Introduction
Prepared by Nabil-Fareed Alikhan. Originally presented by Natacha Couto and Julio Diaz Caballero. Last updated 2024-03-28
This advanced tutorial has been adapted from content presented in the Digital Epidemiology Workshop, hosted in Colombia in September 2023. In this series of exercises, you will use Microreact to gain knowledge regarding a large collection of Klebsiella pneumoniae isolates, sampled from Colombia, between 2013 and 2019. At the end of this series of exercises, you will be able to identify a high risk clone circulating in the country.
Note
For Microreact documentation, visit https://docs.microreact.org/
Microreact features demonstrated
- Opening a Microreact project
- Creating your own copy of a project
- Creating a new panel
- Creating a standard stacked bar plot
- Creating a new chart
- Customising a chart
- Updating an existing view
- Saving changes to a Microreact project
- Showing metadata along side a phylogeny
- Customising metadata blocks
Getting started
Warning
You must use either Google Chrome or Mozilla Firefox as your internet browser.
The dataset used through these recipes is already available on Microreact. Go to microreact.org/project/kpncolombia and explore the collection of isolates. We will use these data for a series of recipes:
- Create an editable project.
- Present whole genome sequencing quality control (WGS QC) statistics in a chart.
- Explore what are the dominating sequence types (STs) in Colombia.
- Plot metadata blocks for the carbapenamase genes CTX-M-15, NDM-1, KPC and OXA to answer what are the prevalent AMR mechanisms detected.
- Explore which STs are associated with the presence of carbapenamase genes.
This is a screenshot (above) of a Microreact project called "Klebsiella pneumoniae Colombia". Notice the main panels in this project: the map, the tree, the timeline and the saved views.
Info
You can save these recipes as a pdf, by using your browser's print function and choosing Save as pdf as the printer.