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      Evaluation of the Sepsis Flow Chip assay for the diagnosis of blood infections

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          Abstract

          Background

          Blood infections are serious complex conditions that generally require rapid diagnosis and treatment. The big challenge is to reduce the time necessary to make a diagnosis with current clinical microbiological methods so as to improve the treatment given to patients.

          Methods

          In this study, we assess for the first time the Sepsis Flow Chip assay, which is a novel diagnostic assay for simultaneous rapid-detection of the vast majority of bloodstream pathogens, including Gram-positive and Gram-negative bacteria and fungi, in the same assay, and for the detection of most common antibiotic resistance genes. The SFC assay is based on multiplex PCR and low density DNA arrays.

          Results

          Positive blood cultures from 202 consecutive bacteremia patients were analyzed by SFC assay and the results were compared with the results obtained by the gold standard methodology used in clinical microbiology diagnostic laboratories (EUCAST guidelines). SFC assay overall sensitivity and specificity for bacterial identification were 93.3% and 100% respectively and sensitivity and specificity for the identification of antibiotic genetic resistance determinants were 93.6% and 100% respectively.

          Conclusions

          This is the first evaluation of SFC assay in clinical samples. This new method appears to be very promising by combining the high number of distinct pathogens and genetic resistance determinants identified in a single assay. Further investigations should be done to evaluate the usefulness of this assay in combination with clinical multidisciplinary groups (stewardship), in order for the results to be applied appropriately to the management of patients`infectious processes.

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          Most cited references37

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          Carbapenemases in Klebsiella pneumoniae and other Enterobacteriaceae: an evolving crisis of global dimensions.

          L Tzouvelekis, A Markogiannakis, M Psichogiou … (2012)
          The spread of Enterobacteriaceae, primarily Klebsiella pneumoniae, producing KPC, VIM, IMP, and NDM carbapenemases, is causing an unprecedented public health crisis. Carbapenemase-producing enterobacteria (CPE) infect mainly hospitalized patients but also have been spreading in long-term care facilities. Given their multidrug resistance, therapeutic options are limited and, as discussed here, should be reevaluated and optimized. Based on susceptibility data, colistin and tigecycline are commonly used to treat CPE infections. Nevertheless, a review of the literature revealed high failure rates in cases of monotherapy with these drugs, whilst monotherapy with either a carbapenem or an aminoglycoside appeared to be more effective. Combination therapies not including carbapenems were comparable to aminoglycoside and carbapenem monotherapies. Higher success rates have been achieved with carbapenem-containing combinations. Pharmacodynamic simulations and experimental infections indicate that modification of the current patterns of carbapenem use against CPE warrants further attention. Epidemiological data, though fragmentary in many countries, indicate CPE foci and transmission routes, to some extent, whilst also underlining the lack of international collaborative systems that could react promptly and effectively. Fortunately, there are sound studies showing successful containment of CPE by bundles of measures, among which the most important are active surveillance cultures, separation of carriers, and assignment of dedicated nursing staff.
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            Carbapenem-resistant Enterobacteriaceae: epidemiology and prevention.

            Neil Gupta, Brandi M. Limbago, Jean B Patel … (2011)
            Over the past 10 years, dissemination of Klebsiella pneumoniae carbapenemase (KPC) has led to an increase in the prevalence of carbapenem-resistant Enterobacteriaceae (CRE) in the United States. Infections caused by CRE have limited treatment options and have been associated with high mortality rates. In the previous year, other carbapenemase subtypes, including New Delhi metallo-β-lactamase, have been identified among Enterobacteriaceae in the United States. Like KPC, these enzymes are frequently found on mobile genetic elements and have the potential to spread widely. As a result, preventing both CRE transmission and CRE infections have become important public health objectives. This review describes the current epidemiology of CRE in the United States and highlights important prevention strategies. © The Author 2011. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved.
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              EUCAST expert rules in antimicrobial susceptibility testing.

              R Leclercq, R Canton, D.F.J. Brown … (2013)
              EUCAST expert rules have been developed to assist clinical microbiologists and describe actions to be taken in response to specific antimicrobial susceptibility test results. They include recommendations on reporting, such as inferring susceptibility to other agents from results with one, suppression of results that may be inappropriate, and editing of results from susceptible to intermediate or resistant or from intermediate to resistant on the basis of an inferred resistance mechanism. They are based on current clinical and/or microbiological evidence. EUCAST expert rules also include intrinsic resistance phenotypes and exceptional resistance phenotypes, which have not yet been reported or are very rare. The applicability of EUCAST expert rules depends on the MIC breakpoints used to define the rules. Setting appropriate clinical breakpoints, based on treating patients and not on the detection of resistance mechanisms, may lead to modification of some expert rules in the future. © 2011 The Authors. Clinical Microbiology and Infection © 2011 European Society of Clinical Microbiology and Infectious Diseases.
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                Author and article information

                Contributors
                Yung-Fu Chang: Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (iso-abbrev): PLoS ONE
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, CA USA )
                ISSN (Electronic): 1932-6203
                Publication date (Electronic): 18 May 2017
                Publication date Collection: 2017
                Volume: 12
                Issue: 5
                Electronic Location Identifier: e0177627
                Affiliations
                [1 ]Department of Microbiology, Hospital General Universitario de Elche, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) Elche, Spain
                [2 ]Department of Microbiology, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL - FISABIO), Alicante, Spain
                [3 ]Department of Infectious Diseases, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL - FISABIO), Alicante, Spain
                Cornell University, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Conceptualization: A Galiana JCR.

                • Data curation: JC A Gimeno EM.

                • Formal analysis: NMG A Gimeno JC GR.

                • Funding acquisition: A Galiana JCR.

                • Investigation: A Galiana FR NMG JC.

                • Methodology: A Galiana.

                • Project administration: JCR.

                • Resources: A Galiana JCR A Gimeno FR.

                • Software: A Galiana NMG.

                • Supervision: JCR GR.

                • Validation: A Galiana A Gimeno JC.

                • Visualization: A Galiana JCR.

                • Writing – original draft: A Galiana EM.

                • Writing – review & editing: A Galiana JCR A Gimeno JC NMG.

                Article
                Publisher ID: PONE-D-16-25902
                DOI: 10.1371/journal.pone.0177627
                PMC ID: 5436663
                PubMed ID: 28542614
                SO-VID: 80b6d566-95e3-4bb6-b8ba-54e34fc02446
                Copyright © © 2017 Galiana et al
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 28 June 2016
                Date accepted : 1 May 2017
                Page count
                Figures: 1, Tables: 3, Pages: 12
                Funding
                Funded by: Hospital general Universitario Alicante
                Award ID: UGP-14-270
                Award Recipient :
                Funded by: Fundación Soria Melguizo
                Award Recipient :
                Funded by: Fundación para el Fomento de la investigación sanitaria y biomédica de la Comunidad Valenciana
                Award ID: UGP-14-216
                Award Recipient :
                This work was supported by Hospital General Universitario de Alicante (UGP-14-270) http://alicante.san.gva.es/; Fundación Soria Melguizo (no number) http://www.f-soria.es/; and FISABIO (UGP-14-216) http://fisabio.san.gva.es/.
                Categories
                Subject: Research Article
                Subject: Biology and Life Sciences
                Subject: Anatomy
                Subject: Body Fluids
                Subject: Blood
                Subject: Medicine and Health Sciences
                Subject: Anatomy
                Subject: Body Fluids
                Subject: Blood
                Subject: Biology and Life Sciences
                Subject: Physiology
                Subject: Body Fluids
                Subject: Blood
                Subject: Medicine and Health Sciences
                Subject: Physiology
                Subject: Body Fluids
                Subject: Blood
                Subject: Biology and Life Sciences
                Subject: Microbiology
                Subject: Microbial Control
                Subject: Antimicrobial Resistance
                Subject: Antibiotic Resistance
                Subject: Medicine and Health Sciences
                Subject: Pharmacology
                Subject: Antimicrobial Resistance
                Subject: Antibiotic Resistance
                Subject: Biology and Life Sciences
                Subject: Genetics
                Subject: Heredity
                Subject: Genetic Determinism
                Subject: Biology and Life Sciences
                Subject: Genetics
                Subject: Microbial Genetics
                Subject: Biology and Life Sciences
                Subject: Microbiology
                Subject: Bacteriology
                Subject: Gram Negative Bacteria
                Subject: Biology and Life Sciences
                Subject: Organisms
                Subject: Bacteria
                Subject: Streptococcus
                Subject: Pneumococcus
                Subject: Biology and Life Sciences
                Subject: Microbiology
                Subject: Medical Microbiology
                Subject: Microbial Pathogens
                Subject: Bacterial Pathogens
                Subject: Streptococcus
                Subject: Pneumococcus
                Subject: Medicine and Health Sciences
                Subject: Pathology and Laboratory Medicine
                Subject: Pathogens
                Subject: Microbial Pathogens
                Subject: Bacterial Pathogens
                Subject: Streptococcus
                Subject: Pneumococcus
                Subject: Biology and Life Sciences
                Subject: Organisms
                Subject: Fungi
                Subject: Yeast
                Subject: Candida
                Subject: Candida Albicans
                Subject: Biology and Life Sciences
                Subject: Microbiology
                Subject: Medical Microbiology
                Subject: Microbial Pathogens
                Subject: Fungal Pathogens
                Subject: Candida Albicans
                Subject: Medicine and Health Sciences
                Subject: Pathology and Laboratory Medicine
                Subject: Pathogens
                Subject: Microbial Pathogens
                Subject: Fungal Pathogens
                Subject: Candida Albicans
                Subject: Biology and Life Sciences
                Subject: Mycology
                Subject: Fungal Pathogens
                Subject: Candida Albicans
                Subject: Research and Analysis Methods
                Subject: Experimental Organism Systems
                Subject: Yeast and Fungal Models
                Subject: Candida Albicans
                Subject: Biology and Life Sciences
                Subject: Microbiology
                Subject: Bacteriology
                Subject: Gram Positive Bacteria
                Custom metadata
                Data Availability All relevant data are within the paper and its Supporting Information files.

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