An Example of Activity Design for Laboratory Genomics Training

This activity was designed by Mihir Kekre and was included in a course on Genomic Surveillance of AMR, organised by the Centre for Genomic Pathogen Surveillance and Wellcome Advanced Courses and was funded by National Institute for Health Research in the UK.

The learning outcomes addressed by the activity included the following: Learners should be able to

1. To design and deliver activities specific to laboratory work in genomic surveillance of antimicrobial resistance: plating live bacteria, bacteria identification and susceptibility testing.
2. To troubleshoot problems that might arise during NGS sequencing of bacterial genomes.
3. To budget appropriately a project on bacterial genomic sequencing.

This was a scenario-based exercise, run in groups: “A scientist is assembling a team tasked with creating a surveillance network to monitor Methicillin-resistant Staphylococcus aureus cases originating from the local hospitals. He needs to establish a baseline for the kind of strains present in the country, as well as the antibiotic resistance patterns displayed. He is running a pilot study using a collection of 4,000 MRSA isolates sampled between 2014 and 2018. The ID and AMR profiles of these isolates have already been determined phenotypically. The aim is to perform whole-genome sequencing (WGS) and use genomic data to determine AMR trends. The budget of the project is $400,000, and the expected timeframe for the pilot study is 24-months. Your task is to submit a project plan detailing how the sequencing will be carried out in the lab, how long it might take to complete and what it will cost him to run this retrospective survey. The objective is to design a LABORATORY ACTION PLAN you wish to carry out in order to be able to sequence the 4,000 isolates of Staphylococcus aureus.”

The planned activity in the example was assessed based on the accuracy of the proposed plan, the level of detail and on how realistic it was.