Metagenomic Cell-free DNA Sequencing for Treatment Monitoring in Sepsis

TL;DR

This study shows that metagenomic sequencing of cell-free DNA can help monitor sepsis by detecting pathogens and organ injury, even after antibiotics are started.

Contribution

The study introduces SIFT-seq, a method that reduces contamination and enables accurate pathogen and organ injury detection in sepsis.

Findings

SIFT-seq identified sepsis-causing pathogens consistent with pre-antibiotic blood cultures.

The method revealed elevated immune activity and organ injury in sepsis patients.

Combining SIFT-seq with the SOFA score improved diagnostic performance (AUC = 0.874).

Abstract

Sepsis is a life-threatening organ dysfunction caused by a dysregulated response to infection. Early identification of pathogens and accurate assessment of organ injury are critical for improving outcomes, but current methods are often inadequate, especially after initiation of antibiotic treatment. Metagenomic sequencing of cell-free DNA (cfDNA) offers a promising alternative, enabling simultaneous pathogen detection and tissue-of-origin profiling. Contamination, however, can limit its accuracy in low-biomass samples. Here, we apply the Sample-Intrinsic Microbial DNA Found by Tagging and Sequencing (SIFT-seq) assay, which reduces contamination and allows detection of pathogens and organ injury simultaneously. We analyzed 142 plasma specimens: 105 from sepsis patients, 103 collected after initiation of antibiotic treatment, 24 from non-sepsis ICU controls, and 13 from healthy controls. SIFT-seq identified sepsis-causing pathogens in good agreement with pre-antibiotic blood cultures, revealed elevated immune activity and organ injury in sepsis patients, and, when combined with the SOFA score in a multivariate model, improved diagnostic performance (AUC = 0.874). These findings highlight the potential of integrated cfDNA profiling to enhance sepsis diagnosis.

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