677 - Plasma Metagenomic Next Generation Sequencing Assay for Identifying Pathogens: A Retrospective Review of Test Utilization in a Large Children’s Hospital

Background: Plasma cell-free metagenomic next generation sequencing (pNGS) is a newer diagnostic method used to potentially identify multiple pathogens with a single DNA-based diagnostic test. The test is expensive and little is understood about where it fits in the diagnostic schema of an infectious workup. We describe our experience at Texas Children’s Hospital with the pNGS assay by Karius from Redwood, CA and attempt to determine what additional diagnostic value is offered by pNGS when it is performed in the same time frame as conventional microbiological testing.

Methods: We performed a retrospective review of all patients who had pNGS testing from April to June of 2019. Results for pNGS testing, collection time, and result time were compared to that of conventional testing (culture, serology, PCR, anatomic pathology) performed one week before and one week after the pNGS testing. Any discordant results were further reviewed to determine if there was a change in antimicrobials due to the additional organism(s) identified by pNGS.Study design for retrospective review of plasma metagenomic sequencing at large pediatric hospital


Results: Sixty patients had pNGS testing; the majority were immunosuppressed (62%) or had a primary immunodeficiency (6.7%). There was a 54% positive agreement and a 62% negative agreement between pNGS and conventional testing. When test results matched, result time in the electronic medical record (EMR) were 3.5 days earlier for conventional testing than pNGS. Overall turnaround time was shorter by conventional testing than pNGS testing (1.8 days vs 4.0 days). When additional organism(s) were identified by pNGS (38% of cases), antimicrobials were changed 26% of the time.Types of organisms identified by pNGS and conventional testing
Number of organisms identified per patient for pNGS and conventional Testing
Turnaround time for organisms identified by pNGS and conventional testing


Conclusion: We found that conventional testing provided the same results sooner compared to pNGS. Additional organisms identified by pNGS only lead to a change in management in a few cases. We advocate for order restriction for pNGS to better delineate which patients may benefit most from pNGS thereby avoiding unnecessary testing and costs.