Experimental Evolution: Identifying Pathways of Viral Resistance

Experimental Evolution: Identifying Pathways of Viral Resistance

By: Dasyre Sires    Email:  sire1910@vandals.uidaho.edu

Home Town: Moscow, Idaho    High School: Kennewick

Major: Psychology
Department: Psychology/Communication Studies, Biological Sciences
College: College of Letters, Arts and Social Sciences, College of Science


Phage therapy and antibiotics have been used in treating
bacterial infections for nearly a century. However, bacterial mutations over
time have allowed bacteria to advance in fitness and, in turn, resistance to
these treatments. In this experiment we evolve phage-resistant bacteria to
observe the mutations present on a genomic level. Pairing these observations
with previous research regarding phage infection mechanisms will hopefully aid
in the understanding and control of bacterial fitness.

From laboratory host Escherichia coli, we have isolated colonies that demonstrated resistance to each of 10 selected types of bacteriophage (Table 1.). We carried out plate evolution experiments with individual host colonies and each of 10 phage isolated from each of the bacteriophage strains. The genome of a resistant host from each experiment was sequenced in its entirety and analyzed for a total of 100 genomes. Sequencing artifacts where then identified in these colonies and compared to the ancestral strain to identify mutations. Similarities and differences in mutations are now being identified and analyzed to help us better understand factors of phage resistance.


The objective of this project is to identify mutations in E. Coli C colonies resistant to one of ten different strains of bacteriophage. The bacteriophage strains we are using are listed in Table 1 and include eight ssDNA microviruses and two dsDNA phage, T7 and T3. This allows us to observe differences in mutations based on the phages’ infection mechanisms. Based on background research, I believe we will find more similar mutations between the host bacteria resistant to phage with more similar infection mechanisms. Additionally, I suspect that there will be a correlation between proximity of phage in the phylogenetic tree and similarities in mutations of the respective resistant E.-coli (See Figure 1). The tree below was made from a gene H (pilot protein) alignment and does not include T7 or T3.

I also would predict the infection mechanism of the phage type will partly determine which mutations are effective. Receptor mutations on the E. coli cell surface or enhancements in defense systems such as the CRISPR system may be more present against one type of mechanism.


The procedure for this project has been broken down into two separate parts. The first part has just recently been completed and is outlined in the figure below. During this first part, we isolated colonies resistant to different phage types. After verifying resistance, these genomes where sent out for sequencing.

The second part of this project has involved working through the genome sequences of each resistant colony and comparing them to the ancestral genome. The discrepancies were flagged for further investigation to identify mutations. We are now in the process of identifying the various types of mutations and the effect of the mutation on the colonies. Understanding this will allow us to better infer how these mutations may be contributing to increased resistance.


Ultimately, I hope that the results and analysis of this experiment will aid in understanding the various pathways of viral resistance or aid others in related research.

As will be demonstrated in this study, mutations that
increase bacteria’s resistance to phage are not uncommon and may even be increasing.
This presents concerns in regard to treating life threatening bacterial
infections with phage therapy. This avenue of treatment utilizes phage’s
ability to kill bacteria cells as a method of combating infection. This
treatment strategy is gaining traction and becoming a very plausible
alternative to antibiotics. However, if the bacterial cells are growing in
resistance, then this approach will become increasingly ineffective.

Though antibiotics are another form of treatment, they often
have more side effects than phage therapy. Unfortunately, antibiotic resistant
mutations are also continuously evolving. This research may identify common
pathways of resistance and could offer insight on ways we can reduce bacterial
fitness from a general stand point. This would not just increase the
effectivity of phage therapy, but antibiotic treatment as well. The results of
this experiment will hopefully provide further understanding on how to combat
bacterial resistance to bacteriophage and, in turn, help increase the
effectivity of phage therapy. It is also possible that the experimental approach
of this study and its findings may offer some insight for those looking to
explore and study antibiotic resistance.

About Dasyre Sires

Dasyre SiresI am a senior pre-med student majoring in Psychology with a minor in addictions and Spanish. In addition to my college career, I work at Schweitzer Engineering and lead a production team. However, after I obtain my degree I hope to attend medical school in pursuit of a career as a neurosurgeon. I spend the free time I do have writing a research book I have been working on and managing a small business my wife and I began a few years back. I enjoy playing with my dog, working on my home, riding my Harley, and really just getting out in nature as much as possible.

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Additional Project Information:

Year in College Project Started:  Senior

Faculty Advisor:   Criag  Miller

Faculty Advisor Email:   crmiller@uidaho.edu

Faculty Advisor Website:  

Funding Source: 

External Link to Project Information:  

Project Location:   Moscow, Idaho