Molecular Profiling of Innate Immune Response Mechanisms in Ventilator-associated Pneumonia

Unlike bronchoalveolar lavages (BAL), the molecular composition of more readily accessible endotracheal aspirates (ETA) has been poorly studied in the context of ventilator-associated pneumonia. In this work, longitudinal ETA and BAL collections from patients under mechanical ventilation were subjected to proteomics and metabolomics analysis. Our integrative omics approach identified signatures of neutrophil mediated induction of host-innate immunity in response to pathogens a day prior to clinical diagnosis. [Display omitted] Highlights •ETA present a diverse proteome and metabolome and can be employed for longitudinal studies of nosocomial infections affecting the lungs.•The proteome and metabolome of ETA and BAL share comparable features that may be leveraged for diagnostics.•ETA carries early signatures of host innate immunity against ventilator-associated pneumonia. Ventilator-associated pneumonia (VAP) is a common hospital-acquired infection, leading to high morbidity and mortality. Currently, bronchoalveolar lavage (BAL) is used in hospitals for VAP diagnosis and guiding treatment options. Although BAL collection procedures are invasive, alternatives such as endotracheal aspirates (ETA) may be of diagnostic value, however, their use has not been thoroughly explored. Longitudinal ETA and BAL were collected from 16 intubated patients up to 15 days, of which 11 developed VAP. We conducted a comprehensive LC–MS/MS based proteome and metabolome characterization of longitudinal ETA and BAL to detect host and pathogen responses to VAP infection. We discovered a diverse ETA proteome of the upper airways reflective of a rich and dynamic host-microbe interface. Prior to VAP diagnosis by microbial cultures from BAL, patient ETA presented characteristic signatures of reactive oxygen species and neutrophil degranulation, indicative of neutrophil mediated pathogen processing as a key host response to the VAP infection. Along with an increase in amino acids, this is suggestive of extracellular membrane degradation resulting from proteolytic activity of neutrophil proteases. The metaproteome approach successfully allowed simultaneous detection of pathogen peptides in patients' ETA, which may have potential use in diagnosis. Our findings suggest that ETA may facilitate early mechanistic insights into host-pathogen interactions associated with VAP infection and therefore provide its diagnosis and treatment.