The upper and lower respiratory tract microbiome in severe aspiration pneumonia

Area of Science:

• Microbiology
• Critical Care Medicine
• Genomics

Background:

• Aspiration pneumonia is a common complication in mechanically ventilated patients.
• The role of anaerobic bacteria as pathogens in aspiration pneumonia remains unclear.
• Understanding respiratory tract microbiota is crucial for managing severe pneumonia.

Purpose of the Study:

• To investigate the role of anaerobic bacteria in aspiration pneumonia.
• To compare microbiota profiles and host responses in different pneumonia types.
• To identify microbial signatures associated with patient outcomes.

Main Methods:

• Nested case-control study of mechanically ventilated patients.
• 16S rRNA gene sequencing of upper and lower respiratory tract microbiota.
• Analysis of bacterial diversity, oxygen requirements, and host-response biomarkers.
• Unsupervised clustering using Dirichlet Multinomial Models (DMM).

Main Results:

• Macro-aspiration pneumonia (MAsP) and non-macro-aspiration pneumonia (NonMAsP) showed similar microbiota and host-response profiles.
• DMM identified distinct bacterial clusters in the respiratory tract.
• Low-diversity clusters enriched in facultative anaerobes correlated with higher SPD and sCD14 levels and poorer survival.
• No significant difference in 60-day survival between MAsP and NonMAsP groups.

Conclusions:

• Anaerobic bacteria do not appear to be primary drivers of aspiration pneumonia.
• Distinct respiratory microbiome profiles, particularly low-diversity clusters, are associated with severe pneumonia and worse outcomes.
• Microbiome analysis offers potential for patient sub-phenotyping and precision medicine in severe pneumonia.