Introduction: Otitis media (OM), an infection of the middle ear, disproportionately impacts disadvantaged populations globally, including Australian First Nations children. Chronic or recurring OM is the leading cause of preventable hearing loss, with standard interventions unable to prevent this increased health burden. Clinical outcomes may depend on not only presence or absence of pathogenic bacteria, but also the broader microbial diversity and their interactions, which therefore warrant further investigation.
Methods: Aboriginal and Torres Strait Islander children (2-7 years old) were recruited from two Queensland communities (one regional, one remote), with paired upper respiratory tract swabs collected alongside ear health examinations. One swab was used for culturomics analyses using selective media and MALDI-TOF identification. A parallel swab was used for pathogen-specific qPCR and 16S (V3/V4) amplicon sequencing analyses. Streptococcus pneumoniae and Haemophilus influenzae isolates underwent whole genome sequencing, with genomic predictions confirmed using gold-standard laboratory protocols.
Results: 103 children were recruited, of which 16.8% presented with healthy ears and no record of previous OM. In total, 2451 bacterial isolates were obtained, representing 237 species. Culture data showed higher prevalence and specific bacterial species correlating with healthy ears, which was also reflected in the 16S data. An otopathogen (S. pneumoniae, H. influenzae, Moraxella catarrhalis) was detected in 81% of children, spanned across all study OM subgroups, and differed in prevalence and load between children from the two communities. Overall nasal microbiota was significantly different in context of OM status and nasal symptoms. Sequences likely representing a recently described species (Candidatus Ornithobacterium hominis) clustered with otopathogens and were rarely found in healthy children’s samples. Most H. influenzae isolates were non-typable, with multiple genotypes often co-colonising. Conversely, 23 S. pneumoniae serotypes were predicted from genomic analyses, with 21/23 predictions confirmed by Quellung reaction. Of note, some children carried serotypes included in the 23vPPV vaccine, despite having been vaccinated.
Conclusions:
The co-occurrence of Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum in the upper respiratory tract correlated with healthy ears, with microbial ecological complexity likely impacting on ear health and disease. Otopathogen presence alone is not an indicator of upper respiratory tract disease.