An interview with Emily Addington
Emily Addington is a PhD student at the University of Strathclyde and a member of the Microbiology Society. In this interview she tells us about her research which includes looking at novel products that can be produced from microbes, tells us about her role in the ‘Dive for Antibiotics’ Project and how she is working to try and understand pathogenic organisms in more depth.
What is your role and area of research?
I’ve just begun my third year as a PhD student at Strathclyde Institute of Pharmacy and Biomedical Sciences in Professor Paul Hoskisson’s lab. My PhD project is looking at characterising the role of the mammalian cell entry operon of Streptomyces coelicolor. We believe the Mycobacterium tuberculosis mammalian cell entry (mce) operon of Streptomyces coelicolor is a nutrient uptake system for lipids which aids the bacterium in colonizing the rhizosphere. However, copies of the mce operon are also present in pathogenic Actinobacteria such as Mycobacterium tuberculosis (Mtb), where the system has a role in virulence.
Part of my project is trying to understand how the mce genes function in Streptomyces to help us understand how they may have evolved into a virulence factor. Mtb. Streptomyces is also the genus best known for producing two thirds of the antibiotics used in clinical practice today, so my interests also extend to natural product discovery from Actinobacteria.
Why is your research important?
Mycobacterium tuberculosis is the world’s most deadly bacterial pathogen and is showing increasing antimicrobial resistance. Determining how systems such as the mce operon function is vital for understanding how a pathogenic organism such as Mtb arose and how it infects and causes disease in its host. Understanding how the mce operon functions in non-pathogenic bacteria may lead us to discover more about how virulence factors evolve.
How did you come about initiating the ‘Dive for Antibiotics’ Project? Why did you decide to focus on marine research?
I’d already been working on Streptomyces for about a year prior to becoming interested in antibiotic discovery. A team from the BBC had collected some soil samples from the River Tay in Dundee as part of their program – The River: A Year in the life of the River Tay – and were visiting our lab.
I offered to isolate Actinobacteria from the sample, something I hadn’t had an opportunity to do previously, and was fascinated by the sheer number and diversity of actinobacterial isolates the small bit of soil produced. I had only just become aware of Scotland’s extensive diving community around the same time, and I had met a few active divers. I thought it would be interesting to see what Actinobacteria we could isolate from the plethora of sea lochs and diving sites Scotland has to offer.
I was also delving into literature I hadn’t previously, about isolation of Actinobacteria from the marine biosphere, which is relatively under sampled in comparison with the terrestrial environment. This made me realize and become interested in the vast potential of the marine environment to produce novel antimicrobial compounds.
As the Actinobacteria that we were isolating were also growing to produce some beautiful structures and bright pigments, I began photographing the isolates and putting them on social media. This resulted in a number of divers getting in contact with us, to know how they could be part of sample collection and expressed an interest in learning more about microbes and antibiotics.
The potential for interesting results and the enthusiasm of the divers to be involved led to me starting the Dive for Antibiotics project, so we could sample and process our isolates in a more organised way, whist also engaging the public in science and antibiotic discovery.
Why is it important to actively look for new antibiotics?
Other than global warming, the antimicrobial resistance (AMR) crisis is the largest single issue facing the world today. The O’Neill Report on AMR predicts that by 2050, 10 million people per year will die as a result of antibiotic resistant infections. It’s truly frightening the number of pathogens showing extensive resistance to antibiotics when we rely on antibiotics for treating everything, from minor ear infections to life-threatening illnesses such as sepsis and meningitis.
There hasn’t been great success in synthesising antibiotics from scratch, and unfortunately, we’ve extensively explored and exploited all common and terrestrially sourced natural products. We need to look new places and try new things if we are to introduce novel antibiotics to the clinic.
What are the challenges you encountered during the project and how did you overcome them?
It was difficult to allocate attention to both the Dive for Antibiotics project and my own PhD research, and I relied on careful organization and time management. At the same time, I had to be flexible about when divers could get samples back to the lab. I initially thought a month would be enough time for divers to return samples, but this ended up being extended quite a bit as I didn’t factor in such things as poor weather, or that some divers aimed to travel quite far to collect their sample from a specific dive site that interested them.
I ended up just having to be prepared to process the samples when they came in. It was also a challenge to convey what was occurring in the lab in a way that was accessible and informative to our social media followers who didn’t have a background in science. Of all the divers and general public, I spoke to about the project, all were aware of antibiotic resistance, but not of how it arose and why. They were most certainly surprised to learn that most of our antibiotics actually come from bacteria themselves.
Have you had any promising results from the samples collected by the divers?
A number of the isolates that divers collected for us have been bioactive against pathogens like MRSA and E. coli, and we’ve had two which are able to kill Pseudomonas aeruginosa.
Pseudomonas is particularly quite hard to kill and is also a common nosocomial pathogen showing multi-drug resistance, so I was quite excited to find isolates that were bioactive against it. Fellow PhD student David Mark is looking at anti-pseudomonad activity of actinobacterial isolates, so I was able to pass those strains onto him and hopefully, more long-term, we’ll be able to look at what specialised metabolites these bacteria are producing. 16S sequencing suggests that one is a Micromonospora whilst the other is a species of Streptomyces, isolated from marine sediment collected in Scotland and England respectively.
It was also very interesting to see how many Actinobacteria could be isolated from marine sediment collected 80 meters below surface, and that one of our bioactive isolates struggled to grow without high levels of salt in the growth medium. It makes you very curious if there are far more novel marine Actinobacteria to be discovered which are adapted to extreme marine environments.
How does the process of discovering novel products from the samples look like?
There are many different techniques that can be used to find bioactive secondary metabolites; the method I used is to screen isolates against some of the ESKAPE pathogens. This type of assay, referred to as an antimicrobial production screening bioassay, takes an agar plug of the potentially bioactive isolate and measures the zone of inhibition it creates in a lawn of the growing pathogen.
Actinobacteria switch on specialised metabolite synthesis at the same time they are erecting aerial hyphae in preparation for sporulation. Taking a plug from a sporulated plate of Actinobacteria means that any specialised metabolites have had the opportunity to diffuse into the medium and will come into contact with the pathogenic cells you’re screening against. How big the zone of inhibition produces depends on the bioactivity of the secondary metabolites; if there is no zone, then the secondary metabolites produced by that isolate are not bioactive against that pathogen, whilst if there is a zone of inhibition, you know that compounds are being produced which are capable of killing the pathogen. Different isolates will be bioactive against different pathogens, and may not produce some specialised metabolites unless stressed, or grown on a particular type of growth medium.
Once you’ve determined that your isolate produces a bioactive compound, you want to extract this metabolite, and again there are many different ways to do this, such as using a range of extraction solvents. You then apply more chemical-based methods such as liquid chromatography–mass spectrometry (LC-MS) and nuclear magnetic resonance (NMR) to determine the chemical nature and structure of the metabolite. The issue is in discovering truly novel products, which is rare, it is easy to rediscover known metabolites. My PI told me when I started this project: “If finding novel antimicrobial metabolites was easy, we wouldn’t have an antibiotic resistance crisis.”
Why is it important to be a member of an organisation like the Microbiology Society?
I’ve been a member of the Microbiology Society since I was a master’s student in 2014. Over the years the Society has offered me to the opportunity to engage in public outreach, attend conferences to present my work and keep up to date with what is happening in my research field. Without the support and funding of the Microbiology Society, I wouldn’t have been able to run the Dive for Antibiotics project. The Society opens up a wealth of opportunities and fosters growth and collaboration; being a member has been highly beneficial for me personally.
Why does microbiology matter?
This is a difficult question, just because I think it’s difficult to put in perspective just how much microbiology matters. Putting aside antibiotics, microbiology still impacts basically every part of our lives; microbiology is vital in dentistry and medicine, in disease and agriculture and biotechnology. From affecting the climate to producing the beer you drink; microbes are doing pretty much everything. There are more microbial cells in our body than human ones and more micro-diversity in 10g of soil than there is macro-diversity on the whole planet. Studying microbiology tells us so much about our world and about ourselves and is so absolutely vital.