Background: Glucosamine modification of Bordetella pertussis lipid A stimulates host-specific immunity. Results: Charged amino acids mediate host-specific responses to glucosamine modification, whereas uncharged amino acids are critical for responses to B. pertussis lipid A. Conclusion: Multiple sites of interaction, both conserved and unique, are utilized for discrimination of lipid A variants. Significance: This is the first study to systematically dissect penta-acylated lipid A recognition.