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      Comparison of two commercial and one in-house real-time PCR assays for the diagnosis of bacterial gastroenteritis

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          Abstract

          Introduction

          The aim of the study was a comparative evaluation of in-house real-time PCR and commercial real-time PCR (Fast Track Diagnostics (FTD), ampliCube/Mikrogen) targeting enteropathogenic bacteria from stool in preparation of Regulation (EU) 2017/746 on in vitro diagnostic medical devices.

          Methods

          Both 241 stool samples from patients and 100 samples from German laboratory control schemes (“Ringversuche”) were used to comparatively assess in-house real-time PCR, the FTD bacterial gastroenteritis kit, and the ampliCube gastrointestinal bacterial panels 1&2 either with the in-house PCRs as gold standard and as a test comparison without gold standard applying latent class analysis. Sensitivity, specificity, intra- and inter-assay variation and Cohen’s kappa were assessed.

          Results

          In comparison with the gold standard, sensitivity was 75–100% for strongly positive samples, 20–100% for weakly positive samples, and specificity ranged from 96 to 100%. Latent class analysis suggested that sensitivity ranges from 81.2 to 100% and specificity from 58.5 to 100%. Cohen’s kappa varied between moderate and nearly perfect agreement, intra- and inter-assay variation was 1–3 to 1–4 Ct values.

          Conclusion

          Acceptable agreement and performance characteristics suggested replaceability of the in-house PCR assays by the commercial approaches.

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          Most cited references 36

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          The measurement of observer agreement for categorical data.

           G Koch,  J R Landis (1977)
          This paper presents a general statistical methodology for the analysis of multivariate categorical data arising from observer reliability studies. The procedure essentially involves the construction of functions of the observed proportions which are directed at the extent to which the observers agree among themselves and the construction of test statistics for hypotheses involving these functions. Tests for interobserver bias are presented in terms of first-order marginal homogeneity and measures of interobserver agreement are developed as generalized kappa-type statistics. These procedures are illustrated with a clinical diagnosis example from the epidemiological literature.
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            European Society of Clinical Microbiology and Infectious Diseases (ESCMID): data review and recommendations for diagnosing Clostridium difficile-infection (CDI).

             E. Kuijper,  M. Crobach,  Alexander H. Wilcox … (2009)
            The aim of the present systematic review was to evaluate the available evidence on laboratory diagnosis of CDI and to formulate recommendations to optimize CDI testing. In comparison with cell culture cytotoxicity assay (CCA) and toxigenic culture (TC) of stools, we analyzed the test characteristics of 13 commercial available enzyme immunoasssays (EIA) detecting toxins A and/or B, 4 EIAs detecting Clostridium difficile glutamate dehydrogenase (GDH), and a real-time PCR for C. difficile toxin B gene. In comparison with CCA and TCA and assuming a prevalence of CDI of 5%, PPV and NPV varied between 0.28-0.77, 0.12-0.65 and 0.98-1.00, 0.97-1.00, respectively. Only if the tests were performed in a population with a CDI prevalence of 50 percent, would PPVs be acceptable (ranging from 0.71 to 1.00).To overcome the problem of a low PPV, we propose a two step approach, with a second test or a reference method in case of a positive first test. Further reducing the number of false negative results would require either retesting of all subjects with a negative first test, or re-testing all subjects with a negative second test, after an initially positive test. This approach resulted in non-significant improvements, and emphasizes the need for better diagnostic tests. Further studies to validate the applicability of two-step testing, including assessment of clinical features, are required.
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              Comparison of nine commercially available Clostridium difficile toxin detection assays, a real-time PCR assay for C. difficile tcdB, and a glutamate dehydrogenase detection assay to cytotoxin testing and cytotoxigenic culture methods.

               P Else,  Mark Wilcox,  Andre Charlett … (2009)
              The continuing rise in the incidence of Clostridium difficile infection is a cause for concern, with implications for patients and health care systems. Laboratory diagnosis largely relies on rapid toxin detection kits, although assays detecting alternative targets, including glutamate dehydrogenase (GDH) and toxin genes, are now available. Six hundred routine diagnostic diarrheal samples were tested prospectively using nine commercial toxin detection assays, cytotoxin assay (CYT), and cytotoxigenic culture (CYTGC) and retrospectively using a GDH detection assay and PCR for the toxin B gene. The mean sensitivity and specificity for toxin detection assays were 82.8% (range, 66.7 to 91.7%) and 95.4% (range, 90.9 to 98.8%), respectively, in comparison with CYT and 75.0% (range, 60.0 to 86.4%) and 96.1% (91.4 to 99.4%), respectively, in comparison with CYTGC. The sensitivity and specificity of the GDH assay were 90.1% and 92.9%, respectively, compared to CYT and 87.6% and 94.3%, respectively, compared to CYTGC. The PCR assay had the highest sensitivity of all the tests in comparison with CYT (92.2%) and CYTGC (88.5%), and the specificities of the PCR assay were 94.0% and 95.4% compared to CYT and CYTGC, respectively. All kits had low positive predictive values (range, 48.6 to 86.8%) compared with CYT, assuming a positive sample prevalence of 10% (representing the hospital setting), which compromises the clinical utility of single tests for the laboratory diagnosis of C. difficile infection. The optimum rapid single test was PCR for toxin B gene, as this had the highest negative predictive value. Diagnostic algorithms that optimize test combinations for the laboratory diagnosis of C. difficile infection need to be defined.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Eur J Microbiol Immunol (Bp)
                Journal ID (iso-abbrev): Eur J Microbiol Immunol (Bp)
                Journal ID (publisher-id): EUJMI
                Title: European Journal of Microbiology & Immunology
                Publisher: Akadémiai Kiadó (Budapest )
                ISSN (Print): 2062-509X
                ISSN (Electronic): 2062-8633
                Publication date (Electronic): 05 December 2020
                Publication date Collection: 31 December 2020
                Volume: 10
                Issue: 4
                Pages: 210-216
                Affiliations
                [1 ] Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg , Hamburg, Germany
                [2 ] Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock , Rostock, Germany
                Author notes
                *Corresponding author. E-mail: Frickmann@ 123456bni-hamburg.de
                Article
                DOI: 10.1556/1886.2020.00030
                PMC ID: 7753976
                PubMed ID: 33279885
                Copyright statement: © 2020, The Author(s)
                License:

                Open Access. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License ( https://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted use, distribution, and reproduction in any medium for non-commercial purposes, provided the original author and source are credited, a link to the CC License is provided, and changes - if any – are indicated.

                Page count
                Figures: 0, Tables: 3, Equations: 0, References: 36, Pages: 7
                Categories
                Subject: Original Research Paper

                Data availability:

                Keywords: real-time pcr, nucleic acid amplification testing, gastrointestinal pathogens, comparative evaluation

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