Pneumococcal Colonization and the Nasopharyngeal Microbiota of Children in Botswana

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

30153231

DOI Digital object identifier for electronic documents.

10.1097/INF.0000000000002174

URI

Authors

Kelly MS, Surette MG, Smieja M, Rossi L, Luinstra K, Steenhoff AP, Goldfarb DM, Pernica JM, Arscott-Mills T, Boiditswe S, Mazhani T, Rawls JF, Cunningham CK, Shah SS, Feemster KA, Seed PC

Journal

The Pediatric infectious disease journal

Year

2018

BACKGROUND: Nasopharyngeal colonization precedes infections caused by Streptococcus pneumoniae. A more detailed understanding of interactions between S. pneumoniae and the nasopharyngeal microbiota of children could inform strategies to prevent pneumococcal infections. METHODS: We collected nasopharyngeal swabs from children 1 to 23 months of age in Botswana between August 2012 and June 2016. We tested samples for S. pneumoniae and common respiratory viruses using polymerase chain reaction. We sequenced the V3 region of the bacterial 16S ribosomal RNA gene and used random forest models to identify clinical variables and bacterial genera that were associated with pneumococcal colonization. RESULTS: Mean age of the 170 children included in this study was 8.3 months. Ninety-six (56%) children were colonized with S. pneumoniae. Pneumococcal colonization was associated with older age (P = 0.0001), a lack of electricity in the home (P = 0.02) and household use of wood as a cooking fuel (P = 0.002). Upper respiratory symptoms were more frequent in children with S. pneumoniae colonization (60% vs. 32%; P = 0.001). Adjusting for age, nasopharyngeal microbiota composition differed in colonized and noncolonized children (P = 0.001). S. pneumoniae colonization was associated with a higher relative abundance of Moraxella (P = 0.001) and lower relative abundances of Corynebacterium (P = 0.001) and Staphylococcus (P = 0.03). A decision tree model containing the relative abundances of bacterial genera had 81% sensitivity and 85% specificity for the determination of S. pneumoniae colonization status. CONCLUSIONS: S. pneumoniae colonization is associated with characteristic alterations of the nasopharyngeal microbiota of children. Prospective studies should determine if nasopharyngeal microbial composition alters the risk of pneumococcal colonization and thus could be modified as a novel pneumonia prevention strategy.

Experiment 1

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Curated date: 2021/01/10

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Subjects

Location of subjects: Botswana

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Nasopharynx Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Pneumonia acute pneumonia,chest infection due to pneumonia,pneumonia,Pneumonia (disorder),Pneumonia (disorder) [Ambiguous],Pneumonia due to other specified organism,Pneumonia due to other specified organisms,Pneumonia due to other specified organisms (disorder),Pneumonia NOS,Pneumonia NOS (disorder),pneumonia with infectious disease,Pneumonitis,Pneumonitis (disorder),Pneumonia

Group 0 name Corresponds to the control (unexposed) group for case-control studies: negative

Group 1 name Corresponds to the case (exposed) group for case-control studies: S.pneumoniae positive

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: clinical pneumonnia

Group 0 sample size Number of subjects in the control (unexposed) group: 74

Group 1 sample size Number of subjects in the case (exposed) group: 96

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: Logistic Regression

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

Matched on Factors on which subjects have been matched on in a case-control study: primary care clinic, date

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Chao1 Abundance-based estimator of species richness: unchanged

Richness Number of species: unchanged

Signature 1

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Curated date: 2021/01/10

Curator: Fatima Zohra

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Source: Figure 3

Description: Relative abundance of highly abundant genera by S. pneumoniae colonization

Abundance in Group 1: increased abundance in S.pneumoniae positive

NCBI	Quality Control	Links
Moraxella
Streptococcus

Revision editor(s): WikiWorks

Signature 2

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Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks

Source: Figure 3

Description: Relative abundance of highly abundant genera by S. pneumoniae colonization

Abundance in Group 1: decreased abundance in S.pneumoniae positive

NCBI	Quality Control	Links
Corynebacterium
Staphylococcus

Revision editor(s): WikiWorks