Bronchoalveolar Lavage Metagenomic Sequencing in the Early Post-Lung Transplantation Period: A Pilot Comparison with Microbiologic Culture
- 1University of Pittsburgh
Abstract
Conventional bronchoalveolar lavage (BAL) culture has limited sensitivity in lung transplant recipients due to universal antimicrobial prophylaxis and inability to detect non-culturable organisms. We prospectively enrolled 19 adult lung transplant recipients undergoing serial bronchoscopies during the immediate post-transplant period. BAL samples (N=33) were tested in parallel with conventional culture, microbial cell-free DNA (mcfDNA) sequencing with quantitative analysis, and long-read sequencing, using a unified three-tier organism classification framework. BAL host-response biomarkers were profiled concurrently. mcfDNA sequencing detected pathogens in 19 of 33 episodes (58%) versus 8 of 33 by conventional culture (24%); organism-level concordance was low (Cohens kappa 0.18). In 16 episodes where mcfDNA detected a pathogen not recovered by culture, 8 across 3 participants represented predictive detections -- the same organism subsequently confirmed as causing invasive infection 2-46 days later, including fatal extensively drug-resistant Pseudomonas pneumonia, vancomycin-resistant Enterococcal surgical site infection, and candidemia. Long-read sequencing had low yield due to contaminating human DNA. Quantitative mcfDNA burden correlated positively with multiple alveolar inflammatory biomarkers. BAL mcfDNA metagenomics identified clinically relevant pathogens not recovered by conventional culture, including predictive detections and non-culturable organisms, supporting a role for metagenomic surveillance in the early post-transplant period.
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BibTeX
@misc{kitsios2026bronchoalveolar,
title = {{Bronchoalveolar Lavage Metagenomic Sequencing in the Early Post-Lung Transplantation Period: A Pilot Comparison with Microbiologic Culture}},
author = {G. Kitsios and M. A. Sy and X. Wang and A. Craig and A. Rizzo and J. R. Francisco and S. Qin and M. Hensley and K. H. Kramer and K. Noda and P. Benos and C. Hage and P. Sanchez and A. Morris and G. Haidar and M. E. Snyder},
howpublished = {medRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.17.26363318},
url = {https://www.medrxiv.org/content/10.64898/2026.09.17.26363318v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Bronchoalveolar Lavage Metagenomic Sequencing in the Early Post-Lung Transplantation Period: A Pilot Comparison with Microbiologic Culture
AU - G. Kitsios
AU - M. A. Sy
AU - X. Wang
AU - A. Craig
AU - A. Rizzo
AU - J. R. Francisco
AU - S. Qin
AU - M. Hensley
AU - K. H. Kramer
AU - K. Noda
AU - P. Benos
AU - C. Hage
AU - P. Sanchez
AU - A. Morris
AU - G. Haidar
AU - M. E. Snyder
PY - 2026
DA - 2026/09/17
PB - medRxiv
DO - 10.64898/2026.09.17.26363318
UR - https://www.medrxiv.org/content/10.64898/2026.09.17.26363318v1
AB - Conventional bronchoalveolar lavage (BAL) culture has limited sensitivity in lung transplant recipients due to universal antimicrobial prophylaxis and inability to detect non-culturable organisms. We prospectively enrolled 19 adult lung transplant recipients undergoing serial bronchoscopies during the immediate post-transplant period. BAL samples (N=33) were tested in parallel with conventional culture, microbial cell-free DNA (mcfDNA) sequencing with quantitative analysis, and long-read sequencing, using a unified three-tier organism classification framework. BAL host-response biomarkers were profiled concurrently. mcfDNA sequencing detected pathogens in 19 of 33 episodes (58%) versus 8 of 33 by conventional culture (24%); organism-level concordance was low (Cohens kappa 0.18). In 16 episodes where mcfDNA detected a pathogen not recovered by culture, 8 across 3 participants represented predictive detections -- the same organism subsequently confirmed as causing invasive infection 2-46 days later, including fatal extensively drug-resistant Pseudomonas pneumonia, vancomycin-resistant Enterococcal surgical site infection, and candidemia. Long-read sequencing had low yield due to contaminating human DNA. Quantitative mcfDNA burden correlated positively with multiple alveolar inflammatory biomarkers. BAL mcfDNA metagenomics identified clinically relevant pathogens not recovered by conventional culture, including predictive detections and non-culturable organisms, supporting a role for metagenomic surveillance in the early post-transplant period.
ER -