Maimuna Carrim
Senior Medical Scientist; NICD
Maimuna Carrim is a senior medical scientist working at the National Institute for Communicable Diseases in South Africa in the Centre for Respiratory Disease and Meningitis. She has completed her Master’s degree at the University of the Witwatersrand, where she explored the prevalence of bacteria causing atypical pneumonia in South Africa. She is pursuing her PhD which focuses on understanding the carriage and transmission of Streptococcus pneumoniae through a community cohort study in South Africa. She is also working on determining aberrations in the nasopharyngeal microbiome in influenza-positive individuals.
Abstract
Background: The nasopharyngeal microbiota plays an important role in respiratory health. We describe changes in the nasopharyngeal microbiota and relative abundance of Streptococcus genus during influenza infection.
Methods: We conducted a household community cohort study (PHIRST) in South Africa during 2017. Nasopharyngeal swabs were collected twice-weekly and tested by PCR for respiratory pathogens. We randomly selected 40/90 (44%) influenza-positive households. Ninety-two individuals had a PCR-positive influenza episode at least once during the study period. 16S-rRNA sequencing of the V4-region was performed for 2 samples collected before, all samples during, and 2 samples after the influenza episode (N=452). Alpha and beta diversity were assessed using the Shannon index and permutational multivariate analysis of variance (PERMANOVA) respectively, assessing changes in the microbial community composition in relation to influenza infection. Statistical differences by influenza-infection time period were calculated using a linear mixed effects model, controlling for age and repeated measures
Results: Within all samples sequenced, we observed a total of 1,084 amplicon sequence variants representing 16 phyla. Proteobacteria was the most abundant phylum detected in all periods. Moraxella was the most abundant ASV. After adjusting for age and repeated measures there was no statistical differences in alpha-diversity over time period. Overall beta diversity differed by time period (p=0.02). No significant differences in the relative abundance of the top 6 genera by time period including Streptococcus genus (before-during, p=0.8; before-after, p=1.0; during-after, p=0.7).
Conclusions: We observed differences in Beta diversity but these were not translated into alpha diversity changes in the 6 major genera, including Streptococcus. Further ASV-level analyses are required to pinpoint the origin of community-level differences.