DNA analysis of bacteria and Viruses
THE STORY BEHIND THE STORY
The Team MMM Story represents just a small part of the huge amount of work that goes on, and the many, many different people who contribute to what we do.
We have strived for scientific accuracy where possible, (though admittedly DNA doesn’t always turn out pink). Whilst we have nominated particular groups for particular steps, in reality many people are involved at multiple stages- our Research Assistants analyse data, our Post Docs do Bioinformatics…
If you want to read the Journal articles which inspired the story here they are:
Sequencing bacterial genomes can be used to study Tuberculosis outbreaks:
Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007-12, with whole pathogen genome sequences: an observational study. Lancet Respir Med. 2014
Genome sequences can be used to predict antibiotic resistance:
Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing. J Clin Microbiol. 2014
Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. J Antimicrob Chemother. 2013
Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study. 2015
The Team we’ve portrayed is the Modernising Medical Microbiology team based in Oxford – the Crook/Peto Research Group, part of the Nuffield Department of Medicine in the University of Oxford. We’re also part of a larger collaboration with groups in Birmingham, Brighton and Leeds, who work to develop experimental science into techniques that can improve the treatment of patients with infections.
Originally we wanted to show our results being used to directly inform patient care, however this work is cutting edge, and at this moment in time our results are not being used directly by the Doctors looking after patients. However they are reported to Public Health England, who use the information to help them look for sources of Tuberculosis spread. Our research group has been at the forefront of turning this technique into a valuable tool for use in patient care. Together with Researchers in Birmingham, it will be trialled by the Department of Health
Some exciting work is coming out of our pilot suggesting we will be able to use genomics to predict antibiotic resistance in Tuberculosis. Watch this space!
Our original plans also had our group leads and heads in the middle of everything, supporting every step as 10-armed octopuses… They are involved every step of the way, from discussing what type of chemicals to use to extract DNA, to how phylogenetic trees are put together, to how we securely store terabytes of genomic data… Team MMM relies on their continuous awesomeness to function.
Even making the comic strip was a teamwork exercise in itself. Once the idea was put out, our Assistant Lab Manager, Ali Vaughan recruited a group of interested individuals to help with the project. A number of ideas were brainstormed, together with a narrative, and we decided upon the comic-book narrative. Ali managed to persuade, cajole and guide each group into posing for a picture, with varying degrees of enthusiasm… Our scientists acted as a reality-and-scientific-accuracy check throughout, and the whole thing was put together by a couple of our team, Amy Mason and Nicola Fawcett, using nothing more fancy than standard iPhone Apps and Microsoft Office tools.
The main message we wanted to portray is how many different disciplines are involved in the work we do. Genomics at a small scale is difficult enough. However if you’ll be responsible for sequencing hundreds of samples a month, storing all the data securely, and conducting the analysis, you really need a well-oiled team working together.
The team represented can be found in the Oxford Staff section (in no particular order) lead by:
Group Heads and PIs:
Senior Statistician and unofficial Head-of-most-things:
And there will be many, many more people involved who we haven’t directly mentioned here, but without whom our work wouldn’t be possible.
We hope you enjoy it! Any feedback or discussion, please contact or tweet us: @modmedmicro or via this website
The MMM Team
-originally published 2014, updated Dec2015