680 - The Use of Plasma Next-Generation Sequencing Test in the Management of Immunocompetent and Immunocompromised Patients – A Single Center Retrospective Study

Background: Microbiological culture data is a longstanding gold standard in diagnostics. Unfortunately, yield from cultures have been inconsistent and slow, prompting the need for newer tests including the plasma-based next-generation sequencing (NGS) tool. This study aims to describe the use of NGS and the corresponding change in management.

Methods: A descriptive retrospective study was done on hospitalized adults at CHI-Baylor St. Luke’s in Houston, Texas with NGS tests from Jan 1, 2017 to Dec 31, 2018.Graph 1 - Next Generation Sequencing Test Breakdown


Results: There were 167 NGS tests performed. Most patients were non-Hispanic (n=129) Caucasian (n=106) males (n=116) with a mean age of 52. Furthermore, 61 were immunocompromised patients [solid organ transplant (n=30), HIV-AIDS (n=14) and rheumatology patients on immunosuppression (n=12)].

During the study, the hospital staff prepared a list of indications for NGS testing including: systemic or deep seated infection where a biopsy or other workup is negative or not possible (n=50), fever of unknown origin (n=26), culture negative endocarditis (n=15), HIV/AIDS with fever (n=10), transplant patient with fever (n=5). There were 60 cases where the indications were not on this list (36%).

Results showed that 118/167 (71%) were positive. The most common organisms identified were gram-negative bacteria (54/118; 46%) followed by viruses (49/118; 42%), gram-positive bacteria (48/118; 41%), fungi (16/118; 14%), atypical bacteria (9/118; 8%), mycobacterium (4/118; 3%), and parasites (4/118; 3%). Blood cultures were concurrently obtained in 148/167 (89%) of the cases and returned negative in 137/148 (93%) of cases.

In terms of change of management, the largest change was found in glycopeptide use (36 fewer patients after NGS results). Next was on anti-mycobacterial drugs where 27 were added among 8 instances. Only 36 patients were taken off antibiotics, even though 49 patients had negative results. In total, 120 out of 160 cases had antibiotic changes.Table 1 - Demographic and Laboratory Characteristics
Graph 2 - Change in Number of Antibiotics (Total: Before and After)
Graph 3 - Indications for Testing and Change in Number of Antibiotics


Conclusion: We observed a large decrease in glycopeptide use after NGS results which suggests physicians’ comfort in withdrawing MRSA coverage. In addition, anti-mycobacterial coverage increased corresponding to early mycobacterial detection with NGS. This study highlights the importance of clinical judgement in the age of rapid diagnostics.