Spatial-temporal and phylogenetic analyses of epidemiologic data to help understand the modes of transmission of endemic typhoid fever in Samoa
Fig 2
Spatial-temporal and genomic analysis of typhoid fever cases (burden) in Samoa from April 2018 through June 2020.
(A) Using ArcGIS Pro v2.9, household GPS coordinates of acute cases of S. Typhi (n = 260) from April 27, 2018 to June 9, 2020 are plotted on a map of Samoa and colored according to S. Typhi genotype/sub-lineage. A point density heatmap is inferred from case coordinates. The four prominent hotspots are identified with arrows labeled 1–4, which also indicate aerial perspectives shown in the reconstructions in panel B. (B) Coordinates were binned into space-time cubes of 1km2 x 2-months (see panel C and S1 Text for additional details) and tested for significant clustering by the emerging hotspot analysis implemented in ArcGIS Pro. The resulting 3D space-time hotspots were visualized from an aerial view of 20,000 meters and 10,000 meters focusing on the four typhoid hotspots identified in panel A. In the 3D renderings, each vertical column on the map represents a stack of cubes over 1 km2 area and with a height representing 2 months of time, totaling 13 time steps, or all 26 months of this study. Aggregation of points in both space and time generate a space-time hotspot, visible as a red cube or band of several adjacent cubes. The intensity of red shading indicates statistical confidence. (C) To generate space-time cubes, points were graphed in a 3-dimensional plane based on coordinates and time, and then binned into cubes of space and time dimensions. Counts within each cube were compared to nearby cubes to extrapolate hot and cold spots with statistical support (99%, 95%, 90%, not significant). Hotspots in the x-y plane occur within a time slice. Hotspots inferred from the z-direction fall within a time series. Adapted with permission from Esri (Redlands, CA: Environmental Systems Research Institute, Inc.). Base layer map available from https://planet.openstreetmap.org.