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Bachmann I, Behrmann O, Klingenberg-Ernst M, Rupnik M, Hufert FT, Dame G, Weidmann M. Rapid Isothermal Detection of Pathogenic Clostridioides difficile Using Recombinase Polymerase Amplification. Anal Chem 2024; 96:3267-3275. [PMID: 38358754 DOI: 10.1021/acs.analchem.3c02985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Nosocomial-associated diarrhea due to Clostridioides difficile infection (CDI) is diagnosed after sample precultivation by the detection of the toxins in enzyme immunoassays or via toxin gene nucleic acid amplification. Rapid and direct diagnosis is important for targeted treatment to prevent severe cases and recurrence. We developed two singleplex and a one-pot duplex fluorescent 15 min isothermal recombinase polymerase amplification (RPA) assays targeting the toxin genes A and B (tcdA and tcdB). Furthermore, we adapted the singleplex RPA to a 3D-printed microreactor device. Analytical sensitivity was determined using a DNA standard and DNA extracts of 20 C. difficile strains with different toxinotypes. Nineteen clostridial and gastrointestinal bacteria strains were used to determine analytical specificity. Adaptation of singleplex assays to duplex assays in a 50 μL volume required optimized primer and probe concentrations. A volume reduction by one-fourth (12.4 μL) was established for the 3D-printed microreactor. Mixing of RPA was confirmed as essential for optimal analytical sensitivity. Detection limits (LOD) ranging from 119 to 1411 DNA molecules detected were similar in the duplex tube format and in the singleplex 3D-printed microreactor format. The duplex RPA allows the simultaneous detection of both toxins important for the timely and reliable diagnosis of CDI. The 3D-printed reaction chamber can be developed into a microfluidic lab-on-a-chip system use at the point of care.
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Affiliation(s)
- Iris Bachmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany
| | - Ole Behrmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany
| | | | - Maja Rupnik
- Center for Medical Microbiology, Department for Microbiological Research, National Laboratory for Health, Environment and Food, Prvomajska ulica 1, 2000 Maribor, Slovenia
- Faculty of Medicine, Maribor, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia
| | - Frank T Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany
- Department of Virology, University Medical Center, Kreuzbergring 57, 37075 Göttingen, Germany
- Brandenburg University of Technology Cottbus - Senftenberg, Universitätsplatz 1, 01968 Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Gregory Dame
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Manfred Weidmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany
- Department of Virology, University Medical Center, Kreuzbergring 57, 37075 Göttingen, Germany
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Behrmann O, Lisec T, Gojdka B. Towards Robust Thermal MEMS: Demonstration of a Novel Approach for Solid Thermal Isolation by Substrate-Level Integrated Porous Microstructures. Micromachines (Basel) 2022; 13:mi13081178. [PMID: 35893176 PMCID: PMC9332110 DOI: 10.3390/mi13081178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 01/27/2023]
Abstract
Most current thermal MEMS use fragile structures such as thin-film membranes or microcantilevers for thermal isolation. To increase the robustness of these devices, solid thermal insulators that are compatible with MEMS cleanroom processing are needed. This work introduces a novel approach for microscale thermal isolation using porous microstructures created with the recently developed PowderMEMS wafer-level process. MEMS devices consisting of heaters on a thin-film membrane were modified with porous microstructures made from three different materials. A thermal model for the estimation of the resulting thermal conductivity was developed, and measurements for porous structures in ambient air and under vacuum were performed. The PowderMEMS process was successfully used to create microscale thermal insulators in silicon cavities at the wafer level. Measurements indicate thermal conductivities of close to 0.1 W/mK in ambient air and close to 0.04 W/mK for porous structures under vacuum for the best-performing material. The obtained thermal conductivities are lower than those reported for both glass and porous silicon, making PowderMEMS a very interesting alternative for solid microscale thermal isolation.
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Lisec T, Behrmann O, Gojdka B. PowderMEMS—A Generic Microfabrication Technology for Integrated Three-Dimensional Functional Microstructures. Micromachines 2022; 13:mi13030398. [PMID: 35334690 PMCID: PMC8950110 DOI: 10.3390/mi13030398] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 02/04/2023]
Abstract
A comprehensive overview of PowderMEMS—a novel back-end-of-line-compatible microfabrication technology—is presented in this paper. The PowderMEMS process solidifies micron-sized particles via atomic layer deposition (ALD) to create three-dimensional microstructures on planar substrates from a wide variety of materials. The process offers numerous degrees of freedom for the design of functional MEMSs, such as a wide choice of different material properties and the precise definition of 3D volumes at the substrate level, with a defined degree of porosity. This work details the characteristics of PowderMEMS materials as well as the maturity of the fabrication technology, while highlighting prospects for future microdevices. Applications of PowderMEMS in the fields of magnetic, thermal, optical, fluidic, and electrochemical MEMSs are described, and future developments and challenges of the technology are discussed.
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El Wahed AA, Patel P, Maier M, Pietsch C, Rüster D, Böhlken-Fascher S, Kissenkötter J, Behrmann O, Frimpong M, Diagne MM, Faye M, Dia N, Shalaby MA, Amer H, Elgamal M, Zaki A, Ismail G, Kaiser M, Corman VM, Niedrig M, Landt O, Faye O, Sall AA, Hufert FT, Truyen U, Liebert UG, Weidmann M. Suitcase Lab for Rapid Detection of SARS-CoV-2 Based on Recombinase Polymerase Amplification Assay. Anal Chem 2021; 93:2627-2634. [PMID: 33471510 PMCID: PMC7839158 DOI: 10.1021/acs.analchem.0c04779] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/11/2021] [Indexed: 12/30/2022]
Abstract
In March 2020, the SARS-CoV-2 virus outbreak was declared as a world pandemic by the World Health Organization (WHO). The only measures for controlling the outbreak are testing and isolation of infected cases. Molecular real-time polymerase chain reaction (PCR) assays are very sensitive but require highly equipped laboratories and well-trained personnel. In this study, a rapid point-of-need detection method was developed to detect the RNA-dependent RNA polymerase (RdRP), envelope protein (E), and nucleocapsid protein (N) genes of SARS-CoV-2 based on the reverse transcription recombinase polymerase amplification (RT-RPA) assay. RdRP, E, and N RT-RPA assays required approximately 15 min to amplify 2, 15, and 15 RNA molecules of molecular standard/reaction, respectively. RdRP and E RT-RPA assays detected SARS-CoV-1 and 2 genomic RNA, whereas the N RT-RPA assay identified only SARS-CoV-2 RNA. All established assays did not cross-react with nucleic acids of other respiratory pathogens. The RT-RPA assay's clinical sensitivity and specificity in comparison to real-time RT-PCR (n = 36) were 94 and 100% for RdRP; 65 and 77% for E; and 83 and 94% for the N RT-RPA assay. The assays were deployed to the field, where the RdRP RT-RPA assays confirmed to produce the most accurate results in three different laboratories in Africa (n = 89). The RPA assays were run in a mobile suitcase laboratory to facilitate the deployment at point of need. The assays can contribute to speed up the control measures as well as assist in the detection of COVID-19 cases in low-resource settings.
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Affiliation(s)
- Ahmed Abd El Wahed
- Institute
of Animal Hygiene and Veterinary Public Health, University of Leipzig, 04103 Leipzig, Germany
- Division
of Microbiology and Animal Hygiene, Georg-August-University, 37077 Goettingen, Germany
| | - Pranav Patel
- Expert
Molecular Diagnostics, 82256Fürstenfeldbruck, Germany
| | - Melanie Maier
- Institute
of Medical Microbiology and VirologyLeipzig
University Hospital, 04103 Leipzig, Germany
| | - Corinna Pietsch
- Institute
of Medical Microbiology and VirologyLeipzig
University Hospital, 04103 Leipzig, Germany
| | - Dana Rüster
- Institute
of Animal Hygiene and Veterinary Public Health, University of Leipzig, 04103 Leipzig, Germany
| | - Susanne Böhlken-Fascher
- Division
of Microbiology and Animal Hygiene, Georg-August-University, 37077 Goettingen, Germany
| | - Jonas Kissenkötter
- Division
of Microbiology and Animal Hygiene, Georg-August-University, 37077 Goettingen, Germany
| | - Ole Behrmann
- Institute
of Microbiology & Virology, Brandenburg Medical School, 01968 Senftenberg, Germany
| | - Michael Frimpong
- Kumasi Centre
for Collaborative Research in Tropical Medicine, Department of Molecular
Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Martin Faye
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Ndongo Dia
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Mohamed A. Shalaby
- Virology
Department, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
| | - Haitham Amer
- Virology
Department, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
| | - Mahmoud Elgamal
- Virology
Department, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
| | - Ali Zaki
- Department
of Medical Microbiology and Immunology, Faculty of Medicine, Ain Shams University, 11591 Cairo, Egypt
| | - Ghada Ismail
- Department
of Clinical Pathology, Faculty of Medicine, Ain Shams University, 11591 Cairo, Egypt
| | - Marco Kaiser
- GenExpress Gesellschaft für Proteindesign, 12103 Berlin, Germany
| | - Victor M. Corman
- Charité−Universitätsmedizin
Berlin, Institute
of Virology, Berlin, Germany
- German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | | | | | - Ousmane Faye
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Amadou A. Sall
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Frank T. Hufert
- Institute
of Microbiology & Virology, Brandenburg Medical School, 01968 Senftenberg, Germany
| | - Uwe Truyen
- Institute
of Animal Hygiene and Veterinary Public Health, University of Leipzig, 04103 Leipzig, Germany
| | - Uwe G. Liebert
- Institute
of Medical Microbiology and VirologyLeipzig
University Hospital, 04103 Leipzig, Germany
| | - Manfred Weidmann
- Institute
of Microbiology & Virology, Brandenburg Medical School, 01968 Senftenberg, Germany
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Behrmann O, Bachmann I, Hufert F, Dame G. Schnellnachweis von SARS-CoV-2 mit recombinase polymerase amplification. Biospektrum 2020; 26:624-627. [PMID: 33078045 PMCID: PMC7556600 DOI: 10.1007/s12268-020-1458-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AbstractThe COVID-19 pandemic highlights the need for fast and simple assays for nucleic acid detection. As an isothermal alternative to RT-qPCR, we outline the development of a detection scheme for SARS-CoV-2 RNA based on reverse transcription recombinase polymerase amplification (RT-RPA) technology. RPA uses recombination proteins in combination with a DNA polymerase for rapid amplification of target DNA at a constant temperature (39–42 °C) within 10 to 20 minutes and can be monitored in real-time with fluorescent probes.
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Affiliation(s)
- Ole Behrmann
- Institut für Mikrobiologie und Virologie, Medizinische Hochschule Brandenburg Theodor Fontane (MHB), Universitätsplatz 1, D-01968 Senftenberg, Deutschland
- Professur für Sensoren, Institut für Mikrosystemtechnik (IMTEK), Universität, Freiburg, Deutschland
| | - Iris Bachmann
- Institut für Mikrobiologie und Virologie, Medizinische Hochschule Brandenburg Theodor Fontane (MHB), Universitätsplatz 1, D-01968 Senftenberg, Deutschland
| | - Frank Hufert
- Institut für Mikrobiologie und Virologie, Medizinische Hochschule Brandenburg Theodor Fontane (MHB), Universitätsplatz 1, D-01968 Senftenberg, Deutschland
| | - Gregory Dame
- Institut für Mikrobiologie und Virologie, Medizinische Hochschule Brandenburg Theodor Fontane (MHB), Universitätsplatz 1, D-01968 Senftenberg, Deutschland
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Affiliation(s)
- Ole Behrmann
- Brandenburg Medical School Theodor Fontane, 16816 Neuruppin, Germany.
| | - Martin Spiegel
- Brandenburg Medical School Theodor Fontane, 16816 Neuruppin, Germany
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Behrmann O, Bachmann I, Spiegel M, Schramm M, Abd El Wahed A, Dobler G, Dame G, Hufert FT. Rapid Detection of SARS-CoV-2 by Low Volume Real-Time Single Tube Reverse Transcription Recombinase Polymerase Amplification Using an Exo Probe with an Internally Linked Quencher (Exo-IQ). Clin Chem 2020; 66:1047-1054. [PMID: 32384153 PMCID: PMC7239256 DOI: 10.1093/clinchem/hvaa116] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 05/05/2020] [Indexed: 01/22/2023]
Abstract
Background The current outbreak of SARS-CoV-2 has spread to almost every country with more than three million confirmed cases and over two hundred thousand deaths as of April 28, 2020. Rapid first-line testing protocols are needed for outbreak control and surveillance. Methods We used computational and manual design to generate a suitable set of reverse transcription recombinase polymerase amplification (RT-RPA) primer and exonuclease probe, internally quenched (exo-IQ) probe sequences targeting the SARS-CoV-2 N gene. RT-RPA sensitivity was determined by amplification of in vitro transcribed RNA standards. Assay selectivity was demonstrated with a selectivity panel of 32 nucleic acid samples derived from common respiratory viruses. To validate the assay against full-length SARS-CoV-2 RNA, total viral RNA derived from cell culture supernatant and 19 nasopharyngeal swab samples (8 positive and 11 negative for SARS-CoV-2) were screened. All results were compared to established RT-qPCR assays. Results The 95% detection probability of the RT-RPA assay was determined to be 7.74 (95% CI: 2.87 - 27.39) RNA copies per reaction. The assay showed no cross-reactivity to any other screened coronaviruses or respiratory viruses of clinical significance. The developed RT-RPA assay produced 100% diagnostic sensitivity and specificity when compared to RT-qPCR (n=20). Conclusion With a run time of 15 to 20 minutes and first results being available in under 7 minutes for high RNA concentrations, the reported assay constitutes one of the fastest nucleic acid based detection methods for SARS-CoV-2 to date and may provide a simple to use alternative to RT-qPCR for first-line screening at the point of need.
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Affiliation(s)
- Ole Behrmann
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
| | - Iris Bachmann
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
| | - Martin Spiegel
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany.,Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, Göttingen, Germany
| | - Marina Schramm
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
| | - Ahmed Abd El Wahed
- Division of Microbiology and Animal Hygiene, University of Göttingen, Germany.,Institute of Animal Hygiene and Veterinary Public Health, University of Leipzig, Leipzig, Germany
| | - Gerhard Dobler
- Bundeswehr Institute of Microbiology (IMB), Munich, Germany
| | - Gregory Dame
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany.,Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
| | - Frank T Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany.,Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
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Behrmann O, Hügle M, Eckardt F, Bachmann I, Heller C, Schramm M, Turner C, Hufert FT, Dame G. 3D Printed Monolithic Microreactors for Real-Time Detection of Klebsiella pneumoniae and the Resistance Gene blaNDM-1 by Recombinase Polymerase Amplification. Micromachines (Basel) 2020; 11:mi11060595. [PMID: 32560308 PMCID: PMC7344889 DOI: 10.3390/mi11060595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 05/07/2023]
Abstract
We investigate the compatibility of three 3D printing materials towards real-time recombinase polymerase amplification (rtRPA). Both the general ability of the rtRPA reaction to occur while in contact with the cured 3D printing materials as well as the residual autofluorescence and fluorescence drift in dependence on post curing of the materials is characterized. We 3D printed monolithic rtRPA microreactors and subjected the devices to different post curing protocols. Residual autofluorescence and drift, as well as rtRPA kinetics, were then measured in a custom-made mobile temperature-controlled fluorescence reader (mTFR). Furthermore, we investigated the effects of storage on the devices over a 30-day period. Finally, we present the single- and duplex rtRPA detection of both the organism-specific Klebsiella haemolysin (khe) gene and the New Delhi metallo-β-lactamase 1 (blaNDM-1) gene from Klebsiella pneumoniae. Results: No combination of 3D printing resin and post curing protocol completely inhibited the rtRPA reaction. The autofluorescence and fluorescence drift measured were found to be highly dependent on printing material and wavelength. Storage had the effect of decreasing the autofluorescence of the investigated materials. Both khe and blaNDM-1 were successfully detected by single- and duplex-rtRPA inside monolithic rtRPA microreactors printed from NextDent Ortho Clear (NXOC). The reaction kinetics were found to be close to those observed for rtRPA performed in a microcentrifuge tube without the need for mixing during amplification. Singleplex assays for both khe and blaNDM-1 achieved a limit of detection of 2.5 × 101 DNA copies while the duplex assay achieved 2.5 × 101 DNA copies for khe and 2.5 × 102 DNA copies for blaNDM-1. Impact: We expand on the state of the art by demonstrating a technology that can manufacture monolithic microfluidic devices that are readily suitable for rtRPA. The devices exhibit very low autofluorescence and fluorescence drift and are compatible with RPA chemistry without the need for any surface pre-treatment such as blocking with, e.g., BSA or PEG.
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Affiliation(s)
- Ole Behrmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 16816 Neuruppin, Germany; (O.B.); (M.H.); (F.E.); (I.B.); (C.H.); (M.S.); (F.T.H.)
- Laboratory for Sensors, Department of Microsystems Engineering - IMTEK, University of Freiburg, 79110 Freiburg, Germany
| | - Matthias Hügle
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 16816 Neuruppin, Germany; (O.B.); (M.H.); (F.E.); (I.B.); (C.H.); (M.S.); (F.T.H.)
- Laboratory for Sensors, Department of Microsystems Engineering - IMTEK, University of Freiburg, 79110 Freiburg, Germany
| | - Franz Eckardt
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 16816 Neuruppin, Germany; (O.B.); (M.H.); (F.E.); (I.B.); (C.H.); (M.S.); (F.T.H.)
| | - Iris Bachmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 16816 Neuruppin, Germany; (O.B.); (M.H.); (F.E.); (I.B.); (C.H.); (M.S.); (F.T.H.)
| | - Cecilia Heller
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 16816 Neuruppin, Germany; (O.B.); (M.H.); (F.E.); (I.B.); (C.H.); (M.S.); (F.T.H.)
| | - Marina Schramm
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 16816 Neuruppin, Germany; (O.B.); (M.H.); (F.E.); (I.B.); (C.H.); (M.S.); (F.T.H.)
| | - Carrie Turner
- National Infections Service, Public Health England, Porton Down SP4 0JG, UK;
| | - Frank T. Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 16816 Neuruppin, Germany; (O.B.); (M.H.); (F.E.); (I.B.); (C.H.); (M.S.); (F.T.H.)
| | - Gregory Dame
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 16816 Neuruppin, Germany; (O.B.); (M.H.); (F.E.); (I.B.); (C.H.); (M.S.); (F.T.H.)
- Correspondence:
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Hügle M, Behrmann O, Raum M, Hufert FT, Urban GA, Dame G. A lab-on-a-chip for free-flow electrophoretic preconcentration of viruses and gel electrophoretic DNA extraction. Analyst 2020; 145:2554-2561. [DOI: 10.1039/c9an02333j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A lab-on-a-chip for FFE preconcentration of viruses and gel electrophoretic DNA extraction: complete preparation of amplifiable DNA from dilute specimens.
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Affiliation(s)
- Matthias Hügle
- Laboratory for Sensors
- Department of Microsystems Engineering (IMTEK)
- University of Freiburg
- Freiburg
- Germany
| | - Ole Behrmann
- Laboratory for Sensors
- Department of Microsystems Engineering (IMTEK)
- University of Freiburg
- Freiburg
- Germany
| | - Madlen Raum
- Laboratory for Sensors
- Department of Microsystems Engineering (IMTEK)
- University of Freiburg
- Freiburg
- Germany
| | - Frank T. Hufert
- Institute of Microbiology and Virology
- Brandenburg Medical School Theodor Fontane
- Neuruppin
- Germany
| | - Gerald A. Urban
- Laboratory for Sensors
- Department of Microsystems Engineering (IMTEK)
- University of Freiburg
- Freiburg
- Germany
| | - Gregory Dame
- Institute of Microbiology and Virology
- Brandenburg Medical School Theodor Fontane
- Neuruppin
- Germany
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Behrmann O, Hügle M, Bronsert P, Herde B, Heni J, Schramm M, Hufert FT, Urban GA, Dame G. A lab-on-a-chip for rapid miRNA extraction. PLoS One 2019; 14:e0226571. [PMID: 31856234 PMCID: PMC6922460 DOI: 10.1371/journal.pone.0226571] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 11/28/2019] [Indexed: 12/16/2022] Open
Abstract
We present a simple to operate microfluidic chip system that allows for the extraction of miRNAs from cells with minimal hands-on time. The chip integrates thermoelectric lysis (TEL) of cells with native gel-electrophoretic elution (GEE) of released nucleic acids and uses non-toxic reagents while requiring a sample volume of only 5 μl. These properties as well as the fast process duration of 180 seconds make the system an ideal candidate to be part of fully integrated point-of-care applications for e.g. the diagnosis of cancerous tissue. GEE was characterized in comparison to state-of-the-art silica column (SC) based RNA recovery using the mirVana kit (Ambion) as a reference. A synthetic miRNA (miR16) as well as a synthetic snoRNA (SNORD48) were subjected to both GEE and SC. Subsequent detection by stem-loop RT-qPCR demonstrated a higher yield for miRNA recovery by GEE. SnoRNA recovery performance was found to be equal for GEE and SC, indicating yield dependence on RNA length. Coupled operation of the chip (TEL + GEE) was characterized using serial dilutions of 5 to 500 MCF7 cancer cells in suspension. Samples were split and cells were subjected to either on-chip extraction or SC. Eluted miRNAs were then detected by stem-loop RT-qPCR without any further pre-processing. The extraction yield from cells was found to be up to ~200-fold higher for the chip system under non-denaturing conditions. The ratio of eluted miRNAs is shown to be dependent on the degree of complexation with miRNA associated proteins by comparing miRNAs purified by GEE from heat-shock and proteinase-K based lysis.
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Affiliation(s)
- Ole Behrmann
- Department of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
- Laboratory for Sensors, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
| | - Matthias Hügle
- Department of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
- Laboratory for Sensors, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
| | - Peter Bronsert
- Institute for Surgical Pathology, Medical Center–University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, Freiburg, Germany
| | - Bettina Herde
- Institute for Surgical Pathology, Medical Center–University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julian Heni
- Laboratory for Sensors, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
| | - Marina Schramm
- Department of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
| | - Frank T. Hufert
- Department of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
| | - Gerald A. Urban
- Laboratory for Sensors, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
| | - Gregory Dame
- Department of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
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Cai D, Behrmann O, Hufert F, Dame G, Urban G. Capacity of rTth polymerase to detect RNA in the presence of various inhibitors. PLoS One 2018; 13:e0190041. [PMID: 29293599 PMCID: PMC5749758 DOI: 10.1371/journal.pone.0190041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 12/07/2017] [Indexed: 11/19/2022] Open
Abstract
The full potential of the real-time reverse transcription polymerase chain reaction (RT-PCR) as a rapid and accurate diagnostic method is limited by DNA polymerase inhibitors as well as reverse transcriptase inhibitors which are ubiquitous in clinical samples. rTth polymerase has proven to be more resistant to DNA polymerase inhibitors present in clinical samples for DNA detection and also exhibits reverse transcriptase activity in the presence of Mn2+ ions. However, the capacity of rTth polymerase, which acts as DNA polymerase and reverse transcriptase, to detect RNA in the presence of various inhibitors has not been investigated in detail. Herein, the inhibitors originating from various clinical samples such as blood, urine, feces, bodily fluids, tissues and reagents used during nucleic acid extraction were employed to evaluate the capacity of rTth polymerase to detect RNA. The results show that the inhibitors have different inhibitory effects on the real-time RT-PCR reactions by rTth polymerase, and the inhibitory effects are concentration dependent. Additionally, the capacity of rTth polymerase to detect RNA in the presence of various inhibitors is better or at least comparable with its capacity to detect DNA in the presence of various inhibitors. As a consequence, RNA may be directly detected in the presence of co-purified inhibitors or even directly from crude clinical samples by rTth polymerase.
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Affiliation(s)
- Dongyang Cai
- Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Baden-Württemberg, Germany
| | - Ole Behrmann
- Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Baden-Württemberg, Germany
| | - Frank Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Neuruppin, Brandenburg, Germany
| | - Gregory Dame
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Neuruppin, Brandenburg, Germany
- * E-mail: (GU); (GD)
| | - Gerald Urban
- Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Baden-Württemberg, Germany
- * E-mail: (GU); (GD)
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Hügle M, Dame G, Behrmann O, Rietzel R, Karthe D, Hufert FT, Urban GA. Correction: A lab-on-a-chip for preconcentration of bacteria and nucleic acid extraction. RSC Adv 2018; 8:26817. [PMID: 35544022 PMCID: PMC9083332 DOI: 10.1039/c8ra90058b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 07/04/2018] [Indexed: 11/21/2022] Open
Abstract
Correction for ‘A lab-on-a-chip for preconcentration of bacteria and nucleic acid extraction’ by M. Hügle et al., RSC Adv., 2018, 8, 20124–20130.
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Affiliation(s)
- M. Hügle
- Laboratory for Sensors
- Department of Microsystems Engineering (IMTEK)
- University of Freiburg
- Freiburg
- Germany
| | - G. Dame
- Institute of Microbiology and Virology
- Brandenburg Medical School Theodor Fontane
- Neuruppin
- Germany
| | - O. Behrmann
- Laboratory for Sensors
- Department of Microsystems Engineering (IMTEK)
- University of Freiburg
- Freiburg
- Germany
| | - R. Rietzel
- Laboratory for Sensors
- Department of Microsystems Engineering (IMTEK)
- University of Freiburg
- Freiburg
- Germany
| | - D. Karthe
- Helmholtz-Centre for Environmental Research
- Magdeburg
- Germany
- German-Mongolian Institute of Resources and Technology
- Nalaikh
| | - F. T. Hufert
- Institute of Microbiology and Virology
- Brandenburg Medical School Theodor Fontane
- Neuruppin
- Germany
| | - G. A. Urban
- Laboratory for Sensors
- Department of Microsystems Engineering (IMTEK)
- University of Freiburg
- Freiburg
- Germany
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Hügle M, Dame G, Behrmann O, Rietzel R, Karthe D, Hufert FT, Urban GA. A lab-on-a-chip for preconcentration of bacteria and nucleic acid extraction. RSC Adv 2018; 8:20124-20130. [PMID: 35541671 PMCID: PMC9080779 DOI: 10.1039/c8ra02177e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/27/2018] [Accepted: 05/22/2018] [Indexed: 11/21/2022] Open
Abstract
To improve detection sensitivity, molecular diagnostics require preconcentration of low concentrated samples followed by rapid nucleic acid extraction. This is usually achieved by multiple centrifugation, lysis and purification steps, for instance, using chemical reagents, spin columns or magnetic beads. These require extensive infrastructure as well as time consuming manual handling steps and are thus not suitable for point of care testing (POCT). To overcome these challenges, we developed a microfluidic chip combining free-flow electrophoretic (FFE) preconcentration (1 ml down to 5 μl) and thermoelectric lysis of bacteria as well as purification of nucleic acids by gel-electrophoresis. The integration of these techniques in a single chip is unique and enables fast, easy and space-saving sample pretreatment without the need for laboratory facilities, making it ideal for the integration into small POCT devices. A preconcentration efficiency of nearly 100% and a lysis/gel-electrophoresis efficiency of about 65% were achieved for the detection of E. coli. The genetic material was analyzed by RT-qPCR targeting the superfolder Green Fluorescent Protein (sfGFP) transcripts to quantify mRNA recovery and qPCR to determine DNA background. A lab-on-a-chip combining free-flow electrophoretic preconcentration and thermoelectric lysis of bacteria as well as purification of nucleic acids by gel-electrophoresis.![]()
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Affiliation(s)
- M. Hügle
- Laboratory for Sensors
- Department of Microsystems Engineering (IMTEK)
- University of Freiburg
- Freiburg
- Germany
| | - G. Dame
- Institute of Microbiology and Virology
- Brandenburg Medical School Theodor Fontane
- Neuruppin
- Germany
| | - O. Behrmann
- Laboratory for Sensors
- Department of Microsystems Engineering (IMTEK)
- University of Freiburg
- Freiburg
- Germany
| | - R. Rietzel
- Laboratory for Sensors
- Department of Microsystems Engineering (IMTEK)
- University of Freiburg
- Freiburg
- Germany
| | - D. Karthe
- German-Mongolian Institute of Resources and Technology
- Mongolia
| | - F. T. Hufert
- Institute of Microbiology and Virology
- Brandenburg Medical School Theodor Fontane
- Neuruppin
- Germany
| | - G. A. Urban
- Laboratory for Sensors
- Department of Microsystems Engineering (IMTEK)
- University of Freiburg
- Freiburg
- Germany
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Hakenberg S, Hügle M, Meyer P, Behrmann O, Dame G, Urban G. Fenton fragmentation for faster electrophoretic on chip purification of amplifiable genomic DNA. Biosens Bioelectron 2015; 67:49-52. [DOI: 10.1016/j.bios.2014.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/22/2014] [Accepted: 06/01/2014] [Indexed: 12/01/2022]
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