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Objective: To describe whether detecting plasma microbial cell-free DNA by next-generation sequencing (NGS) provided additional information compared to routine cultures or led to change in antimicrobial management. Design and setting: This is a retrospective cohort study evaluating NGS tests performed on patients who were admitted to an 11-acute care hospital health system in the greater Houston area between May 2022 and May 2023. Repeat tests on the same patient encounter were included if >7 days from previous test. Routine microbiology data was compared if test was collected within 7 days before or after NGS testing. Results: During the study period there were 135 unique patient encounters identified with an NGS order. Of which, 74.1% were ≥18 years of age and 46.7% were immunocompromised. A total of 143 NGS tests were ordered, with 4 not being run due to quality control issues. Out of 139 NGS tests completed, 76 (54.7%) were positive for at least one organism. When compared to routine testing, NGS alone was positive in 29 (20.9%) instances, routine testing alone was positive in 17 (12.2%) instances, both were positive in 44 (31.7%) instances, and both were negative in 49 (35.3%) instances. In the 44 instances that both NGS and routine testing were positive, 15 (34.1%) were concordant for all organisms. In total, NGS identified 92 more organisms (69 bacterial, 8 fungal, and 15 viral) compared to routine testing and routine testing identified 42 more organisms (28 bacterial, 6 fungal, 11 viral, and 1 parasite) compared to NGS. Fifty-six changes to antibiotic therapy were made within 48 hours of the NGS test resulting, with 16 of these changes being directly attributed to NGS test. Nine of these changes being escalations and seven being de-escalations. Conclusion: NGS may aid in determining further testing, earlier detection of pathogens, and detection of pathogens outside of routine testing resulting in direct changes to antimicrobials. However, results need to be interpreted with caution. NGS can miss pertinent pathogens and is difficult to interpret when commensal organisms are detected, both of which can lead to unnecessary testing or treatment. There is an absence of a clear algorithm for the use of NGS testing and the test comes with a high price and unclear utility. Further studies are needed to determine which patients may most benefit from NGS testing.

Abstract Objective: 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. Design and Setting: 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. Patients: 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. Results: 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%]). Conclusions: 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.