Fig. 3: Dissemination patterns are associated with primary and secondary site similarity, clonal expansion, increased bacterial tissue burden, and disease stage.

Mice were infected with KPPR1-STAMPR, in a model of pneumonia that progresses to bacteremia. Tissues were harvested 24-hours (A–G) or 48-hours (H–N) post-infection and analyzed with quantitative culture and the STAMPR pipeline. A, H The extent of replication evenness within the lung is estimated by log₁₀(N_s/N_b) for each mode of dissemination, metastatic (dark purple closed circles) and direct (pink open circles). B, C, I, J Genetic distance (GD) and number of barcodes shared (FRD) between the lung:spleen (B, I) or the lung:liver (C, J) are displayed for each mouse, with indications for defining dissemination patterns as metastatic or direct, further defined in Supplementary Fig. 3. Lines connect values from the same mouse. Bacterial burden, displayed as log₁₀ CFU, is compared across the lung (D, K), spleen (E, L), liver (F, M), or blood (G, N). For (A, D–G, H, K–N), data is represented as a box plot with points representing individual animals, whisker end points indicating the minimum and maximum observed values, box boundaries representing the 25th and 75th percentile, and the middle line representing the median value. For (A, D–G), comparisons between metastatic and direct groups were assessed by two-tailed unpaired t-tests and corrected for multiple comparisons; p-values are displayed above each comparison. In (A–G), n = 17 mice infected across five independent trials; in (H–N), n = 9 mice in a single trial. STAMPR analysis was excluded for one mouse with no detectable blood CFU, and any sample with low sequencing quality. Source data are provided within the Source Data file.