Biofilms contribute to Pseudomonas aeruginosa persistence in a variety of diseases, including cystic fibrosis, burn wounds, and chronic suppurative otitis media. However, few studies have directly addressed P. aeruginosa biofilms in vivo. We used a chinchilla model of otitis media, which has previously been used to study persistent Streptococcus pneumoniae and Haemophilus influenzae infections, to show that structures formed in vivo are biofilms of bacterial and host origin within a matrix that includes Psl, a P. aeruginosa biofilm polysaccharide. We evaluated three biofilm and/or virulence mediators of P. aeruginosa known to affect biofilm formation in vitro and pathogenesis in vivobis-(3,5)-cyclic dimeric GMP (c-di-GMP), flagella, and quorum sensing-in a chinchilla model. We show that c-di-GMP overproduction has a positive impact on bacterial persistence, while quorum sensing increases virulence. We found no difference in persistence attributed to flagella. We conclude from these studies that a chinchilla otitis media model provides a means to evaluate pathogenic mediators of P. aeruginosa and that in vitro phenotypes should be examined in multiple infection systems to fully understand their role in disease.The formation of biofilms facilitates chronic bacterial infections and reduces the efficacy of antimicrobial therapy (20, 39). The Gram-negative pathogen Pseudomonas aeruginosa is a model organism for biofilm studies and causes both acute and chronic infections by exploiting deficiencies in host immunity. P. aeruginosa is thought to exist as a biofilm during infections of the cystic fibrosis (CF) airway (5, 48), in acute burn wounds (45), and in chronic suppurative otitis media (13). Biofilm formation in P. aeruginosa is regulated by a complex network of signals that includes small molecules, two-component systems, small RNAs, and nutritional cues (27). As a result of these signals, a matrix that consists predominately of polysaccharides and extracellular DNA is formed (1,17,25,33,35,52). While P. aeruginosa biofilms have been studied extensively in vitro, there have been few studies characterizing biofilm formation in vivo (31,45,48,53).The chinchilla model has been widely used to study Haemophilus influenzae and Streptococcus pneumoniae otitis media infections, establishing that these pathogens form biofilms in vivo (3,15,19,24,26,42). Addressing biofilms in the context of an intact immune system and the complex environmental and structural features present in a mammalian host is necessary to determine if in vitro phenotypes are relevant to clinical infections. We used a chinchilla otitis media model to characterize P. aeruginosa biofilm formation and then focused on three systems involved in pathogenesis and/or biofilm formationbis-(3Ј,5Ј)-cyclic dimeric GMP (c-di-GMP), flagella, and quorum sensing-in order to understand their contribution to P. aeruginosa infection.The intracellular second messenger c-di-GMP positively regulates aggregation and biofilm formation in P. aeruginosa (22,30,51) and mediates ...