Little is known about the effect of antibiotics on eradication of carriage and development of resistance in Haemophilus influenzae in individuals with chronic obstructive pulmonary disease (COPD). Our goals were to assess antibiotic susceptibilities, prevalence of resistance genes, and development of resistance in H. influenzae and to evaluate the effect of macrolide and fluoroquinolone administration on H. influenzae eradication. Data were from a 15-year longitudinal study of COPD. Genome sequence data were used to determine genotype and identify resistance genes. MICs of antibiotics were determined by reference broth microdilution. Generalized linear mixed models were used to evaluate associations between antibiotic use and H. influenzae eradication. We examined 267 H. influenzae isolates from 77 individuals. All newly acquired H. influenzae isolates were susceptible to azithromycin. C hronic obstructive pulmonary disease (COPD) affects approximately 24 million people in the United States and is the third leading cause of death worldwide (1, 2). Disease is characterized by intermittent acute exacerbations of COPD (AECOPD) that result in missed work, clinic visits, emergency room visits, hospital admissions, and respiratory failure requiring mechanical ventilation. Approximately half of AECOPD cases are caused by bacterial infection, with nontypeable Haemophilus influenzae being the most common pathogen (3, 4). H. influenzae also colonizes the lower airways of individuals with COPD for extended periods and contributes to inflammation, impaired pulmonary function, and increases in daily respiratory symptoms (3-6).Clinical studies indicate that antibiotic therapy results in accelerated recovery and reduced complications of moderate and severe exacerbations (7,8). Thus, antibiotics, particularly oral macrolides and fluoroquinolones, are commonly prescribed for treatment of AECOPD (4,(8)(9)(10). Several recent clinical trials demonstrated that daily azithromycin results in fewer exacerbations and improved quality of life, and thus, azithromycin is increasingly administered prophylactically to many COPD patients (11)(12)(13).In spite of widespread administration of antibiotics for treatment and prophylaxis of infection in COPD, remarkably little is known about the effect of antibiotics on carriage and eradication of respiratory tract pathogens, particularly H. influenzae. Prior studies suggested that fluoroquinolones were superior to macrolides in eradicating H. influenzae (14-17). However, a significant limitation of these studies is that eradication was assumed if the patient was unable to produce sputum and/or was determined by a single posttreatment sputum culture. This study design misses the possibility of H. influenzae persistence in spite of negative culture, a scenario known to be common in COPD (3). When microbiologic confirmation was obtained, the strains were not genotyped, precluding determination of whether a positive culture represented unsuccessful bacterial eradication or acquisition of a new strain...