Microbiome-guided Prophylaxis to Reduce Ventilator-Associated Pneumonia in Intensive Care Units: A Pilot Randomized Controlled Trial

Critical Illness, Mechanical Ventilation

Ventilator-associated pneumonia, Microbiome, Critical Illness, Inhaled Antibiotics

Ventilator-associated pneumonia (VAP) remains the most common hospital-acquired infection worldwide, affecting up to 40% of mechanically ventilated patients and contributing to increased morbidity, prolonged hospital stays, and high mortality rates. Standard prevention strategies rely on VAP prevention "bundles", which focus on general supportive care measures such as head-of-bed elevation, sedation interruption, and oral care. While these measures reduce some risk, they do not specifically target the underlying microbial mechanisms driving VAP. Emerging evidence supports the use of inhaled antibiotic (iABx) prophylaxis to suppress or eliminate airway pathogens. Several randomized controlled trials have shown that inhaled antimicrobials can reduce the incidence of VAP. However, the effectiveness of this approach is inconsistent when applied to all ventilated patients. Studies indicate that the greatest benefit occurs when inhaled antimicrobials are targeted toward patients with airway colonization by specific VAP pathogens. Traditional airway microbiome diagnostics have been a major barrier to implementing targeted prophylaxis because they are slow, costly, and require advanced expertise. Recently, a novel diagnostic method-ON-Time rapid microbiome sequencing-has been developed, offering accurate, cost-effective, and rapid (approximately 4.2 hours) results that can identify key VAP pathogens within the airway microbiome of ICU patients such as Enterobacteriaceae organisms, Pseudomonas spp., Acinetobacter spp., Stenotrophomonas maltophilia, Staphylococcus aureus, and others. The ability to define the airway microbiome of ICU patients including whether they harbour potential VAP pathogens provides a unique opportunity to tailor prophylactic antibiotics in a personalized and timely manner. Thus, microbiome-guided prophylaxis represents a novel precision medicine approach to preventing VAP by selecting the right patient. This pilot trial aims to test the feasibility of implementing such an approach to prevent VAP in critically ill patients.

Research Question: Is it feasible and safe to implement a randomized controlled trial of microbiome-guided inhaled antimicrobial prophylaxis to prevent VAP in mechanically ventilated ICU patients? Primary Objective: To assess the feasibility of conducting a full-scale randomized controlled trial, including protocol adherence, timely microbiome result reporting, and timely initiation and completion of the assigned intervention, and safety. Secondary Objectives: To explore the impact of microbiome-guided inhaled prophylaxis on airway microbiome composition and to estimate clinical outcomes including VAP incidence, ventilator-free days, ICU and hospital length of stay, and mortality up to 28 days. Hypothesis: Microbiome-guided inhaled antimicrobial prophylaxis is feasible and may be superior to standard care in reducing airway pathogen burden and VAP incidence. Methods: This is a single-centre, randomized, placebo-controlled pilot trial enrolling 70 mechanically ventilated adult ICU patients at Foothills Medical Centre in Calgary, AB, Canada. Participants will be randomized 1:1 to microbiome-guided inhaled antibiotic prophylaxis (intervention arm) or matching placebo (control arm). Endotracheal aspirates (ETA) will be collected at enrolment for rapid microbiome sequencing and analysis. In the intervention arm, participants with airway microbiome positive for VAP pathogens will receive inhaled tobramycin, participants with airway S. aureus will receive inhaled vancomycin, while those without pathogens will receive inhaled saline placebo. Treatment responsiveness will be determined on day 3 with repeat airway microbiome sequencing and analysis, and in participants with persistent airway pathogens, inhaled tobramycin will be changed to inhaled aztreonam, while those with airway S. aureus will continue to receive inhaled vancomycin. Total duration of intervention will be 5 days. Participants randomized to control arm, will undergo identical ETA sampling for airway microbiome sequencing but results will remain blinded, and participants will receive inhaled saline placebo for 5 days. Clinicians and participants will be blinded to microbiome results and allocation. Participants will be followed for up to 28 days for primary feasibility and safety outcomes (see section below for additional details), as well as secondary clinical outcomes and biological outcomes (airway microbiome and immune analyses).

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