Nasopharyngeal microbiome composition by SARS-CoV-2 presence and severity

Area of Science:

• Microbiology
• Virology
• Human Microbiome

Background:

• The relationship between SARS-CoV-2 infection and the nasopharyngeal microbiome remains largely unexplored.
• Understanding this interaction is crucial for comprehending COVID-19 pathogenesis and host response.

Purpose of the Study:

• To investigate the influence of SARS-CoV-2 on the nasopharyngeal microbiome composition and bacterial concentrations.
• To explore potential bidirectional interactions between SARS-CoV-2 and nasopharyngeal bacteria.

Main Methods:

• Nasopharyngeal swabs from Dutch healthcare workers and respiratory outpatients were analyzed using 16S rRNA amplicon sequencing.
• Samples were tested for SARS-CoV-2 and other respiratory viruses using multiplex PCR.
• Bacterial estimated concentrations (ECs) were correlated with viral presence and disease severity.

Main Results:

• In healthcare workers, SARS-CoV-2 presence correlated with a slight increase in Corynebacterium ECs.
• Dolosigranulum ECs were higher in asymptomatic SARS-CoV-2 cases compared to uninfected controls but decreased with increasing COVID-19 severity.
• Nasopharyngeal microbiome composition in patients was primarily influenced by comorbidities, not SARS-CoV-2 severity.

Conclusions:

• Dolosigranulum ECs may decrease with increasing SARS-CoV-2 severity, though clinical significance is uncertain.
• Comorbidities significantly shape the nasopharyngeal microbiome in patients with respiratory symptoms.
• Further research is needed to elucidate the clinical relevance of observed microbiome alterations in COVID-19.