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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | e211-e218 |
| Journal | Pediatric Infectious Disease Journal |
| Volume | 36 |
| Issue number | 9 |
| DOIs | |
| State | Published - Sep 1 2017 |
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Keywords
- children
- microbial communities
- microbiota
- pneumonia
- respiratory infections
ASJC Scopus subject areas
- Pediatrics, Perinatology, and Child Health
- Microbiology (medical)
- Infectious Diseases
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The Nasopharyngeal Microbiota of Children with Respiratory Infections in Botswana. / Kelly, Matthew S.; Surette, Michael G.; Smieja, Marek; Pernica, Jeffrey M.; Rossi, Laura; Luinstra, Kathy; Steenhoff, Andrew P.; Feemster, Kristen A.; Goldfarb, David M.; Arscott-Mills, Tonya; Boiditswe, Sefelani; Rulaganyang, Ikanyeng; Muthoga, Charles; Gaofiwe, Letang; Mazhani, Tiny; Rawls, John F.; Cunningham, Coleen K.; Shah, Samir S.; Seed, Patrick C.
In: Pediatric Infectious Disease Journal, Vol. 36, No. 9, 01.09.2017, p. e211-e218.Research output: Contribution to journal › Article
TY - JOUR
T1 - The Nasopharyngeal Microbiota of Children with Respiratory Infections in Botswana
AU - Kelly, Matthew S.
AU - Surette, Michael G.
AU - Smieja, Marek
AU - Pernica, Jeffrey M.
AU - Rossi, Laura
AU - Luinstra, Kathy
AU - Steenhoff, Andrew P.
AU - Feemster, Kristen A.
AU - Goldfarb, David M.
AU - Arscott-Mills, Tonya
AU - Boiditswe, Sefelani
AU - Rulaganyang, Ikanyeng
AU - Muthoga, Charles
AU - Gaofiwe, Letang
AU - Mazhani, Tiny
AU - Rawls, John F.
AU - Cunningham, Coleen K.
AU - Shah, Samir S.
AU - Seed, Patrick C.
PY - 2017/9/1
Y1 - 2017/9/1
N2 - 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.
AB - 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.
KW - children
KW - microbial communities
KW - microbiota
KW - pneumonia
KW - respiratory infections
UR - http://www.scopus.com/inward/record.url?scp=85017460730&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85017460730&partnerID=8YFLogxK
U2 - 10.1097/INF.0000000000001607
DO - 10.1097/INF.0000000000001607
M3 - Article
C2 - 28399056
AN - SCOPUS:85017460730
VL - 36
SP - e211-e218
JO - Pediatric Infectious Disease Journal
JF - Pediatric Infectious Disease Journal
SN - 0891-3668
IS - 9
ER -