The Impact of Respiratory Infection on the Nasal Microbiota

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Moslinger, Emily
Nasal Microbiota , SARS-CoV-2 , Next Generation Sequencing
Background: Viral respiratory infections represent a significant burden of illness with high morbidity and mortality, which has been further magnified in recent years by the emergence of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Viruses including SARS-CoV-2, Influenza A Virus (Flu-A), and Respiratory Syncytial Virus (RSV) utilize the nasopharynx for viral entry, replication and infection. The nasopharynx epithelial cell mucous membrane harbors a diverse community of bacteria, called the nasal microbiota (NM). Flu-A can modulate changes in the NM community and lead to pathobiont enrichment. Therefore, here we aim to investigate the NM of individuals with SARS-CoV-2, Flu-A and RSV infection, and identify correlates between the NM community and viral load (VL) and SARS-CoV-2 variants of concern (VOC). Methods: Nasopharyngeal (NP) swabs were collected and tested for SARS-CoV-2, Flu-A, and RSV by validated real-time PCR (RT-PCR) assays. RNA extraction was performed using a Maxwell automatic nucleic acid extractor followed by 16S rRNA Illumina Next Generation Sequencing (NGS) library sample preparation for NGS on a MiSeq Sequencer. QIIME II, Microbiome Analyst and PRISM 9.0.0 were used for data analysis. Results: NP swabs from 118 SARS-CoV-2, 40 Flu-A, 26 RSV positive and 45 negative controls (NC) were included. An increase in alpha and beta bacterial diversity (p<0.001) was observed in the NM of SARS-CoV-2 patients and an enrichment in Streptococcus and Staphylococcus species and depletion of Bifidobacterium and Moraxella species compared to NC’s (p<0.001). Compared to Flu-A and RSV patients, SARS-CoV-2 positives showed enrichment in Streptococcus, and depletion in Haemophilus species (p<0.002). 73/118 SARS-CoV-2 specimens were further sequenced to identify VOC lineage and stratified by VL. No significance in bacterial richness, diversity, or abundance correlated to VL. Only a significant difference in beta diversity was observed between the alpha/delta and omicron cohorts (p<0.001). Conclusions: This study demonstrates that the NM community is different in individuals with respiratory illness and distinct between SARS-CoV-2, Flu-A and RSV infected individuals. This study also demonstrated that NM beta diversity was different between individuals with different SARS-CoV-2 lineages, suggesting virus-NM interplay that may be important in explaining differences in transmission potentials and pathogenesis between SARS-CoV-2 VOCs.
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