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

Abstract

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. pneumoniae are poorly described. In this study, we sought to identify interspecies interactions that modify the risk of S. pneumoniae colonization 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. pneumoniae colonization using a species-specific PCR assay. We detect S. pneumoniae colonization 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 Corynebacterium within the infant nasopharyngeal microbiome and the risk of S. pneumoniae colonization. Using in vitro cultivation experiments, we demonstrate growth inhibition of S. pneumoniae by secreted factors from strains of several Corynebacterium species isolated from these infants. Finally, we demonstrate that antibiotic exposures and the winter season are associated with a decline in the relative abundance of Corynebacterium within the nasopharyngeal microbiome, while breastfeeding is associated with an increase in the Corynebacterium relative abundance. Our findings provide novel insights into the interspecies interactions that contribute to colonization resistance to S. pneumoniae and 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.

Corynebacterium Species Inhibit Streptococcus pneumoniae Colonization and Infection of the Mouse Airway

“…A recent survey of morphologically distinct Corynebacterium strains collected from infants showed that cell-free supernatants from four different lipophilic species, including C. accolens , inhibited S. pneumoniae growth in vitro ( Kelly et al, 2021 ). However, supernatants from only 20% of the Corynebacterium isolates tested in this study were inhibitory, indicating that not all Corynebacterium strains mediate S. pneumoniae growth restriction in vitro .…”

“…However, non-C. diphtheriae species are more often associated with respiratory health, as the abundance of Corynebacterium species in nasopharynx correlates with reduced S. pneumoniae colonization and infection in several studies (Laufer et al, 2011;Pettigrew et al, 2012;Bomar et al, 2016;Kelly et al, 2017;Xu et al, 2021). Longitudinal studies tracking upper airway microbiome dynamics in children over time indicate that Corynebacterium abundance is predictive of both S. pneumoniae carriage and risk of respiratory tract infection (Biesbroek et al, 2014;Teo et al, 2015;Bosch et al, 2017;Kelly et al, 2021). Both children and adults with a higher abundance of Corynebacterium also have more stable airway microbiomes, compared to those with a predominance of opportunistic pathogens including S. pneumoniae (Bosch et al, 2017;Piters et al, 2019;Kelly et al, 2021).…”

“…Longitudinal studies tracking upper airway microbiome dynamics in children over time indicate that Corynebacterium abundance is predictive of both S. pneumoniae carriage and risk of respiratory tract infection (Biesbroek et al, 2014;Teo et al, 2015;Bosch et al, 2017;Kelly et al, 2021). Both children and adults with a higher abundance of Corynebacterium also have more stable airway microbiomes, compared to those with a predominance of opportunistic pathogens including S. pneumoniae (Bosch et al, 2017;Piters et al, 2019;Kelly et al, 2021). Together, these studies indicate that Corynebacterium species may play an important role in microbiome-mediated protection against pathogens such as S. pneumoniae, thereby reducing susceptibility to pneumonia.…”

“…Interruption of the potential protective benefit of Corynebacterium species in the airway is of particular concern for patients receiving antibiotics, as antibiotic therapy selectively reduces the Corynebacterium population while pathogens including S. pneumoniae are enriched ( Teo et al, 2015 ; Prevaes et al, 2016 ; Kelly et al, 2021 ). Mechanistically, several Corynebacterium species can directly inhibit growth of S. pneumoniae in vitro ( Bomar et al, 2016 ; Kelly et al, 2021 ; Xu et al, 2021 ). Among these, Corynebacterium accolens inhibits S. pneumoniae growth by expression of a bacterial lipase called LipS1, which hydrolyses host triacylglycerols, releasing free fatty acids that kill S. pneumoniae ( Bomar et al, 2016 ).…”

“…Two non-lipophilic Corynebacterium species, which do not require host lipids for growth, were recently shown to inhibit S. pneumoniae in vitro , though the mechanisms were not identified ( Xu et al, 2021 ). Another non-lipophilic species, Corynebacterium amycolatum , is frequently isolated from the human nasopharynx ( Kaspar et al, 2016 ; Kelly et al, 2021 ) but is unusual in that it lacks mycolic acid, a long chain fatty acid which is a major component of the cell wall in almost all other Corynebacterium ( Collins et al, 1988 ; Marrakchi et al, 2014 ). It is unclear whether FA production by bacterial lipases are universally required for Corynebacterium -mediated inhibition of S. pneumoniae , or whether diverse Corynebacterium species, including those less dependent on exogenous lipids, utilize similar mechanisms.…”