Pneumococcal phase variation of 37 middle ear and 31 nasopharyngeal isolates obtained from children with acute otitis media was examined in the absence of intervening culture. The fraction of the opaque colonies was significantly higher in middle ear isolates than in nasopharyngeal isolates. The difference is probably the result of the pneumococci adapting to differential selective environments.Streptococcus pneumoniae first colonizes the mucosal surface of the human nasopharynx and can then infect the middle ear cavity via the Eustachian tubes to cause acute otitis media (AOM). In 1994, Weiser et al. reported spontaneous, reversible intrastrain phase variation of pneumococci in colony opacity on transparent agar surfaces (15). Transparent variants associated with low levels of capsular polysaccharide are able to most efficiently colonize the nasopharynx in animal models of pneumococcal carriage (8). In contrast, opaque variants associated with greater amounts of capsular polysaccharide colonize poorly in animals and provide greater resistance to clearance by phagocytes but at the same time decrease the adherence of opaque variants to host cells (2, 4). Thus, the intrastrain phase shifts of pneumococci are hypothesized to be adaptations to different stages in the pathogenesis of infections (1,8,10,13,14). However, the phase shifts have never been clearly demonstrated with human samples. A study in 2001 examined 19 "minimally passaged" paired nasal and blood isolates, but no statistical association was observed between the phase and body isolation site (P ϭ 0.51) (12). The present study was designed to investigate the morphological phase of pneumococci by plating them on transparent agar immediately upon their isolation from the nasopharynx and middle ear of children with AOM. By avoiding any growth between isolation and plating, we hoped to minimize the effects of bacterial growth in vitro on bacterial phase. The study focused on samples from young children because of their high rates of pneumococcal carriage and AOM.Middle ear and nasopharyngeal cultures were collected from all children between 5 and 70 months of age who presented at our clinic with AOM from 2008 to 2010 and who had not previously been treated with antibiotics. No subsequent cultures were collected for the study from any patients at later clinic visits. The swabs used to collect cultures were stored on transport agar with charcoal media (Eiken Chemical Co., Tokyo, Japan) at room temperature and transported to the laboratory for processing, and within 18 h of collection, they were plated on tryptic soy agar (TSA) plates for phase determination (with no intervening culture).Samples were obtained from 42 children, 25 males and 17 females, with a median age of 21.5 months. The children were all unrelated to each other, and only one culture from the nasopharynx and one from each ear were included in the study for a single patient, when available from the patient. All together, from the 42 children, 37 middle ear and 31 nasopharyngeal cultures were e...