Fragment Ends of Circulating Microbial DNA as Signatures for Pathogen Detection in Sepsis.

Area of Science:

• Genomics
• Molecular Biology
• Infectious Disease Diagnostics

Background:

• Cell-free DNA (cfDNA) in plasma exhibits non-random fragmentation patterns linked to its origin.
• DNASE1L3 enzyme influences nuclear cfDNA fragmentation, favoring CC-end motifs.
• Fragment end properties and clinical implications of microbial cfDNA are largely unexplored.

Purpose of the Study:

• To investigate the fragmentation characteristics of microbial cfDNA in sepsis patients.
• To explore the potential of microbial cfDNA fragment end motifs for clinical diagnostics.

Main Methods:

• Analysis of microbial cfDNA fragment end motifs in plasma samples from sepsis patients.
• Application of a sequence context-based normalization method to mitigate analysis bias.

Main Results:

• Microbial cfDNA end motifs resemble nuclear cfDNA, with a preference for the CC-end motif, suggesting DNASE1L3 involvement.
• Differential end motifs distinguish pathogenic microbial cfDNA (CC-enriched) from contaminating microbial DNA (random).
• Fragment end signatures achieved high accuracy (AUC 0.99) in differentiating pathogens from contaminants, outperforming abundance-based methods.

Conclusions:

• Fragmentomic features of microbial cfDNA can differentiate true pathogens from contaminants in sepsis.
• Microbial cfDNA fragmentomics holds significant potential for metagenomic analysis and improved sepsis diagnostics.