Abstract
There is growing concern that interventions that alter microbial ecology can adversely affect health. We characterised the impact of the seven-valent pneumococcal conjugate vaccine (PCV7) on pneumococcal carriage and the bacterial component of the nasopharyngeal microbiome during infancy. Newborns were recruited into three groups as follows: Group1 (n = 33) was the control group and comprised infants who received PCV7 after 6 months and came from unvaccinated communities. Group 2 (n = 30) came from unvaccinated communities and Group 3 (n = 39) came from vaccinated communities. Both group 2 and 3 received PCV7 at 2, 3 and 4 months. Culture and 16 S rRNA gene sequencing were performed on nasopharyngeal specimens collected at regular intervals from infants. Nasopharyngeal carriage of PCV7 serotypes in Group 1 was significantly higher than in Group 2 and 3 (p < 0.01). However, pneumococcal carriage remained comparable due to an expansion of non-vaccine serotypes in Groups 2 and 3. Determination of phylogenetic dis(similarities) showed that the bacterial community structures were comparable across groups. A mixed effects model showed no difference in community richness (p = 0.15) and Shannon α-diversity (p = 0.48) across the groups. Immediate replacement of pneumococcal vaccine serotypes with non-vaccine serotypes may mitigate the impact of PCV7 on nasopharyngeal bacterial community structure and ecology.
Highlights
There is growing concern that interventions that alter microbial ecology can adversely affect health
Few studies have reported changes in the epidemiology of bacterial diseases associated with widespread use of PCV714–16; it is unclear how these changes are related to nasopharyngeal microbial colonisation
There is growing concern that vaccination and antimicrobial treatment strategies that alter the normal balance of microbial communities could have temporal or pervasive adverse effects on health[20]. In this unique study of infants followed up from birth to 1 year with intensive sampling, we have demonstrated that while PCV7 vaccination effectively reduces the nasopharyngeal carriage of vaccine serotypes, pneumococcal carriage remains high among vaccinated infants due to an immediate expansion of non-vaccine serotypes throughout the first year of life
Summary
Carriage of serotype 15B was most common among Group 3 infants who came from heavily vaccinated villages and received PCV at 2, 3 and 4 months (Fig. 2G). The top ten genera, which included Streptococcus, Staphylococcus, Corynebacterium, Pseudomonas, Moraxella and Haemophilus, accounted for more than 70% of the microbiota throughout the first 12 months of life (Fig. 3B) These microbes form the backbone of the infant nasopharyngeal microbiome while there are numerous low abundance microbes, which may account for most of the diversity within and across individuals. A total of 9 OTUs representing Streptococcus, Moraxella, Dolosigranulum, Haemophilus, Pseudomonas and Pelomonas genera had significantly different abundance across the vaccination groups after controlling for confounders in a mixed effect model performed as described above (Table 2). Group 2 and Group 3 infants had reduced abundance of 7 of the 9 OTUs compared to Group 1 infants
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