Fig. 3: Distinct phage and antibiotic timescales collapse multidrug-resistant Pseudomonas and restore a lower-burden chronic state.

a–c Quantification of bacterial dynamics in sputum. a Relative abundance of Pseudomonas in metagenomes. b Absolute abundance normalized to human reads, revealing bacterial load reductions otherwise obscured by dominance. c Layered area chart of mucoid (blue) and nonmucoid (yellow) subpopulations, expressed as colony-forming units (CFU) per mL of sputum. Persistent layering of mucoid behind nonmucoid counts indicates phenotype dominance. Vertical dashed lines mark key events: ciprofloxacin initiation (day –4), phage initiation (day 0), and end of co-therapy (day 14). d Heatmap of isolate susceptibilities to phages P1A, PYO2, and ciprofloxacin (CIP), separated by phenotype and collection day. Plaque formation indicates sensitivity (yellow); absence indicates resistance (maroon). Asterisks denote isolates analyzed by automated antibiotic susceptibility testing (AST; values in Table S2).