A new method using rapid Nanopore metagenomic cell-free DNA sequencing to diagnose bloodstream infections: a prospective observational study
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- Evaluated articles (Rapid Reviews Infectious Diseases)
Abstract
Background
Bloodstream infections (BSIs) remain a major cause of mortality, in part due to many patients developing sepsis or septic shock. To survive sepsis, it is paramount that effective antimicrobial therapy is initiated rapidly to avoid excess mortality, but the current gold-standard to identify the pathogen in BSIs, blood culturing, has great limitations with a long turnaround time and a poor sensitivity. This delay to correct empiric broad-spectrum antimicrobial treatments leads to excess mortality and antimicrobial resistance development.
Methods
In this study we developed a metagenomic next-generation sequencing (mNGS) assay utilizing the Oxford Nanopore Technologies platform to sequence microbial cell-free DNA from blood plasma. The method was evaluated in a prospective observational clinical study (n=40) in an emergency ward setting, where a study sample was taken from the same venipuncture as a blood culture sample from patients with a suspected BSI.
Findings
Nanopore mNGS confirmed all findings in patients with a positive blood culture (n=11), and identified pathogens relevant to the acute infection in an additional 11 patients with a negative blood culture. In an analysis of potential impact on the antibiotic treatment, we found that 59% (n=13) of mNGS positive answers could have impacted the treatment, with five cases of a change from ineffective to effective therapy.
Interpretation
This study demonstrates that culture-independent Nanopore mNGS directly on blood plasma could be a feasible alternative to blood culturing for infection diagnostics for patients admitted with a severe infection or sepsis. The method identified a relevant pathogen in patients with a broad range of etiologies including urinary tract infections and lower respiratory tract infections. With a turnaround time of 6 hours the method could provide unprecedented speed and sensitivity in BSI diagnostics.
Article activity feed
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Barry Lutz, Qin Wang, Rhett Britton
Review 5: "A New Method Using Rapid Nanopore Metagenomic Cell-free DNA Sequencing to Diagnose Bloodstream Infections: A Prospective Observational Study"
Reviewers agree that the methodology is well-designed and the evidence is reliable. However, they suggest including more technical details and caution against overestimating the method's capabilities while emphasizing its supplementary role alongside blood cultures.
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Zoe Weiss, Sean Harford
Review 4: "A New Method Using Rapid Nanopore Metagenomic Cell-free DNA Sequencing to Diagnose Bloodstream Infections: A Prospective Observational Study"
Reviewers agree that the methodology is well-designed and the evidence is reliable. However, they suggest including more technical details and caution against overestimating the method's capabilities while emphasizing its supplementary role alongside blood cultures.
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Yeon Joo Lee
Review 3: "A New Method Using Rapid Nanopore Metagenomic Cell-free DNA Sequencing to Diagnose Bloodstream Infections: A Prospective Observational Study"
Reviewers agree that the methodology is well-designed and the evidence is reliable. However, they suggest including more technical details and caution against overestimating the method's capabilities while emphasizing its supplementary role alongside blood cultures.
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Nadia Urosevir
Review 2: "A New Method Using Rapid Nanopore Metagenomic Cell-free DNA Sequencing to Diagnose Bloodstream Infections: A Prospective Observational Study"
Reviewers agree that the methodology is well-designed and the evidence is reliable. However, they suggest including more technical details and caution against overestimating the method's capabilities while emphasizing its supplementary role alongside blood cultures.
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Francesco Santoro, David Pinzauti
Review 1: "A New Method Using Rapid Nanopore Metagenomic Cell-free DNA Sequencing to Diagnose Bloodstream Infections: A Prospective Observational Study"
Reviewers agree that the methodology is well-designed and the evidence is reliable. However, they suggest including more technical details and caution against overestimating the method's capabilities while emphasizing its supplementary role alongside blood cultures.
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Strength of evidence
F Santoro(Università degli Studi di Siena)&D Pinzauti(The Bioarte ltd.)|📗📗📗📗◻️
N Urosevir(University of Western Australia)|📗📗📗📗◻️
Y Joo Lee(Memorial Sloan Hospital)|📒📒📒◻️◻️
Z Weiss&S Harford(Tufts)|📗📗📗📗◻️
B Lutz&Q Wang&R Britton(University of Washington)|📗📗📗📗◻️ -
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