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For: Eigner U, Nörz D, Reucher S, Furrer J, Sun J, Chu K, Kolb M, Hefner N, Pfefferle S, Lütgehetmann M. Detection of C. difficile toxin as a model assay for performing fully automated high-throughput RT-PCR on clinical stool samples. J Microbiol Methods 2020;172:105882. [DOI: 10.1016/j.mimet.2020.105882] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 02/27/2020] [Accepted: 02/27/2020] [Indexed: 01/02/2023]

For:	Eigner U, Nörz D, Reucher S, Furrer J, Sun J, Chu K, Kolb M, Hefner N, Pfefferle S, Lütgehetmann M. Detection of C. difficile toxin as a model assay for performing fully automated high-throughput RT-PCR on clinical stool samples. J Microbiol Methods 2020;172:105882. [DOI: 10.1016/j.mimet.2020.105882] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 02/27/2020] [Accepted: 02/27/2020] [Indexed: 01/02/2023]

Number

Cited by Other Article(s)

Köffer J, Frontzek A, Eigner U. Development and validation of a bacterial gastrointestinal multiplex RT-PCR assay for use on a fully automated molecular system. J Microbiol Methods 2023;210:106754. [PMID: 37263528 DOI: 10.1016/j.mimet.2023.106754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/03/2023]

Abstract

PCR-based enteric multiplex panels represent a rapid and reliable alternative to conventional "classical" phenotypic stool diagnostics. The aim of this study was to establish a laboratory-developed non-commercial multiplex Real-Time-PCR panel for the detection of the most important bacterial stool pathogens, Salmonella spp., Shigella spp., Yersinia enterocolitica/ pseudotuberculosis and Campylobacter jejuni/coli. on the "open" cobas omni Utility Channel (UC) of the cobas 6800 system (Roche). The aim was to replace the laborious phenotypical stool diagnostics with a high throughput Real-Time PCR method. The respective primers and probes were designed to cover conserved genomic regions of the pathogens and validated using Ultramer oligonucleotides, positive stool material and reference strains. To further validate the multiplex PCR-assay, the following parameters were evaluated: analytical-sensitivity and -specificity, cross-reactivity, linearity and inter- and intra-assay variance as well as limit of detection (LOD). In addition a retrospective analysis of culture positive and negative samples from daily routine was performed using 745 native stool samples. The Gastro assay was linear over a 5-log-unit and within the expected dynamic range with amplification efficiencies ranging from 94.6% to 120%. In addition, all targets showed excellent coefficients of repeatability (≤ 1.11%), intermediate precision (≤ 1.02%) and total variance (≤ 1.39%). In terms of analytical sensitivity the assay demonstrated detection limits ranging from 7.83 copies per reaction to 14.4 copies per reaction. The assay showed excellent agreement with culture methods (>95%) and a 100% sensitivity and specificity after resolution of discrepant results. The multiplex-PCR assay provides a comprehensive, rapid and sensitive alternative to conventional methods for the detection of the major bacterial stool pathogens in diagnostic laboratories.

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Nörz D, Grunwald M, Tang HT, Olearo F, Günther T, Robitaille A, Fischer N, Grundhoff A, Aepfelbacher M, Pfefferle S, Lütgehetmann M. Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. Diagnostics (Basel) 2021;11:1818. [PMID: 34679517 PMCID: PMC8534837 DOI: 10.3390/diagnostics11101818] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 12/23/2022] Open

Affiliation(s)

Dominik Nörz Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
Moritz Grunwald Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
Hui Ting Tang Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
Flaminia Olearo Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
Thomas Günther Virus Genomics, Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (T.G.); (A.R.); (A.G.)
Alexis Robitaille Virus Genomics, Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (T.G.); (A.R.); (A.G.)
Nicole Fischer Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
Adam Grundhoff Virus Genomics, Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (T.G.); (A.R.); (A.G.)
Martin Aepfelbacher Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
Susanne Pfefferle Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
Marc Lütgehetmann Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)

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Pushing beyond specifications: Evaluation of linearity and clinical performance of the cobas 6800/8800 SARS-CoV-2 RT-PCR assay for reliable quantification in blood and other materials outside recommendations. J Clin Virol 2020;132:104650. [PMID: 33011643 PMCID: PMC7510425 DOI: 10.1016/j.jcv.2020.104650] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/15/2020] [Accepted: 09/21/2020] [Indexed: 12/18/2022]

Abstract

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Effective reduction of SARS-CoV-2 infectivity by chemical inactivation without affecting assay performance.

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SARS-CoV-2 IVD for the cobas 6800/8800 is linear over up to six log steps in different materials including human plasma.

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Minimal variance of CT values between testing sites indicates high comparability of quantification results.

Background

The ongoing SARS-CoV-2 pandemic presents a unique challenge to diagnostic laboratories. There are preliminary studies correlating qRT-PCR results from different materials to clinical outcomes, yet, comparability is limited due to the plethora of different assays used for diagnostics. In this study we evaluate clinical performance and linear range for the SARS-CoV-2 IVD (cobas6800/8800 system, a fully automated sample-to-result platform) in different clinically relevant matrix materials outside official specifications.

Methods

Assay performance was assessed in human plasma, BAL/BL and transport medium following chemical inactivation. For analytical evaluation, respective matrix materials were spiked with SARS-CoV-2 RNA in ten-fold dilution series. The efficacy of chemical inactivation by guanidine hydrochloride solution was confirmed in cell culture infectivity experiments. For correlation, a total of 289 predetermined clinical samples including respiratory swabs, plasma and lower respiratory tract specimens were subjected to the SARS-CoV-2 IVD test and results were compared.

Results

The SARS-CoV-2 IVD showed excellent linearity over four to six log steps depending on matrix material. Chemical inactivation resulted in a reduction in plaque forming units of at least 3.5 log steps, while having no significant impact on assay performance. Inter-run consistency from three different testing sites demonstrated excellent comparability of RT-PCR results (maximum deviation was 1.53 CT). Clinical evaluation for respiratory swabs showed very good agreement with the comparator assay (Positive agreement 95.7 %, negative agreement 98.9 %).

Conclusion

The SARS-CoV-2 IVD test for the cobas6800/8800 systems offers excellent linear range and inter-run consistency for quantification of SARS-CoV-2 RNA in different matrices outside official specifications.

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