Lung Microbiome Profiling: A Promising Approach to Enhance Diagnostic Precision for Ventilator-Associated Pneumonia

Georgios Kitsios, MD, PhD

Ventilator-associated pneumonia (VAP) remains a critical challenge in intensive care units (ICUs), affecting up to 50% of patients requiring invasive mechanical ventilation (IMV) and significantly increasing mortality rates, antibiotic use, and hospital stays.¹ The COVID-19 pandemic has further underscored the urgency of understanding respiratory infections in critically ill patients, particularly as severe cases often necessitate prolonged IMV and are susceptible to developing VAP.²

In response to these challenges, I have launched the innovative Lung CovID-19 Interactions with Microbiota and Host (LUCID-IMHO) study. Funded by a $200,000 COVID-19 Respiratory Virus Research Award from the American Lung Association, this 2-year project aims to develop a novel, microbiome-based diagnostic framework for VAP in critically ill patients.

The LUCID-IMHO study leverages a high-dimensional, multi-omic dataset from 110 patients with severe respiratory failure requiring IMV. These patients underwent longitudinal sampling of the lower respiratory tract at 3 key intervals: baseline (0-2 days post-intubation), middle (days 3-7), and late (days 8-12). This comprehensive sampling strategy allows for detailed temporal analysis of microbial and host factors associated with VAP development.

A key innovation of the LUCID-IMHO study is its use of untargeted DNA metagenomics with rapid sequencing platforms, including the portable MiNION Mk1c sequencer by Oxford Nanopore Technologies. This approach enables systematic and comprehensive profiling of microbial communities, including bacteria, viruses, and fungi, without relying on traditional culture methods. Importantly, it allows for real-time data generation, potentially reducing the time from sample acquisition to diagnosis from days to hours.

Interim results of the LUCID-IMHO study, recently published in Nature Communications, provide significant insights into the microbiome dynamics of critically ill patients.³ The study conducted a longitudinal, multi-compartment assessment of host-microbiota interactions across 3 body sites—oral cavity, lungs, and gut—in 479 patients with acute respiratory failure receiving IMV. Findings were validated in 2 independent cohorts of critically ill COVID-19 patients.

Key findings from this interim analysis include:

1. Progressive dysbiosis in oral, lung, and gut microbiota of critically ill patients, characterized by reduced microbial diversity and alterations in composition over time.
2. The lung microbiome emerged as the strongest independent predictor of important clinical outcomes, outperforming oral and gut microbiota.
3. Specific clinical factors, including chronic obstructive pulmonary disease (COPD), immunosuppression, and antibiotic exposure, were associated with distinct dysbiotic patterns.
4. Anaerobe-targeting antibiotics were associated with anaerobic bacteria depletion in both respiratory and intestinal tracts, correlating with worse clinical outcomes.
5. The oral cavity was identified as the main source of microbial seeding in the lungs, with a small subset of patients (8.3%) showing enrichment for gut-origin bacteria associated with worse survival outcomes.
6. Dirichlet Multinomial Mixture (DMM) models stratified patients into distinct microbial clusters, revealing high-diversity clusters associated with better outcomes and low-diversity clusters linked to worsened clinical trajectories.
7. A Dysbiosis Index derived from these clusters successfully classified microbiota profiles in independent cohorts, including COVID-19 patients, demonstrating associations with inflammatory biomarkers and clinical outcomes.

These findings highlight the potential of microbiome analysis in critical care medicine, particularly for improving VAP diagnosis and management. The lung microbiome's strong predictive value for clinical outcomes, independent of traditional clinical predictors and host-response subphenotypes, suggests that integrating microbiome data into clinical decision-making could significantly enhance risk stratification and resource allocation in intensive care units.

Moreover, the study's insights into the effects of antibiotics on microbial communities underscore the importance of rational antibiotic use in critically ill patients. The observed associations between anaerobic bacteria depletion and worse clinical outcomes highlight potential unintended consequences of broad-spectrum antibiotic use and suggest avenues for more targeted therapeutic approaches.

The LUCID-IMHO study's approach aligns with recent advances in the field, such as the multi-institutional study published in Nature Medicine that defined clinically informative lung microbiome signatures associated with acute respiratory distress syndrome (ARDS) and hospital-acquired pneumonia (HAP).⁴ Together, these studies underscore the potential for microbiome-targeted therapies in critically ill patients.

As the LUCID-IMHO study progresses, its findings could lead to the development of a microbiome-based diagnostic framework for VAP, enabling more precise and timely interventions. This approach has the potential to revolutionize clinical practice by reducing unnecessary antibiotic use, improving patient outcomes, and alleviating the burden of antibiotic resistance in intensive care settings.

Kitsios has received research funding from Karius, Inc., Pfizer, Inc., and Genentech, Inc.

References

1. ^{Ranzani OT, Niederman MS, Torres A. Ventilator-associated pneumonia. Intensive Care Med. 2022;48(9):1222-1226. doi:10.1007/s00134-022-06773-3}
2. ^{Niederman MS. What COVID-19 Has Taught Us: Ventilator-associated Pneumonia Is Back! Am J Respir Crit Care Med. 2022;206(2):132-134. doi:10.1164/rccm.202204-0799ED}
3. ^{Kitsios GD, Sayed K, Fitch A, et al. Longitudinal multicompartment characterization of host-microbiota interactions in patients with acute respiratory failure. Nat Commun. 2024;15(1):4708. doi:10.1038/s41467-024-48819-8}
4. ^{Montassier E, Kitsios GD, Radder JE, et al. Robust airway microbiome signatures in acute respiratory failure and hospital-acquired pneumonia. Nat Med. 2023;29(11):2793-2804. doi:10.1038/s41591-023-02617-9}