Blood microbial DNA as a non-invasive diagnostic surrogate for pneumonia pathogens in immunocompromised patients: A real-world outcomes analysis

Abstract While blood testing is a non-invasive tool for pneumonia diagnosis, its utility depends on specific clinical conditions. Given the invasiveness of bronchoalveolar lavage fluid (BALF) sampling, this study investigates whether blood-based microbial DNA sequencing could serve as a viable alternative for pathogen detection in pneumonia, particularly in immunocompromised (ICP) patients post-allogeneic hematopoietic stem cell transplantation compared to immunocompetent (ICT) controls. We compared microbial DNA sequence diversity in paired blood and BALF samples from ICP and ICT patients. Striking differences emerged in microbial alpha and beta diversity between blood and BALF in ICP patients, but not in ICT patients. ICP BALF samples exhibited significantly greater microbial diversity and abundance (859 upregulated microbes) than ICT BALF. Furthermore, a higher proportion of microbial DNA sequences detected in ICP blood were also present in paired BALF, a pattern not observed in ICT patients. These findings may reflect alveolar-capillary barrier disruption in ICP patients, supported by downregulation of genes critical to barrier integrity —such as NABA CORE MATRISOME, extracellular matrix organization, and cell-cell adhesion pathways. Concurrent upregulation of VEGFA-VEGFR2 signaling and Rho GTPase pathways—associated with vascular permeability—and markers of excessive inflammation further corroborate this mechanism. Notably, 419 microbial DNA sequences in ICP blood strongly predicted lower respiratory tract origin (≥70% certainty). Overall, the difference in microbial sequence diversity between paired blood-BALF was significantly influenced by the host's immune status, and the microbial DNA sequence markers found in the blood have the potential to aid the diagnosis of pneumonia pathogens. This is the first study to compare microbial not limited to pathogenic DNA sequence diversity between the paired blood and BALF in humans, providing a novel approach to identifying blood biomarkers for diagnosing pneumonia pathogens. Blood microbial DNA testing may reduce the need for invasive BALF procedures in ICP patients, potentially improving early diagnosis and clinical outcomes.