A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children

Abstract

A longitudinal study was undertaken in infants living in the Maela refugee camp on the Thailand-Myanmar border between 2007 and 2010. Nasopharyngeal swabs were collected monthly, from birth to 24 months of age, with additional swabs taken if the infant was diagnosed with pneumonia according to WHO clinical criteria. At the time of collection, swabs were cultured for Streptococcus pneumoniae and multiple serotype carriage was assessed. The bacterial 16S rRNA gene profiles of 544 swabs from 21 infants were analysed to see how the microbiota changes with age, respiratory infection, antibiotic consumption and pneumococcal acquisition. The nasopharyngeal microbiota is a somewhat homogenous community compared to that of other body sites. In this cohort it is dominated by five taxa: Moraxella, Streptococcus, Haemophilus, Corynebacterium and an uncharacterized Flavobacteriaceae taxon of 93% nucleotide similarity to Ornithobacterium. Infant age correlates with certain changes in the microbiota across the cohort: Staphylococcus and Corynebacterium are associated with the first few months of life while Moraxella and the uncharacterised Flavobacteriaceae increase in proportional abundance with age. Respiratory illness and antibiotic use often coincide with an unpredictable perturbation of the microbiota that differs from infant to infant and in different illness episodes. The previously described interaction between Dolosigranulum and Streptococcus was observed in these data. Monthly sampling demonstrates that the nasopharyngeal microbiota is in flux throughout the first two years of life, and that in this refugee camp population the pool of potential bacterial colonisers may be limited.

Fig 1. Aggregate of all routine swabs from all infants, proportional abundance of the 15 OTUs that account for >98% of the cohort microbiota, by age in months (1–24).

OTUs are colour grouped by phylum: Actinobacteria (orange), Bacteroidetes (yellow), Firmicutes (green), Proteobacteria (blue).

Fig 2. NMDS plot based on Jaccard distance (a-c) and Bray-Curtis dissimilarity (d-f), coloured according to age.

a) and d) show 50% ellipses and centroids of the first 12 months of life as an overlay on the full 24-month dataset, while b) and e) show ellipses for 13–24 months overlaid on the full 24-month dataset. Ellipses and datapoints are presented in corresponding colours. Significant OTUs driving the ordination (p<0.0001 and with vector length >0.25) are shown in d) and f). Increasing age is significantly correlated with both x and y axis.

Fig 3. Boxplots of proportional abundances in routine swabs of a) Staphylococcus, b) Corynebacterium II, c) Moraxella II, d) unclassified Flavobacteriaceae I, e) Streptococcus I, f) Moraxella I.

Fig 4. Microbiota profile of one child from 1–24 months of age.

Swabs taken during a pneumonia episode are highlighted by boxes. Where cultured, pneumococcal serotype in the sample is indicated in the top pane. OTUs are colour grouped by phylum: Actinobacteria (orange), Bacteroidetes (yellow), Firmicutes (green), Proteobacteria (blue).

Fig 5. Proportional abundances of a) Corynebacterium II, b) Dolosigranulum, c) Staphylococcus, d) Streptococcus I, grouped by the presence/absence of cocolonisers.

There is some support for the observation that Dolosigranulum is negatively associated with Streptococcus pneumoniae in the squat distributions seen in (d) however Corynebacterium II does not appear to play a part in that interaction.

Fig 6. Heatmap of pneumococcal serotypes detected in culture per infant.

The mean number of types acquired per child over the study period is 7.4.