Identifying ecological factors that drive the evolution of innate versus adaptive immunity in bacteria

Lead Research Organisation: University of Exeter
Department Name: Biosciences

Abstract

How are we going to deal with bacterial infections if pathogens are resistant to antibiotics? And how do we protect bacteria that are useful for industrial production of cheese and yoghurt against their parasites (bacteriophages, the viruses of bacteria)? These are questions of great societal and economic importance that need to be addressed in the near future. The answer to the first question may well lie in the application of parasites that cause the economic problems in industry that is referred to in the second question.

Like all organisms bacteria face infectious diseases caused by parasites (bacteriophages) that abuse host resources for their own benefit. These bacteriophages sometimes cause severe problems in food industry, but can perhaps also be applied to fight bacterial infections in humans, or bacterial infections of crops in agriculture. However, bacteria evolved several mechanisms to acquire immunity against bacteriophages.

Understanding how bacteriophage immunity evolves in bacteria is one of the key objectives of my research. I am particularly interested in the evolution of two distinct immune mechanisms: bacterial innate and adaptive immunity. I will test how environmental variables impact on the evolution of either immunity mechanism. This will hopefully lead us to conditions where both immune systems of the bacterial host are ineffective, which will aid the use of bacteriophages to combat bacterial infections. On the other hand, my research will likely also identify conditions where the immune system of bacteria is highly effective, which can then be used in food industry to avoid that bacteria that produce our food (e.g. yoghurt) become infected with bacteriophage, which results in severe economic losses. Hence, my research will reveal how, when and why ecological factors drive the evolution of bacterial immunity against bacteriophages.

This information is only one step away from applications in industry, where bacteria need to be protected from bacteriophages. Bioreactors could be designed in such a way that bacterial immunity levels are optimal, which would strongly reduce the frequency of bacteriophage infections and the concomitant economic losses. For the purpose of treating patients that are infected with antibiotic resistant bacterial pathogens, phages can be used as an alternative treatment (phage therapy). In this context, my research will provide clues what the optimal treatment method may be in order to avoid or at least reduce the evolution of bacterial immunity against the bacteriophages. Although phage therapy is not yet used on patients, many believe this to be the medicine of the future and a promising alternative for antibiotics. Nevertheless, phage therapy is already being applied in agriculture, to protect crops from bacterial infections, and in food preservations, for example to avoid contamination of food with pathogenic bacteria. Hence, the knowledge gained from my research can be directly implemented to optimize the procedures of applying bacteriophages to combat unwanted bacteria.

Apart from these important applications, my research will also provide fundamental insights into the evolution of immunity mechanisms and how their evolution is affected by ecological factors. This may provide general insights that are also applicable to other systems. For example, it will help us to understand how immune systems evolve in nature and what their importance is in controlling diseases and how they influence the evolution and spread of parasites.

Planned Impact

Impact on scientific community:
Scientific output will be disseminated to the academic community through publication in scientific journals and presentation at (inter)national conferences. The field of CRISPR-Cas has received considerable attention, as attested by the high number of high-impact papers on this topic. Nevertheless, studying CRISPR-Cas in a community context is an entirely unexplored field of study that is important both from a fundamental scientific point of view as well as for applications in phage therapy and starter culture protection.

Impact on the general public through the use of media:
The applicability of the findings from the proposed research in phage therapy and industry makes that they can easily be tailored for coverage by the popular press. I have followed a course in communicating with the press and have always been very active in communicating my research (see pathways to impact). I will continue to pursue these opportunities as they arise (e.g. after an important discovery), since it provides an excellent forum to inform the general public of science, which directly benefits the general awareness of scientific developments and its societal implications.

Impact on patients:
The high frequency of antibiotic resistant bacteria has caused a resurgence of interest in the use of phages as therapeutic and prophylactic antimicrobials in clinical and agricultural contexts. Being a member of PHAGE (Phages For Human Application Group Europe; P.H.A.G.E; http://www.p-h-a-g-e.org), enables me to disseminate my research data to the general public and may facilitate applying phage in a medical setting. This may have direct implications for cystic fibrosis patients who may benefit from phage therapy in the future (see below).

Impact on companies:
1. Starter culture protection.
CRISPR-Cas systems are used to protect bacterial starter cultures in dairy industry. I am setting up collaborations with Phillipe Horvath at DuPont, to optimize these applications, which will help to minimize economic losses in the food industry. In particular, I am interested in further improving starter cultures protection using CRISPR-Cas. Fundamental research on CRISPR-Cas has already led to the development of a new starter culture series by DuPont based on patented CRISPR Technology: CHOOZIT-TM SWIFT, which has reduced issues related with phage infections resulting in better yields, optimized process time and minimization of product downgrades. Further improvement of the application of CRISPR-Cas for these purposes requires more detailed knowledge on (i) when CRISPR-Cas is (in)effective in immunity; (ii) the costs and benefits associated with CRISPR-Cas and (iii) how these costs and benefits depend on ecological factors, such as phage diversity and abundance. The cost associated with expressing CRISPR-Cas is a key determinant for successful application of CRISPR-Cas in dairy industry. Fitness costs associated with expression of resistance determinants has for example limited the generation of resistant plant species, since it resulted in severely reduced crop yields (Gur et al, Trends Biotech 2005). Understanding the costs and benefits of CRISPR-Cas can have direct impact on industry, allowing optimization of the use of CRISPR-Cas in culture protection.

2. Phage therapy.
Data from my research can be directly applied in phage therapy. The University of Exeter is ideally suited to realize these applications: Excellent collaborations of Prof. Buckling exist with phage therapy laboratories in Belgium and Georgia, where trials are currently running. Furthermore, Dr. Koskella has excellent contacts with Novolytics, a phage therapy company in the UK. I will be able to use this existing network to realize the applications in phage therapy; once I identify variables altering CRISPR-Cas efficacy, they can readily be tested in phage therapy. As such, the proposed research can directly benefit phage therapy companies.

Publications

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Chabas H (2019) Variability in the durability of CRISPR-Cas immunity in Philosophical Transactions of the Royal Society B: Biological Sciences

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Chevallereau A (2019) The effect of bacterial mutation rate on the evolution of CRISPR-Cas adaptive immunity in Philosophical Transactions of the Royal Society B: Biological Sciences

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Common J (2019) CRISPR-Cas immunity leads to a coevolutionary arms race between Streptococcus thermophilus and lytic phage in Philosophical Transactions of the Royal Society B: Biological Sciences

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Høyland-Kroghsbo NM (2017) Quorum sensing controls the Pseudomonas aeruginosa CRISPR-Cas adaptive immune system. in Proceedings of the National Academy of Sciences of the United States of America

 
Description We have identified conditions where CRISPR-Cas adaptive immunity is favoured over surface based innate immunity and vice versa, and demonstrated that each of these responses is associated with unique coevolutionary consequences. We also made important progress in understanding how CRISPR systems lead to patterns of local adaptation between bacteria and phage. Finally, we examined how these systems are regulated across different environments.

We have further identified drivers of CRISPR-based resistance evolution. Examined the coevolutionary consequences in the context of phage that can transmit both horizontally and vertically, and examined the impact of phage-encoded anti-CRISPR genes.
Exploitation Route Understanding when CRISPR-Cas is important and its consequences will help to generate effective fermentation protection strategies.
Sectors Agriculture, Food and Drink

 
Description I am currently in contact with Folium Biosciences, who would like to use CRISPR in the context of food production. Together with Dr. van Houte, I have had intensive contact with Folium Biosciences. We wrote a grant proposal for a BBSRC IPA. Unfortunately, Folium Biosciences pulled out only days before the submission deadline as they did not have the financial means to continue. I have not generated any other non-academic impact.
First Year Of Impact 2018
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description ERC starter grant
Amount € 1,500,000 (EUR)
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 01/2017 
End 01/2022
 
Description Gave a public lecture to an audience of >500 members of the public about ethics of CRISPR-Cas genome editing 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact I was invited to give together with Prof. Jennifer Doudna this lecture "NWO publiekslezing" at Wageningen University, the Netherlands. The audience far exceeded 500, and consisted of members of the general public.
Year(s) Of Engagement Activity 2016
URL https://wurtv.wur.nl/p2gplayer/Player.aspx?id=bzGxs4
 
Description Talk for lay public in Leusden 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact I have 3 lectures on CRISPR of 1 hour each to a lay audience. This included a discussion about the possibilities, risks and ethical concerns associated with this novel technology. I covered CRISPR biology, its use in genome editing of somatic and germline tissue, ecological engineering including removal of antibiotics resistance genes, and use of CRISPR gene drives to control mosquitoes. The lectures helped the public to better understand the subject. The public included members of a charitable donor, whose decision making will be impacted by the knowledge gained on this subject.
Year(s) Of Engagement Activity 2018
URL https://isvw.nl/activiteit/frontiers-life-sciences/
 
Description Writing article for Microbiology Today on CRISPR-Cas 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact I wrote an article for Microbiology, following the invitation below:

I hope you are well. I am contacting you today as editor in Chief of Microbiology Today the professional magazine of the Microbiology Society based in the UK. We are really lucky that the magazine has a readership of >4ooo and it is distributed to scientists and microbiologist, politicians, policymakers, publics and schools and teachers across the globe. Our next edition will be focused on how Microbes and microbial systems have transformed techniques used in modern biological research. The articles are all about 1200 words or so and have an accessible easy to read style. We hope to make this edition an interactive affair and know that it will highlight attention on research being carried out in this area One of the articles I am really keen to sign up is to focus on CRISPR-Cas piece. As you know this technology is transforming science, and is highly topical and relevant to our readers and beyond. I am aware that you are an expert in this field and Malcolm White in St Andrews and the Editorial board agree that it would be an utter coup to get an article written by you and/or your lab as a world class leader in the field. I have researched you through your website and your publications, and I realise that they are absolutely right: your expertise is perfect!. I am hoping that you by yourself, or more likely, with a colleague would be prepared to write an article for us MT? I hope you will consider this request and just to let you know that I would be happy to support you and/or with a colleague with writing an article for this sort of audience if you would feel happy checking the science if that helps? This article of MT will be innovative and we genuinely feel that it will get a high readership and that it is an opportunity to add impact to your work.

I would like the article to describe how developments in microbiology/biology/molecular biology made this possible. and how it works. The deadline is 6 weeks or so? ( 1200 is can be a bit less or a bit more and a simple overview of what it is and how it works, would be amazing).
Year(s) Of Engagement Activity 2016
URL http://www.microbiologysociety.org/news/society-news.cfm/microbiology-today-future-tech