Diagnostic Value of 16S Ribosomal RNA Gene Polymerase Chain Reaction/Sanger Sequencing in Clinical Practice

• Published in: Clinical infectious diseases 2021-09, Vol.73 (6), p.961-968
• Main Authors: Fida, Madiha, Khalil, Sarwat, Abu Saleh, Omar, Challener, Douglas W, Sohail, Muhammad Rizwan, Yang, Joshua N, Pritt, Bobbi S, Schuetz, Audrey N, Patel, Robin
• Format: Article
• Language: English
• Subjects: Bacterial Infections - diagnosis; DNA, Bacterial - genetics; Genes, rRNA; Humans; Major and Commentaries; Polymerase Chain Reaction; Retrospective Studies; RNA, Ribosomal, 16S - genetics
• ISSN: 1058-4838; 1537-6591
• DOI: 10.1093/cid/ciab167

Accurate microbiologic diagnosis is important for appropriate management of infectious diseases. Sequencing-based molecular diagnostics are increasingly used for precision diagnosis of infections. However, their clinical utility is unclear. We conducted a retrospective analysis of specimens that underwent 16S ribosomal RNA (rRNA) gene polymerase chain reaction (PCR) followed by Sanger sequencing at our institution from April 2017 through March 2019. A total of 566 specimens obtained from 460 patients were studied. Patients were considered clinically infected or noninfected based on final diagnosis and management. In 17% of patients, 16S rRNA PCR/sequencing was positive and in 5% of patients, this test led to an impact on clinical care. In comparison, bacterial cultures were positive in 21% of patients. Specimens with a positive Gram stain had 12 times greater odds of having a positive molecular result than those with a negative Gram stain (95% confidence interval for odds ratio, 5.2-31.4). Overall, PCR positivity was higher in cardiovascular specimens (37%) obtained from clinically infected patients, with bacterial cultures being more likely to be positive for musculoskeletal specimens (P