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.

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.

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.

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.

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 selection pressure 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

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