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

Abstract

ABSTRACTMicrobial 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.