Diagnostic Yield and Impact on Antimicrobial Management of 16S rRNA Testing of Clinical Specimens

16S rRNA gene sequencing is increasingly used in clinical practice for bacterial identification of clinical specimens. However, studies on its applicability to direct clinical specimens are limited. Here, we studied the diagnostic yield and impact of 16S rRNA gene sequencing from direct clinical specimens on antimicrobial management. Adult inpatients whose attending physician requested 16S rRNA gene sequencing and corresponding bacterial culture from a direct clinical specimen between January and December 2021 in a university hospital were prospectively included in this study. A total of 434 specimens from 374 patients were requested. Of these, 253 (58.3%) specimens were collected from patients whose final diagnosis indicated a bacterial infection, whereas 181 (41.7%) specimens were from nonbacterial infections. Using the final diagnosis as a “gold standard,” the sensitivity and specificity of 16S rRNA gene sequencing were 38.3% and 93.9%, respectively. Among the bacterial infection cases, the proportion of 16S rRNA gene sequencing-positive and culture-positive cases was 32.4%, and the proportion of sequencing-positive and culture-negative cases was 5.9%. The impact on antimicrobial management was evident in 10 (2.3%) specimens, which all resulted in the continuation of antibiotics. The impact on antimicrobial management was highest in skin and soft tissue infections, followed by bone and joint infections. In this study, the long turnaround time of 16S rRNA gene sequencing of clinical specimens was a limiting factor. In conclusion, the overall diagnostic yield of 16S rRNA gene sequencing in bacterial infection cases was fair, being useful in selected cases. Restrictions on test requests may improve test utilization in this setting. IMPORTANCE 16S rRNA gene sequencing has been increasingly used in clinical practice. Using the final diagnosis as a gold standard, the sensitivity of 16S rRNA gene sequencing was fair. In the setting with no 16S rRNA gene sequencing test ordering restrictions, only small percentages of the test results had an impact on antimicrobial management. Restrictions on test requests should be developed to maximize the benefit of the test.