Figure 4. Hypothetical time trees indicating transmission links (TLs).

(A) (Left) The complete phylogeny, including all bacterial isolates and displaying multiple transmission events over time (located at nodes for simplification). This scenario allows the reconstruction of a tree (middle) with several tips and multiple TLs (as the summary of all the events). A continuous distribution of clustered cases by different pairwise distances is retrieved (right) as observed in the Valencia region and Malawi. (B) A complete phylogeny (left) in which transmission is either too old or recent and few (or no) transmission events occurred in the middle time, led to the reconstruction of a tree (middle) in which few samples reach the present and fewer nodes are observed all over the tree. This scenario provides a bimodal distribution of clustered cases by pairwise distance (right) as observed for Oxfordshire. (C) Time tree highlighting TLs over time before the most recent sample (BMRS). The table (bottom) shows the number of links counted in each time period and the median distance range among the samples within the links for the three settings analyzed. For the period between the most recent sample (MRS) and 50 y BMRS, links within (gClusters) and outside gClusters (No gClusters) are indicated. Vertical red lines indicate periods of time, horizontal dashed lines indicate missing samples, shaded areas indicate sampling period, and circles indicate transmission events with colors specified in the legend.