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Ventilator-associated pneumonia (VAP) is one of the commonest hospital-acquired infections associated with high mortality. VAP pathogenesis is closely linked to organisms colonizing the endotracheal tube (ETT) such as  Staphylococcus epidermidis  and  Pseudomonas aeruginosa , the former a common commensal with pathogenic potential and the latter a known VAP pathogen. However, recent gut microbiome studies show that pathogens rarely function alone. Hence, we determined the ETT microbial consortium co-colonizing with  S. epidermidis  or  P. aeruginosa  to understand its importance in the development of VAP and for patient prognosis. Using bacterial 16S rRNA and fungal ITS-II sequencing on ETT biomass showing presence of  P. aeruginosa  and/or  S. epidermidis  on culture, we found that presence of  P. aeruginosa  correlated inversely with patient survival and with bacterial species diversity. A decision tree, using 16S rRNA and patient parameters, to predict patient survival was generated. Patients with a relative abundance of  Pseudomonadaceae  <4.6% and of  Staphylococcaceae  <70.8% had the highest chance of survival. When  Pseudomonadaceae  were >4.6%, age of patient <66.5 years was the most important predictor of patient survival. These data indicate that the composition of the ETT microbiome correlates with patient prognosis, and presence of  P. aeruginosa  is an important predictor of patient outcome.

The endotracheal tube microbiome associated with Pseudomonas aeruginosa or Staphylococcus epidermidis