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

J Clin Microbiol. 2020 Oct 21;58(11):e00794-20. doi: 10.1128/JCM.00794-20. Print 2020 Oct 21.


Plasma metagenomic next-generation sequencing (mNGS) is a new 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 into the diagnostic schema. We describe our experience at Texas Children's Hospital with the mNGS assay by Karius from Redwood City, CA, to determine whether mNGS offers additional diagnostic value when performed within 1 week before or after conventional testing (CT) (i.e., concurrently). We performed a retrospective review of all patients who had mNGS testing from April to June of 2019. Results for mNGS testing, collection time, time of result entry into the electronic medical record, and turnaround time were compared to those for CT performed concurrently. Discordant results were further reviewed for changes in antimicrobials due to the additional organism(s) identified by mNGS. Sixty patients had mNGS testing; the majority were immunosuppressed (62%). There was 61% positive agreement and 58% negative agreement between mNGS and CT. The mean time of result entry into the electronic medical record for CT was 3.5 days earlier than the mean result time for mNGS. When an additional organism(s) was identified by mNGS, antimicrobials were changed 26% of the time. On average, CT provided the same result as mNGS, but sooner than mNGS. When additional organisms were identified by mNGS, there was no change in management in the majority of cases. Overall, mNGS added little diagnostic value when ordered concurrently with CT.

Keywords: Karius; cell-free DNA; metagenomics; pediatrics; plasma metagenomic sequencing; plasma next-generation sequencing.

MeSH terms

  • Child
  • High-Throughput Nucleotide Sequencing*
  • Hospitals
  • Humans
  • Metagenomics*
  • Retrospective Studies
  • Sensitivity and Specificity
  • Texas