The nasopharynx is an important reservoir of microbes some of which can cause serious mucosal and invasive disease. The impact of the 7-Valent Pneumococcal Conjugate Vaccine (PCV-7) on pharyngeal microbial ecology is not well characterized. The aim of this study is characterize the infant nasopharyngeal microbiome and subsequently to address the hypothesis that PCV-7 vaccination influences its development. Nasopharyngeal (NP) swabs were collected from neonates at birth, bi-weekly from zero to six months and bi-monthly from six to twelve months. High co-carriage of Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis was confirmed by species-specific PCR. Molecular-fingerprinting of the infant NP microbial communities combined with partial 16S rRNA gene showed that microbes are acquired rapidly after birth and that there are distinct microbial profiles over time and across individuals. Bar-coded 454 pyrosequencing of the 16S rRNA gene showed over 800 operational taxonomic units (genera). Streptococcus was the only genus present in all the NP communities. Six genera including Streptococcus, Haemophilus, Moraxella and Staphylococcus comprised over 80% of the infant NP microbiome. Most genera had low relative abundance (<1%) and their variable accounted for much of the diversity between individuals. Although early PCV-7 intervention did not appear to alter the abundance of Streptococcus, overall, the abundance of microbes was less turbulent among infants vaccinated early, before four months. Early intervention also appeared to alter the interactions between Streptococcus and several OTUs. Streptococcus was negatively correlated with Staphylococcus, Corynebacterium and Pseudomonas; this could play a major role in replacement. Preliminary data suggests that PCV-7 intervention may alter the development of the microbiome and microbial interactions within the nasopharynx. The long term implications of this finding for PCV-7 vaccination are yet to be determined, but continued surveillance of replacement in carriage and disease is necessary as immunisation with vaccines covering more serotypes are implemented
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