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      Next-Generation Sequencing for the Diagnosis of Challenging Culture-Negative Endocarditis

      case-report

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          Abstract

          Diagnosis of culture-negative infective endocarditis usually implies indirect pathogen identification by serologic or molecular techniques. Clinical metagenomics, relying on next-generation sequencing (NGS) is an emerging approach that allows pathogen identification in challenging situations, as evidenced by a clinical case. We sequenced the DNA extracted from the surgically-removed frozen valve tissue from a patient with suspected infective endocarditis with negative blood and valve cultures. Mapping of the sequence reads against reference genomic sequences, a 16S rRNA gene database and clade-specific marker genes suggested an infection caused by Cardiobacterium hominis.

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          Most cited references15

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          Infective endocarditis in adults.

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            Next-generation sequencing diagnostics of bacteremia in septic patients

            Background Bloodstream infections remain one of the major challenges in intensive care units, leading to sepsis or even septic shock in many cases. Due to the lack of timely diagnostic approaches with sufficient sensitivity, mortality rates of sepsis are still unacceptably high. However a prompt diagnosis of the causative microorganism is critical to significantly improve outcome of bloodstream infections. Although various targeted molecular tests for blood samples are available, time-consuming blood culture-based approaches still represent the standard of care for the identification of bacteria. Methods Here we describe the establishment of a complete diagnostic workflow for the identification of infectious microorganisms from seven septic patients based on unbiased sequence analyses of free circulating DNA from plasma by next-generation sequencing. Results We found significant levels of DNA fragments derived from pathogenic bacteria in samples from septic patients. Quantitative evaluation of normalized read counts and introduction of a sepsis indicating quantifier (SIQ) score allowed for an unambiguous identification of Gram-positive as well as Gram-negative bacteria that exactly matched with blood cultures from corresponding patient samples. In addition, we also identified species from samples where blood cultures were negative. Reads of non-human origin also comprised fragments derived from antimicrobial resistance genes, showing that, in principle, prediction of specific types of resistance might be possible. Conclusions The complete workflow from sample preparation to species identification report could be accomplished in roughly 30 h, thus making this approach a promising diagnostic platform for critically ill patients suffering from bloodstream infections. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0326-8) contains supplementary material, which is available to authorized users.
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              Blood culture-negative endocarditis

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                Author and article information

                Contributors
                Journal
                Front Med (Lausanne)
                Front Med (Lausanne)
                Front. Med.
                Frontiers in Medicine
                Frontiers Media S.A.
                2296-858X
                20 September 2019
                2019
                : 6
                : 203
                Affiliations
                [1] 1Service of General Internal Medicine, Geneva University Hospitals (HUG) , Geneva, Switzerland
                [2] 2Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals , Geneva, Switzerland
                [3] 3Bacteriology Laboratory, Service of Laboratory Medicine, Geneva University Hospitals , Geneva, Switzerland
                [4] 4Service of Infectious Diseases, Geneva University Hospitals , Geneva, Switzerland
                [5] 5Institute of Medical Microbiology, University of Zurich , Zurich, Switzerland
                [6] 6Service of Cardiovascular Surgery, Geneva University Hospitals , Geneva, Switzerland
                Author notes

                Edited by: Vitali Sintchenko, University of Sydney, Australia

                Reviewed by: Matthew Watts, New South Wales Health Pathology, Australia; Jianfeng Xie, Southeast University, China

                *Correspondence: Jacques Schrenzel jacques.schrenzel@ 123456hcuge.ch

                This article was submitted to Infectious Diseases - Surveillance, Prevention and Treatment, a section of the journal Frontiers in Medicine

                †These authors have contributed equally to this work

                Article
                10.3389/fmed.2019.00203
                6763761
                31616669
                a92b7a72-5630-437e-a312-83c8e165e0aa
                Copyright © 2019 Kolb, Lazarevic, Emonet, Calmy, Girard, Gaïa, Charretier, Cherkaoui, Keller, Huber and Schrenzel.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 13 June 2019
                : 29 August 2019
                Page count
                Figures: 1, Tables: 1, Equations: 0, References: 23, Pages: 4, Words: 2831
                Categories
                Medicine
                Case Report

                next-generation sequencing,culture-negative endocarditis,clinical metagenomics,cardiobacterium hominis,diagnosis

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