Plasma Microbial Cell-free DNA Sequencing from Over 15,000 Patients Identified a Broad Spectrum of Pathogens

Abstract

Microbial cell-free DNA (mcfDNA) sequencing is an emerging infectious disease diagnostic tool which enables unbiased pathogen detection from plasma. The Karius Test®, a commercial mcfDNA sequencing assay developed by and available since 2017 from Karius, Inc. (Redwood City, CA), detects and quantifies mcfDNA as molecules/μl in plasma. The commercial sample data and results for all tests conducted from April 2018 through mid-September 2021 were evaluated for laboratory performance metrics, reported pathogens, and data from test requisition forms. A total of 18,690 reports were generated from 15,165 patients in a hospital setting among 39 states and the District of Columbia. The median time from sample receipt to reported result was 26 hours (IQR 25–28), and 96% of samples had valid test results. Almost two-thirds (65%) of patients were adults, and 29% at the time of diagnostic testing had ICD10 codes representing a diverse array of clinical scenarios. There were 10,752 (58%) reports that yielded at least one taxon for a total of 22,792 detections spanning 701 unique microbial taxa. The 50 most common taxa detected included 36 bacteria, 9 viruses, and 5 fungi. Opportunistic fungi (374Aspergillusspp., 258Pneumocystis jirovecii, 196Mucorales, and 33 dematiaceous fungi) comprised 861 (4%) of all detections. Additional diagnostically challenging pathogens (247 zoonotic and vector borne pathogens, 144Mycobacteria, 80Legionellaspp., 78 systemic dimorphic fungi, 69Nocardiaspp., and 57 protozoan parasites) comprised 675 (3%) of all detections. We report the largest cohort of patients tested using plasma mcfDNA sequencing. The wide variety of pathogens detected by plasma mcfDNA sequencing reaffirm our understanding of the ubiquity of some infections while also identifying taxa less commonly detected by conventional methods.

Analytical and Clinical Validation of Direct Detection of Antimicrobial Resistance Markers by Plasma Microbial Cell-free DNA Sequencing

“…The copyright holder for this preprint this version posted March 18, 2024. ; https://doi.org/10.1101/2024.03.14.24303933 doi: medRxiv preprint plasma for >1,000 pathogens including bacteria, DNA viruses, fungi, and parasites within a clinically relevant time frame, with a median time from specimen collection to report of 2.6 days (10). The analytical and clinical validation of the test has been previously reported (11).…”

“…The Karius Test® is an analytically and clinically validated mcfDNA sequencing test, commercially available since December 2016 as a laboratory developed test. The test identifies and quantitates mcfDNA in plasma for >1,000 pathogens including bacteria, DNA viruses, fungi, and parasites within a clinically relevant time frame, with a median time from specimen collection to report of 2.6 days (10). The analytical and clinical validation of the test has been previously reported (11).…”

Amebic encephalitis and meningoencephalitis: an update on epidemiology, diagnostic methods, and treatment

“…An additional B. mandrillaris GAE case in the United States was diagnosed by performing microbial cell-free DNA testing of a serum sample using NGS methods by Karius, Inc. [47]. In a 2023 preprint article published by researchers from Karius, Inc., the private company reported detection of Acanthamoeba , B. mandrillaris , and N. fowleri in one patient sample each between 2018 and 2021 [48]. Although this may suggest utility in serum NGS testing in some cases, the proportion of patients with GAE or PAM that have detectable DNA in the serum is currently unknown.…”

Detection of Mpox Virus Using Microbial Cell-Free DNA: The Potential of Pathogen-Agnostic Sequencing for Rapid Identification of Emerging Pathogens

“…Microbial cell-free DNA (mcfDNA) metagenomic sequencing from plasma has been used for pathogen-agnostic infectious disease diagnostics [ 18 ] and has been demonstrated to detect diagnostically challenging clinical infections [ 19–21 ]. The pathogen-agnostic nature of mcfDNA testing may support detecting emerging infections.…”