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Ahuja S, Tallur S, Kondabagil K. Simultaneous microbial capture and nucleic acid extraction from wastewater with minimal pre-processing and high recovery efficiency. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170347. [PMID: 38336063 DOI: 10.1016/j.scitotenv.2024.170347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/22/2023] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
The COVID-19 pandemic accelerated research towards developing low-cost assays for automated urban wastewater monitoring assay that can be integrated into an environmental surveillance system for early warning of frequent disease outbreaks and future pandemics. Microbial concentration is one of the most challenging steps in wastewater surveillance, due to the sample heterogeneity and low pathogen load. Keeping in mind the requirements of large-scale testing in densely populated low- or middle-income countries (LMICs), such assays would need to be low-cost and have rapid turnaround time with high recovery efficiency. In this study, two such methods are presented and evaluated against commercially available kits for pathogen detection in wastewater. The first method utilizes paper dipsticks while the second method comprises of a PTFE membrane filter (PMF) integrated with a peristaltic pump. Both methods were used to concentrate and isolate nucleic acids from different microbes such as SARS-CoV-2, pepper mild mottle virus (PMMoV), bacteriophage Phi6, and E. coli from wastewater samples with minimal or no sample pre-processing. While the paper dipstick method is suitable for sub-milliliter sample volume, the PMF method can be used with larger volumes of wastewater sample (40 mL) and can detect multiple microbes with recovery efficiency comparable to commercially available kits.
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Affiliation(s)
- Shruti Ahuja
- Centre for Research in Nanotechnology & Science (CRNTS), IIT Bombay, Powai, Mumbai 400076, Maharashtra, India.
| | - Siddharth Tallur
- Department of Electrical Engineering, IIT Bombay, Powai, Mumbai 400076, Maharashtra, India.
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, Maharashtra, India.
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2
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Rivera J, Mu Y, Gordon CA, Jones MK, Cheng G, Cai P. Current and upcoming point-of-care diagnostics for schistosomiasis. Trends Parasitol 2024; 40:60-74. [PMID: 38000956 DOI: 10.1016/j.pt.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023]
Abstract
Point-of-care (POC) diagnostics are simple and effective portable tools that can be used for fast mapping of helminthic diseases and monitoring control programs. Most POC tests (POCTs) available for schistosomiasis diagnosis are lateral flow immunoassays (LFIAs). The emergence of simple and rapid DNA isolation methods, along with isothermal nucleic acid amplification strategies - for example, loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA) - and recent clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic methods facilitate the development of molecular-based POC diagnostics for schistosomiasis. Furthermore, smartphone-based techniques increase real-time connectivity and readout accuracy of POCTs. This review discusses the recent advances in immunological-, molecular-based POCTs and mobile phone microscopes for the diagnosis/screening of schistosomiasis.
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Affiliation(s)
- Jonas Rivera
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | - Yi Mu
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Catherine A Gordon
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia; School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Malcolm K Jones
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia; School of Veterinary Science, The University of Queensland, Brisbane, Australia
| | - Guofeng Cheng
- Shanghai Tenth People's Hospital, Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Pengfei Cai
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, Australia.
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3
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Zou Y, Mason MG, Botella JR. A low-cost, portable, dual-function readout device for amplification-based point-of-need diagnostics. Appl Environ Microbiol 2023; 89:e0090223. [PMID: 38047632 PMCID: PMC10734478 DOI: 10.1128/aem.00902-23] [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: 05/29/2023] [Accepted: 09/25/2023] [Indexed: 12/05/2023] Open
Abstract
IMPORTANCE The first critical step in timely disease management is rapid disease identification, which is ideally on-site detection. Of all the technologies available for disease identification, nucleic acid amplification-based diagnostics are often used due to their specificity, sensitivity, adaptability, and speed. However, the modules to interpret amplification results rapidly, reliably, and easily in resource-limited settings at point-of-need (PON) are in high demand. Therefore, we developed a portable, low-cost, and easy-to-perform device that can be used for amplification readout at PON to enable rapid yet reliable disease identification by users with minimal training.
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Affiliation(s)
- Yiping Zou
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael Glenn Mason
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Jose Ramon Botella
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, Australia
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Aula OP, McManus DP, Jones MK, You H, Cai P, Gordon CA. Optimisation of the DNA dipstick as a rapid extraction method for Schistosoma japonicum in infected mice samples and spiked human clinical samples. Infect Dis Poverty 2023; 12:71. [PMID: 37550723 PMCID: PMC10405380 DOI: 10.1186/s40249-023-01118-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/04/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Schistosomiasis remains a public health issue and the need for accurate and affordable diagnostics is crucial in the elimination of the disease. While molecular diagnostics are highly effective, they are expensive, with the main costs been associated with DNA extraction. The DNA dipstick is a rapid, affordable and simple purification method that allows DNA to be extracted from diagnostic samples within 30 s. We aimed to optimise the DNA dipstick method for samples from mice and egg-spiked human samples. METHODS Urine, blood and faeces were collected from mice exposed to Schistosoma japonicum infection at weekly intervals from Day 0 to Day 42. Urine and faecal samples were also collected from volunteer, uninfected humans and spiked with S. japonicum eggs. All samples were subject to several optimisation procedures and DNA extracted with the DNA dipstick. Amplification of the target DNA was carried out using LAMP and visualised using agarose gel electrophoresis and flocculation. RESULTS The DNA dipstick successfully identified S. japonicum from infected mice and human clinical samples spiked with cracked eggs or genomic DNA from S. japonicum. Amplification was observed from week 4 post infection in infected mice. For human samples, amplification was observed in sieved faecal samples, filtered urine samples heated at 95 °C for 30 min, and sera samples heated at 95 °C for 30 min. CONCLUSIONS The DNA dipstick combined with LAMP has huge potential in providing cost-effective, simple and accurate detection of schistosomiasis infection in endemic regions. This will allow for rapid treatment, tracking outbreaks-such as occur after typhoons, leading to better health outcomes and contributing to control and eventual elimination of schistosomiasis.
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Affiliation(s)
- Oyime P Aula
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
- School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, Australia.
| | - Donald P McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Malcolm K Jones
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Veterinary Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Hong You
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Veterinary Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Pengfei Cai
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Catherine A Gordon
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
- School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Australia.
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5
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Batra AR, Cottam D, Lepesteur M, Dexter C, Zuccala K, Martino C, Khudur L, Daniel V, Ball AS, Soni SK. Development of A Rapid, Low-Cost Portable Detection Assay for Enterococci in Wastewater and Environmental Waters. Microorganisms 2023; 11:microorganisms11020381. [PMID: 36838346 PMCID: PMC9960780 DOI: 10.3390/microorganisms11020381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Waterborne diseases are known as a leading cause of illness and death in both developing and developed countries. Several pathogens can be present in contaminated water, particularly waters containing faecal material; however, routine monitoring of all pathogens is not currently possible. Enterococcus faecalis, which is present in the microflora of human and animals has been used as a faecal indicator in water due to its abundance in surface water and soil. Accurate and fast detection methods are critical for the effective monitoring of E. faecalis in the environment. Although conventional and current molecular detection techniques provide sufficient sensitivity, specificity and throughput, their use is hampered by the long waiting period (1-6 days) to obtain results, the need for expensive laboratory equipment, skilled personnel, and cold-chain storage. Therefore, this study aimed to develop a detection system for E. faecalis that would be simple, rapid, and low-cost, using an isothermal DNA amplification assay called recombinase polymerase amplification (RPA), integrated with a lateral flow assay (LFA). The assay was found to be 100% selective for E. faecalis and capable of detecting rates as low as 2.8 × 103 cells per 100 mL from water and wastewater, and 2.8 × 104 cells per 100 mL from saline water. The assay was completed in approximately 30 min using one constant temperature (38 °C). In addition, this study demonstrated the quantitation of E. faecalis using a lateral flow strip reader for the first time, enhancing the potential use of RPA assay for the enumeration of E. faecalis in wastewater and heavily contaminated environmental waters, surface water, and wastewater. However, the sensitivity of the RPA-LFA assay for the detection of E. faecalis in tap water, saline water and in wastewater was 10-1000 times lower than that of the Enterolert-E test, depending on the water quality. Nevertheless, with further improvements, this low-cost RPA-LFA may be suitable to be used at the point-of-need (PON) if conjugated with a rapid field-deployable DNA extraction method.
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Affiliation(s)
- Alka Rani Batra
- ARC Training Centre for the Transformation of Australia’s Biosolids Resource, School of Science, RMIT University, Bundoora West, VIC 3083, Australia
- Environment Protection Authority Victoria, Centre for Applied Sciences, Ernest Jones Drive, Macleod, VIC 3085, Australia
- School of Science, RMIT University, Melbourne, VIC 3083, Australia
- Correspondence: ; Tel.: +61-399256594
| | - Darren Cottam
- Environment Protection Authority Victoria, Centre for Applied Sciences, Ernest Jones Drive, Macleod, VIC 3085, Australia
| | - Muriel Lepesteur
- Environment Protection Authority Victoria, Centre for Applied Sciences, Ernest Jones Drive, Macleod, VIC 3085, Australia
| | - Carina Dexter
- Environment Protection Authority Victoria, Centre for Applied Sciences, Ernest Jones Drive, Macleod, VIC 3085, Australia
| | - Kelly Zuccala
- Environment Protection Authority Victoria, Centre for Applied Sciences, Ernest Jones Drive, Macleod, VIC 3085, Australia
| | - Caroline Martino
- Environment Protection Authority Victoria, Centre for Applied Sciences, Ernest Jones Drive, Macleod, VIC 3085, Australia
| | - Leadin Khudur
- ARC Training Centre for the Transformation of Australia’s Biosolids Resource, School of Science, RMIT University, Bundoora West, VIC 3083, Australia
| | - Vivek Daniel
- School of Science, RMIT University, Melbourne, VIC 3083, Australia
| | - Andrew S. Ball
- ARC Training Centre for the Transformation of Australia’s Biosolids Resource, School of Science, RMIT University, Bundoora West, VIC 3083, Australia
| | - Sarvesh Kumar Soni
- ARC Training Centre for the Transformation of Australia’s Biosolids Resource, School of Science, RMIT University, Bundoora West, VIC 3083, Australia
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Deconinck D, Robbens J, Volckaert FA, Derycke S. Rapid and low-cost identification of common sole (Solea solea) in the field using a fast DNA isolation protocol and loop-mediated isothermal amplification (LAMP). J Food Compost Anal 2023. [DOI: 10.1016/j.jfca.2023.105166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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7
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Dual-mode visual detection strategies of viable pathogens for point-of-care testing. Biosens Bioelectron 2022; 221:114904. [DOI: 10.1016/j.bios.2022.114904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/31/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
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8
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Lu M, Lan H, Cai Z, Wu Z, Sun Y, Tu M, Pan D. Rapid solid phase microextraction of DNA using mesoporous metal–organic framework coating for PCR-based identification of meat adulteration. Mikrochim Acta 2022; 189:433. [DOI: 10.1007/s00604-022-05531-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 10/07/2022] [Indexed: 11/29/2022]
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9
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Botella JR. Point-of-Care DNA Amplification for Disease Diagnosis and Management. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:1-20. [PMID: 36027938 DOI: 10.1146/annurev-phyto-021621-115027] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Early detection of pests and pathogens is of paramount importance in reducing agricultural losses. One approach to early detection is point-of-care (POC) diagnostics, which can provide early warning and therefore allow fast deployment of preventive measures to slow down the establishment of crop diseases. Among the available diagnostic technologies, nucleic acid amplification-based diagnostics provide the highest sensitivity and specificity, and those technologies that forego the requirement for thermocycling show the most potential for use at POC. In this review, I discuss the progress, advantages, and disadvantages of the established and most promising POC amplification technologies. The success and usefulness of POC amplification are ultimately dependent on the availability of POC-friendly nucleic acid extraction methods and amplification readouts, which are also briefly discussed in the review.
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Affiliation(s)
- José R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia;
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10
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Nguyen HA, Choi H, Lee NY. A Rotatable Paper Device Integrating Reverse Transcription Loop-Mediated Isothermal Amplification and a Food Dye for Colorimetric Detection of Infectious Pathogens. BIOSENSORS 2022; 12:bios12070488. [PMID: 35884291 PMCID: PMC9313173 DOI: 10.3390/bios12070488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022]
Abstract
In this study, we developed a rotatable paper device integrating loop-mediated isothermal amplification (RT-LAMP) and a novel naked-eye readout of the RT-LAMP results using a food additive, carmoisine, for infectious pathogen detection. Hydroxyl radicals created from the reaction between CuSO4 and H2O2 were used to decolor carmoisine, which is originally red. The decolorization of carmoisine can be interrupted in the presence of DNA amplicons produced by the RT-LAMP reaction due to how DNA competitively reacts with the hydroxyl radicals to maintain the red color of the solution. In the absence of the target DNA, carmoisine is decolored, owing to its reaction with hydroxyl radicals; thus, positive and negative samples can be easily differentiated based on the color change of the solution. A rotatable paper device was fabricated to integrate the RT-LAMP reaction with carmoisine-based colorimetric detection. The rotatable paper device was successfully used to detect SARS-CoV-2 and SARS-CoV within 70 min using the naked eye. Enterococcus faecium spiked in milk was detected using the rotatable paper device. The detection limits for the SARS-CoV-2 and SARS-CoV targets were both 103 copies/µL. The rotatable paper device provides a portable and low-cost tool for detecting infectious pathogens in a resource-limited environment.
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Development of a Highly Sensitive Loop-Mediated Isothermal Amplification Incorporated with Flocculation of Carbon Particles for Rapid On-Site Diagnosis of Blood Disease Bacterium Banana. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bananas are one of the most crucial fruit crops worldwide and significantly contribute to food security in developing countries. However, blood disease of bananas caused by Ralstonia syzygii subspecies celebensensis has become a threat to banana production. Rapid and accurate diagnosis of BDB for on-site detection is pivotal at an early stage for an effective disease control strategy. This study developed LAMP with specific primers targeting BDB, followed by a flocculation assay for visualising positive amplification in the LAMP assay. The assay was sensitive to picogram amounts of gDNA (0.5 pg). LAMP assay on BDB gDNA showed flocculation, but negative results on Fusarium oxysporus cubense and Ralstonia solanacaerum confirming the specificity of the assays. Field testing conducted at MARDI headquarters and Taman Pertanian Universiti discovered that the LAMP-flocculation assays were successful in detecting BDB on symptomatic samples as well as on samples from a healthy plot with no symptom observed at the sampling stage, revealing that this assay can detect BDB at an early infection stage. The validation results showed that the LAMP-flocculation assay was comparable with the PCR technique. This newly developed technique is highly specific and sensitive for the early detection of BDB for the adoption of precautionary control measures.
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Rogers MJ, McManus DP, Muhi S, Gordon CA. Membrane Technology for Rapid Point-of-Care Diagnostics for Parasitic Neglected Tropical Diseases. Clin Microbiol Rev 2021; 34:e0032920. [PMID: 34378956 PMCID: PMC8404699 DOI: 10.1128/cmr.00329-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Parasitic neglected tropical diseases (NTDs) affect over one billion people worldwide, with individuals from communities in low-socioeconomic areas being most at risk and suffering the most. Disease management programs are hindered by the lack of infrastructure and resources for clinical sample collection, storage, and transport and a dearth of sensitive diagnostic methods that are inexpensive as well as accurate. Many diagnostic tests and tools have been developed for the parasitic NTDs, but the collection and storage of clinical samples for molecular and immunological diagnosis can be expensive due to storage, transport, and reagent costs, making these procedures untenable in most areas of endemicity. The application of membrane technology, which involves the use of specific membranes for either sample collection and storage or diagnostic procedures, can streamline this process, allowing for long-term sample storage at room temperature. Membrane technology can be used in serology-based diagnostic assays and for nucleic acid purification prior to molecular analysis. This facilitates the development of relatively simple and rapid procedures, although some of these methods, mainly due to costs, lack accessibility in low-socioeconomic regions of endemicity. New immunological procedures and nucleic acid storage, purification, and diagnostics protocols that are simple, rapid, accurate, and cost-effective must be developed as countries progress control efforts toward the elimination of the parasitic NTDs.
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Affiliation(s)
- Madeleine J. Rogers
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Donald P. McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Stephen Muhi
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Catherine A. Gordon
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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13
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Nguyen HA, Lee NY. Polydopamine aggregation: A novel strategy for power-free readout of loop-mediated isothermal amplification integrated into a paper device for multiplex pathogens detection. Biosens Bioelectron 2021; 189:113353. [PMID: 34049080 DOI: 10.1016/j.bios.2021.113353] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/23/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) has been widely used for detecting pathogens. However, power-free and clear visualization of results still remain challenging. In this study, we developed a paper device integrated with power-free DNA detection strategy realized by polydopamine aggregation. In the presence of DNA amplicons, the polymerization of dopamine into aggregated polydopamine was hindered, while in the absence of DNA amplicons, polydopamine aggregation is facilitated. The porosity of the paper enabled the capillary flow of dispersed polydopamine for positive sample, while aggregated polydopamine remained at the bottom of the paper strip due to large size of the aggregates for negative sample. Based on this mechanism, we fabricated a slidable paper device integrating LAMP with dopamine polymerization for the naked-eye detection, operated in a seamless manner. Moreover, the introduced paper device was successfully used to detect DNA extracted from Escherichia coli O157:H7 and SARS-CoV-2 within 25 min, as well as Enterococcus faecium within 35 min. The detection limits of both Escherichia coli O157:H7 and SARS-CoV-2 were 10-4 ng/μL. The introduced paper device can be used as a simple and sensitive tool for detecting multiple infectious pathogens, making it an ideal tool particularly for resource-limited environment.
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Affiliation(s)
- Hanh An Nguyen
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, South Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, South Korea.
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14
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Aula OP, McManus DP, Mason MG, Botella JR, Gordon CA. Rapid parasite detection utilizing a DNA dipstick. Exp Parasitol 2021; 224:108098. [PMID: 33713659 DOI: 10.1016/j.exppara.2021.108098] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/15/2021] [Accepted: 03/07/2021] [Indexed: 01/14/2023]
Abstract
Molecular diagnostics are powerful tools for disease detection but are typically confined to the laboratory environment due to the cumbersome methods required to extract nucleic acids from biological samples. Accurate diagnosis is essential for early detection of parasitic worm infections and for monitoring control programs, particularly during new transmission outbreaks to limit infection spread. We optimized the recently developed DNA dipstick technology to purify Schistosoma japonicum DNA from different life stages in <60 s. We successfully detected DNA from adult worms, eggs and infected snails. The speed and simplicity of this method enables the point-of-care detection of S. japonicum.
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Affiliation(s)
- Oyime Poise Aula
- QIMR Berghofer Medical Research Institute, Molecular Parasitology Laboratory, Brisbane, Australia; University of Queensland, Faculty of Medicine, Herston, 4006, QLD, Australia
| | - Donald Peter McManus
- QIMR Berghofer Medical Research Institute, Molecular Parasitology Laboratory, Brisbane, Australia
| | - Michael Glenn Mason
- University of Queensland, School of Agriculture and Food Sciences, Brisbane, Australia
| | - José Ramón Botella
- University of Queensland, School of Agriculture and Food Sciences, Brisbane, Australia
| | - Catherine Amy Gordon
- QIMR Berghofer Medical Research Institute, Molecular Parasitology Laboratory, Brisbane, Australia.
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15
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Wang L, He K, Sadak O, Wang X, Wang Q, Xu X. Visual detection of in vitro nucleic acid replication by submicro- and nano-sized materials. Biosens Bioelectron 2020; 169:112602. [PMID: 32947078 DOI: 10.1016/j.bios.2020.112602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/29/2020] [Accepted: 09/06/2020] [Indexed: 12/15/2022]
Abstract
The rapid growth of in vitro nucleic acid replication has offered a powerful tool for clinical diagnosis, food safety detection and environmental monitorning. Successful implementation of various isothermal nucleic acid amplification methods enables rapid replication of target sequences without the participant of a thermal cycler. Point-of-need analysis possesses great superiorities in user-friendly, instant results analysis, low manufacturing, and consumable costs. To meet the great challenge of point-of-need analysis, developing simple and rapid visual methods becomes crucial. Submicro- and nanomaterials possess unique surface properties, which enables their rapid response to DNA amplicons. Their unique optical, magnetic, catalytic, and other physical/chemical properties have been frequently employed for the visual detection of in vitro nucleic acid replications. Herein, we aim to review the submicro- and nanomaterials-based visual methods for detection of nucleic acid amplification. The visual methods are classified according to the designing strategies (e.g. LSPR, bridging flocculation, luminescence, catalytic reaction, separation, etc.). The basic principles, merits and drawbacks of each strategy are described. The application in analysis of nucleic acid targets and non-nucleic acid targets are discussed. The main challenges and future research directions are also highlighted in this rapidly emerging field.
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Affiliation(s)
- Liu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Kaiyu He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Omer Sadak
- Department of Electrical and Electronics Engineering, Ardahan University, 75000, Turkey
| | - Xinquan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Qiang Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiahong Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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16
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Mason MG, Botella JR. Rapid (30-second), equipment-free purification of nucleic acids using easy-to-make dipsticks. Nat Protoc 2020; 15:3663-3677. [PMID: 33005038 PMCID: PMC7528719 DOI: 10.1038/s41596-020-0392-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/31/2020] [Indexed: 01/22/2023]
Abstract
The complexity of current nucleic acid isolation methods limits their use outside of the modern laboratory environment. Here, we describe a fast and affordable method to purify nucleic acids from animal, plant, viral and microbial samples using a cellulose-based dipstick. Nucleic acids can be purified by dipping in-house-made dipsticks into just three solutions: the extract (to bind the nucleic acids), a wash buffer (to remove impurities) and the amplification reaction (to elute the nucleic acids). The speed and simplicity of this method make it ideally suited for molecular applications, both within and outside the laboratory, including limited-resource settings such as remote field sites and teaching institutions. Detailed instructions for how to easily manufacture large numbers of dipsticks in house are provided. Using the instructions, readers can create more than 200 dipsticks in <30 min and perform dipstick-based nucleic acid purifications in 30 s.
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Affiliation(s)
- Michael G Mason
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, Australia.
| | - José R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, Australia.
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Zou Y, Mason MG, Botella JR. Evaluation and improvement of isothermal amplification methods for point-of-need plant disease diagnostics. PLoS One 2020; 15:e0235216. [PMID: 32598374 PMCID: PMC7323990 DOI: 10.1371/journal.pone.0235216] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 06/10/2020] [Indexed: 01/01/2023] Open
Abstract
A number of isothermal DNA amplification technologies claim to be ideal for point-of-need (PON) applications as they enable reactions to be performed using a single-temperature heat source (e.g. water bath). Thus, we examined several isothermal amplification methods focusing on simplicity, cost, sensitivity and reproducibility to identify the most suitable method(s) for low resource PON applications. A number of methods were found unsuitable as they either involved multiple temperature incubations, were relatively expensive or required relatively large amounts target DNA for amplification. Among the methods examined, loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA) were found to be the most suitable for PON applications as they are both single step methods that provide highly sensitive and reproducible amplifications. The speed of LAMP reactions was greatly enhanced, up to 76%, with the addition of loop primers while the presence of swarm primers and the sequestration of free magnesium ions with nucleotides also enhanced the amplification speed. In contrast, we were unable to enhance RPA's performance from the original published literature. While both RPA and LAMP have some drawbacks, either isothermal technology can reliably be used for on-site diagnostics with minimal equipment.
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Affiliation(s)
- Yiping Zou
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Michael Glenn Mason
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jose Ramon Botella
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
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Zhu H, Fohlerová Z, Pekárek J, Basova E, Neužil P. Recent advances in lab-on-a-chip technologies for viral diagnosis. Biosens Bioelectron 2020; 153:112041. [PMID: 31999560 PMCID: PMC7126858 DOI: 10.1016/j.bios.2020.112041] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/13/2020] [Accepted: 01/20/2020] [Indexed: 12/12/2022]
Abstract
The global risk of viral disease outbreaks emphasizes the need for rapid, accurate, and sensitive detection techniques to speed up diagnostics allowing early intervention. An emerging field of microfluidics also known as the lab-on-a-chip (LOC) or micro total analysis system includes a wide range of diagnostic devices. This review briefly covers both conventional and microfluidics-based techniques for rapid viral detection. We first describe conventional detection methods such as cell culturing, immunofluorescence or enzyme-linked immunosorbent assay (ELISA), or reverse transcription polymerase chain reaction (RT-PCR). These methods often have limited speed, sensitivity, or specificity and are performed with typically bulky equipment. Here, we discuss some of the LOC technologies that can overcome these demerits, highlighting the latest advances in LOC devices for viral disease diagnosis. We also discuss the fabrication of LOC systems to produce devices for performing either individual steps or virus detection in samples with the sample to answer method. The complete system consists of sample preparation, and ELISA and RT-PCR for viral-antibody and nucleic acid detection, respectively. Finally, we formulate our opinions on these areas for the future development of LOC systems for viral diagnostics.
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Affiliation(s)
- Hanliang Zhu
- Ministry of Education Key Laboratory of Micro/Nano Systems for Aerospace, Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Zdenka Fohlerová
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic
| | - Jan Pekárek
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic
| | - Evgenia Basova
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic
| | - Pavel Neužil
- Ministry of Education Key Laboratory of Micro/Nano Systems for Aerospace, Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China; Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic.
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