Duke University
Pediatrics
Dr. Kelly is a pediatrician and physician-scientist trained in infectious diseases, global health, and human microbial ecology. He received his MD degree from Harvard Medical School and his MPH degree from the Harvard School of Public Health before completing his pediatrics training at the Boston Combined Residency Program in Pediatrics. He was a David N. Pincus Pediatric Global Health Fellow through the Children's Hospital of Philadelphia, during which he worked as a pediatric hospitalist in Gaborone, Botswana and started a research program focused on childhood pneumonia. He completed pediatric infectious diseases training at Duke University with a focus on the role of the microbiome in the prevention of common infections among children. Dr. Kelly is now an Associate Professor of Pediatrics and Associate Research Professor of Global Health at Duke University. His long-term career goal is to develop novel microbiome-based strategies for the prevention and treatment of childhood infections, particularly those for which the highest burden is among children in low- and middle-income countries. His research focuses on understanding the roles of the upper respiratory microbiome and host-microbe interactions within the upper respiratory tract in modifying the risk and severity of childhood respiratory infections.

Presenter Of 1 Presentation

O087 - SYNERGISM BETWEEN RESPIRATORY VIRUSES AND PNEUMOCOCCUS: A POTENTIAL ROLE FOR THE UPPER RESPIRATORY MICROBIOME? (ID 266)

Session Type
Parallel Session
Date
Wed, 22.06.2022
Session Time
15:05 - 16:35
Room
Grand Ballroom West
Lecture Time
15:10 - 15:20

Abstract

Background

Respiratory viruses predispose to infections caused by pneumococcus. Although this viral-pneumococcal synergism was first recognized during the 1918 influenza pandemic, most subsequent studies have focused on the effect of respiratory viruses on host pneumococcal immunity. The respiratory microbiome is a complementary and potentially modifiable mechanism by which respiratory viruses may promote pneumococcal colonization.

Methods

We conducted a longitudinal study of mother-infant pairs (n=266) in Gaborone, Botswana. We collected infant nasopharyngeal swabs every 1-2 months during the first year of life and tested these samples (n=1,901) for pneumococcus (lytA gene) and respiratory viruses (Table 1) by PCR. We used 16S ribosomal RNA gene sequencing to evaluate associations between respiratory virus infection and the relative abundances of bacterial genera within the nasopharyngeal microbiome.

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Results

Pneumococcus was identified more frequently (68% vs. 43%; p<0.0001) and at higher colonization density (7.2 vs. 6.7 log copies/mL; p<0.0001) in samples with one or more respiratory viruses than in samples without respiratory viruses. In multivariable analyses, respiratory virus detection was associated with a 46% higher hazard of pneumococcal colonization (Cox proportional hazards model; HR: 1.46, 95% CI: 1.01-2.19). Respiratory virus infection was associated with losses of genera containing key bacterial commensals (Corynebacterium, Lactobacillus) and enrichment of the nasopharyngeal microbiome by Streptococcus and other genera containing common bacterial pathobionts (Figure 1).

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Conclusions

Respiratory viruses contribute to population-level trends in pneumococcal colonization during infancy. Our data provide new insights into the dynamic interactions that exist between respiratory viruses, the nasopharyngeal microbiome, and pneumococcus within the upper respiratory tract.

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