Assessment of the Clinical Utility of Plasma Metagenomic Next-Generation Sequencing in a Pediatric Hospital Population

Background Metagenomic next-generation sequencing (mNGS) of plasma cell-free DNA (cfDNA) is commercially available, but its role in the workup of infectious diseases is unclear. Methods To understand the clinical utility of plasma mNGS, we retrospectively reviewed patients tested at a pediatric institution over 2 years to evaluate the clinical relevance of the organism(s) identified and impact on antimicrobial management. We also investigated the effect of pre-test antimicrobials and interpretation of molecules of microbial cfDNA per microliter (MPM) plasma. Results 29/59 (49%) mNGS tests detected organism(s), and 28/51 (55%) organisms detected were clinically relevant. Median MPM of clinically relevant organisms was 1533 versus 221 for irrelevant organisms (p=0.01). mNGS test sensitivity and specificity were 53% and 79%, respectively, with a positive predictive value (PPV) of 72% and negative predictive value (NPV) of 50%. 14% of tests impacted clinical management by changing antimicrobial therapy. Immunocompromised status was the only patient characteristic that trended towards a significant clinical impact (p=0.056). No patients with culture-negative endocarditis had organisms identified by mNGS. There were no significant differences in antimicrobial pre-test duration between tests with clinically relevant organism(s) versus those that returned negative, nor was the MPM different between pre-treated and un-treated organisms, suggesting that 10 days of antimicrobial therapy as observed in this cohort did not sterilize testing; however, no pre-treated organisms identified resulted in a new diagnosis impacting clinical management Conclusions Plasma mNGS demonstrated higher utility for immunocompromised patients, but given the low PPV and NPV, cautious interpretation and Infectious Diseases consultation are prudent. Summary We evaluate the test performance characteristics and clinical utility of plasma metagenomic next-generation sequencing in a pediatric hospital cohort and demonstrate sensitivity and specificity of 53% and 79%, with 14% of tests impacting antimicrobial management.