Comparison of the nasopharynx microbiome between influenza and non‐influenza cases of severe acute respiratory infections: A pilot study

AIMS: Influenza A virus (IAV) can cause severe acute respiratory infection (SARI), and disease outcome may be associated with changes in the microbiome of the nasopharynx. This is a pilot study to characterize the microbiome of the nasopharynx in patients hospitalized with SARI, infected and not infected by IAV. METHODS AND RESULTS: Using target sequencing of the 16S rRNA gene, we assessed the bacterial community of nasopharyngeal aspirate samples and compared the microbiome of patients infected with IAV with the microbiome of patients who were negative for IAV. We observed differences in the relative abundance of Proteobacteria and Firmicutes between SARI patients, with Streptococcus being enriched and Pseudomonas underrepresented in IAV patients compared with patients who were not infected with IAV. CONCLUSION: Pseudomonas taxon seems to be in high frequency on the nasopharynx of SARI patients with non‐IAV infection and might present a negative association with Streptococcus taxon. Microbial profile appears to be different between SARI patients infected or not infected with IAV.