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Yin K, Ding X, Xu Z, Li Z, Wang X, Zhao H, Otis C, Li B, Liu C. Multiplexed colorimetric detection of SARS-CoV-2 and other pathogens in wastewater on a 3D printed integrated microfluidic chip. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 344:130242. [PMID: 34121812 PMCID: PMC8183101 DOI: 10.1016/j.snb.2021.130242] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 05/04/2023]
Abstract
Severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic has become a global public health emergency. The detection of SARS-CoV-2 and human enteric pathogens in wastewater can provide an early warning of disease outbreak. Herein, a sensitive, multiplexed, colorimetric detection (termed "SMCD") method was established for pathogen detection in wastewater samples. The SMCD method integrated on-chip nucleic acid extraction, two-stage isothermal amplification, and colorimetric detection on a 3D printed microfluidic chip. The colorimetric signal during nucleic acid amplification was recorded in real-time and analyzed by a programmed smartphone without the need for complicated equipment. By combining two-stage isothermal amplification assay into the integrated microfluidic platform, we detected SARS-CoV-2 and human enteric pathogens with sensitivities of 100 genome equivalent (GE)/mL and 500 colony-forming units (CFU)/mL, respectively, in wastewater within one hour. Additionally, we realized smart, connected, on-site detection with a reporting framework embedded in a portable detection platform, which exhibited potential for rapid spatiotemporal epidemiologic data collection regarding the environmental dynamics, transmission, and persistence of infectious diseases.
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Affiliation(s)
- Kun Yin
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Xiong Ding
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Zhiheng Xu
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Ziyue Li
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Xingyu Wang
- Department of Civil & Environmental Engineering, University of Connecticut, Storrs, CT, 06269-3037, USA
| | - Hui Zhao
- Department of Mechanical Engineering, University of Nevada, Las Vegas, NV, 89154, USA
| | - Clifford Otis
- Department of Civil & Environmental Engineering, University of Connecticut, Storrs, CT, 06269-3037, USA
| | - Baikun Li
- Department of Civil & Environmental Engineering, University of Connecticut, Storrs, CT, 06269-3037, USA
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
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2
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Nieuwkerk DM, Korajkic A, Valdespino EL, Herrmann MP, Harwood VJ. Critical review of methods for isothermal amplification of nucleic acids for environmental analysis. J Microbiol Methods 2020; 179:106099. [PMID: 33159993 DOI: 10.1016/j.mimet.2020.106099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/27/2020] [Accepted: 10/31/2020] [Indexed: 10/23/2022]
Abstract
The past 30 years have seen the emergence and proliferation of isothermal amplification methods (IAMs) for rapid, sensitive detection and quantification of nucleic acids in a variety of sample types. These methods share dependence on primers and probes with quantitative PCR, but they differ in the specific enzymes and instruments employed, and are frequently conducted in a binary, rather than quantitative format. IAMs typically rely on simpler instruments than PCR analyses due to the maintenance of a single temperature throughout the amplification reaction, which could facilitate deployment of IAMs in a variety of environmental and field settings. This review summarizes the mechanisms of the most common IAM methods and their use in studies of pathogens, harmful algae and fecal indicators in environmental waters, feces, wastewater, reclaimed water, and tissues of aquatic animals. Performance metrics of sensitivity, specificity and limit of detection are highlighted, and the potential for use in monitoring and regulatory contexts is discussed.
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Affiliation(s)
- Dana M Nieuwkerk
- University of South Florida, Department of Integrative Biology, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Asja Korajkic
- US Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Erika L Valdespino
- University of South Florida, Department of Integrative Biology, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Michael P Herrmann
- US Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Valerie J Harwood
- University of South Florida, Department of Integrative Biology, 4202 E. Fowler Ave, Tampa, FL 33620, USA.
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3
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Robène I, Maillot-Lebon V, Chabirand A, Moreau A, Becker N, Moumène A, Rieux A, Campos P, Gagnevin L, Gaudeul M, Baider C, Chiroleu F, Pruvost O. Development and comparative validation of genomic-driven PCR-based assays to detect Xanthomonas citri pv. citri in citrus plants. BMC Microbiol 2020; 20:296. [PMID: 33004016 PMCID: PMC7528614 DOI: 10.1186/s12866-020-01972-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/08/2020] [Indexed: 01/07/2023] Open
Abstract
Background Asiatic Citrus Canker, caused by Xanthomonas citri pv. citri, severely impacts citrus production worldwide and hampers international trade. Considerable regulatory procedures have been implemented to prevent the introduction and establishment of X. citri pv. citri into areas where it is not present. The effectiveness of this surveillance largely relies on the availability of specific and sensitive detection protocols. Although several PCR- or real-time PCR-based methods are available, most of them showed analytical specificity issues. Therefore, we developed new conventional and real-time quantitative PCR assays, which target a region identified by comparative genomic analyses, and compared them to existing protocols. Results Our assays target the X. citri pv. citri XAC1051 gene that encodes for a putative transmembrane protein. The real-time PCR assay includes an internal plant control (5.8S rDNA) for validating the assay in the absence of target amplification. A receiver-operating characteristic approach was used in order to determine a reliable cycle cut-off for providing accurate qualitative results. Repeatability, reproducibility and transferability between real-time devices were demonstrated for this duplex qPCR assay (XAC1051-2qPCR). When challenged with an extensive collection of target and non-target strains, both assays displayed a high analytical sensitivity and specificity performance: LOD95% = 754 CFU ml− 1 (15 cells per reaction), 100% inclusivity, 97.2% exclusivity for XAC1051-2qPCR; LOD95% = 5234 CFU ml− 1 (105 cells per reaction), 100% exclusivity and inclusivity for the conventional PCR. Both assays can detect the target from naturally infected citrus fruit. Interestingly, XAC1051-2qPCR detected X. citri pv. citri from herbarium citrus samples. The new PCR-based assays displayed enhanced analytical sensitivity and specificity when compared with previously published PCR and real-time qPCR assays. Conclusions We developed new valuable detection assays useful for routine diagnostics and surveillance of X. citri pv. citri in citrus material. Their reliability was evidenced through numerous trials on a wide range of bacterial strains and plant samples. Successful detection of the pathogen was achieved from both artificially and naturally infected plants, as well as from citrus herbarium samples, suggesting that these assays will have positive impact both for future applied and academic research on this bacterium.
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Affiliation(s)
| | | | - Aude Chabirand
- Unit for Tropical Pests and Diseases, Plant Health Laboratory (LSV), French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Saint-Pierre, Reunion Island, France
| | - Aurélie Moreau
- Unit for Tropical Pests and Diseases, Plant Health Laboratory (LSV), French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Saint-Pierre, Reunion Island, France
| | - Nathalie Becker
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Sorbonne Université, EPHE, Université des Antilles, CNRS, Paris, France
| | - Amal Moumène
- Université de La Réunion, UMR PVBMT, Saint-Pierre, Reunion Island, France
| | - Adrien Rieux
- CIRAD, UMR PVBMT, Saint-Pierre, Reunion Island, France
| | - Paola Campos
- CIRAD, UMR PVBMT, Saint-Pierre, Reunion Island, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Sorbonne Université, EPHE, Université des Antilles, CNRS, Paris, France
| | | | - Myriam Gaudeul
- Herbier national (P), Muséum National d'Histoire Naturelle, Paris, France
| | - Claudia Baider
- Ministry of Agro Industry and Food Security, Mauritius Herbarium, R.E. Vaughan Building (MSIRI compound) Agricultural Services, Réduit, Mauritius
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Simple lysis of bacterial cells for DNA-based diagnostics using hydrophilic ionic liquids. Sci Rep 2019; 9:13994. [PMID: 31570727 PMCID: PMC6768989 DOI: 10.1038/s41598-019-50246-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/09/2019] [Indexed: 12/20/2022] Open
Abstract
The extraction of nucleic acids from microorganisms for subsequent molecular diagnostic applications is still a tedious and time-consuming procedure. We developed a method for the rapid preparation of genomic DNA from bacteria based on hydrophilic ionic liquids (ILs). First, we tested eight ILs in different buffer systems for their inhibitory effects on quantitative PCR. The cell lysis potential of different IL/buffer combinations was assessed by application on Enterococcus faecalis as a model organism for Gram-positive bacteria. The two best ILs, choline hexanoate and 1-ethyl-3-methylimidazolium acetate, were compared with the reference enzymatic method and two commercial DNA extraction kits. All methods were evaluated on four Gram-positive and four Gram-negative bacterial species that are highly relevant for environmental, food, or clinical diagnostics. In comparison to the reference method, extraction yields of the IL-based procedure were within one order of magnitude for most of the strains. The final protocol for DNA extraction using the two ILs is very low-cost, avoids the use of hazardous chemicals and can be performed in five minutes on a simple heating block. This makes the method ideal for high sample throughput and offers the opportunity for DNA extraction from bacteria in resource-limited settings or even in the field.
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Martzy R, Kolm C, Krska R, Mach RL, Farnleitner AH, Reischer GH. Challenges and perspectives in the application of isothermal DNA amplification methods for food and water analysis. Anal Bioanal Chem 2019; 411:1695-1702. [PMID: 30617408 PMCID: PMC6453865 DOI: 10.1007/s00216-018-1553-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/09/2018] [Accepted: 12/14/2018] [Indexed: 12/04/2022]
Abstract
Molecular diagnostic tools in the field of food and water quality analysis are becoming increasingly widespread. Usually, based on DNA amplification techniques such as polymerase chain reaction (PCR), these methods are highly sensitive and versatile but require well-equipped laboratories and trained personnel. To reduce analysis time and avoid expensive equipment, isothermal DNA amplification methods for detecting various target organisms have been developed. However, to make molecular diagnostics suitable for low-resource settings and in-field applications, it is crucial to continuously adapt the working steps associated with DNA amplification, namely sample preparation, DNA extraction, and visualization of the results. Many novel approaches have been evaluated in recent years to tackle these challenges, e.g., the use of ionic liquids for the rapid isolation of nucleic acids from organisms relevant for food and water analysis or the integration of entire analytical workflows on microfluidic chips. In any event, the future of applications in the field of isothermal amplification will probably lie in ready-to-use cartridges combined with affordable handheld devices for on-site analysis. This trend article aims to make prospective users more familiar with this technology and its potential for moving molecular diagnostics from the laboratory to the field. Graphical abstract ᅟ.
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Affiliation(s)
- Roland Martzy
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Molecular Diagnostics Group, Department of Agrobiotechnology (IFA-Tulln), 3430, Tulln, Austria
- ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
| | - Claudia Kolm
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Molecular Diagnostics Group, Department of Agrobiotechnology (IFA-Tulln), 3430, Tulln, Austria
- ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
| | - Rudolf Krska
- University of Natural Resources and Life Sciences, Vienna (BOKU), Department of Agrobiotechnology (IFA-Tulln), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
- Queen's University Belfast, Institute for Global Food Security, School of Biological Sciences, Belfast, Northern Ireland, BT71NN, UK
| | - Robert L Mach
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Research Area Biochemical Technology, Research Group of Synthetic Biology and Molecular Biotechnology, 1060, Vienna, Austria
| | - Andreas H Farnleitner
- ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
- Karl Landsteiner University of Health Sciences, Research Unit Water Quality and Health, 3500, Krems, Austria
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Research Area Biochemical Technology, Research Group of Environmental Microbiology and Molecular Diagnostics, 1060, Vienna, Austria
| | - Georg H Reischer
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Molecular Diagnostics Group, Department of Agrobiotechnology (IFA-Tulln), 3430, Tulln, Austria.
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Research Area Biochemical Technology, Research Group of Environmental Microbiology and Molecular Diagnostics, 1060, Vienna, Austria.
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Kolm C, Martzy R, Führer M, Mach RL, Krska R, Baumgartner S, Farnleitner AH, Reischer GH. Detection of a microbial source tracking marker by isothermal helicase-dependent amplification and a nucleic acid lateral-flow strip test. Sci Rep 2019; 9:393. [PMID: 30674936 PMCID: PMC6344534 DOI: 10.1038/s41598-018-36749-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/23/2018] [Indexed: 11/25/2022] Open
Abstract
Over the last decades, various PCR-based methods have been proposed that can identify sources of faecal pollution in environmental waters. These microbial source tracking (MST) methods are powerful tools to manage water quality and support public health risk assessment. However, their application is limited by the lack of specialized equipment and trained personnel in laboratories performing microbiological water quality assessment. Here, we describe a novel molecular method that combines helicase-dependent amplification (HDA) with a strip test for detecting ruminant faecal pollution sources. Unlike quantitative PCR (qPCR), the developed HDA-strip assay only requires a heating block to amplify the ruminant-associated Bacteroidetes 16S rRNA marker (BacR). Following HDA, the reaction mixture can be directly applied onto the test strip, which detects and displays the amplification products by marker-specific hybridization probes via an on-strip colorimetric reaction. The entire assay takes two hours and demands no extensive practical training. Furthermore, the BacR HDA-strip assay achieved comparable results in head-to-head performance tests with the qPCR reference, in which we investigated source-sensitivity and source-specificity, the analytical limit of detection, and the sample limit of detection. Although this approach only yields qualitative results, it can pave a way for future simple-to-use MST screening tools.
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Affiliation(s)
- Claudia Kolm
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Molecular Diagnostics Group, Department IFA-Tulln, Tulln, Austria
- ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
| | - Roland Martzy
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Molecular Diagnostics Group, Department IFA-Tulln, Tulln, Austria
- ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
| | - Manuela Führer
- University of Natural Resources and Life Sciences, Vienna (BOKU), Department IFA-Tulln, Center for Analytical Chemistry, Tulln, Austria
| | - Robert L Mach
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Research Division Biochemical Technology, Research Group Synthetic Biology and Molecular Biotechnology, Vienna, Austria
| | - Rudolf Krska
- University of Natural Resources and Life Sciences, Vienna (BOKU), Department IFA-Tulln, Center for Analytical Chemistry, Tulln, Austria
- Queen's University Belfast, School of Biological Sciences, Institute for Global Food Security, Belfast, Northern Ireland, United Kingdom
| | - Sabine Baumgartner
- University of Natural Resources and Life Sciences, Vienna (BOKU), Department IFA-Tulln, Center for Analytical Chemistry, Tulln, Austria
| | - Andreas H Farnleitner
- ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
- Karl Landsteiner University of Health Sciences, Research Unit Water Quality and Health, Krems, Austria
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Research Division Biochemical Technology, Research Group of Environmental Microbiology and Molecular Diagnostics, Vienna, Austria
| | - Georg H Reischer
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Molecular Diagnostics Group, Department IFA-Tulln, Tulln, Austria.
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Research Division Biochemical Technology, Research Group of Environmental Microbiology and Molecular Diagnostics, Vienna, Austria.
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Huang X, Lin X, Urmann K, Li L, Xie X, Jiang S, Hoffmann MR. Smartphone-Based in-Gel Loop-Mediated Isothermal Amplification (gLAMP) System Enables Rapid Coliphage MS2 Quantification in Environmental Waters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:6399-6407. [PMID: 29738236 PMCID: PMC5990930 DOI: 10.1021/acs.est.8b00241] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 04/12/2018] [Accepted: 05/08/2018] [Indexed: 05/03/2023]
Abstract
Model coliphages (e.g., ΦX174, MS2, and PRD1) have been widely used as surrogates to study the fate and transport of pathogenic viruses in the environment and during wastewater treatment. Two groups of coliphages (F-specific and somatic) are being explored as indicators of viral fecal pollution in ambient water. However, the detection and quantification of coliphages still largely rely on time-consuming culture-based plaque assays. In this study, we developed an in-gel loop-mediated isothermal amplification (gLAMP) system enabling coliphage MS2 quantification within 30 min using standard laboratory devices. Viral particles (MS2) were immobilized with LAMP reagents in polyethylene glycol hydrogel, and then viral RNAs were amplified through a LAMP reaction. Due to the restriction effect of the hydrogel matrix, one viral particle would only produce one amplicon dot. Therefore, the sample virus concentrations can be determined based on the number of fluorescent amplicon dots using a smartphone for imaging. The method was validated by using artificially spiked and naturally contaminated water samples. gLAMP results were shown to correlate well with plaque assay counts ( R2 = 0.984, p < 0.05) and achieved similar sensitivity to quantitative reverse-transcription polymerase chain reaction (RT-qPCR; 1 plaque-forming unit per reaction). Moreover, gLAMP demonstrated a high level of tolerance against inhibitors naturally present in wastewater, in which RT-qPCR was completely inhibited. Besides MS2, gLAMP can also be used for the quantification of other microbial targets (e.g., Escherichia coli and Salmonella). Considering its simplicity, sensitivity, rapidity, and versatility, gLAMP holds great potential for microbial water-quality analysis, especially in resource-limited settings.
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Affiliation(s)
- Xiao Huang
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
| | - Xingyu Lin
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
| | - Katharina Urmann
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
| | - Lijie Li
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
| | - Xing Xie
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
- School
of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Sunny Jiang
- Department
of Civil and Environmental Engineering, Henry Samueli School of Engineering, University of California, Irvine, California 92697, United States
| | - Michael R. Hoffmann
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
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