Inferring evolutionary pathways and directed genotype networks of foodborne pathogens
Fig 2
The directed network based on genetic and temporal distances between MLVA profiles, where each directed edge is obtained from Bayesian inference.
The network comprises 690 connected nodes and 1,020 directed edges, with each node representing an MLVA profile and each edge representing an inferred evolutionary step. In addition, each profile may be associated with a cluster of other profiles within a genetic distance G. Formally, the cluster Ci associated with node i is given by Ci = {j: Gij ≤ Gmax}, for some threshold Gmax (Materials and methods). The size of the nodes represents the average prevalence within this cluster approximating the average virulence across closely related strains. In this network, the node associated with the most prevalent cluster (profile 3-9-7-17-523) is highlighted and circled in orange. The color of all other nodes illustrates their genetic distance to this reference node, from light green (closest) to dark (farthest). The layout of nodes is given by Cytoscape’s edge-weighted spring-embedded algorithm, which groups together cliques of nodes. From this graph, we can capture a potential evolutionary path between two connected nodes as a sequence of directed edges between them, as described in Model. We highlight three case studies as paths in magenta, blue, and red that contain eleven, nine, and five STM strains respectively. These paths include profiles associated with outbreaks previously investigated by the Australian Department of Health (see Materials and methods). The path shown in magenta includes (as the 9th node) profile 3-10-7-14-523, which caused a significant outbreak in October 2013. The origin node of the blue path is profile 3-12-9-10-550, which was the source of an outbreak in January 2011. The origin profile of the red path is 3-16-9-11-523, which is associated with at least two outbreaks in February 2014 and September 2015. In addition to the case studies above, we illustrate the longest path (17 nodes) inferred from the dataset as a dashed black line with a source node near the top-left of the network. The origin of this path is profile 3-12-9-12-523, which was consistently detected from January 2008 to November 2016, spanning the entire dataset.