Design of effective interventions is complicated by the polymicrobial nature of otitis media. Vaccination strategies have successfully targeted single pathogens, but have failed to significantly reduce otitis media prevalence because of rapid bacterial replacement. Antibiotic therapies target multiple pathogens, but frequent treatment failures – despite good compliance and pathogen susceptibility – indicate the existence of a more complex ecology promoting the disease state. Greater understanding of the polymicrobial nature of otitis media is required if more effective interventions are to be achieved.

Most otitis media studies successfully use culture-based technologies to isolate and identify important individual pathogens. While such methods provide valuable species-specific data, the technical limitations of culture preclude more extensive investigation of polymicrobial interactions. For example, culture-based studies have clearly demonstrated the importance of Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catharralis in otitis media aetiology, but we do not know how these pathogens initially succeed in the complex microbial communities of the upper respiratory tract – the first stage of the infective process.

The aim of this study is to describe changes in the upper respiratory microbiota at two important stages of otitis media disease progression - i) at onset of otitis media in the first weeks of life and ii) following successful and failed antibiotic treatment. This will be done using culture-independent molecular technologies including sequencing of 16S-rRNA gene libraries; T-RFLP; and 454-sequencing. The use of culture-independent methods will allow extensive description of the pathogenic and commensal microbiota. This will provide a basis for future investigation of synergistic and antagonistic microbial interactions associated with pathogen colonisation and persistence in the upper respiratory tract. The long-term aim of our research is to provide data that will lead to better otitis media interventions.