable, the revolution started. One just gives it the DNA for desired modification, and
lets CRISPR do the work. It is remarkable because it could be the cure for all diseases, stop
aging, create designer babies, etc. But there is still a long way to go, and many roadblocks in the
way such as ethical and moral concerns, etc.
Application to Research: This user-friendly video made CRISPR easy to understand, and it
thoroughly explained the huge significance of CRISPR. Once we have taken full reign of it, we
will be able to create a world without disease, resulting in antibiotic resistance becoming simply
a laughing matter.

Kurzgesagt, I. A. N. (2016, March 16). The antibiotic apocalypse explained [Video file].
Retrieved from https://www.youtube.com/watch?v=xZbcwi7SfZE
Summary: In this video, antibiotic resistance and the workings of bacteria are explained. It goes
in depth about how antibiotics work, and how bacteria are coming up with defense mechanisms
for them. It states that bacteria are among the oldest life forms on the planet, so they would have
definitely come up with evolutionary tricks by now. Millions used to die from bacterial
infections, but then antibiotics were invented, as well as vaccines. Antibiotics kill most harmful
bacteria, leaving small amounts for our immune system to deal with. It describes the methods of
the antibiotic to be shutting down the production of new DNA or cellular matter, tearing apart
the membrane of the bacteria, slowing metabolism and growth, etc. Some bacterial defenses are
creating molecules that intercept antibiotic particles and render them harmless, making cellular
pumps that get rid of the antibiotic in the bacteria, etc. Immune system deals with these rogue
resistors, but the chance of spreading immunity is very high. Immunity can be spread through
plasmids. Plasmids are small DNA loops containing the gene for resistance, and can be passed
from bacterium to bacterium by simply touching. It can be spread like wildfire and can even be
spread between bacterial species like this. Bacteria can also use transformation, harvesting useful
DNA from dead bacterium. Antibiotics are taken too freely and without care. They are not
seen as a miracle anymore, but only as a common everyday object. Antibiotics should only be
used as a last resort. Antibiotics are being used in our food supply as well, providing bacteria
with more practice to develop resistance. If humanity plays its cards right, superbugs might not
turn out to be very super after all.
Application to Research: This is extremely reliable information that is more varied and more in
depth than any other source I have seen so far. It will be greatly needed in my paper, like
explaining how antibiotics and resistance work, etc.

Loc-Carillo, C., & Abedon, S. T. (2011). Pros and cons of phage therapy. PMC, 1(2), 111-114.
https://dx.doi.org/10.4161%2Fbact.1.2.14590

Summary: This scholarly journal article details the pros and cons of phage therapy. Phage
therapy is the use of bacteriophages that exist in nature, engineering them to attack nuisance
bacteria. Bacteriophages are naturally predatory of bacteria, but phage therapy is different
because in nature, bacteriophages invade bacteria to insert their DNA into the bacteria and take it
over, producing more viruses. In phage therapy, the mechanism of the bacteriophage that is used
to penetrate the cell wall of the bacteria is engineered to take out major chunks of the cell wall,
eventually killing the bacteria. Now on to the pros and cons of phage therapy. The major pros are
that phages are bactericidal agents, they can auto dose (Phages are capable of increasing their
numbers when needed, and automatically setting the desired dosage.), they have low inherent
toxicity, there is minimal disruption of normal flora (There is a minimal chance that phages will
attack health-protecting normal flora bacteria.), they have a narrower potential for reducing
resistance (There is limited ways in which bacteria can develop resistance, and even using those
methods will overall negatively harm the bacteria.), there is lack of cross-resistance with
antibiotics, phages are easily discovered and abundant, they are versatile (Can be used in creams,
liquids, etc.), they have the ability to clear biofilms, they have single dose potential, phages can
transfer to other people or animals curing them as well, they utilise single-hit kinetics (Only one
phage is needed to kill one bacterium.), they have low environmental impact, they are natural
products, they are relatively cheap, and they are not antibiotics. Phages are not completely the
golden bullet, as there are some minor downsides. Some major cons of phage therapy are that not
all phages make for good therapeutics, the problem of narrow host range, they trigger immune
responses (Many other pharmaceuticals that have already been approved have this quality.), and
the biggest one of all is the Western medical establishments unfamiliarity with the use of phages
as therapeutic drugs.
Application to Research: This article is extremely useful in highlighting the real-world
applications of bacteriophages, and shows the legitimacy of phage therapy.

MacDonald, F. (2017, January 21). Scientists just announced our best shot at ending antibiotic
resistance to date. Retrieved January 21, 2017, from Science Alert website:
 http://www.sciencealert.com/scientists-just-announced-our-best-shot-at-ending-antibiotic
-resistance-to-date

Summary: This website article details a new scientific discovery, a molecule that reverses
antibiotic resistance. This is very promising, and could not have come at a better time, because
the United Nations has declared it a fundamental issue, as 300 million people are projected to die
of it by 2050. Many bacterial strains are developing resistance at an alarming rate, and the more
scientists look for new antibiotics, the more they realize that they cannot find any new
antibiotics. One way that bacteria develop resistance is through an enzyme known as NDM-1.
This enzyme makes bacteria resistant to carbapenems, or last-resort drugs. Scientists have
created a new molecule that is a type of PPMO (peptide-conjugated phosphorodiamidate
morpholino oligomer) it disables NDM-1. This enzyme targets a resistance mechanism shared by
many different strains of bacteria. This PPMO is applied to bacteria, and then carbapenems are
used. The PPMO restores the susceptibility of antibiotics, and the carbapenems kill the bacteria.
Application to Research: This article shows a new type of solution in the avenue of biochemistry,
that can help tremendously in reversing and disabling antibiotic resistance genes.

Nelson, D. (2016). A bacteriophage endolysin that eliminates intracellular streptococci. eLife, 5.

http://dx.doi.org/10.7554/eLife.13152

Summary: This scholarly journal article by Dr. Daniel Nelson of the University of Maryland
details how endolysins or enzybiotics can help fight the battle against antibiotic resistant
bacteria. The experiment that was conducted revolved around the bacteria Streptococcus
pyogenes (Spy), and PlyC, a bacteriophage-encoded endolysin. A bacteriophage is a virus that
invades and multiplies inside a bacteria. For the bacteriophage to to invade the bacteria, it must
first create an opening in the cell wall of the bacteria to enter. It uses an enzyme to do this, and
Dr. Nelson and his team have harnessed an enzyme that the bacteriophage uses to enter the
bacteria. The PlyC enzyme lyses the cell wall of the bacteria upon contact. If enough of the cell
wall of the bacteria is lysed, the insides of the bacteria cannot be contained anymore, and the
bacterial insides spill out, killing the bacteria. As Dr. Nelson said, it is like steel girders in a
building, if you take out too many, the building collapses. The enzyme PlyC uses cell
penetrating peptides to accomplish this. This is remarkable, as bacteria do not currently have a
genotypically defined or phenotypically defined trait to counter this. The same is true of bacteria,
and this a discovery that has the potential to turn the world of antibiotics in its head. The
engineering of the bacteriophage enzyme PlyC to accomplish this is truly a scientific work that
deserves more credit.
Application to Research: This is a remarkable discovery that has lead me to a host of other
scientific papers. It is amazing because this is a real and viable solution to the threat of antibiotic
resistance, and has the potential to save us all.
New Molecule Circumvents Antibiotic Resistance. (2017, January 19). Retrieved January 21,
2017, from Genetic Engineering and Biotechnology News website:
http://www.genengnews.com/gen-news-highlights/new-molecule-circumvents-antibiotic-
resistance/81253741

Summary: This website article details a new molecule discovered by scientists that reverses
antibiotic resistance. This new molecule was created by researchers at Oregon State University,
it destroys a bacterias ability to fight antibiotics. -lactamases are a type of enzyme used by
many bacterial strains to fight antibiotics. This family of enzymes is also responsible for
multidrug resistance in in many bacterial strains. The new molecule that they have created is
called PPMO, and it acts to make antibiotic resistant pathogens more susceptible to antibiotics,
they are coupled with antibiotics that then kill those pathogens. The ability of this PPMO was
demonstrated in vitro. It has restored our ability to fight antibiotic resistant microbes again by
neutralizing their ability to resist antibiotics.
Application to Research: This article shows a new method of combatting antibiotic resistance, a
molecule that neutralize the bacterias ability to fight antibiotic resistance, adding a new
dimension to the the solutions.

Olena, A. (2016, December 8). Phages Carry Antibiotic Resistance Genes. Retrieved December
14, 2016, from The Scientist website: http://www.the-scientist.com/ ?article.view/ar/
ticleNo/47698/title/Phages-Carry-Antibiotic-Resistance-Genes/

Summary: This news article details a discovery in the field of antibiotic resistance. It details that
a special, experimental treatment option might not be what we thought it would end up to be.
Prior to this discovery, we were very hopeful in a treatment option known as bacteriophages or
phages. Bacteriophages are a naturally occurring specimen in nature, and the most abundant life
form in the biosphere. What they are are viruses that invade bacterial cells. We had developed a
strategy that we would be able to efficiently kill bacteria by using their ability to break cell walls
in cell lysis of the bacterial cell. It was a great idea because they are abundant, cheap, easy to
use, etc. But, according to a study that was published recently, bacteriophages might contain
antibiotic resistance genes. This might be a major roadblock in the institution of phages as a
viable treatment option in the Western medical establishment. If this study is followed up and
shown to be correct and produces the same results, then we could see the disappearance of
phages as a treatment option all together. The antibiotic resistance genes might cause even more
resistance to antibiotics, worsening our problem. Phages are a very useful and amazing
discovery, but they might only be our short-term solution as we work toward a more viable one.
Application to Research: This article and my findings apply to my research by showing another
aspect of phage treatment for bacterial infections that was not previously known.

L. (2016, July 04). Will Antibiotic-Resistant Superbugs Kill Us All? - YouTube. Retrieved
September 15, 2016, from https://www.youtube.com/watch?v=ByEjq7L5Ue4
Summary: In this video, the creator of the video explains the topic of antibiotic resistant
superbugs, and how many there are, and how dangerous they are. He says that bacteria that are
becoming resistant to antibiotics are called superbugs. Every year, 2,000,000 people get sick
from superbug, and 23,000 die from it in the US alone. All bacteria can turn into superbugs,
highlighting the importance of finding a solution to this problem, as bacteria are literally
everywhere. They are even inside of us. A great example is the C. Diff bacteria, they live in our
intestines. The good bacteria in their keep us from getting sick, but when you take antibiotics,
you kill the good bacteria. With no good bacteria, the C Diff. takes over, and the use of
antibiotics only makes it worse. Antibiotics would help the C. Diff become more resistant, and
kill off more of the good bacteria in our intestines, leading to have some very bad repercussions,
from life threatening diarrhea to having to get your intestines removed. Also, a bacteria called
CRE is resistant to almost all known antibiotics. It is so severe, it warranted a terrifying comment
from the CDC, One of the most urgent public health threats that we currently have. Bacteria
are evolving, and mutations in genomes can cause resistance to antibiotics. Another explanation
is the concept of plasmids. Plasmids are parts of bacterial DNA, and they are the ones
responsible for passing on the gene of antibacterial resistance. What is more terrifying is that
they can pass from different bacterial species to the next, making it very difficult for us to do
anything about it. The health industry needs to do something, and they need to do it fast.
Application to Research: I was so pleased to have found this source by a YouTuber with such a
huge following. His video was very informative and very easy to understand, it was even
entertaining to watch. It taught me so much, and suggested information for me to look into later
for later reading reports. I am extremely happy to have found this source!

Now - HowStuffWorks. (2016, September 14). Retrieved September 15, 2016, from
http://now.howstuffworks.com/2016/09/14/watch-bacteria-mutate-drugresistant-superbugs
Summary: In the above website, Harvard Medical School has created a short video and there is
an article underneath relating to the topic of antibiotic resistant superbugs. The scientists set up a
2x4 rectangular petri dish which they separated into nine segments. The farthest out were given
one part of antibiotics, and it kept increasing by 10x on each side until it reached a tremendously
huge amount by the time it got to the very middle, 1000x the concentration of the segments
farthest out. The very center segment was also the segment that had 1000x the amount of
antibiotics that E. coli can regularly survive. At the beginning, the bacteria (E. coli) were very
plentiful on each side, and smaller mutations cropped up along the way as it made its way to the
center. As it made its way to the center, it began developing an extraordinary resistance to the
antibiotics, and against all odds, kept moving towards the center. Once the bacteria hit a part that
was deadly to it, it stopped, but not for long. Soon after, its genes mutated and it kept crossing
those barriers, moving on to the next segment of the petri dish. Slowly by slowly, step by step,
the bacteria made it across to the center of the board, their genes constantly mutating, constantly
becoming more and more resistant. This experiment illustrates that if bacteria is given time to
mutate and evolve, it can develop a resistance to antibiotics that are thousands or more times
what scientists believed it was capable of withstanding. This experiment shows that we have to
be more careful in the way that we use our antibiotics, as it could and will lead to the evolution
of bacteria into unstoppable superbugs. Ten days and a whole bunch of antibiotics. was all it
needed.
Application to Research: I was stumbling along the internet until I found this, published by a
credible site reporting on the findings of a credible institution. I hit the jackpot! It is a very brief
experiment and article, but there is a massive wealth of information that can help me in this
source, and I am happy that I have found it.
Plasmids 101: Plasmids 101: A Desktop Resource (2nd ed., Vol. 1) (Addgene, Comp.). (2015).
Retrieved from http://www.addgene.org
Summary: I used pages 7-14 in this e-book, these pages detail what a plasmid is, and many other
aspects of a plasmid. It also runs through some aspects of antibiotic resistance. It says that a
plasmid is a small, circular piece of DNA found in bacterial cells. In 1952, Joshua Lederberg
came up with the term plasmid, what he meant by plasmid was a generic term for any
extrachromosomal hereditary determinant. Plasmids can be found naturally in bacteria, archaea,
eukaryotes, yeast, plants, etc. All plasmids in someway, shape, or form are a perk to their host.
Some provide antibiotic resistance. All plasmids contain an origin of replication. When an
antibiotic directly kills bacteria, it is called bactericidal, when it slows growth or causes cell
division, that is called bacteriostatic. The origin of replication is where DNA replication begins,
as the plasmid replicates to survive within the bacteria. Plasmids rely on host mechanics to
replicate. Antibiotic resistance genes are used to transform plasmids into E.coli, as it makes it
more efficient. Also, antibiotic resistance genes are used to make the plasmid more advantageous
to the bacteria to have the plasmid inside of it and to use resources to replicate and maintain it.
Plasmids can be easily passed from one bacteria to another, even across special lines. This makes
it easier for the antibiotic resistance gene to pass, making it worse for us.
Application to Research: This ebook is very useful in explaining in-depth the uses of plasmids,
the history of plasmids, and everything associated with plasmids. A lot can be learned from this
source.

Rowlands, L. (2016, May 24). Economic Interests Harming Global Health: WHO Chief. Inter
Press Service News Agency. Retrieved from SIRS Knowledge Source database.
Summary: This article starts with a statement from Margaret Chan, the Director-General of the
World Health Organization. She warned health professionals that putting economic interests over
health concerns could lead to major disasters. She not only points to antibiotic resistance as an
effect of economic prioritisation over public health, but also points to climate change, and
lifestyle disease, caused by poor diet and exercise. "These are not natural disasters. They are
man-made disasters created by policies that place economic interests above concerns about the
well-being of human lives and the planet that sustains them," she said. The article says that
antibiotic resistance has the world most concerned, Chan said that it threatens to throw the world
back into the health dark ages. Antibiotics are beginning to fail more and more frequently,
infectious diseases are becoming more and more volatile, and Chan says that the global health
system was not as prepared as it should be. She pointed to Ebola, Zika, Dengue, Yellow Fever,
and Chikungunya. She points the rise of mosquito-borne illnesses on massive policy failure in
the 70s. The overuse and the misuse of antibiotics has created so many opportunities for the
microbial world to arm themselves against us, just as natural selection dictates. Major food
supply companies are giving massive amounts of antibiotics to their animals because of the
living conditions they are in and for profit, and claim that antibiotics have no effect of the
development of resistance. The drive for money will drive the world into an age where
antibiotics will eventually not work anymore. As Chan says, "changes in the way humanity
inhabits the planet (that) have given the volatile microbial world multiple new opportunities to
exploit."
Application to Research: This is a very useful tool because it is an account from possibly one of
the most respected health officials in the world. This can be an account of what the medical
world is doing to acknowledge and begin to fight antibiotic resistance.

Schmieder, R., & Edwards, R. (n.d.). Insights into Antibiotic Resistance Through
Metagenomic Approaches. Medscape. http://dx.doi.org/2012;7(1):73-89.
Schmieder, R., & Edwards, R. (n.d.). Insights into Antibiotic Resistance Through Metagenomic

Approaches. Medscape. http://dx.doi.org/2012;7(1):73-89.

Summary: In this scholarly journal, it discusses recent findings and future challenges in the
study of antibiotic resistance through metagenomic approaches. Bacteria use many different
methods to resist antibiotics, and some of them are the inactivation or modification of the
antibiotic, an alteration in the target site of the antibiotic that reduces its binding capacity, the
modification of metabolic pathways to circumvent the antibiotic effect, and the reduced
intracellular antibiotic accumulation by decreasing permeability and/or increasing active efflux
of the antibiotic. When a bacteria develops resistance to antibiotics by mutating existing genes,
it is called vertical evolution. When it develops antibiotic resistance by acquiring genes or
plasmids from other bacteria or other species, it is called horizontal gene transfer. Phages and
transposons, as well as plasmids, help with horizontal gene transfer.
Application to Research: This source is very useful, as it goes in-depth about all of the aspects of
antibiotic resistance. It also provides new ideas for research, such as the use of transposons and
phages in horizontal gene transfer.
SciShow (Producer). (2016). CRISPR: A Gene-Editing Superpower [Video file]. Retrieved from
https://www.youtube.com/watch?v=UfA_jAKV29g

Summary: This youtube video details the gene editing tool/process known as CRISPR and its
significance. The video says that CRISPR is an extremely efficient gene editing process that
allows them to edit genes like never before. But, being able to change the genome of any
organism at will raises ethical concerns. The way that CRISPR, or CRISPR-CAS9 works is that
they were originally described as a form of immune system in in archaea. When the bacteria is
attacked by a virus and survives, it stores part of the viral DNA in what is known as a CRISPR
locus. It then creates RNA copies of the original stored viral DNA, and sends it to a protein
known as CAS9. CAS9 is a nuclease protein, it is very precise and cuts wherever the RNA tells it
to. When the virus comes again, the RNA tells CAS9 to cut up the viral DNA and destroy it.
CRISPR can be used by simply giving the CAS9 protein an RNA strand, and that RNA strand
dictates the changes and how to make a new 3D DNA strand. CAS9 can also be used as a light
switch to turn the gene on and off. It can be used across a multitude of applications from
genetically predisposed diseases to stopping aging, and anything imaginable. But there are some
obstacles, CAS9 may sometimes cut at the wrong places, add new pieces of DNA, and/or
completely delete pieces of DNA. CRISPR is already being used in creating a form of gene
therapy for patients to cure cancer, etc, But if CRISPR makes a mistake in editing DNA, it could
be disastrous. Scientists are currently working to combine the processes of CRISPR with the
concept of immunotherapy. The trials take a patients immune cells, and use CRISPR to give the
immune cells a boost, then they are put back into the patients to set about the healing process.
Scientists can also use CRISPR to alter mosquitos to make them less prone to transferring
disease, through a mechanism called a gene drive. This would change the genes of an entire
insect population through multiple generations regardless of natural selection. They can also
change human embryos, which raises ethical concerns, but regardless, CRISPR has broadened
the scientific field and the health field to immense proportions. It used to be that the sky was the
limit, but now there is nothing that we cannot accomplish.
Application to Research: This video was very useful and helpful in breaking down how CRISPR
works, and how we can use it in the future, It can be very useful in every endeavor we pursue,
but specifically it will be extremely helpful in combatting antibiotic resistance.

Scutti, S. (2016, July 12). Second U.S. patient had antibiotic-resistant superbug infection.
Retrieved September 21, 2016, from CNN website:
http://www.cnn.com/2016/07/12/health/superbug-second-us-patient/
Summary: This article tells about how a group of scientists have identified a superbug in a
Pennsylvania woman, and how another group of scientists working for JMI laboratories have
identified a gene called mcr-1. This gene gives bacteria the ability to stand up to the drug
colistin, the most powerful antibiotic that we have. It also says that the scientists are concerned
because the gene is located on a piece of DNA that can move from bacteria to bacteria,
transferring the resistance gene to different species. "The fear is that it will transfer to bacteria
that are already resistant to most other antibiotics," explained Patrick McGann, chief of
molecular research and diagnostics at Walter Reed Army Institute of Research. If what McGann
has stated concerns for above really does happen, then we will be in a world of trouble.The
previously stated combination would create a bacteria so powerful that it will be resistant to all
antibiotics of the modern day, creating the ultimate unstoppable superbug. The frequency of the
mcr-1 gene in the 21,000 strains analyzed was only 2%, so the frequency was not enough to
conclude that the gene is really taking off. Also, scientists were already aware of this genes
existence in other parts of the world. It is not an imminent threat, but is a clear warning that it
will soon very well become an imminent threat. If nothing is done about it, then more people will
die of superbugs than cancer by 2050, and already 700,000 die per year of these superbugs. As
resistance builds, common wounds will begin to become fatal. Dr. James Kirby of Harvard
suggests that we develop a multi-pronged approach to dealing with the issue from the animals to
people, etc. ahead of when it becomes a disaster.
Application to Research: This article is a very good article with very good opinions from high
ranking professionals in the field. It is a news article with up to date news about the current
affairs of the issue. It seems very reliable, and will prove to be a very good source.

Strom, S. (2016, August 2). Major Poultry Producer Defends Its Use of Antibiotics. The New
York Times. Retrieved from SIRS Knowledge Source database.
Summary: This article details how the poultry industry is reacting to criticism in its use of
antibiotics in raising and maintaining livestock. It says that they have lowered their use of
antibiotics in recent years due to criticisms from the public, government, and health officials
about the rise of antibiotic resistance in its meats. But the article says that a major poultry
producer, Sanderson Farms, is now defending its use of the antibiotics, and has created a
campaign to let people know. Sanderson Farms is the third-largest poultry producer in the United
States, and calls its competitors' efforts in the other direction a "marketing gimmick" aimed at
charging higher prices. This is said to heat up the battle over the use of antibiotics in food even
more, as many customers, special interest groups, and corporations like Mcdonalds or
Chick-fil-a have stated that they only want to buy meat from a source that does not use
antibiotics in the raising of their meat. Most major poultry producers, faced with the loss of
major corporate consumers, have been working to eliminate the use of antibiotics in their meat.
Tyson farms plans to completely cut use of antibiotics by September 2017, and Perdue has
already cut the administration of antibiotics to over half of its flock. But Sanderson Farms
continues to defend the use of antibiotics. The President and COO of Sanderson stated "There is
not any credible science that leads us to believe we're causing antibiotic resistance in humans,
But the CDC and other scientific research worldwide has affirmed that there is indeed a link
between the two. He also said that cutting antibiotics would also lead to higher mortality rates in
his flock, more barns, more electricity, more grain, more feed, etc. He is saying that this is
against sustainability, but he might just be trying to defend profits. He says that it is only to
keep them healthy, not to make them grow. FDA has been trying to regulate use of antibiotics.
All Sanderson chickens receive germaticin while still in the egg. Sanderson has conducted
surveys, finding that most people do not know the issue of antibiotic resistance and the use of it
in our meat supply.
Application to Research: This article is a very important finding because it shows how the
private industry is reacting to the calls for antibiotic free meat. It shows one of the solutions to
this problem, peoples opinions, etc. This is a very important finding and will lead me to further
research on the specifics of this article.
Warmflash, D. (2016, August 22). CRISPR genome editing could be game changer in war
against antibiotic resistance. Retrieved December 14, 2016, from Genetic Literacy
Project website: https://www.geneticliteracyproject.org/2016/08/22/crispr-genome-editi/
ng-game-changer-war-antibiotic-resistance/

Summary: This website article details the issue of antibiotic resistance, its history, and treatment
options and solutions that scientists are trying to find. In the article, it details two possible
treatment options that could solve the problem of antibiotic resistance for the modern world
moving forward. The two treatment options stated in the article were conventional methods, or
by attacking the bacteria in vivo. Conventional methods are simply continuing to administer
antibiotics, or creating new ones. Conventional methods are out of the question, because that is
what has gotten us into this mess in the first place. They will only trigger further bacterial
evolution, and are not a viable option to fight antibiotic resistance. The second option is to use
bacteriophages, or attack the bacteria in vivo. The article describes the use of phages as using
them to infect and inject the bacterial cells with plasmids that kill the bacteria, acting as a trojan
horse of sorts. These phages would be administered through the blood stream, but there is as
much chance of them killing essential bacteria as harmful bacteria, and are not necessarily safe
enough to be used. The article suggests that none of these are the best options, but using CRISPR
gene editing is the best option. The idea of CRISPR-based approaches is to enact
sequence-specific antimicrobial activity, placing selective pressure against genes that are bad
rather than conserved bacterial targets, says MITs Timothy Lu, Professor of Biological and
Electrical Engineering. Scientists in Tel Aviv, Israel have also begun using CRISPR to edit
bacteria to have qualities that would make the edited bacteria go after bacteria that are resistant
to antibiotics, changing the dynamics of the population. This could prove to be a roadblock for
bacteria, and a viable option for us humans.
Application to Research: This article is very helpful in highlighting the main downside of
phages, they are uncontrollable in which bacteria they kill. It also provides a new option that can
be prove to be very useful, CRISPR.
Webber, M. A., & Piddock, L. J.V. (2003). The importance of efflux pumps in bacterial
antibiotic resistance. Journal of Antimicrobial Chemotherapy, 51(1), 9-11.
http://dx.doi.org/10.1093/jac/dkg050

Summary: This scholarly journal article goes in-depth into how a phenotypically defined trait of
antibiotic resistance helps the bacteria resist antibiotics. This trait is the efflux pump, a transport
protein, which is an extremely efficient way to get harmful things inside of the bacteria out.
Efflux means to move the material out, so efflux pumps pump harmful substrates out of the
bacteria. There are five major families of efflux transporter in bacteria: MF, MATE, RND, SMR,
and ABC. The ABC family uses ATP hydrolysis to efflux, but the others use proton motive
force. Regulatory genes are in charge of the efflux pumps, making sure that they do not
overexpress, or pump more than they have to. Because if the pumps pump more than they have
to, they also pump out essential nutrients, minerals, vitamins, etc. Plasmids can carry genetic
information for efflux pumps, but the bacteria already have that information in their
chromosome, so that they would have an intrinsic mechanism to defend themselves against
harmful substrates. If a pump is ever exposed to any substrate that is in its profile to efflux, it
develops a cross-resistance to any other substrate with the same profile of the pump. This could
lead to MDR (multiple drug resistance). Bacteria that have these pumps to resist antibiotics are
better suited to live in antibiotic saturated places, and develop mutations that change the target
sites of antibiotics. If the efflux pump is overexpressing, and the target areas of antibiotics are
altered, the beacteria would become extremely difficult to treat. The expression of these pumps is
most when the bacteria are stressed, e.g. growth in a nutrient poor-medium, growth to stationary
phase or osmotic shock. Research into efflux pump inhibitors has started, and since efflux
pumps have mostly the same structural homology, one inhibitor should be able to work across
multiple classes of pumps. The effluxability of drugs has to be kept in mind when developing
antibiotics in the future, as these phenotypically defined traits are very dangerous.
Application to Research: This journal article details efflux pumps in-depth, and is extremely
useful in understanding the efflux pump and what it signifies going forward.

Blzquez E, Rodrguez C, Rdenas J, Prez de Rozas A, Segals J, et al. (2017) Ultraviolet (UV-C)
inactivation of Enterococcus faecium, Salmonella choleraesuis and Salmonella typhimurium in porcine
plasma. PLOS ONE 12(4): e0175289. https://doi.org/10.1371/journal.pone.0175289