this is a review about evolution of antibiotic resistance. I tried to answer how bacteria acquire new genes to resist, how they choose, what are people doing to prevent this increasing resistance levels.

1. Evolution of Antibiotic Resistance
A Report
By Ahmet VARIS, BSc
Introduction
Antibiotics were investigated for saving lives from microbial diseases. But as a result of
evolution they have to be fit to nature to stay alive. So resistance genes started to be acquired by
bacteria which have not resistant to antibiotics. Researches show that these resistance can be
caused from horizontal gene transfer or some spontaneous mutations. Nowadays databases and
artificial evolution used for estimation for future of evolution of antibiotic resistance.
How Resistance Evolution Started
The world is evolving every moment. The evolutions may result of natural effects or artificial
effects. Antibiotics which are using as drug, are a part of artificial evolution. First antibiotic had
been discovered, just before a few years than first event about antibiotic resistance (4). In 1928
penicillin was discovered by Alexander Flemings. But at 1940 which after years from penicillin
published and started to be used by as pharmaceutical drug, penicillinase was discovered by the
members of penicillin team (9). In 1994 an antibiotic, called streptomycin, used to treat
tuberculosis. But the evolution has come to Mycobacterium tuberculosis. Mutant version of this
bacteria have resistance to therapeutic concentration of streptomycin (8).
Question is, where these bacteria get resistant genes. The most important part of this evolution
arisen from Horizontal Gene Transfer (HGT is a process that the transfer of genetic material
without reproduction). Origin of antibiotic resistance which is result of HGT may come from
non-pathogenic bacteria or some antibiotics are produced from bacteria, it is understood that the
bacteria have resistance to that antibiotics (5). These type of resistance actually had been used by
bacteria, before discovery of antibiotics. So resistant genes exist in nature.

2. Figure 1: How HGT work. Transformation: free DNA parts taken by bacteria and these make
bacterial plasmid. One of these free parts can have resistance gene. Transduction: A bacterial
virus bind to bacteria and give its genetic material which consist resistance genes and it turns to
plasmid for bacteria. Conjugation: A bacterium give another one its plasmid which already have
resistance genes.
“This situation implies the existence of three different landscapes important in the
evolution of resistance” (The role of natural environments in the evolution of resistance traits in
pathogenic bacteria, Jose L. Martinez, 2009);
First level is microbiosphere where all micro-organisms have interactions between each other.
Nature has its own antibiotics so micro-organism try to be fit against these antibiotics with
interacting to others which have resistance gene. This communication may about their live-dead
decision. And also this level is starting point of whole evolution (5).Second level is
microbiosphere where touch to human. This may be soil, activated sludge, human gut, and oral
microbiomes etc. It is important to understand relation between human and environment to show
how human pathogens acquire antibiotic resistance genes (3). Third level is treated patient. At this
level commensalism is important. Antibiotics are designed as less harmful as do not hurt the
patient body. And mostly the organisms which is inside of patient have resistant that antibiotics.
So pathogens get resistance genes from bacteria which patients have.

3. Other way of getting resistance is spontaneous mutations. This is Darwinian evolution driven by
natural selection which is that wild types are killing by antibiotics and mutant ones live. The
mutant genes pass through the next generations with vertical gene transfer. The rate for this type
of mutations is 10-8
- 10-9
. For example at E.coli it is estimated that the streptomycin resistance
frequency is 10-9
while using high concentration of antibiotics (11).
Where Are We Now
“Consequently, we face the prospect of returning to a preantibiotic era, where an increasing
number of infections can no longer be treated effectively with our current arsenal of drugs”
(Moly K. Gibson et al. Improved annotation of antibiotic resistance determinants reveals
microbial resistomes cluster by ecology, 2014)
Every antibiotic changes the fitness of the nature for that affected ones by antibiotics. This is like
a loop. Firstly antibiotic given to nature, organisms which have r genes will live and increase
their number if they are threat for you, make another antibiotic for them and here we come to first
step.
There have been a lot of researches about evolution of antibiotic resistance. Directed evolution,
genome-wide analysis, databases etc. But the r genes is not clearly understood. One of these
researches is Genome-wide analysis captures the determinants of the antibiotic cross-resistance
interaction network (2). At this experiment they try to understand how evolution of resistance or r genes
work spontaneously. So it is a directed evolution. Directed evolutions can help us to predict the
mechanisms of nature (7). At this experiment they also made experiment with different dosages of 12
antibiotics with using E.coli to realize the relation between cross-resistance and parallel evolution. As a
result of this experiment they said individual mutations and laboratory-evolved lines are 62% overlap (2).
So we can figure that out, mostly, mutations which organisms have against antibiotics are similar. Doesn’t
matter if it has natural evolved genes from an ancestor which already has r genes or it has r genes as a
result of a spontaneous mutation.

4. Another experiment which is prediction of antibiotic resistance by gene expression profiles (S.Suziki et.
al, 2014) try to understand relation between mutations. They made experiment with ten antibiotics and
antibiotic free cases. And also for every antibiotics there are 4 cases. With that process they can compare
cases for each antibiotics (1).
The result for that experiment is, in every cases there are different evolved mutations which is shown at
Figure 2.
Figure 2: this figure shows the mutational differences between cases which can be same antibiotics or
different antibiotics. For example at Cefoperazone cases, there are 4 different evolution of mutations. For
the first one synonymous mutations occur but at others there is none. And also numbers of mutations are
shown differentiate for each cases. The AF (antibiotic free) cases shows that there can be spontaneous
mutations where there was no effect of antibiotics.

5. For the control of the evolution of antibiotic resistance, clinics and companies make public databases
which can be used by everyone. The most important database is Antibiotic Resistance Gene Database
(ARDB). (6)
CONCLUSION
Antibiotic resistance is a problem which permanently increase. And the evolution will continue
until the end of the world. Because the bacteria are living organisms and our body has ten times
more bacteria than our cells. It means that the bacterial environment will continue and resistance
will not be end. But no one can see tomorrow if the differences between pathogenic and non-
pathogenic bacteria are fully investigated, the pathogenic bacteria can be destroyed. Or maybe we
will use viruses for destroying bacteria. Actually this is a war between human being and nature.
Homo sapiens try to control the nature. But nature gives its answer every time with another
evolution. The war will not be end until human give up.
REFERENCES
1. S. Suziki et al., Prediction of antibiotic resistance by gene expression analysis,
2014
2. Viktoria L., Istvan N. et al., Genome wide analysis captures the determinants of
antibiotic-resistance interaction network, 2014
3. Gibson MK, Forsberg KJ, Dantas G, Improved annotation of antibiotic resistance
determinants reveals microbial resistomes cluster by ecology, 2014
4. Tugce O, Aysegul G et al., Strength of selectionpressure is an important parameter
contributing to the complexity of antibiotic resistance evolution, 2014
5. Jose L. Martinez, The role of natural environment in the evolution of resistance
traits in pathogenic bacteria, 2009
6. McArthur AG et al.,The comprehensive antibiotic resistance databases, 2013

6. 7. Mc Orencia et al.,Predicting the emergence of antibiotic resistance by directed
evolution and structural analysis, 2001
8. Davies & Davies, The origin and evolution of antibiotic resistance, 2010
9. E. P. ABRAHAM & E. CHAIN an Enzyme from Bacteria able to Destroy
Penicillin, 1940
10.Ryan T Cirz, Jodie K Chin et al., Inhibition of mutation and combating the
evolution of antibiotic resistance, 2005
11.Anita H. Melnyk, Alex Wong and Rees Kassen, The fitness cost of antibiotic
resistance mutations, 2010