Understanding the nasopharyngeal carriage dynamics of Streptococcus pneumoniae and other microbiota in Malawian children and adults

Streptococcus pneumoniae naturally colonises the human nasopharynx, where it normally resides as a commensal. However, any change in the bacterial and host condition in the nasopharynx may lead to invasive pneumococcal disease. The human nasopharynx is also home to a broad range of other microbiota, which interact with S. pneumoniae, consequently impacting on its carriage dynamics. This thesis investigated the carriage of S. pneumoniae and other microbiota in the nasopharynx of Malawian children and adults, and factors that may impact on this. To characterise S. pneumoniae in carriage, a microarray was used, whereas the nasopharyngeal microbiota were characterised using 16SrRNA gene sequencing. Results demonstrated a broad range of carriage pneumococcal serotypes in Malawian children and adults. Carriage of nontypeable serotypes was higher in adults (~20%) compared to children (~1%). Based on carriage data only, PCV13 coverage was 60% in children and 30% in adults. The low PCV13 coverage demonstrates a high prevalence of non-vaccine serotypes in circulation, which may provide the scope for serotype replacement post vaccination. For the first time in Malawi, we have demonstrated that multiple carriage is not only common but also higher in children (40%) than in adults (19%). The study did not find any significant impact on serotype specific carriage or the degree of multiple carriage by HIV status. Despite the high levels of multiple carriage, there was no evidence of capsule switching in our setting. However CPS locus variants of 8 serotypes including the vaccine serotype 6B, 19A and 20 were identified. It is not known whether these variants have the improved ability to colonise or cause invasive disease, thereby necessitating further analysis. Studying other microorganisms in carriage showed that the Malawian nasopharyngeal microbiota was dominated by four phyla in both adults and children, namely Firmicutes (79%), Proteobacteria (17%), Actinobacteria (3%) and Bacteroidetes (1%). The data demonstrated no significant difference in the distribution of phyla between adults and children, however there was broader microbial diversity amongst HIV negative subjects compared to HIV positive subjects. Specifically, HIV infection was associated with a lower prevalence of Actinobacteria. Although anti-retroviral therapy (ART) did not impact the nasopharyngeal microbiota, our data showed differences in phyla distribution in children‟s samples collected from Karonga and Blantyre. Samples from Karonga demonstrated a significantly higher carriage of Actinobacteria and Proteobacteria, while Firmicutes were predominant in Blantyre. This diversity could possibly be attributed to existing differences in age and HIV prevalence between the two sample groups. In conclusion, our study has demonstrated a high degree of serotype diversity and multiple carriage in the Malawian population, which suggests a greater likelihood of serotype replacement post-vaccination. This study therefore, recommends further carriage surveillance studies post PCV13 in the Malawian population. Such studies should evaluate the impact of PCV13 on carriage in the Malawian population, which in turn, will provide an estimate of herd immunity. The study has also generated important preliminary findings on dominant phyla in carriage, however further studies are recommended to evaluate the impact of other microbiota on pneumococcal carriage dynamics