Bronchoalveolar Lavage Metagenomic Sequencing in the Early Post-Lung Transplantation Period: A Pilot Comparison with Microbiologic Culture

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 (Cohen’s 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.