Outbreaks

List of outbreaks

The Outbreaks section displays automatically detected clusters of isolates that may indicate potential outbreaks based on genomic similarity and temporal patterns.

Navigate to the Outbreaks menu item on the left sidebar. The main panel shows a searchable and sortable list of outbreak clusters.

Outbreaks are identified using cgMLST profiles and a species-specific allele cutoff, specified in the cluster name. E.g. the cluster name “yer_1_10” refers to the Yersinia enterocolitica cluster number 1, using a cutoff of 10 alleles differences.

If you wish to get notified when outbreak clusters are added or updated, please click the button on the top right.

Outbreaks are listed by species, based on a cgMLST schema. To change the species of interest, use the species dropdown button.

Species-specific tree

To view an unrooted tree of all the outbreaks within a species, click on the button next to the species name. The resulting view might be useful to identify closely related outbreaks just above the cutoff threshold (example below).

The tree can be rearranged by manually dragging nodes or by clicking on . It can also be downloaded by clicking on .

You may also download the distance matrix file for a species by clicking on “Download matrix file” at the top of the tree.

Oubreak view

Select a cluster to view its general information, table of isolates and cgMLST-based minimum spanning tree. The cluster name reflects the species, cluster number and number of alleles used as a cutoff (10 in the example below). The information panel on the left indicates the first detection date and when the cluster was last updated. You can download the table of allelic distances using the Download button next to “Matrix distance”.

Tree and distance matrix

Click on the button on the top-right. Under “Unrooted tree”, select “Color by” to color the tree nodes based on a field (e.g. isolation source, isolation year, quality etc).

Click on “Heatmap” to view the distance matrix.

Adjust visible columns in the table

Click on the button on the top-right to adjust the visible fields (columns in the isolates table). Already visible fields are highlighted with a gray background. Click on any field to make it visible in the table.