Post-mortem Nasopharyngeal Microbiome Analysis of Zambian Infants with and without Respiratory Syncytial Virus Disease: A Nested Case Control Study

ABSTRACT Background Respiratory Syncytial Virus (RSV) is the most common cause of bronchiolitis and lower respiratory tract infections in children in their first year of life, disproportionately affecting infants in developing countries. Previous studies have found that the nasopharyngeal microbiome of infants with RSV infection has specific characteristics that correlate with disease severity, including lower biodiversity, perturbations of the microbiota and differences in relative abundance. These studies have focused on infants seen in clinical or hospital settings, predominantly in developed countries. Methods We conducted a nested case control study within a random sample of 50 deceased RSV+ infants with age at death ranging from 4 days to 6 months and 50 matched deceased RSV-infants who were all previously enrolled in the Zambia Pertussis and RSV Infant Mortality Estimation (ZPRIME) study. All infants died within the community or within 48 hours of facility admittance. As part of the ZPRIME study procedures, all decedents underwent one-time, post-mortem nasopharyngeal sampling. The current analysis explored the differences between the nasopharyngeal microbiome profiles of RSV+ and RSV-decedents using 16S ribosomal DNA sequencing. Results We found that Moraxella was more abundant in the nasopharyngeal microbiome of RSV+ decedents than in RSV-decedents. Additionally, Gemella and Staphylococcus were less abundant in RSV+ decedents than in RSV-decedents. Conclusion These results support previously reported findings of the association between the nasopharyngeal microbiome and RSV and suggest that changes in the abundance of these microbes are likely specific to RSV and may correlate with mortality associated with the disease.