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...

The upper respiratory tract microbiome of indigenous Orang Asli in north-eastern Peninsular Malaysia

“…The significant proportion of individuals who harbour profiles that are being considered to be potentially protective either in terms of acute respiratory infections 55 or chronic disease such as asthma 56 – 58 , is intriguing. Similar profiles were observed in Fijian children with either Dolosigranulum or Haemophilus / Corynebacterium dominant profiles 53 although there are important contrasts, remembering that these were observed in older children and adults, we observed Corynebacterium and Corynebacterium / Dolosigranulum profiles in the Orang Asli. Lastly, while Delftia is not uncommon as an oral bacterium 59 , given the common finding of Delftia and Ochrobactrum as contaminants in microbiome research 60 we interpret these four samples with extreme caution.…”

“…A similar interaction may also explain the absence of Streptococci 50 —although we recognise in both cases that our hypothesis requires further testing due to the identification of both S. aureus and pneumococcal carriage among our participants. A Moraxella dominated profile similar to CST6, is also present in the Orang Asli, a profile which has also been observed in healthy adults in a European setting 51 , as well as in both Kenyan 52 and Fijian children 53 (where it is more common in iTaukei, the indigenous Fijians). We also saw a Moraxella - Haemophilus profile which hasn’t been described previously.…”

Nasopharyngeal Microbiota Profiles in Rural Venezuelan Children Are Associated With Respiratory and Gastrointestinal Infections

“…However, the top 15 most abundant OTUs in our study contained several bacteria that are not commonly observed in developed regions, including multiple Acinetobacter species. Interestingly, other studies performed in populations that reside in humid tropical regions also reported Acinetobacter presence in the upper respiratory tract of young children [ 25 , 26 ], most likely because wet environments, such as moist soil, water plants, and seawater, are known environmental reservoirs for Acinetobacter [ 27 ]. This suggests a location-specific bacterial colonization pattern, which might have important implications for preventive and therapeutic strategies.…”

“…Interestingly, several of the bacteria that were associated with the absence of RTIs included environmental bacteria not commonly observed in developed regions such as Acinetobacter , Caulobacteraceae , and Pseudomonas . A recent study in young Fijian children residing on a tropical island also reported Pseudomonas to be abundantly present in the nasopharynx of healthy children [ 26 ]. Like Acinetobacter , Pseudomonas is present in watery environments, particularly in rivers during the period just before heavy rainfalls that lead to an influx of water into the river [ 30 ].…”

Upper Respiratory Tract Microbiome and Otitis Media Intertalk: Lessons from the Literature

“…NP swabs were collected from 132 total children belonging to the two ethnic groups that were further divided in two subgroups based on whether children had been previously vaccinated or not with PCV-7. The vaccination had no overall impact on microbial diversity or composition, but significant modifications were evident when stratifying by ethnicity: vaccinated iTaukei children had a lower relative abundance of Streptococcus and Haemophilus compared with unvaccinated ones, while vaccinated Indian descent children had a higher relative abundance of Dolosigranulum compared with those unvaccinated [55].…”