Taking a deep dive into vaccine effects on the respiratory microbiome in Fiji

Published in Microbiology
Taking a deep dive into vaccine effects on the respiratory microbiome in Fiji

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BioMed Central
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The association between pneumococcal vaccination, ethnicity, and the nasopharyngeal microbiota of children in Fiji - Microbiome

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.

Streptococcus pneumoniae (the pneumococcus) is a significant global pathogen that can also live harmlessly in the nose of healthy people. In 2011, about one third of the 1.3 million pneumonia deaths in young children were caused by pneumococcus.

The story behind our paper began over a decade ago with the Fiji Pneumococcal Project, a randomised control trial in Fiji that examined various pneumococcal vaccine schedules. While the population in Fiji is small – around 850,000 people – diseases caused by pneumococci (such as pneumonia and meningitis) are a significant problem. In our vaccine trial, we proved that the pneumococcal conjugate vaccine was effective, ultimately leading to introduction of the 10-valent pneumococcal conjugate vaccine in Fiji in 2012.

Our group, based at the Murdoch Children’s Research Institute, has continued to collaborate with the Fiji Ministry of Health & Medical Services on numerous projects to investigate the burden of invasive pneumococcal disease, pneumococcal carriage, and the impact of vaccine introduction.

Pneumococcal conjugate vaccines reduce pneumococcal disease as well as pneumococcal carriage. However, they only protect against a subset of the 90+ known pneumococcal serotypes. Following vaccine introduction, carriage of vaccine-serotypes decreases, whereas carriage of serotypes not included in PCVs increases in a phenomenon known as serotype replacement. Knowing that PCV can have ecological effects on pneumococcal colonisation has led us and others to wonder whether PCV possibly has more broad effects on the nasopharyngeal microbiota. We also knew from our previous studies in Fiji that the two main ethnic groups in Fiji – indigenous Fijians (iTaukei) and Fijians of Indian descent (FID) – experience different prevalence of pneumococcal carriage and disease. In a follow-up study, we found that the effects of the pneumococcal polysaccharide vaccine on bacterial carriage also differed by ethnicity. These observations raised some interesting questions:

  1. Does pneumococcal conjugate vaccination affect the nasopharyngeal microbiota?
  2. Do the effects of pneumococcal conjugate vaccination differ depending on ethnic group?


Sample collection in Fiji

We decided to investigate. Our first challenge was determining which samples to use. We conducted cross-sectional carriage surveys before and after PCV10 introduction, however we were concerned that temporal differences and secular trends in bacterial carriage may confound our attempts to investigate vaccine effects. Therefore, we returned to our samples from the original vaccine trial to answer these questions, as nasopharyngeal swabs from vaccinated children and unvaccinated controls had been collected contemporaneously. Fortunately, they had been kept frozen at -80°C with minimal freeze-thaw in the years since the trial finished.

The next challenge was for us to conduct microbiome analyses: despite being experienced microbiologists, we did not have microbiome analysis established in our laboratory. Fortunately, Laura Boelsen, a PhD student with a background in microbiology and a penchant for bioinformatics, was up to the task. Our collaborative team from Australia and Fiji enlisted fellow pneumococcologists and microbiome experts at the Institute for Infectious Diseases in Bern, Switzerland, and Laura visited them for 3 weeks to learn from their experience in microbiome studies of the respiratory tract. Laura returned to Melbourne, conducted the bench work to prepare the samples, liaised with our in-house genomics facility for sequencing, and performed the analysis.

Coat of arms of the City of Bern, Switzerland. Source Wikipedia.

So what did we find? Children who received PCV had a similar microbiota to unvaccinated controls, suggesting that PCV did not affect the nasopharyngeal microbiota overall. The two ethnic groups had distinct differences in microbiota – in both microbial composition and structure. Intriguingly, PCV was associated with different microbiota within each ethnic group – in iTaukei children PCV was associated with lower relative abundance of Streptococcus, and in FID children PCV was associated with higher relative abundance of Dolosigranulum which has been associated with healthy nasopharyngeal microbiota. Ultimately, our observations suggest that PCV has beneficial but differing effects for both ethnic groups, and underscores the public health importance of vaccination.

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