The Nasopharyngeal Microbiota of Children With Respiratory Infections in Botswana

Abstract

Background: Nearly half of child pneumonia deaths occur in sub-Saharan Africa. Microbial communities in the nasopharynx are a reservoir for pneumonia pathogens and remain poorly described in African children.

Methods: Nasopharyngeal swabs were collected from children with pneumonia (N = 204), children with upper respiratory infection symptoms (N = 55) and healthy children (N = 60) in Botswana between April 2012 and April 2014. We sequenced the V3 region of the bacterial 16S ribosomal RNA gene and used partitioning around medoids to cluster samples into microbiota biotypes. We then used multivariable logistic regression to examine whether microbiota biotypes were associated with pneumonia and upper respiratory infection symptoms.

Results: Mean ages of children with pneumonia, children with upper respiratory infection symptoms and healthy children were 8.2, 11.4 and 8.0 months, respectively. Clustering of nasopharyngeal microbiota identified 5 distinct biotypes: Corynebacterium/Dolosigranulum-dominant (23%), Haemophilus-dominant (11%), Moraxella-dominant (24%), Staphylococcus-dominant (13%) and Streptococcus-dominant (28%). The Haemophilus-dominant [odds ratio (OR): 13.55; 95% confidence interval (CI): 2.10-87.26], the Staphylococcus-dominant (OR: 8.27; 95% CI: 2.13-32.14) and the Streptococcus-dominant (OR: 39.97; 95% CI: 6.63-241.00) biotypes were associated with pneumonia. The Moraxella-dominant (OR: 3.71; 95% CI: 1.09-12.64) and Streptococcus-dominant (OR: 12.26; 95% CI: 1.81-83.06) biotypes were associated with upper respiratory infection symptoms. In children with pneumonia, HIV infection was associated with a lower relative abundance of Dolosigranulum (P = 0.03).

Conclusions: Pneumonia and upper respiratory infection symptoms are associated with distinct nasopharyngeal microbiota biotypes in African children. A lower abundance of the commensal genus Dolosigranulum may contribute to the higher pneumonia risk of HIV-infected children.

Figure 1. Comparison of bacterial alpha diversity measures by disease status

Nasopharyngeal microbiota richness (a), as measured by the Chao1 index, and diversity (b), as measured by the Shannon Diversity Index, among children with URI symptoms, healthy children, and children with pneumonia. URI, upper respiratory infection

Figure 2. Relative abundances of frequently occurring genera by disease status

Relative abundances of genera in healthy children and children with pneumonia (a), by HIV exposure status in children with pneumonia (b), in healthy children and children with URI symptoms (c), and by age categories in healthy children (d). URI, upper respiratory infection, HIV-EU, HIV-exposed uninfected

Figure 3. Nasopharyngeal microbiota biotypes by disease status

Relative abundances of frequently occurring genera in microbiota biotypes (a), and the distribution of nasopharyngeal samples from children with pneumonia, children with URI symptoms, and healthy children with these microbiota biotypes (b). In panel (b), the medoids are shown as large points with white centers; all other points correspond to individual nasopharyngeal swab samples. URI, upper respiratory infection