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Aim  This study aims to describe the microbiology of middle ear fluid ( MEF ) in a cohort of children vaccinated with   S   treptococcus pneumoniae  conjugate vaccine ( PCV 7) having ventilation tube insertion. Nasopharyngeal ( NP ) carriage of otopathogens in these children is compared with children without history of otitis media.    Methods  Between  M ay and  N ovember 2011,  MEF  and  NP  samples from 325 children aged <3 years were collected in three major centres in New Zealand at the time of ventilation tube insertion. An age‐matched non‐otitis‐prone comparison group of 137 children had  NP  samples taken. A questionnaire was completed by both groups.    Results  Immunisation coverage with at least one dose of  PCV 7 was 97%.   H   aemophilus influenzae  was cultured in 19.4% of  MEF  and was polymerase chain reaction (PCR) positive in 43.4%.   S   . pneumoniae  and   M   oraxella catarrhalis  were cultured in <10% of  MEF  samples but were PCR positive for 23.1% and 38.7%, respectively.   H   . influenzae  was the most common organism isolated from  NP  samples (60%) in the grommet group, while   M   . catarrhalis  (56%) was the most common in the non‐otitis prone group.   S   . pneumoniae  was more commonly found in the nasopharynx of children with ear disease (41% vs. 29%). 19 F  was the most prominent   S   . pneumoniae  serotype in  NP  samples of both groups, but no serotype dominated in  MEF . Ninety‐five per cent of   H   . influenzae  isolates were confirmed to be non‐typeable   H   . influenzae.Conclusion  In this cohort of children with established ear disease requiring surgical intervention, non‐typeable   H   . influenzae  is the dominant pathogen in both the nasopharynx and  MEF .

What is behind the ear drum? The microbiology of otitis media and the nasopharyngeal flora in children in the era of pneumococcal vaccination