Knowledge about human-associated microbiota, defined as the microorganisms inhabiting specific organ and body system niches, has increased rapidly in recent years. Microbiome studies have been used to longitudinally characterize patients with Cystic Fibrosis, COPD and other lung pathologies. In this project, we will longitudinally assess intensive care patients who require mechanical ventilation, and assess the feasibility of using microbiological, microbiome and immunological tracheal aspirate markers to predict disease onset and/or severity of Ventilator associated Pneumonia (VAP). No previous studies of microbiome in VAP have been published to our knowledge.
We designed an observational cohort study where 17 intubated patients were enrolled and 3 tracheal aspirate samples were obtained on days 1, 3 and 5 post intubation (51 samples). We performed molecular identification of bacteria in serial tracheal aspirate samples by isolating rRNA genes harvested by PCR to determine the composition and the timing of acquisition of bacterial communities in the lower airways. We compared these results to those obtained by clinically indicated standard laboratory cultures and describe the timing of antibiotic administration in relation to the identification of airway bacterial communities. Routine Microbiology, 16S rRNA gene pyrosequencing and V-PLEX Proinflammatory Panel 1 (human) Kit of the 51 study samples were conducted. VAP criteria was daily assessed in all of these intubated patients requiring mechanical ventilation using CDC criteria.
36 patients were enrolled and 17 completed 3 samples post intubation. Their average age was 59.7 years. Their average length of intubation was 11 days. VAP incidence by CDC criteria was 6/17. Antibiotic exposure was common accounting for on 17/17 intubated patients, most commonly broad spectrum antibiotics such as Piperacillin/Tazobactam, Vancomycin and Ceftriaxone. Mixed flora along with S. aureus and Gram negative rods were the microorganisms more commonly isolated. Microbiome data showed that Herbaspirillum was highly prevalent whereas Serratia, Moraxella and Pseudomonas was sporadically abundant. Immune studies are currently in process.
In our microbiology studies, more microbiology diversity was observed as patients remained intubated longer; towards day 5 post intubation, there was more microbiology diversity, as opposed as seen in COPD patients; antibiotic exposure did not seem to affect this diversity. Gram negative rods were isolated in patients who developed VAP (E coli, Pseudomonas, Proteus, Citrobacter) more frequently that in patients who did not. In our microbiome studies, Herbaspirillum was highly prevalent (indicating likely contamination) whereas Serratia, Moraxella and Pseudomonas was sporadically abundant. However, no genera was both highly prevalent and highly abundant; while the patients that went on to develop VAP did manifest bacterial taxa that others have tied to VAP, e.g. P. aeruginosa, it is possible that what was not in the VAP microbiome might be more indicative of poor prognosis than what was. Our immune studies are pending at this time.
G. O'toole, None