Week E: Experimental Plan#

Week E will be less structured than the other weeks on the course - this is the week for students to design their own experiments and do their own analysis.

Instructions for students#

Remember you are trying to biologically test the predictions from your genome annotation. You need to have a clear logical link between the bioinformatic analysis and your experiments - your experimental design must be based on the predictions from your genome, not be a random unconnected experiment.

There a detailed protocol for antibiotic disc sensitivity testing in Hudzicki J. Kirby-Bauer Disk Diffusion Susceptibility Test Protocol. American Society of Microbiology. 2016. We provide the PDF.

Read this really carefully and decide what you will need to do to perform this protocol. I have also put a link to to some commercially available antibiotic diffusion discs. You will need to send a list of the antibiotic disks you would like us to order in order for you to carry out the experiment.

Things to think about:#

  • Which strain of bacteria are you going to work with? Are you doing both B and C, or concentrating on one strain only?

  • Which AMR genes are you going to focus on? Most of you had predictions of multiple AMR genes - are you going to test all of them or a subset? Either is fine, but you need to have a plan.

  • Which antibiotics are you going to test? The bioinformatic analysis predicts resistance to classes of antibiotics i.e. multiple similar compounds. You will need to pick specific compounds to test that belong to an appropriate class of antibiotic. Are you going to test one antibiotic per class or multiple antibiotics?

  • What concentrations of antibiotics are you going to use? What are you going to use as positive or negative controls? We will have E.coli K12 available as well as the clinical strains.

  • Are you going to quantify your results? How are you going to do this?

It is better to do a simple experiment well rather than to make things too complicated and have results that don’t make sense or your protocol can’t be completed within the time.