A cell-free DNA metagenomic sequencing assay that integrates the host injury response to infection

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 116; no. 37; pp. 18738 - 18744
• Main Authors: Cheng, Alexandre Pellan, Burnham, Philip, Lee, John Richard, Cheng, Matthew Pellan, Suthanthiran, Manikkam, Dadhania, Darshana, De Vlaminck, Iwijn
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 10.09.2019
• Subjects: Assaying; Bacteria; Bacterial infections; Bacterial Infections - diagnosis; Bacterial Infections - microbiology; Bacterial Infections - urine; Biological Sciences; Biomarkers - urine; Bisulfite; Bladder; Cell-Free Nucleic Acids - genetics; Cell-Free Nucleic Acids - isolation & purification; Cell-Free Nucleic Acids - urine; Deoxyribonucleic acid; Diagnosis, Differential; Differential diagnosis; DNA; DNA methylation; DNA Methylation - genetics; DNA sequencing; DNA, Bacterial - genetics; DNA, Bacterial - isolation & purification; DNA, Bacterial - urine; DNA, Viral - genetics; DNA, Viral - isolation & purification; DNA, Viral - urine; Female; Genomes; High-Throughput Nucleotide Sequencing; Host-Pathogen Interactions - genetics; Host-Pathogen Interactions - immunology; Humans; Infections; Infectious diseases; Information processing; Kidney - cytology; Kidney - immunology; Kidney - microbiology; Kidney - pathology; Kidney Failure, Chronic - surgery; Kidney transplantation; Kidney Transplantation - adverse effects; Kidneys; Leukocytes (neutrophilic); Male; Metagenome - genetics; Metagenomics - methods; Neutrophil Infiltration - immunology; Next-generation sequencing; Postoperative Complications - diagnosis; Postoperative Complications - immunology; Postoperative Complications - microbiology; Postoperative Complications - urine; Tissues; Transplant Recipients; Urinary Bladder - cytology; Urinary Bladder - immunology; Urinary Bladder - microbiology; Urinary Bladder - pathology; Urinary tract; Urinary Tract Infections - diagnosis; Urinary Tract Infections - immunology; Urinary Tract Infections - microbiology; Urinary Tract Infections - urine; Urogenital system; Viral infections; Virus Diseases - diagnosis; Virus Diseases - immunology; Virus Diseases - urine; Virus Diseases - virology; host injury; cell-free DNA; metagenomics
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1906320116

High-throughput metagenomic sequencing offers an unbiased approach to identify pathogens in clinical samples. Conventional metagenomic sequencing, however, does not integrate information about the host, which is often critical to distinguish infection from infectious disease, and to assess the severity of disease. Here, we explore the utility of high-throughput sequencing of cell-free DNA (cfDNA) after bisulfite conversion to map the tissue and cell types of origin of host-derived cfDNA, and to profile the bacterial and viral metagenome. We applied this assay to 51 urinary cfDNA isolates collected from a cohort of kidney transplant recipients with and without bacterial and viral infection of the urinary tract. We find that the cell and tissue types of origin of urinary cfDNA can be derived from its genome-wide profile of methylation marks, and strongly depend on infection status. We find evidence of kidney and bladder tissue damage due to viral and bacterial infection, respectively, and of the recruitment of neutrophils to the urinary tract during infection. Through direct comparison to conventional metagenomic sequencing as well as clinical tests of infection, we find this assay accurately captures the bacterial and viral composition of the sample. The assay presented here is straightforward to implement, offers a systems view into bacterial and viral infections of the urinary tract, and can find future use as a tool for the differential diagnosis of infection.