A phagocyte that engulfs a bacterium has not finished its job; it must kill what it has swallowed. Neutrophils and macrophages kill through two systems that work together. The first is the oxidative burst. When the phagocyte engulfs a particle, the NADPH oxidase complex assembles on the phagosomal membrane and transfers electrons from NADPH to molecular oxygen, producing superoxide (O2−). Superoxide dismutase converts it to hydrogen peroxide (H2O2), and myeloperoxidase uses H2O2 plus chloride to make hypochlorous acid (HOCl), the same reactive molecule as household bleach. These reactive oxygen species damage bacterial DNA, proteins, and membranes. The second system is non-oxidative: antimicrobial peptides such as defensins, proteases such as cathepsin G and elastase, and lysozyme degrade the bacterial cell wall and proteins inside the phagosome.
When NADPH oxidase is defective — as in chronic granulomatous disease — the phagocyte still ingests bacteria normally, but the oxidative burst fails. Catalase-positive organisms such as Staphylococcus aureus, Serratia marcescens, Burkholderia cepacia, and Aspergillus species survive inside the phagocyte, and the body responds by walling them off in granulomas. The result is recurrent abscesses in the skin, lymph nodes, liver, and lungs, often beginning in early childhood. The key point is that ingestion and killing are separate steps; a defect in killing produces infection even though the phagocyte reaches the bacterium and takes it in.