Young adult chinchillas were atraumatically inoculated with Moraxella catarrhalis via the nasal route. Detailed histopathologic examination of nasopharyngeal tissues isolated from these M. catarrhalis-infected animals revealed the presence of significant inflammation within the epithelium. Absence of similar histopathologic findings in sham-inoculated animals confirmed that M. catarrhalis was exposed to significant host-derived factors in this environment. Twenty-four hours after inoculation, viable M. catarrhalis organisms were recovered from the nasal cavity and nasopharynx of the animals in numbers sufficient for DNA microarray analysis. More than 100 M. catarrhalis genes were upregulated in vivo, including open reading frames ( M oraxella catarrhalis is a Gram-negative mucosal pathogen that has attracted increased interest within the scientific and medical communities for its role in several clinically significant human infections. The bacterium is a cause of upper respiratory tract infections including sinusitis and otitis media in healthy children (10, 17, 62). More recently, M. catarrhalis has been shown to be involved in conjunctivitis in children (9) and in acute exacerbations of chronic sinusitis in adults (11). Additionally, in adults, it is an important etiologic agent of exacerbations of chronic obstructive pulmonary disease (COPD) (54,55,62). It has been estimated that M. catarrhalis is responsible for up to 10% of exacerbations of COPD in the United States, a finding which translates into as many as 4 million infections per year (43).For M. catarrhalis to cause clinical disease, it typically must spread from its initial site of colonization in the nasopharynx into either the middle ear or the lower respiratory tract. It is believed that biofilm formation is an important event involved in colonization of the nasopharynx, and a recent study demonstrated that M. catarrhalis was present in a biofilm in the middle ear of children with chronic otitis media (25). It is likely that M. catarrhalis exists in a biofilm together with other normal flora in the nasopharynx. Until relatively recently, no studies had been performed in an in vivo environment to identify and better characterize the bacterial factors involved with colonization of the nasopharynx by M. catarrhalis. However, utilizing a chinchilla model, Luke et al. (36) demonstrated that type IV pili are important for colonization by M. catarrhalis in this animal model.Previous studies have examined the human antibody response to known surface proteins of M. catarrhalis as a surrogate for identification of bacterial genes expressed in vivo (for a representative example, see reference 42), and one study was able to detect mRNA from a small number of selected M. catarrhalis genes in nasopharyngeal secretions from young children with acute respiratory tract illness (39). The demonstration that the chinchilla nasopharynx can be colonized by M. catarrhalis (5, 36), together with the development of M. catarrhalis DNA microarrays (19,65), presented the op...