iScience (Jun 2023)
The upper and lower respiratory tract microbiome in severe aspiration pneumonia
- Georgios D. Kitsios,
- Vi D. Nguyen,
- Khaled Sayed,
- Nameer Al-Yousif,
- Caitlin Schaefer,
- Faraaz A. Shah,
- William Bain,
- Haopu Yang,
- Adam Fitch,
- Kelvin Li,
- Xiaohong Wang,
- Shulin Qin,
- Heather Gentry,
- Yingze Zhang,
- Jack Varon,
- Antonio Arciniegas Rubio,
- Joshua A. Englert,
- Rebecca M. Baron,
- Janet S. Lee,
- Barbara Methé,
- Panayiotis V. Benos,
- Alison Morris,
- Bryan J. McVerry
Affiliations
- Georgios D. Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA; University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA; Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA; Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA; Corresponding author
- Vi D. Nguyen
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA; University of California Los Angeles, Department of Medicine, Internal Medicine Residency Program, Los Angeles, CA90095, USA
- Khaled Sayed
- University of PittsburghDepartment of Computational & Systems Biology, Pittsburgh, PA15213, USA; Department of Epidemiology, University of Florida, Gainesville, FL32611, USA
- Nameer Al-Yousif
- University of Pittsburgh Medical Center Mercy, Department of Medicine, Pittsburgh, PA15219, USA
- Caitlin Schaefer
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA; Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
- Faraaz A. Shah
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA; University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA; Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA; Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA15240, USA
- William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA; University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA; Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA; Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA15240, USA
- Haopu Yang
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA; School of Medicine, Tsinghua University, Beijing, China
- Adam Fitch
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
- Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
- Xiaohong Wang
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- Shulin Qin
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA; Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
- Heather Gentry
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA; Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
- Jack Varon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA02115, USA
- Antonio Arciniegas Rubio
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA02115, USA
- Joshua A. Englert
- Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University Wexner Medical Center, Columbus, OH43210, USA
- Rebecca M. Baron
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA02115, USA
- Janet S. Lee
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO63110, USA
- Barbara Methé
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA; Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
- Panayiotis V. Benos
- Department of Epidemiology, University of Florida, Gainesville, FL32611, USA
- Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA; University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA; Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- Bryan J. McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA; University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA; Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA; Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
- Journal volume & issue
-
Vol. 26,
no. 6
p. 106832
Abstract
Summary: Uncertainty persists whether anaerobic bacteria represent important pathogens in aspiration pneumonia. In a nested case-control study of mechanically ventilated patients classified as macro-aspiration pneumonia (MAsP, n = 56), non-macro-aspiration pneumonia (NonMAsP, n = 91), and uninfected controls (n = 11), we profiled upper (URT) and lower respiratory tract (LRT) microbiota with bacterial 16S rRNA gene sequencing, measured plasma host-response biomarkers, analyzed bacterial communities by diversity and oxygen requirements, and performed unsupervised clustering with Dirichlet Multinomial Models (DMM). MAsP and NonMAsP patients had indistinguishable microbiota profiles by alpha diversity and oxygen requirements with similar host-response profiles and 60-day survival. Unsupervised DMM clusters revealed distinct bacterial clusters in the URT and LRT, with low-diversity clusters enriched for facultative anaerobes and typical pathogens, associated with higher plasma levels of SPD and sCD14 and worse 60-day survival. The predictive inter-patient variability in these bacterial profiles highlights the importance of microbiome study in patient sub-phenotyping and precision medicine approaches for severe pneumonia.
