Inflammation of the middle ear, known as otitis media (OM), affects over 80% of children at least once by the age of 3 years and is a major reason for antibiotic prescriptions and childhood surgeries. Children with recurrent acute otitis media (rAOM) experience severe disease, with frequent recurring episodes of ear infection. Although OM is a common disease of childhood, there are children who are exposed to known OM risk factors but who do not develop rAOM. These children appear resistant to the disease. One factor that may determine whether a child is rAOM-prone or rAOM-‘resistant’ is the microbiome of the upper respiratory tract (URT). We hypothesise that ‘resistant’ children carry protective, non-pathogenic bacteria in the URT that contribute to their resistance to developing rAOM.
The aim of this project is to characterise the microbiome of the upper respiratory tract (URT) in these two groups of children using 16S rRNA profiling and whole genome shotgun sequencing techniques. The microbiome profiles of the rAOM-prone (case) and rAOM ‘resistant’ (control) groups, as determined from the 16S rRNA sequence data, are used to select a representative subset of samples to undergo whole genome shotgun sequencing. The whole genome data will allow us to identify protective genes (such as those that code for bacteriocins or molecules that may interfere with other bacteria) in the control samples; as well as pathogenic genes from the case samples that will increase our understanding of the mechanisms of this complex microbial disease. Using both the 16S rRNA and whole genome shotgun sequencing data, candidate commensal bacteria from the controls will be selected and tested in vitro to identify protective microbial factors that may contribute to the healthy children’s apparent resistance. This improved understanding of the role of the microbiome in OM will be used to initiate studies on developing a probiotic prophylaxis for rAOM.