Fragmentation patterns of pathogen-derived cell-free DNA as a promising non-invasive biomarker for bloodstream infection diagnosis.

Background: Bloodstream infections (BSIs) caused by bacteria, viruses, and parasites pose a global health challenge, with high mortality rates. Traditional blood cultures are considered the gold standard but are limited by long turnaround times, low sensitivity, and reliance on culturable pathogens. Cell-free DNA (cfDNA) has emerged as a promising non-invasive biomarker for rapid pathogen detection. Materials and methods: In this study, we analyzed plasma cfDNA from 102 BSI patients (42 bacterial, 34 viral, and 23 parasitic infections) using next-generation sequencing to examine the differences in cfDNA fragmentation patterns across pathogen types. Results: Pathogen-derived cfDNA fragments were shorter than human-derived cfDNA (median: 166 bp), with bacterial cfDNA averaging 126 bp and viral cfDNA 140 bp. Bacterial cfDNA fragments were typically shorter than viral ones, revealing distinctive patterns that could differentiate bacterial from viral infections. Fragment lengths varied among bacterial and viral species, suggesting the potential for pathogen-specific detection. EBV-derived cfDNA, at 163 bp, resembled human cfDNA possibly due to its nucleosome-bound form, while parasite-derived cfDNA had a broader distribution (median: 165 bp), indicating limitations in using cfDNA length for detecting parasitic infections. Conclusions: Our findings demonstrate that pathogen-derived cfDNA exhibits distinct fragmentation patterns, providing a potential non-invasive tool to complement traditional diagnostic methods, particularly for hard-to-culture pathogens. However, further studies with larger sample sizes are needed to refine pathogen-specific fragment length ranges and validate its clinical applicability.