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

Frédéric Schramm,Axel Ursenbach,François Séverac,Yves Hansmann,Nicolas Lefebvre,Xavier Argemi,Yvon Ruch

doi:10.1186/s12879-021-05892-4

Frédéric Schramm, Axel Ursenbach + Show 5 more

Open Access

https://doi.org/10.1186/s12879-021-05892-4

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Abstract

BackgroundPCRs 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.MethodsFrom 2014 to 2018, 806 16S PCR samples were processed, and 191 of those were positive.ResultsOverall, 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).ConclusionIn 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.

Highlights

Bacterial infections in hospitalized patients can lead to sepsis and death [1], when the diagnosis is delayed [2]
From 2014 to 2018, 835 16S Ribosomal DNA (rDNA) Polymerase chain reaction (PCR) were performed in our laboratory, and 197 (24%) were positive with a final bacterial identification
We found clinical impacts of the 16S PCR results in 62/191 (32%) patients, consisting of 31 (50%) ‘Rationalizing’, 24 (39%) ‘Extended spectrums’ and 7 (11%) ‘Interventions’

Summary

Introduction

Bacterial infections in hospitalized patients can lead to sepsis and death [1], when the diagnosis is delayed [2]. Different primers targeting conserved regions of 16S ribosomal DNAs are used to amplify nucleic acids via PCR, followed by sequencing. Variable regions of this gene allow identification to the species level, especially using phylogenetic tree reconstructions [18]. This method has multiple advantages including large implementation in the routine workflow of clinical laboratories and the possibility to detect noncultivable bacteria or not viable bacteria following antibiotic therapy [3], but it is expensive. 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

Results

Discussion

Conclusion