The association between pneumococcal vaccination, ethnicity, and the nasopharyngeal microbiota of children in Fiji

Abstract

Background: Streptococcus pneumoniae is a significant global pathogen that colonises the nasopharynx of healthy children. Pneumococcal conjugate vaccines, which reduce nasopharyngeal colonisation of vaccine-type S. pneumoniae, may have broader effects on the nasopharyngeal microbiota; however, data are limited. In Fiji, nasopharyngeal carriage prevalence of S. pneumoniae and other colonising species differ between the two main ethnic groups. Here, we examined the association between the 7-valent pneumococcal conjugate vaccine (PCV7) and the nasopharyngeal microbiota of children in Fiji, including for each of the two main ethnic groups-indigenous Fijians (iTaukei) and Fijians of Indian descent (FID).

Method: The nasopharyngeal microbiota of 132 Fijian children was examined using nasopharyngeal swabs collected from 12-month-old iTaukei and FID children who were vaccinated (3 doses PCV7) or unvaccinated in infancy as part of a phase II randomised controlled trial. Microbiota composition was determined by sequencing the V4 region of the 16S rRNA gene. Species-specific carriage of S. pneumoniae, Haemophilus influenzae, Moraxella catarrhalis and Staphylococcus aureus was determined using real-time quantitative PCR. Associations between microbiota composition and other host and environmental factors were considered in the analysis.

Results: PCV7 had no overall impact on microbial diversity or composition. However, ethnic differences were observed in both diversity and composition with iTaukei children having higher relative abundance of Moraxella (p = 0.004) and Haemophilus (p = 0.004) and lower relative abundance of Staphylococcus (p = 0.026), Dolosigranulum (p = 0.004) and Corynebacterium (p = 0.003) compared with FID children. Further, when we stratified by ethnicity, associations with PCV7 could be detected: vaccinated iTaukei children had a lower relative abundance of Streptococcus and Haemophilus compared with unvaccinated iTaukei children (p = 0.022 and p = 0.043, respectively); and vaccinated FID children had a higher relative abundance of Dolosigranulum compared with unvaccinated FID children (p = 0.037). Children with symptoms of an upper respiratory tract infection (URTI) had a significantly different microbiota composition to children without symptoms. The microbiota composition of iTaukei children without URTI symptoms was most similar to the microbiota composition of FID children with URTI symptoms.

Conclusions: Associations between PCV7 and nasopharyngeal microbiota differed within each ethnic group. This study highlights the influence that ethnicity and URTIs have on nasopharyngeal microbiota.

Keywords: Ethnicity; Fiji; Nasopharyngeal microbiota; Pneumococcal conjugate vaccination; Streptococcus pneumoniae.

Fig. 1

nMDS of the dissimilarity in microbial composition using both abundance-based and binary-based measures by vaccination status (a and b, respectively), by ethnicity (c and d, respectively), in iTaukei children by vaccination status (e and f, respectively) and in FID children by vaccination status (g and h, respectively). The centre points represent the mean of each group and the lines represent distance from the mean for each sample. p values calculated using PERMANOVA. Stress values for figures are 0.158 (a and c), 0.216 (b and d), 0.154 (e), 0.218 (f), 0.149 (g) and 0.215 (h)

Fig. 2

Top ten most important OTUs (as ranked by mean decrease in accuracy) in random forest models for ethnicity (a) and symptoms of an URTI (b). Only ten OTUs are shown to highlight the most significant OTUs that separate iTaukei and FID children, and children with and without symptoms of an URTI

Fig. 3

nMDS of the dissimilarity in microbial composition by ethnicity and symptoms of an upper respiratory tract infection using abundance-based (a) and binary-based (b) measures. Shown are iTaukei children, with (light blue) or without (dark blue) symptoms of an upper respiratory tract infection, and FID children, with (light brown) or without (dark brown) symptoms of an upper respiratory tract infection. The centre points represent the mean of each group and the lines represent distance from the mean for each sample. There was a significant difference between the four groups (p = 0.001), p value calculated using PERMANOVA. Stress values for figures are 0.158 (a) and 0.216 (b)

Fig. 4

Relative abundance (%) heatmap including all 132 samples. Sample clustering is shown on the left-hand side. Taxa with a relative abundance above 30% in at least one sample are shown at the bottom. Where multiple OTUs are from the same genus ‘.1’ has been used for subsequent OTUs. ‘Others’ represents the remaining taxa in each sample. Clusters for samples have been coloured to show clustered groups: Cluster 1 (shown in dark blue), Cluster 2 (shown in green) dominated by Moraxella, Cluster 3 (shown in yellow) dominated by Dolosigranulum, Cluster 4 (shown in purple) dominated by Dolosigranulum and Corynebacterium, Cluster 5 (shown in orange) dominated by Haemophilus, and Cluster 6 (shown in grey) dominated by Pseudomonas. The vaccination status (unvaccinated—blue; vaccinated—red), ethnicity (iTaukei—turquoise; FID—gold) and whether the child had any symptoms of an upper respiratory tract infection (no URTI—light blue; URTI—brown) are shown in bars on the right of the heatmap

Fig. 5

Network correlation map based on the 100 most common OTUs considering samples from all 132 children. Shown are SparCC correlations with p value < 0.05 and r > 0.3. The main OTUs from the top seven genera are shown by larger node size. Colours of nodes are grey except for the seven most common genera. The edge (connecting line) colour represents a positive (green solid lines) or negative (red dashed lines) correlation between two OTUs, with thicker lines representing stronger correlations. Only those correlations with genus-level classification are shown and are labelled with the OTU genus