Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract
Open accessPublished version of a preprint
Abstract
Urinary tract infections are one of the most common infections in humans. Here we tested the utility of urinary cell-free DNA (cfDNA) to comprehensively monitor host and pathogen dynamics in bacterial and viral urinary tract infections. We isolated cfDNA from 141 urine samples from a cohort of 82 kidney transplant recipients and performed next-generation sequencing. We found that urinary cfDNA is highly informative about bacterial and viral composition of the microbiome, antimicrobial susceptibility, bacterial growth dynamics, kidney allograft injury, and host response to infection. These different layers of information are accessible from a single assay and individually agree with corresponding clinical tests based on quantitative PCR, conventional bacterial culture, and urinalysis. In addition, cfDNA reveals the frequent occurrence of pathologies that remain undiagnosed with conventional diagnostic protocols. Our work identifies urinary cfDNA as a highly versatile analyte to monitor infections of the urinary tract.
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Blood-based microbial DNA can be clinically informative in cancer, including cancers with blood-barrier or lymphatic disruptions.
“There is mounting evidence that blood-based microbial DNA (hereafter “mbDNA”) can be clinically informative in cancer39–44, including those featuring blood-barrier or lymphatic disruptions (e.g. COAD)39”
From RETRACTED ARTICLE: Microbiome analyses of blood and tissues suggest cancer diagnostic approach (2020) · cites this paper as [42]
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References 64 · Cited by 160
- Authors
- Burnham, P., Dadhania, D., Heyang, M., Chen, F., Westblade, L. F., Suthanthiran, M., Lee, J. R., & De Vlaminck, I.
- Affiliations
- Cornell University (US)
- NewYork–Presbyterian Hospital (US)
- Weill Cornell Medicine (US)
- Corresponding author
- Lee, John Richard
- ORCID
- Venue
- Nature Communications
- Published
- 2018-06-20
- Volume
- 9
- Issue
- 1
- Pages
- 2412-2412
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC6010457
- OpenAlex
- W2807732072
- Cited by
- 160
- References
- 64
- Citations by year
- 2026: 7 · 2025: 17 · 2024: 23 · 2023: 12 · 2022: 24 · 2021: 27 · 2020: 30 · 2019: 15 · 2018: 5
- FWCI
- 15.23
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Science Foundation (1144153)
- Noyce Foundation
- National Institutes of Health (1dp2ai138242-01)
- National Institute of Allergy and Infectious Diseases (DP2 AI138242, R21AI133331, K23AI124464, R37AI051652, R21AI124237)
- Topics
- Health Sciences › Medicine › Epidemiology › Urinary Tract Infections Management
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Bacterial Identification and Susceptibility Testing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- urinary cell-free DNA, urinary tract infection, kidney transplant recipients, urinary microbiome, antimicrobial susceptibility, bacterial growth dynamics, host response to infection, infection monitoring, liquid biopsy
- MeSH terms
- Cell-Free Nucleic Acids, DNA, Bacterial, DNA, Viral, Female, Humans, Male, Urinary Tract, Urinary Tract Infections, Cohort Studies, Biomarkers, Sequence Analysis, DNA, Host-Pathogen Interactions, High-Throughput Nucleotide Sequencing, Microbiota
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