Microbial Cell-Free DNA Identifies Etiology of Bloodstream Infections, Persists Longer Than Conventional Blood Cultures, and Its Duration of Detection Is Associated With Metastatic Infection in Patients With Staphylococcus aureus and Gram-Negative Bacteremia

Abstract

Background Microbial cell-free DNA (mcfDNA) sequencing of plasma can identify presence of a pathogen in a host. This study evaluated the duration of pathogen detection by mcfDNA sequencing vs. conventional blood culture in patients with bacteremia. Methods Blood samples from patients with culture-confirmed bloodstream infection were collected within 24 hours of the index positive blood culture and 48 to 72 hours thereafter. mcfDNA was extracted from plasma and next-generation sequencing (NGS) applied. Reads were aligned against a curated pathogen database. Statistical significance was defined with Bonferroni adjustment for multiple comparisons (p < 0.0033). Results A total of 175 patients with Staphylococcus aureus bacteremia (SAB; n=66), Gram-negative bacteremia (GNB; n=74), or non-infected controls (n=35) were enrolled. The overall sensitivity of mcfDNA sequencing compared to index blood culture was 89.3% (125/140) and the specificity was 74.3%. Among patients with bacteremia, pathogen specific mcfDNA remained detectable for significantly longer than conventional blood cultures (median 15 days vs. 2 days; p<0.0001). Each additional day of mcfDNA detection significantly increased the odds of metastatic infection (Odds Ratio [OR]: 2.89; 95% Confidence Interval [CI]: 1.53-5.46; p=0.0011). Conclusions Pathogen mcfDNA identified the bacterial etiology of bloodstream infection for a significantly longer interval than conventional cultures, and its duration of detection was associated with increased risk for metastatic infection. mcfDNA could play a role in the diagnosis of partially treated endovascular infections.

Clinical impact of a metagenomic microbial plasma cell-free DNA next-generation sequencing assay on treatment decisions: a single-center retrospective study

“…This benefit was often derived from situations in which the assay either identified pathogens that were felt to not be clinically relevant, or no pathogen at all (Table 5 ). While different from our study in its scope, a study by Eichenberger et al demonstrated that mcfDNA persisted in plasma well beyond conventional blood cultures in bloodstream infections and that persistence was associated with an increased risk of metastatic infection [ 7 ]. Taken together, the safe de-escalation or discontinuation of antimicrobials in the context of negative or decreasing levels of mcfDNA may highlight a role for mcfDNA in the realm of stewardship or determining antimicrobial course duration.…”

Development and clinical validation of a droplet digital PCR assay for detecting Acinetobacter baumannii and Klebsiella pneumoniae in patients with suspected bloodstream infections

“…This study had certain limitations. First, as the microbial cfDNA is possibly released from dead pathogens and is continuously detected almost 2 weeks after conventional blood cultures report negative results (Eichenberger et al, 2021 ), the presence of microbial cfDNA in the blood does not necessarily indicate the presence of living microorganisms in the bloodstream and may also be derived from a previous BSI. Second, unlike metagenomic NGS that has a wider coverage for detecting causative pathogens, ddPCR can only identify a small number of target pathogens; thus, it is not possible to determine whether a patient has a mono‐microbial infection or polymicrobial infection based on the detection results from the ddPCR assay alone.…”

Clinical Utility and Impact of the Metagenomic Microbial Plasma Cell-Free DNA Next-Generation Sequencing Assay on Treatment Decision: A Single-Center Retrospective Study

“…While different from our study in its scope, a study by Eichenberger, et al demonstrated that mcfDNA persisted in plasma well beyond conventional blood cultures in blood stream infections and that persistence was associated with an increased risk of metastatic infection. 7 Taken together, the safe de-escalation or discontinuation of antimicrobials in the context of negative or decreasing levels of mcfDNA may highlight a role for mcfDNA in the realm of stewardship or determining antimicrobial course duration.…”

“…mcfDNA sequencing has been studied as a complimentary assay in the rapid diagnosis of sepsis, culture-negative endocarditis, pneumonia, invasive fungal infections, brain abscesses and more recently as an adjunct to conventional microbiology cultures in bloodstream infections and prosthetic joint infections. [2][3][4][5][6][7][8] Despite results of recent clinical trials and case reports demonstrating the potential value of mcfDNA as a diagnostic tool, the overall impact of mcfDNA testing on clinical care is less certain. For example, a retrospective cohort study by Hogan and colleagues evaluating the clinical impact of mcfDNA found that despite a positivity rate of 61%, mcfDNA had a positive clinical impact in only 7.3% of cases.…”