ArticleNature microbiology2023
Phage diversity in cell-free DNA identifies bacterial pathogens in human sepsis cases.
Article in Nature microbiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 32 citations in OpenAlex.
- Fast Microbiology: A Pilot Study Comparing Culture-Independent Digital PCR and Blood Culture for Pathogen Detection in Sepsis.International journal of molecular sciences · 2026Article
- DNAviWEB: sequencing-free clinical screening of liquid biopsies.Nucleic acids research · 2026Article
- Prevalent gut phages encode modular adhesins mediating epithelial binding and endoplasmic reticulum trafficking.Nature communications · 2026Article
- Cross-reactive anti-prophage antibodies and bacterial heteroresistance implicated in phage therapeutic failure.Nature medicine · 2026Article
- Bronchoalveolar lavage fluid metagenomic datasets: a multidimensional clinical biomolecular resource.Scientific data · 2025Article
- Metagenomic fingerprints in bronchoalveolar lavage differentiate pulmonary diseases.NPJ digital medicine · 2025Article
- Identification of bacteriophage DNA in human umbilical cord blood.JCI insight · 2025Article
- International consensus statement on microbiome testing in clinical practice.The lancet. Gastroenterology & hepatology · 2025Review
- Transcytosis of T4 Bacteriophage Through Intestinal Cells Enhances Its Immune Activation.Viruses · 2025Article
- Metagenomic and metatranscriptomic profiling of bronchoalveolar lavage fluid identifies microbial and host biomarkers of drug-resistant tuberculosis.Frontiers in cellular and infection microbiology · 2025Article
- Self-assembled carbon monoxide nanogenerators managing sepsis through scavenging multiple inflammatory mediators.Bioactive materials · 2024Article
- Re-visiting humoral constitutive antibacterial heterogeneity in bloodstream infections.The Lancet. Infectious diseases · 2024Review
- InducedFrontiers in microbiology · 2024Article
- Host heterogeneity in humoral bactericidal activity can be complement independent.Frontiers in immunology · 2024Article
- Deciphering the microbial landscape of lower respiratory tract infections: insights from metagenomics and machine learning.Frontiers in cellular and infection microbiology · 2024Article
- Phage therapy: Targeting intestinal bacterial microbiota for the treatment of liver diseases.JHEP reports : innovation in hepatology · 2023Review
- Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
Bacteriophages, viruses that infect bacteria, have great specificity for their bacterial hosts at the strain and species level. However, the relationship between the phageome and associated bacterial population dynamics is unclear. Here we generated a computational pipeline to identify sequences associated with bacteriophages and their bacterial hosts in cell-free DNA from plasma samples. Analysis of two independent cohorts, including a Stanford Cohort of 61 septic patients and 10 controls and the SeqStudy cohort of 224 septic patients and 167 controls, reveals a circulating phageome in the plasma of all sampled individuals. Moreover, infection is associated with overrepresentation of pathogen-specific phages, allowing for identification of bacterial pathogens. We find that information on phage diversity enables identification of the bacteria that produced these phages, including pathovariant strains of Escherichia coli. Phage sequences can likewise be used to distinguish between closely related bacterial species such as Staphylococcus aureus, a frequent pathogen, and coagulase-negative Staphylococcus, a frequent contaminant. Phage cell-free DNA may have utility in studying bacterial infections.
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