Detection of Pathogens through Liquid Biopsy Shotgun Sequencing

Abstract

Pathogens — bacteria, viruses, and fungi — cause a wide range of infectious diseases, from mild to life-threatening. Accurate and timely identification of these pathogens is essential for effective treatment, particularly in vulnerable patients. Traditional diagnostic tools are often limited in speed or sensitivity. This book explores the promise of cell-free DNA (cfDNA) sequencing as a novel, non-invasive method to detect pathogens directly from blood or other body fluids. Focusing on Next-Generation Sequencing (NGS) of cfDNA, this work addresses both laboratory and computational challenges in identifying low-abundance microbial DNA among the overwhelming background of human DNA. Through clinical collaborations, the research investigates real-world applications of cfDNA NGS in two urgent diagnostic contexts: invasive fungal infections in immunocompromised children and bacterial sepsis in newborn foals. The findings demonstrate that cfDNA sequencing can detect Aspergillus fumigatus in lung fluid and blood, and identify bacterial pathogens in foals with sepsis. Additionally, the book presents innovative methods to enrich pathogen-specific DNA fragments, improving sensitivity and efficiency.