Fig 2. Phylogenetic tree of Salmonella Typhimurium isolates obtained from blood culture and household visits performed within the HDSS catchment area.

The phylogenetic tree is based on mapping Salmonella Typhimurium ST313 lineage II to reference strain D23580. The sequencing data from this study is analyzed in the context of 5 diverse African ST313 lineage II strains included as references, isolate DT2B was included to root the phylogenetic tree [30]. The branch tips and names from the isolates obtained in this study are color-coded based on village of collection. Time: The month of isolation is shown as a color gradient in purple. Cluster: clusters and pairs are color coded on household level. Blood/Stool: origin of the paired and clustered isolates whereby red represents blood and yellow represents stool.