Hello, everyone. In this step, we will learn how to use Microreact. Start by opening up a new window in Firefox and typing microreact.org in the address bar. Microreact is a free web tool developed by the Centre for Genomic Pathogen Surveillance at the Wellcome Sanger Institute. The tool allows you to upload, visualize, and explore phylogenetic trees along geographic and temporal data to study the epidemiology of infectious diseases. Now click on the Upload’s app. Here, you can upload your own data. You will need a phylogenetic tree in .nwk formats, like the one shown here, and a table with isolate metadata in .csv format. This table should include at least information on sample IDs, sample collection dates, and geographic coordinates.
You can add additional information such as resistance profiles, presence of AMR genes, and use colours and shapes to define sample attributes.
Remember, you can find more information and how to prepare your own data for Microreact on the Instructions page. In this video, we will use an existing collection of Staphylococcus aureus genomes to show the functionality of Microreact. You will find three panels, the map, the phylogeny, and the timeline panel. You can click, drag, and zoom in and out to navigate inside each panel. The tree panel allows you to view and explore the phylogenetic tree. The controls on this panel allow you to change between different tree layouts. We will keep the rectangular layout. On the Nodes & Labels, click on Show Leaf Labels to make sure sample labels on the tree are displayed.
You will need to zoom in to be able to see the labels of leaves on the tree.
You can also change the text size of these labels.
Click again on the controls button to hide controls. If you are interested in a particular group of samples, you can select the internal node that represents their common ancestor. Note that now samples of the selected clade are highlighted on the tree, map, and timeline panels. Double-click on a blank space to highlight all samples again. Right-click and select Fit in Panel to view the whole tree again. The map panels shows you the geographical locations samples were collected from. Zoom in to get a closer look. Each point represents a sample or group of samples collected from the same location. Points with multiple samples are rendered as pie charts on the map. Click on a point to view details.
And finally, zoom out to get a view of the whole world map again. The side panel, represented with an eye icon on the right hand side of your screen, will allow you to change the label, shape, and colour of samples on all three panels. Clicking on the Label by or Colour by buttons will open a drop-down list with sample attributes. In this data set, samples are colour coded by country of origin as well as antibiotics susceptibilities, where black denotes resistant isolates and white susceptible ones. Keep Country selected as default. The Timeline panel, located at the bottom of the screen, shows when samples were collected.
You can move the mouse over each point to display sample details or click on them to highlight their locations on the phylogeny and map.
If you are interested in a particular time period, you can drag the edge of the slider to set specific dates. Samples collected during the chosen time interval are filtered and highlighted on all three panels.
Another helpful feature of Microreact is the search box located at the top of the screen, which allows you to query all sample attributes at once. For instance, you can find out what genomes carry specific AMR genes.
All sample attributes can be accessed through the data table panel at the bottom of the screen, where each row represents a single sample. You can use the tune button to choose visible columns.
In this case, we will select all columns and also change table display density. So that’s all. Also remember that each Microreact project is assigned a unique URL, which means that projects can be saved, published, and shared. In later steps of the week, we will make use of Microreact to explore real world data sets of bacterial outbreaks.