Fig. 5: AM-associated phage decay and adsorption inhibition assumption.

A Uninfected mice were given clodronate (blue) or EL (red) by intra-tracheal instillation (n = 3–4 each) 4 days prior phage PAK_P1 (5 × 10⁷ PFU) at t = 0 h. Lungs were collected and homogenized at indicated time points. Data fitted using a monoexponential decay model with decay rate values indicated (p values, two-tailed Mann–Whitney U test, are indicated). B Uninfected mice received intranasally PBS (n = 2) or phage PAK_P1 (5 × 10⁷ PFU) (n = 6) at t = 0 h and broncho alveolar lavage was performed 4 h post-administration to sort and count AM and quantify phage DNA by qPCR. C Counts of phage-associated fluorescent signals in individual AM collected from uninfected mice and incubated without (control) or with phage PAK_P1 in absence or presence of cytochalasin B (N = number of AM observed for each condition). Boxplots display median (center line), first and third quartiles (box limits), and whiskers extending to 1.5×IQR from the quartiles (p values, two-tailed Mann–Whitney U test, are indicated). D Representative images from AM incubated with phage PAK_P1 in presence or absence of cytochalasin B. Median dynamics with various adsorption inhibition parameter values after infection and phage treatment for (E) immunocompetent control (i.e. EL) and F AM-depleted mice. Dynamics of bacteria (red), phage (green), alveolar macrophage (AM, light blue), and lung neutrophils (dark blue) based on the model and its median parameters (Fig. 2A, Supplementary Methods), assuming phagocytosis rate value from the inference of the data of Fig. 4A. Line widths increase depending on the maximal adsorption inhibition by AM: 0%, 15%, 30% and 60%, from the thinnest to the widest line. The maximal adsorption inhibition value leading to the best model (i.e., 30%) is represented by solid lines, while the others are represented by dotted lines. The violin and dots represent the distribution and values of observations: CFUs in red and PFUs in green. The limit of detection (LOD) for CFUs is represented by the light red horizontal dashed line (LOD = 2.4 log₁₀ CFU/mL) For AM-depletion, all the observations were below the LOD.