Decoding cell-free DNA in critical illness to profile tissue injury, host response, and infection

Critical illness encompasses heterogeneous symptoms, signs, and syndromes, including sepsis, acute respiratory failure, shock, acute brain injury, and postoperative complications; these often converge on shared biological processes such as tissue injury, dysregulated inflammation, and endothelial dysfunction leading to multiple-organ failure. A major limitation in unraveling the underlying pathophysiology in critical care is that current biomarkers often provide limited mechanistic resolution, reporting inflammation or organ dysfunction without identifying the exact tissue source, extent, or biological nature of ongoing injury. Cell-free DNA (cfDNA) is a promising analyte in this setting because it is released during cellular injury, cleared rapidly from circulation, and retains multiple layers of biological information. In this review, we discuss cfDNA as a systems-level biomarker in critical illness. Beyond total concentration, cfDNA encodes complementary information through tissue-specific methylation patterns, fragmentomic features, genomic signals, and microbial DNA. Together, these layers can inform on injury burden, tissue-of-origin, host response, and pathogen detection from a single analyte. We summarize the principal analytical approaches used to interrogate these signals and review cfDNA applications across major critical care presentations, including respiratory failure, brain, liver, kidney, and cardiac injury, transplantation, major surgery, and suspected infection or sepsis. Across these settings, cfDNA frequently provides information that extends beyond conventional biomarkers by capturing real-time tissue injury, systemic immune activation, and, in infection, both pathogen-derived and host-derived signals. We also discuss key interpretative challenges, including altered clearance, tissue-composition confounding, and pre-analytical variability. Finally, we highlight the need to move beyond identifying where injury occurs toward resolving how it occurs, enabling pathway-aware diagnostics in critical illness.