Clinical Utility of Metagenomic Next-Generation Sequencing of Plasma Microbial Cell-Free DNA: a Single-Center Retrospective Study

Abstract Infectious diseases account for significant morbidity and mortality in healthcare, and metagenomic next-generation sequencing of plasma microbial cell-free DNA has emerged as a promising non-invasive diagnostic tool in this scenario. However, the available data on the real impact of this test in clinical practice is limited and conflicting. In this context, we performed a retrospective evaluation of the utilization of this test at our institution since February 17, 2019. A total of 76 tests were performed in this period in 68 different patients. The mean age of the patients was 9 years old, with 40 being male (58.82%) and 28 female (41.18%). The ordering specialties included infectious diseases (82.90%), hematology/oncology (9.21%), neurology (3.95%), pulmonology (2.63%), and dermatology (1.31%). The vast majority of the tests were ordered as inpatient (73 tests, 96.05%). 45 tests (59.21%) resulted as positive, of which 19 (42.22%) were polymicrobial. The tests were concordant with conventional microbiological studies 47 times (61.84%). Most tests (67 tests, 88.16%) had no significant clinical impact, 8 tests (10.53%) had a positive impact, and one test (1.31%) had an indeterminate impact. No tests were determined to have a negative clinical impact. Overall, our data is consistent with most studies which assessed the clinical utility of metagenomic next-generation sequencing of plasma microbial cell-free DNA in the literature, showing that testing did not have a significant impact on patient care for the majority of cases. There were some cases, however, in which testing showed a positive impact in escalating or de-escalating antibiotic therapy. In conclusion, despite being mostly a bystander, in selected cases and in the right clinical context, the test can be useful to guide antimicrobial treatment without causing significant harm. More studies are needed to further investigate the real utility of the test.