The upper and lower respiratory tract microbiome in severe aspiration pneumonia

Uncertainty persists whether anaerobic bacteria represent important pathogens in aspiration pneumonia. In a nested case-control study of mechanically ventilated patients classified as macro-aspiration pneumonia (MAsP, n = 56), non-macro -aspiration pneumonia (NonMAsP, n = 91), and uninfected controls (n = 11), we profiled upper (URT) and lower respiratory tract (LRT) microbiota with bacterial 16S rRNA gene sequencing, measured plasma host-response biomarkers, analyzed bacterial communities by diversity and oxygen requirements, and per-formed unsupervised clustering with Dirichlet Multinomial Models (DMM). MAsP and NonMAsP patients had indistinguishable microbiota profiles by alpha diversity and oxygen requirements with similar host-response profiles and 60-day survival. Unsupervised DMM clusters revealed distinct bacterial clusters in the URT and LRT, with low-diversity clusters enriched for facultative anaerobes and typical pathogens, associated with higher plasma levels of SPD and sCD14 and worse 60-day survival. The predictive inter-patient variability in these bacterial profiles highlights the importance of microbiome study in patient sub-phenotyping and precision medicine approaches for severe pneumonia.

Automated summary

The importance of anaerobic bacteria as pathogens in aspiration pneumonia remains uncertain. A study conducted on mechanically ventilated patients classified as macro-aspiration pneumonia (MAsP), non-macro-aspiration pneumonia (NonMAsP), and uninfected controls, found that MAsP and NonMAsP patients had similar microbiota profiles and host-response profiles, with comparable 60-day survival rates. However, distinct bacterial clusters in the upper and lower respiratory tracts, enriched with facultative anaerobes and typical pathogens, were associated with higher plasma levels of SPD and sCD14 and worse 60-day survival.