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Peer-reviewedCC BYScientific Reports

Alternative to invasive bronchoscopy: validating tracheal aspirates for microbiome profiling in intensive care unit pneumonia patients

  • Parshatd Govindasamy1
  • Jun Yeun Cho2
  • Jiyoul Yang2
  • Bumhee Yang2
  • Sun-Hyung Kim2
  • Ki Man Lee2
  • Kang Hyeon Choe2
  • Ok-Jun Lee3
  • Eung-Gook Kim4
  • Kalai Mathee5
  • Giri Narasimhan1
  • Yoon Mi Shin2
5 affiliations
  1. 1Bioinformatics Research Group (BioRG), Florida International University
  2. 2Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Chungbuk National University Hospital, Chungbuk National University College of Medicine
  3. 3Department of Pathology, Chungbuk National University Hospital, Chungbuk National University College of Medicine
  4. 4Medical Research Center, Department of Biochemistry, Chungbuk National University College of Medicine
  5. 5Euleris.AI LLC
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Abstract

Pneumonia causes significant mortality in intensive care unit (ICU) patients, yet traditional culture-based pathogen detection lacks sufficient sensitivity. While bronchoalveolar lavage fluid (BAL) provides optimal diagnostic yield, bronchoscopy is often contraindicated in critically ill patients. This study compares the respiratory microbiome profiles of paired tracheal aspirate (ETA) and BAL samples from pneumonia patients in a tertiary hospital ICU (n=23, November 2019–September 2022). Using 16S rRNA next-generation sequencing, we analyzed microbial diversity (Shannon Index), taxonomic composition, and differential abundance (edgeR). Results showed comparable diversity indices and microbial communities between ETA and BAL samples, with ETA successfully capturing key pneumonia-related microbial signatures. These findings validate ETA as a reliable, less invasive alternative to BAL for respiratory microbiome analysis in critically ill patients, establishing the groundwork for future clinical applications.

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Cite

BibTeXRIS
BibTeX
@article{govindasamy2026alternative,
  title = {{Alternative to invasive bronchoscopy: validating tracheal aspirates for microbiome profiling in intensive care unit pneumonia patients}},
  author = {Parshatd Govindasamy and Jun Yeun Cho and Jiyoul Yang and Bumhee Yang and Sun-Hyung Kim and Ki Man Lee and Kang Hyeon Choe and Ok-Jun Lee and Eung-Gook Kim and Kalai Mathee and Giri Narasimhan and Yoon Mi Shin},
  journal = {Scientific Reports},
  year = {2026},
  month = jul,
  doi = {10.1038/s41598-026-60691-8},
  url = {https://doi.org/10.1038/s41598-026-60691-8},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Alternative to invasive bronchoscopy: validating tracheal aspirates for microbiome profiling in intensive care unit pneumonia patients
AU  - Parshatd Govindasamy
AU  - Jun Yeun Cho
AU  - Jiyoul Yang
AU  - Bumhee Yang
AU  - Sun-Hyung Kim
AU  - Ki Man Lee
AU  - Kang Hyeon Choe
AU  - Ok-Jun Lee
AU  - Eung-Gook Kim
AU  - Kalai Mathee
AU  - Giri Narasimhan
AU  - Yoon Mi Shin
PY  - 2026
DA  - 2026/07/01
JO  - Scientific Reports
DO  - 10.1038/s41598-026-60691-8
UR  - https://doi.org/10.1038/s41598-026-60691-8
AB  - Pneumonia causes significant mortality in intensive care unit (ICU) patients, yet traditional culture-based pathogen detection lacks sufficient sensitivity. While bronchoalveolar lavage fluid (BAL) provides optimal diagnostic yield, bronchoscopy is often contraindicated in critically ill patients. This study compares the respiratory microbiome profiles of paired tracheal aspirate (ETA) and BAL samples from pneumonia patients in a tertiary hospital ICU (n=23, November 2019–September 2022). Using 16S rRNA next-generation sequencing, we analyzed microbial diversity (Shannon Index), taxonomic composition, and differential abundance (edgeR). Results showed comparable diversity indices and microbial communities between ETA and BAL samples, with ETA successfully capturing key pneumonia-related microbial signatures. These findings validate ETA as a reliable, less invasive alternative to BAL for respiratory microbiome analysis in critically ill patients, establishing the groundwork for future clinical applications.
SN  - 2045-2322
ER  -