A one-year hospital system review of plasma next-generation sequencing in a mixed population

To describe the use of plasma next-generation sequencing (NGS) and determine if it provided additional information from routine tests or lead to change in antimicrobial management.

This retrospective cohort study evaluated patients with a NGS test performed who were admitted to a hospital health system in the greater Houston area between May 2022 and May 2023.

In total, 143 NGS tests were ordered in the span of one year for 135 unique patients. Most patients were ≥ 18 years (74.1%), White/Caucasian (43.7%), male (61.5%), and immunocompetent (54.1%). Eight patients had repeat tests during the study period, four being after an initial rejected test, and the rest being greater than 7 days from the initial test.

Of the 139 NGS tests performed, 56 (40%) were positive. When compared to routine testing, 49 (35%) were negative when routine testing was negative, 15 (11%) positive were concordant with routine testing, 29 (21%) positive were discordant from routine testing, 17 (12%) negative while routine testing was positive, and 29 (21%) were positive while routine testing was negative. Documented changes in antimicrobial due to NGS occurred after 16 (13.6%) tests, with the majority of these changes occurring in immunocompromised patients (14/16 [88%]).

NGS provided additional data when compared to routine testing but rarely resulted in antimicrobial changes. The majority of changes occurred in immunocompromised patients. Diagnostic stewardship is a vital component for this type of NGS testing and others in which guidelines do not exist.