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

Abstract

Background Metagenomic next-generation sequencing of microbial cell-free DNA (mcfDNA) allows for non-invasive pathogen detection from plasma. However, there is little data describing the optimal role for this assay in real-world clinical decision making. Methods We performed a single-center retrospective cohort study of adult patients for whom a mcfDNA (Karius©) test was sent between May 2019 and February 2021. Clinical impact was arbitrated after review and discussion of each case. Results A total of 80 patients were included. The most common reason for sending the assay was unknown microbiologic diagnosis (78%), followed by avoiding invasive procedures (14%). The test had a positive impact in 34 (43%), a negative impact in 2 (3%), and uncertain or no impact in 44 (55%). A positive impact was observed in solid organ transplant recipients (SOTR, 71.4%, p = 0.003), sepsis (71.4%, p = 0.003), and those receiving antimicrobial agents for less than 7 days prior to mcfDNA testing (i.e., 61.8%, p = 0.004). Positive impact was driven primarily by de-escalation of antimicrobial therapy. Conclusion Clinical impact of mcfDNA testing was highest in SOTR, patients with sepsis and patients who had been on antimicrobial therapy for less than 7 days. Positive impact was driven by de-escalation of antimicrobial therapy which may highlight a potential role for mcfDNA in the realm of stewardship.

Utility of Metagenomic Next-Generation Sequencing in Infective Endocarditis: A Systematic Review

“…As for the five remaining studies, they included only scant clinical information related to the definition of IE, a non-IE focused study, and lacked comparison to the results of conventional IE pathogen identification methods. Three retrospective cohort studies on plasma cell-free DNA-based pathogen identification had a few patients with IE among other infectious syndromes [ 22 , 23 , 24 ]. Million M et al and Bouchiat et al proposed two different steps to enhance the results of mNGS, microdissection combined with human DNA depletion [ 25 ] and a nanopore-based 16S rRNA metagenomic approach [ 26 ].…”

“…The narrow spectrum of specific 16s rRNA sequencing assays limits its usage in clinical practice as it can only amplify genes from certain bacteria only with targeted and predetermined primers or probes. mNGS offers a wider range of microorganisms’ detection, including viruses and fungi [ 20 , 24 , 27 ]. Pathogens that are unexpected, infrequent, or new may avoid identification by serological testing and 16S rRNA PCR.…”

“…The first was performed for multiple infection syndromes and showed that plasma mNGS can impact patient management; however, only 8.5% ( n = 7) of the patients had a suspicion of IE [ 22 ]. In the second, mNGS was used in 16.3% ( n = 13) of IE patients, and led to confirmation of diagnosis in two patients, de-escalation of antimicrobials in four patients, and procedure avoidance in one patient with IE [ 24 ]; and in the third only four patients with BCNE were evaluated [ 23 ], thus results were difficult to construe.…”

Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics

“…Standardization of the methodological and analytical workflows has just started [ 109 , 110 ]. Proof-of-concept studies have shown the potential clinical impact in pathogen identification within culture-negative samples of, e.g., meningitis and encephalitis [ 111 ], sepsis [ 112 , 113 , 114 ], pneumonia [ 115 , 116 ], and prosthetic joint infections [ 117 , 118 ]. The detection limit of shotgun metagenomics is affected by slow-growing microorganisms or if the potential pathogen is present in low abundance.…”

Could cell‐free DNA and host biomarkers assist in antimicrobial stewardship with organ transplant recipients?

“…Moreover, microbial (cf)DNA sequencing has been reported to be able to detect microbes in the bloodstream longer than conventional blood cultures, with each additional day of microbial (cf)DNA detection significantly increasing the odds of metastatic infection, 5 thereby suggesting that a negative test may be used to help shorten antimicrobial duration. A retrospective cohort study examining the clinical impact of (cf)DNA sequencing found that it can promote de‐escalation of antimicrobials in SOT recipients 6 . Similarly, a study evaluating the diagnostic performance of cf(DNA) sequencing in patients with febrile neutropenia found that real time application of sequencing results could have led to antimicrobial narrowing or discontinuation in 27% of the patients 7 .…”