Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis

Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) improves pathogen detection in severe pneumonia-related sepsis, but sampling is invasive and prone to false-positive results. Blood is easier to obtain, and broad-spectrum targeted NGS (tNGS) of microbial cell-free DNA may offer a practical alternative to BALF-based testing. We evaluated the diagnostic and prognostic value of blood-based bstNGS. In this retrospective cohort, 122 adults with suspected severe pneumonia-related sepsis and paired BALF and blood samples underwent BALF-mNGS, blood-bstNGS and blood-mNGS. Pathogens were adjudicated using a composite clinical reference. We assessed blood-BALF concordance, compared diagnostic performance across methods, and examined whether blood-bstNGS could down-weight likely false-positive BALF-only detections and stratify prognosis. BALF-mNGS identified 414 microorganisms; 51% were adjudicated as causative or possibly causative, corresponding to 85.24% of patients. Among these pathogenic microorganisms, blood-bstNGS detected 45.02%, significantly more than blood-mNGS (22.27%), and nearly all pathogens detected by blood-mNGS were also detected by blood-bstNGS. Against the clinical reference, blood-bstNGS showed higher sensitivity (63.46%) than blood-mNGS (35.58%), conventional microbiological tests (CMTs) (49.04%), and blood culture (9.62%). Organisms detected only in BALF but not in blood were less likely to be classified as causative. Patients with concordant blood-bstNGS and BALF-mNGS profiles had significantly lower 30-day and 90-day mortality. In severe pneumonia-related sepsis, blood-bstNGS provides sensitive, non-invasive pathogen detection. It acts as a complementary tool rather than a replacement for BALF-mNGS, offering an important diagnostic alternative when BALF is unavailable and improving specificity and prognostic utility when used in combination.