Respiratory microbiota: interactions with maternal pneumococcal immunisation and live attenuated influenza vaccine (LAIV) in children

Abstract

Respiratory tract infections (RTIs) are a leading cause of mortality in children under five years. The high burden of RTIs is experienced in low and middle-income countries (LMICs). RTIs are caused by bacteria and viruses that are common colonisers of the respiratory microbial ecosystem (microbiome) and generally colonize the nasopharynx asymptomatically. There is increasing evidence from high-income countries (HICs) that the respiratory microbiome plays a critical role in pathogen-resistance and containment, and immune modulation including vaccine-induced immune responses in all stages of life. In addition, there is also increasing evidence that vaccines may alter the composition of the microbiome. However, data illustrating the development of respiratory microbiota, vaccine-microbiome interactions, and the role of the respiratory microbiome in vaccine immunogenicity in children from LMIC settings is limited. Understanding these aspects presents the first steps towards the development of effective intervention strategies targeting the respiratory microbiome in settings with high-disease burden, including enhancing robust immune responses to vaccines. Current understanding asserts that in LMICs, asymptomatic carriage of pathogenic bacteria and viruses including Streptococcus pneumoniae is high and occurs rapidly in early life. In addition, poor vaccine immunogenicity is common; reasons for this are not fully understood but could be linked to the microbiome.

To address these gaps, this thesis describes a series of investigations using data and materials obtained through two longitudinal clinical trials conducted in Gambian children. The first study investigates the interactions between live attenuated influenza vaccine (LAIV) and nasopharyngeal microbiota, including interactions specifically focused on S. pneumoniae, during the first 21 days following immunisation in young children (2-5 years of age). The second study investigates the development of respiratory microbiota in the first nine months of life and the effect of maternal pneumococcal-conjugate vaccination (PCV [Prevenar13™]) on this development in Gambian infants.

Results from the first study showed a high baseline S. pneumoniae carriage rate in both LAIV and control groups (74.9%). By day 21, S. pneumoniae carriage rate increased in response to LAIV (84.5%), but not in controls. An increase in S. pneumoniae density was also seen in LAIV immunized children at day 7 and day 21, but not in the control group. Younger age, the presence of asymptomatic respiratory viruses at baseline, and higher LAIV shedding at day 7 were also associated with higher pneumococcal density. Microbiome analyses showed a temporary impact of LAIV administration on the overall microbial community composition at day 7, which was no longer significant at day 21. In addition, the presence of asymptomatic respiratory viruses at baseline also induced an independent effect on day 7 microbial communities. On taxa level, LAIV administration resulted in modest increases in the abundance of Psychrobacter spp and an oral bacterium, Gracilibacteria spp, with a decrease in Neisseria spp and several less abundant taxa.

In children who received LAIV, baseline microbial community composition did not impact mucosal IgA response but was associated with increases in both Matrix and Nuclear protein (MNP)-specific CD4+ T-cell responses and ex vivo T Follicular Helper (Tfh)-like cells. Microbiota profiles with higher abundances of lactic acid producing bacteria including Dolosigranulum spp. and Corynebacterium propinquum at the time of LAIV receipt were found in seroconvertors, and those with MNP-specific and Tfh-like CD4+ T-cell following vaccination.

Results from the second study showed that, post-partum, the nasopharynx of Gambian infants is initially colonized with mixed bacterial communities. Within the first fourteen days, there is rapid niche differentiation, initially dominated by Staphylococcus with concurrent acquisition of other bacteria including Corynebacterium, Dolosigranulum, Haemophilus, Streptococcus and Moraxella. Season of sampling, presence of young children in the household and sleeping together with other siblings influence the development of the nasopharyngeal microbiota. Interestingly, the effect of maternal PCV13 immunisation on overall microbial composition occurred later, observed at six months of age rather than earlier in life. On taxa level, maternal PCV13 immunisation was associated with modest changes in several microbial taxa during development.

The findings of this thesis show that the impact of LAIV on S. pneumoniae density and nasopharyngeal microbiota in children is modest and exacerbated by pre-existing asymptomatic respiratory viral infection. In addition to illustrating the importance of asymptomatic viral-viral and viral-bacterial interactions in the respiratory tract, these findings provide reassurance for use of LAIV to expand influenza vaccine programmes in LMIC with high pneumococcal carriage. This thesis also demonstrates that nasopharyngeal microbiota composition may play a role in modulating adaptive immunity to LAIV in children. This is an important finding in the context of formulating interventions to improve immunogenicity to intranasal or mucosal administered vaccines in the future. Finally, this thesis adds to the information gap illustrating the development of the nasopharyngeal microbiome and how early life vaccine interventions may affect this process. However, further studies are required to investigate the impact of these effects on early life respiratory health.