Non-diphtheriae Corynebacteriumspecies are associated with decreased risk of pneumococcal colonization during infancy

Autor: Kelly, Matthew S, Plunkett, Catherine, Yu, Yahe, Aquino, Jhoanna N, Patel, Sweta M, Hurst, Jillian H, Young, Rebecca R, Smieja, Marek, Steenhoff, Andrew P, Arscott-Mills, Tonya, Feemster, Kristen A, Boiditswe, Sefelani, Leburu, Tirayaone, Mazhani, Tiny, Patel, Mohamed Z, Rawls, John F, Jawahar, Jayanth, Shah, Samir S, Polage, Christopher R, Cunningham, Coleen K, Seed, Patrick C
Zdroj: The ISME Journal; March 2022, Vol. 16 Issue: 3 p655-665, 11p
Abstrakt: Streptococcus pneumoniae(pneumococcus) is a leading cause of severe infections among children and adults. Interactions between commensal microbes in the upper respiratory tract and S. pneumoniaeare poorly described. In this study, we sought to identify interspecies interactions that modify the risk of S. pneumoniaecolonization during infancy and to describe development of the upper respiratory microbiome during infancy in a sub-Saharan African setting. We collected nasopharyngeal swabs monthly (0–6 months of age) or bimonthly (6–12 months of age) from 179 mother–infant dyads in Botswana. We used 16S ribosomal RNA gene sequencing to characterize the nasopharyngeal microbiome and identified S. pneumoniaecolonization using a species-specific PCR assay. We detect S. pneumoniaecolonization in 144 (80%) infants at a median age of 71 days and identify a strong negative association between the relative abundance of the bacterial genera Corynebacteriumwithin the infant nasopharyngeal microbiome and the risk of S. pneumoniaecolonization. Using in vitro cultivation experiments, we demonstrate growth inhibition of S. pneumoniaeby secreted factors from strains of several Corynebacteriumspecies isolated from these infants. Finally, we demonstrate that antibiotic exposures and the winter season are associated with a decline in the relative abundance of Corynebacteriumwithin the nasopharyngeal microbiome, while breastfeeding is associated with an increase in the Corynebacteriumrelative abundance. Our findings provide novel insights into the interspecies interactions that contribute to colonization resistance to S. pneumoniaeand suggest that the nasopharyngeal microbiome may be a previously unrecognized mechanism by which environmental factors influence the risk of pneumococcal infections during childhood. Moreover, this work lays the foundation for future studies seeking to use targeted manipulation of the nasopharyngeal microbiome to prevent infections caused by S. pneumoniae.
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