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Updated: May 6, 2026
Circulating MicroRNA Quantification Using DNA-binding Dye Chemistry and Droplet Digital PCR
Published on: June 26, 2016
Plasma microbial cell-free DNA characterization in different populations based on the droplet digital PCR method: a
Juan Du1,2, Dong Zhang1,2, Fengliu Wang3
1Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.
Background:
Plasma microbial cell-free DNA (mcfDNA) is a key biomarker for diagnosing bloodstream infections (BSIs), which contribute significantly to morbidity and mortality, particularly in patients with severe trauma, chronic illnesses, or immunosuppressive conditions. However, the baseline distribution of mcfDNA in different populations remains unclear. This study characterizes plasma mcfDNA profiles across various human populations.
Methods:
A total of 300 blood samples were collected from 10 groups: healthy individuals (Group A), patients with chronic diseases but no infections (Group B1-B7), patients with mild-to-moderate infections (Group C), and patients meeting sepsis criteria (Group D). Multiplex droplet digital PCR (ddPCR) was used to detect mcfDNA from 10 common sepsis-causing bacterial species, two fungal species, and three herpesviruses (HSV-1, Epstein-Barr virus [EBV], and Cytomegalovirus [CMV]).
Results:
Most pathogens in all groups showed low mcfDNA copy concentrations (~100 copies/mL), forming a baseline. Group A had no pathogens exceeding this level, while Group B showed elevated E. coli and S. maltophilia (102-104 copies/mL). In Group C, 53 pathogens were detected above baseline, with EBV, CMV, and HSV-1 as the most common (copy concentrations 102-104 copies/mL). In Group D, 57 pathogens exceeded baseline, primarily EBV, K. pneumoniae, A. baumannii, E. faecium, and CMV. Although statistical analysis showed no significant differences in pathogen distribution between Groups C and D, Gram-negative bacteria were more prevalent in Group D (70% vs. 53.3%, OR = 2.03), while viral pathogens were more frequently detected in Group C (93.3% vs. 76.7%, OR = 0.24). The microbial profiles and mcfDNA copy concentrations in Groups C and D were similar (102-104 copies/mL), distinguishing them from Groups A and B.
Conclusion:
This study provides a comprehensive characterization of mcfDNA across different health states, demonstrating the utility of ddPCR in detecting microbial infections. These findings contribute to refining infection diagnostics and improving early detection strategies for BSIs and sepsis.
Insights
Plasma microbial cell-free DNA (mcfDNA) is a biomarker for bloodstream infections. This study characterized mcfDNA profiles in various populations, distinguishing infection states from healthy individuals.
Area of Science:
- Clinical microbiology
- Molecular diagnostics
- Infectious disease epidemiology
Background:
- Plasma microbial cell-free DNA (mcfDNA) is a crucial biomarker for diagnosing bloodstream infections (BSIs).
- BSIs significantly contribute to morbidity and mortality, especially in vulnerable patient groups.
- The baseline distribution of mcfDNA across diverse human populations is not well-established.
Purpose of the Study:
- To characterize plasma mcfDNA profiles in different human populations.
- To establish baseline mcfDNA levels in healthy individuals and patients with varying infection severities.
- To assess the utility of mcfDNA analysis in differentiating infection states.
Main Methods:
- Collected 300 blood samples from 10 groups, including healthy individuals, patients with chronic diseases, mild-to-moderate infections, and sepsis.
- Utilized multiplex droplet digital PCR (ddPCR) for detecting cell-free DNA from common bacterial, fungal, and viral pathogens.
- Quantified mcfDNA copy concentrations for various microbial species.
Main Results:
- Most pathogens showed low baseline mcfDNA concentrations (~100 copies/mL).
- Elevated mcfDNA levels (10^2-10^4 copies/mL) were observed in patients with infections (Groups C and D) compared to healthy (Group A) and non-infected chronic disease (Group B) groups.
- While pathogen distribution showed no significant difference between mild infections and sepsis, Gram-negative bacteria were more prevalent in sepsis, and viral pathogens were more common in mild infections.
Conclusions:
- Plasma mcfDNA analysis effectively characterizes microbial profiles across different health states.
- Droplet digital PCR (ddPCR) is a valuable tool for detecting microbial infections via mcfDNA.
- These findings aid in refining diagnostics and improving early detection of BSIs and sepsis.
