The aim of this study was to explore the upper respiratory tract (URT) microbiota of Australian Indigenous children from a remote Queensland Indigenous community and analyse the impact of season and household occupancy on microbiota composition.
Australian Indigenous children aged from 2-7 years were recruited from a remote Indigenous community in Queensland. Swabs were taken from the nose, buccal cavity and tonsils. We performed culture-based analysis with Vitek MS MALDI-TOF (bioMérieux) to identify isolates. Differences in the presence of bacterial species in relation to season and household occupancy were analysed using logistic regression (STATA/IC 15.0).
A total of 59 children were recruited, mean age = 57 months (SD = 13), 26(44%) were male. The majority attended school/daycare (n=53, 90%). Range of household occupancy r=3-12, mean=5 (SD=2). Samples were collected in spring (n=29, 49%), autumn (n=23, 39%), and winter (n=7, 12%). A total of 163 bacterial species were identified. The most prevalent were Streptococcus mitis/oralis (n=55, 93%), Streptococcus parasanguinis and Streptococcus pneumoniae (both n=44, 75%), and Haemophilus influenzae (n=43, 73%). In relation to season, Gemella haemolysans (OR=2.7), Haemophilus haemolyticus (OR=7.2), Neisseria mucosa (OR=8.4)and Prevotella species (OR=6.1) were detected significantly more often in swabs collected in winter(all p<0.05), . Lactobacillus species were significantly more prevalent in swabs collected in spring (OR=0.4, p=0.04). There was no difference in respiratory pathogens H. influenzae, S. pneumoniae, or M. catarrhalis. We observed a nominal increase in the presence of H. influenzae when household occupancy was >7 (increase from 70 to 86%, p=0.46). Otherwise, no changes to the microbiota were observed in relation to household occupancy.
Using culture-based analysis we demonstrated a broad microbiota in the URT of Australian Indigenous children. Respiratory pathogens were highly prevalent in the cohort. Season appeared to impact the URT microbiota, although not for the main respiratory pathogens. In contrast, we saw no significant effect of household occupancy on URT microbiota.