Outbreaks and Antibiotic Resistance

Dr Sophia David is a Postdoctoral Scientist at the Centre for Genomic Pathogen Surveillance (CGPS) based at the Wellcome Sanger Institute. Her most recent work has been tracking antibiotic resistant bacteria across Europe.

Tell us about your work in up to 10 words

Tracking the spread of antibiotic-resistant bacteria using genome sequencing.

What is the most overused word or phrase in your lab?

One of our most commonly used words must be “outbreak”. We’re always looking out for signs of an outbreak in our data!

Describe the Sanger Institute in up to 10 words

Amazingly diverse community and cutting-edge science on a beautiful campus.

Why did you become a scientist?

I never anticipated becoming a scientist but it happened through a series of steps and decisions. I have been fascinated by genetics since I was at school – in particular, how the incredible diversity of living organisms can be encoded by just four letters! I got my first flavour of scientific research during a summer project working in a Crop Genetics lab at the John Innes Centre. By observing the science going on around me, I witnessed the potential impact that scientists could have on important global issues, and this played a big part in my decision to do a PhD. Then since being at the Sanger Institute (I started my PhD here in 2012), I have become completely hooked on the different projects I have taken on and always enjoy the aspect of discovering new things, however small they might be.

Who is your science hero?

I don’t have a single hero, but I have been very lucky to be surrounded by wonderful people. My PhD supervisors, Julian Parkhill (previously at the Sanger Institute) and Tim Harrison (previously at Public Health England), are both brilliant scientists who taught me a huge amount. I have also been fortunate to work with scientists who have a particularly remarkable ability to innovate and find novel ways of looking at data, and really push the field forward. Simon Harris, previously a Senior Staff Scientist at the Sanger Institute, stands out amongst these. And finally, most scientists have a big passion for their subject but some, like my friend and ex-Sanger PhD student, Mia Petljak, have this in incredible abundance! I have always admired Mia’s tremendous drive and work ethic, and the scientific field is very lucky to have people like her.

What is the most exciting development in your field from the last 10 years?

One of the most exciting things for me has been the development of long-read sequencing by companies such as Pacific Biosciences and Oxford Nanopore. By sequencing longer pieces of DNA, we are now able to piece together our bacterial genomes much more easily, usually enabling assembly of the genome into a full chromosome and any additional plasmids. Previously, using short-read sequencing technologies, our bacterial genomes would be highly fragmented.

I’m particularly interested in the plasmids from bacteria because they can carry antibiotic resistance genes. Plasmids have the ability to spread horizontally between different strains and even different species of bacteria, which has greatly accelerated the spread of antibiotic resistance. However, now we can obtain full-length plasmid sequences using long-read technologies, we are able to track the spread and evolution of plasmids carrying important resistance genes at high resolution. This will be an important factor in our fight-back against antibiotic resistance.

What is the most surprising discovery you have made?

During my PhD, I studied the genomes of a bacterial species called Legionella pneumophila, which can cause Legionnaires’ disease, a severe and potentially life-threatening pneumonia. L. pneumophila is an environmental bacterium that lives in soil and water, and can opportunistically infect humans when it contaminates man-made water systems. By sequencing the genomes of these bacteria from patients, we found that the majority of disease cases were actually caused by bacteria that are extremely related to one another, and that are unrepresentative of the bacterial population in the natural environment. This was surprising to us as it suggests that there are certain clones of L. pneumophila that may be highly adapted to survival in man-made environments but also possibly adapted to human infection too.

If you could time travel to any period in history, which would you pick?

It depends how long you’d make me stay! It would be interesting, but perhaps very alarming too, to go back to perhaps a few thousand years ago when humans had made little visible impact on the environment.

If you were omnipotent for the day, what is the first thing you would do?

I would enable free and high-quality education for everyone on the planet.

Links