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Zhu L, Liang Z, Xu Y, Chen Z, Wang J, Zhou L. Ultrasensitive and Rapid Visual Detection of Escherichia coli O157:H7 Based on RAA-CRISPR/Cas12a System. BIOSENSORS 2023; 13:659. [PMID: 37367024 DOI: 10.3390/bios13060659] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023]
Abstract
Escherichia coli (E. coli) O157:H7 is a major foodborne and waterborne pathogen that can threaten human health. Due to its high toxicity at low concentrations, it is crucial to establish a time-saving and highly sensitive in situ detection method. Herein, we developed a rapid, ultrasensitive, and visualized method for detecting E. coli O157:H7 based on a combination of Recombinase-Aided Amplification (RAA) and CRISPR/Cas12a technology. The CRISPR/Cas12a-based system was pre-amplified using the RAA method, which showed high sensitivity and enabled detecting as low as ~1 CFU/mL (fluorescence method) and 1 × 102 CFU/mL (lateral flow assay) of E. coli O157:H7, which was much lower than the detection limit of the traditional real-time PCR technology (103 CFU/mL) and ELISA (104~107 CFU/mL). In addition, we demonstrated that this method still has good applicability in practical samples by simulating the detection in real milk and drinking water samples. Importantly, our RAA-CRISPR/Cas12a detection system could complete the overall process (including extraction, amplification, and detection) within 55 min under optimized conditions, which is faster than most other reported sensors, which take several hours to several days. The signal readout could also be visualized by fluorescence generated with a handheld UV lamp or a naked-eye-detected lateral flow assay depending on the DNA reporters used. Because of the advantages of being fast, having high sensitivity, and not requiring sophisticated equipment, this method has a promising application prospect for in situ detection of trace amounts of pathogens.
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Affiliation(s)
- Lishan Zhu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Zhenda Liang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yongtao Xu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Zhiquan Chen
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Jiasi Wang
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Li Zhou
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
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Göpfert L, Elsner M, Seidel M. Isothermal haRPA detection of bla CTX-M in bacterial isolates from water samples and comparison with qPCR. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:552-557. [PMID: 33410433 DOI: 10.1039/d0ay02000a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Antibiotic resistant bacteria complicate infection treatment worldwide. Rapid and inexpensive detection of the current occurrence of antibiotic resistant bacteria in surface and irrigation water as well as treated wastewater is essential to minimize exposure and further spread. To reduce cost and analysis time compared to current qPCR (quantitative polymerase chain reaction), isothermal nucleic acid amplification tests are promising bioanalytical methods which can be integrated in simplified molecular biological detection systems. This study establishes heterogeneous asymmetric recombinase polymerase amplification (haRPA) for the detection of antibiotic resistance genes in water. After DNA extraction of bacteria cultivated from water, the target DNA for blaCTX-M cluster 1 was amplified at 39 °C for 40 min on a microfluidic DNA chip. The amplified DNA on each spot was quantified by a flow-based chemiluminescence reaction. Even though slightly less sensitive than conventional qPCR, the haRPA method was successful in identifying the blaCTX-M cluster 1 in bacterial isolates with a limit of detection of 0.013 ng μL-1. In a proof-of-principle study, 37 bacterial isolates from environmental water samples were classified according to blaCTX-M cluster 1 occurrence and gave 100% agreement in cross-reference with PCR. Importantly, haRPA allows for a quick in-field monitoring at low incubation temperatures and by an easy visual readout. This study paves the path to establish haRPA as a quick on-site monitoring option for antibiotic resistance gene occurrence without the need for a thermal cycling device or long data processing.
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Affiliation(s)
- Lisa Göpfert
- Institute of Hydrochemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistr. 17, 81377 Munich, Germany.
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Magnetic nanocomposites: versatile tool for the combination of immunomagnetic separation with flow-based chemiluminescence immunochip for rapid biosensing of Staphylococcal enterotoxin B in milk. Anal Bioanal Chem 2019; 411:4951-4961. [DOI: 10.1007/s00216-019-01808-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/18/2019] [Accepted: 03/25/2019] [Indexed: 12/20/2022]
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Elsäßer D, Ho J, Niessner R, Tiehm A, Seidel M. Heterogeneous asymmetric recombinase polymerase amplification (haRPA) for rapid hygiene control of large-volume water samples. Anal Biochem 2018; 546:58-64. [DOI: 10.1016/j.ab.2018.01.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 01/26/2018] [Accepted: 01/30/2018] [Indexed: 02/06/2023]
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Kober C, Niessner R, Seidel M. Quantification of viable and non-viable Legionella spp. by heterogeneous asymmetric recombinase polymerase amplification (haRPA) on a flow-based chemiluminescence microarray. Biosens Bioelectron 2017; 100:49-55. [PMID: 28863324 DOI: 10.1016/j.bios.2017.08.053] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/01/2017] [Accepted: 08/23/2017] [Indexed: 11/19/2022]
Abstract
Increasing numbers of legionellosis outbreaks within the last years have shown that Legionella are a growing challenge for public health. Molecular biological detection methods capable of rapidly identifying viable Legionella are important for the control of engineered water systems. The current gold standard based on culture methods takes up to 10 days to show positive results. For this reason, a flow-based chemiluminescence (CL) DNA microarray was developed that is able to quantify viable and non-viable Legionella spp. as well as Legionella pneumophila in one hour. An isothermal heterogeneous asymmetric recombinase polymerase amplification (haRPA) was carried out on flow-based CL DNA microarrays. Detection limits of 87 genomic units (GU) µL-1 and 26GUµL-1 for Legionella spp. and Legionella pneumophila, respectively, were achieved. In this work, it was shown for the first time that the combination of a propidium monoazide (PMA) treatment with haRPA, the so-called viability haRPA, is able to identify viable Legionella on DNA microarrays. Different proportions of viable and non-viable Legionella, shown with the example of L. pneumophila, ranging in a total concentration between 101 to 105GUµL-1 were analyzed on the microarray analysis platform MCR 3. Recovery values for viable Legionella spp. were found between 81% and 133%. With the combination of these two methods, there is a chance to replace culture-based methods in the future for the monitoring of engineered water systems like condensation recooling plants.
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Affiliation(s)
- Catharina Kober
- Institute of Hydrochemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, 81377 München, Germany
| | - Reinhard Niessner
- Institute of Hydrochemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, 81377 München, Germany
| | - Michael Seidel
- Institute of Hydrochemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, 81377 München, Germany.
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Kunze A, Dilcher M, Abd El Wahed A, Hufert F, Niessner R, Seidel M. On-Chip Isothermal Nucleic Acid Amplification on Flow-Based Chemiluminescence Microarray Analysis Platform for the Detection of Viruses and Bacteria. Anal Chem 2015; 88:898-905. [PMID: 26624222 DOI: 10.1021/acs.analchem.5b03540] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
This work presents an on-chip isothermal nucleic acid amplification test (iNAAT) for the multiplex amplification and detection of viral and bacterial DNA by a flow-based chemiluminescence microarray. In a principle study, on-chip recombinase polymerase amplification (RPA) on defined spots of a DNA microarray was used to spatially separate the amplification reaction of DNA from two viruses (Human adenovirus 41, Phi X 174) and the bacterium Enterococcus faecalis, which are relevant for water hygiene. By establishing the developed assay on the microarray analysis platform MCR 3, the automation of isothermal multiplex-amplification (39 °C, 40 min) and subsequent detection by chemiluminescence imaging was realized. Within 48 min, the microbes could be identified by the spot position on the microarray while the generated chemiluminescence signal correlated with the amount of applied microbe DNA. The limit of detection (LOD) determined for HAdV 41, Phi X 174, and E. faecalis was 35 GU/μL, 1 GU/μL, and 5 × 10(3) GU/μL (genomic units), which is comparable to the sensitivity reported for qPCR analysis, respectively. Moreover the simultaneous amplification and detection of DNA from all three microbes was possible. The presented assay shows that complex enzymatic reactions like an isothermal amplification can be performed in an easy-to-use experimental setup. Furthermore, iNAATs can be potent candidates for multipathogen detection in clinical, food, or environmental samples in routine or field monitoring approaches.
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Affiliation(s)
- A Kunze
- Institute of Hydrochemistry, Chair of Analytical Chemistry, Technical University of Munich , Marchioninistrasse 17, D-81377 Munich, Germany
| | - M Dilcher
- Department of Virology, University Medical Center, Georg-August-University Göttingen , Kreuzbergring 57, D-37075 Göttingen, Germany
| | - A Abd El Wahed
- Division of Microbiology and Animal Health, Georg-August-University Göttingen , Burckhardtweg 2, D-37077 Göttingen, Germany
| | - F Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane , Grossenhainer Strasse 57, D-01968 Senftenberg, Germany
| | - R Niessner
- Institute of Hydrochemistry, Chair of Analytical Chemistry, Technical University of Munich , Marchioninistrasse 17, D-81377 Munich, Germany
| | - M Seidel
- Institute of Hydrochemistry, Chair of Analytical Chemistry, Technical University of Munich , Marchioninistrasse 17, D-81377 Munich, Germany
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Chemiluminescence microarrays in analytical chemistry: a critical review. Anal Bioanal Chem 2014; 406:5589-612. [DOI: 10.1007/s00216-014-7968-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 05/14/2014] [Accepted: 06/12/2014] [Indexed: 12/26/2022]
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Oligonucleotide microarray chip for the quantification of MS2, ΦX174, and adenoviruses on the multiplex analysis platform MCR 3. Anal Bioanal Chem 2014; 406:3323-34. [PMID: 24577571 DOI: 10.1007/s00216-014-7641-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 01/20/2014] [Indexed: 12/15/2022]
Abstract
Pathogenic viruses are emerging contaminants in water which should be analyzed for water safety to preserve public health. A strategy was developed to quantify RNA and DNA viruses in parallel on chemiluminescence flow-through oligonucleotide microarrays. In order to show the proof of principle, bacteriophage MS2, ΦX174, and the human pathogenic adenovirus type 2 (hAdV2) were analyzed in spiked tap water samples on the analysis platform MCR 3. The chemiluminescence microarray imaging unit was equipped with a Peltier heater for a controlled heating of the flow cell. The efficiency and selectivity of DNA hybridization could be increased resulting in higher signal intensities and lower cross-reactivities of polymerase chain reaction (PCR) products from other viruses. The total analysis time for DNA/RNA extraction, cDNA synthesis for RNA viruses, polymerase chain reaction, single-strand separation, and oligonucleotide microarray analysis was performed in 4-4.5 h. The parallel quantification was possible in a concentration range of 9.6 × 10(5)-1.4 × 10(10) genomic units (GU)/mL for bacteriophage MS2, 1.4 × 10(5)-3.7 × 10(8) GU/mL for bacteriophage ΦX174, and 6.5 × 10(3)-1.2 × 10(5) for hAdV2, respectively, by using a measuring temperature of 40 °C. Detection limits could be calculated to 6.6 × 10(5) GU/mL for MS2, 5.3 × 10(3) GU/mL for ΦX174, and 1.5 × 10(2) GU/mL for hAdV2, respectively. Real samples of surface water and treated wastewater were tested. Generally, found concentrations of hAdV2, bacteriophage MS2, and ΦX174 were at the detection limit. Nevertheless, bacteriophages could be identified with similar results by means of quantitative PCR and oligonucleotide microarray analysis on the MCR 3.
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Mirasoli M, Guardigli M, Michelini E, Roda A. Recent advancements in chemical luminescence-based lab-on-chip and microfluidic platforms for bioanalysis. J Pharm Biomed Anal 2014; 87:36-52. [DOI: 10.1016/j.jpba.2013.07.008] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 07/08/2013] [Accepted: 07/08/2013] [Indexed: 01/27/2023]
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Lengger S, Nießner R, Seidel M. Krankheitserreger im Wasser - anreichern und nachweisen. ACTA ACUST UNITED AC 2012. [DOI: 10.1002/nadc.201290444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Portable chemiluminescence multiplex biosensor for quantitative detection of three B19 DNA genotypes. Anal Bioanal Chem 2012. [DOI: 10.1007/s00216-012-6573-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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Clifford RJ, Milillo M, Prestwood J, Quintero R, Zurawski DV, Kwak YI, Waterman PE, Lesho EP, Mc Gann P. Detection of bacterial 16S rRNA and identification of four clinically important bacteria by real-time PCR. PLoS One 2012; 7:e48558. [PMID: 23139793 PMCID: PMC3490953 DOI: 10.1371/journal.pone.0048558] [Citation(s) in RCA: 165] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 09/26/2012] [Indexed: 12/26/2022] Open
Abstract
Within the paradigm of clinical infectious disease research, Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa represent the four most clinically relevant, and hence most extensively studied bacteria. Current culture-based methods for identifying these organisms are slow and cumbersome, and there is increasing need for more rapid and accurate molecular detection methods. Using bioinformatic tools, 962,279 bacterial 16S rRNA gene sequences were aligned, and regions of homology were selected to generate a set of real-time PCR primers that target 93.6% of all bacterial 16S rRNA sequences published to date. A set of four species-specific real-time PCR primer pairs were also designed, capable of detecting less than 100 genome copies of A. baumannii, E. coli, K. pneumoniae, and P. aeruginosa. All primers were tested for specificity in vitro against 50 species of Gram-positive and –negative bacteria. Additionally, the species-specific primers were tested against a panel of 200 clinical isolates of each species, randomly selected from a large repository of clinical isolates from diverse areas and sources. A comparison of culture and real-time PCR demonstrated 100% concordance. The primers were incorporated into a rapid assay capable of positive identification from plate or broth cultures in less than 90 minutes. Furthermore, our data demonstrate that current targets, such as the uidA gene in E.coli, are not suitable as species-specific genes due to sequence variation. The assay described herein is rapid, cost-effective and accurate, and can be easily incorporated into any research laboratory capable of real-time PCR.
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Affiliation(s)
- Robert J. Clifford
- Multi-drug Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Michael Milillo
- Multi-drug Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Jackson Prestwood
- Multi-drug Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Reyes Quintero
- Multi-drug Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Daniel V. Zurawski
- Department of Wound Infections, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Yoon I. Kwak
- Multi-drug Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Paige E. Waterman
- Multi-drug Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Emil P. Lesho
- Multi-drug Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Patrick Mc Gann
- Multi-drug Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- * E-mail:
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Roda A, Mirasoli M, Dolci LS, Buragina A, Bonvicini F, Simoni P, Guardigli M. Portable Device Based on Chemiluminescence Lensless Imaging for Personalized Diagnostics through Multiplex Bioanalysis. Anal Chem 2011; 83:3178-85. [DOI: 10.1021/ac200360k] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Aldo Roda
- Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
- National Institute for Biostructures and Biosystems (INBB), Viale Medaglie d'Oro 305, 00136 Rome, Italy
| | - Mara Mirasoli
- Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Luisa Stella Dolci
- Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Angela Buragina
- Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | | | - Patrizia Simoni
- National Institute for Biostructures and Biosystems (INBB), Viale Medaglie d'Oro 305, 00136 Rome, Italy
| | - Massimo Guardigli
- Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
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Donhauser SC, Niessner R, Seidel M. Sensitive Quantification of Escherichia coli O157:H7, Salmonella enterica, and Campylobacter jejuni by Combining Stopped Polymerase Chain Reaction with Chemiluminescence Flow-Through DNA Microarray Analysis. Anal Chem 2011; 83:3153-60. [DOI: 10.1021/ac2002214] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simon Christian Donhauser
- Chair for Analytical Chemistry and Institute of Hydrochemistry, Technische Universität München, Marchioninistrasse 17, D-81377 München, Germany
| | - Reinhard Niessner
- Chair for Analytical Chemistry and Institute of Hydrochemistry, Technische Universität München, Marchioninistrasse 17, D-81377 München, Germany
| | - Michael Seidel
- Chair for Analytical Chemistry and Institute of Hydrochemistry, Technische Universität München, Marchioninistrasse 17, D-81377 München, Germany
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Simultaneous determination of four different antibiotic residues in honey by chemiluminescence multianalyte chip immunoassays. Mikrochim Acta 2011. [DOI: 10.1007/s00604-011-0548-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Langer V, Niessner R, Seidel M. Stopped-flow microarray immunoassay for detection of viable E. coli by use of chemiluminescence flow-through microarrays. Anal Bioanal Chem 2010; 399:1041-50. [DOI: 10.1007/s00216-010-4414-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 11/02/2010] [Accepted: 11/02/2010] [Indexed: 11/27/2022]
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Pappert G, Rieger M, Niessner R, Seidel M. Immunomagnetic nanoparticle-based sandwich chemiluminescence-ELISA for the enrichment and quantification of E. coli. Mikrochim Acta 2009. [DOI: 10.1007/s00604-009-0264-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Karsunke XYZ, Niessner R, Seidel M. Development of a multichannel flow-through chemiluminescence microarray chip for parallel calibration and detection of pathogenic bacteria. Anal Bioanal Chem 2009; 395:1623-30. [DOI: 10.1007/s00216-009-2905-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Revised: 06/05/2009] [Accepted: 06/09/2009] [Indexed: 11/24/2022]
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