Clinical Utility of Plasma Microbial Cell-Free DNA Sequencing in Adult Immunocompromised Patients: A Real-World Cohort Study.

Abstract

Background: Plasma metagenomic next generation sequencing (mNGS) enables noninvasive pathogen detection independent of organism viability. Although analytic performance has been described, the real-world clinical impact in immunocompromised hosts remains incompletely defined.

Methods: We conducted a retrospective cohort study of immunocompromised adults undergoing plasma mNGS testing from January 2022 through November 2024 at the Medical University of South Carolina. Immunocompromised conditions included solid organ transplantation, hematopoietic stem cell transplantation, active hematologic malignancy, HIV, or biologic immunosuppressants. Clinical impact was adjudicated by infectious disease physicians as positive, negative, or neutral. Positive results were classified as definite, probable, possible, or unlikely infectious based on clinical correlation and concordance with conventional microbiologic testing (CMT).

Results: Ninety-eight patients were included (median age 60 years [range 18-76]; 63% male), including solid organ transplant (31%), hematopoietic stem cell transplant (8%), HIV (13%), active malignancy (42%), corticosteroids (3%), and biologic therapy (10%). At testing, 85% were receiving antimicrobials and 88% were hospitalized. Plasma mNGS was positive in 62% of cases, with CMT concordance in 30%. Thirty-two percent of tests had positive clinical impact, identifying unrecognized infection or antimicrobial optimization. Sixty-six percent had no treatment impact and 2% had potential negative impact. More than half of discordant positives were deemed possible or unlikely infections. False-negative cases included invasive mold and nontuberculous mycobacterial infections.

Conclusions: In this antimicrobial-exposed immunocompromised cohort, plasma mNGS frequently detected organisms but less often influenced clinical management. Discordant positives were common, and false negatives occurred in selected syndromes, supporting cautious interpretation and stewardship-guided use.