Impact of 16S rDNA sequencing on clinical treatment decisions: a single center retrospective study

Abstract

Background PCRs targeting 16S ribosomal DNA (16S PCR) followed by Sanger’s sequencing can identify bacteria from normally sterile sites and complement standard analyzes, but they are expensive. We conducted a retrospective study in the Strasbourg University Hospital to assess the clinical impact of 16S PCR sequencing on patients’ treatments according to different sample types. Methods From 2014 to 2018, 806 16S PCR samples were processed, and 191 of those were positive. Results Overall, the test impacted the treatment of 62 of the 191 patients (32%). The antibiotic treatment was rationalized in 31 patients (50%) and extended in 24 patients (39%), and an invasive procedure was chosen for 7 patients (11%) due to the 16S PCR sequencing results. Positive 16S PCR sequencing results on cerebrospinal fluid (CSF) had a greater impact on patients’ management than positive ones on cardiac valves (p = 0.044). The clinical impact of positive 16S PCR sequencing results were significantly higher when blood cultures were negative (p < 0.001), and this difference appeared larger when both blood and sample cultures were negative (p < 0.001). The diagnostic contribution of 16S PCR was higher in patients with previous antibiotic treatment (p < 0.001). Conclusion In all, 16S PCR analysis has a significant clinical impact on patient management, particularly for suspected CSF infections, for patients with culture-negative samples and for those with previous antibiotic treatments.

A retrospective observational study of the impact of 16s and 18s ribosomal RNA PCR on antimicrobial treatment over seven years: A tertiary hospital experience

“…One important contributor to our findings was the long turn-around time from sample collection to reporting, with a mean time of 6.8 days. This is significantly longer than reported by Ursenbach et al, who benefited from 16s PCR technology availability within onsite diagnostic services [ 20 ]. Previously, we reported the use of molecular diagnostics with rapid turn-around-times that led to actionable case management; positive use of Abbott ID NOW™ in our Emergency Department leading to reduced admissions and reduction in healthcare associated influenza [ 18 ].…”

“…Our findings are contrary to those from another Irish centre where in 2018 they reported successful de-escalation of therapy in 21% of patients upon adoption of 16s PCR diagnostics in their centre [ 19 ]. In 2021, Ursenbach et al also reported successful change in therapy for 32% of cases with a positive 16s target in a single French centre [ 20 ]. However, these hospitals provided quaternary clinical services with specialist neurosurgical and cardiothoracic departments, in contrast to our general hospital model.…”

“…Notably, Ursenbach et al reported significant changes in antimicrobial treatment choice following positive 16s PCR for CSF samples, albeit in only 21 cases [ 20 ]. In our centre, prior to the introduction of the FilmArray ME Panel (bioMérieux, Marcy l’Étoile, France) in October 2017, bacterial testing for CSF was limited to culture and agglutination test methodologies.…”

Molecular Analysis With 16S rRNA PCR/Sanger Sequencing and Molecular Antibiogram Performed on DNA Extracted From Valve Improve Diagnosis and Targeted Therapy of Infective Endocarditis: A Prospective Study

“…Since the beginning of the 1990s, molecular analysis (MA) based on amplification and sequencing of ribosomal RNA (rRNA) genes (16S rRNA for bacteria and 18S rRNA for fungi) has been used on valve tissue to identify causative microorganisms [ 15 ]. Several studies demonstrated the diagnostic value of MA on HV for etiological diagnosis of IE [ 13–20 ] and its impact on antimicrobial therapy [ 21 , 22 ]. For these reasons, MA has been proposed for inclusion into Duke’s Criteria [ 14 , 23 , 24 ].…”