Inferring evolutionary pathways and directed genotype networks of foodborne pathogens
Fig 1
The 1,673 unique MLVA profiles isolated between 1 January 2008 and 31 December 2016.
Each horizontal line shows the temporal history of a given MLVA profile, with each point showing the day a sample was collected. The dataset contains 17,005 cases of STM, which comprises 98.7% of all isolated cases in NSW over this 3,287 day period. The profiles are sorted according to the date of their first detection—resulting in a diagonal outline—indicating that new MLVA profiles are usually detected regularly throughout the observational period. Once detected, the profiles typically continue to be observed in the dataset. Three actual case studies associated with outbreaks previously investigated by the Australian Department of Health (see Materials and methods) are highlighted in different colors, illustrating distinct MLVA profiles that are grouped according to their genetic and temporal proximity (that is, profiles with the same color lie on the same inferred evolutionary path).