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Rodrigues V, Honrado M, Santos J, Pinto MA, Amaral JS. Development of a loop-mediated isothermal amplification assay for the rapid detection of Styphnolobium japonicum (L.) Schott as an adulterant of Ginkgo biloba (L.). Phytomedicine 2024; 128:155322. [PMID: 38569291 DOI: 10.1016/j.phymed.2023.155322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 04/05/2024]
Abstract
BACKGROUND Species adulteration is a concern in herbal products, especially when plant substitutes of lower economic value replace valuable botanicals. Styphnolobium japonicum is well known as a potential adulterant of Ginkgo biloba, which is one of the most demanded medicinal plants due to its wide use in pharmaceuticals, food supplements, and traditional medicine. Despite bearing some resemblance to ginkgo's flavonol composition, S. japonicum lacks many of G. biloba's desired therapeutic properties. To prevent adulteration practices, it is crucial to implement rigorous quality control measures, including fast and simple diagnostic tools that can be used on-field. PURPOSE This study aims to develop for the first time a species-specific loop-mediated isothermal amplification (LAMP) method for the fast identification of S. japonicum in ginkgo-containing products. METHODS A set of four specific primers (SjF3, SjB3, SjFIP, and SjBIP) and loop primers (SjLF and SjLB) were designed for a LAMP based assay using the 5.8S partial sequence and the internal transcribed spacer 2 of nuclear ribosomal DNA of S. japonicum. RESULTS The successful amplification of the LAMP assay was inspected through visual detection, with the highest intensity recorded at the optimal conditions set at 68 °C for 40 min. The primers showed high specificity and were able to accurately discriminate S. japonicum from G. biloba and 49 other species of medicinal plants. Furthermore, the proposed LAMP assay proved to be fast, selective, and highly sensitive, as demonstrated by the absolute and relative limits of detection, which were reached at 0.5 pg for S. japonicum DNA and 0.01 % S. japonicum in G. biloba, respectively. CONCLUSIONS This novel approach allows easy identification and discrimination of S. japonicum as a potential adulterant of G. biloba, thus being a useful tool for quality control. Compared to chromatographic or PCR-based methods, the assay proved to be fast, sensitive and did not require expensive equipment, thus offering the possibly usage in field analysis.
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Affiliation(s)
- Vânia Rodrigues
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Mónica Honrado
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Bragança, Portugal; LAQV-REQUIMTE & Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Joana Santos
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Bragança, Portugal
| | - M Alice Pinto
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Joana S Amaral
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Bragança, Portugal.
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Almulla N, Soltane R, Alasiri A, Kamal Allayeh A, Alqadi T, Alshehri F, Hamad Alrokban A, Zaghlool SS, Zayan AZ, Abdalla KF, Sayed AM. Advancements in SARS-CoV-2 detection: Navigating the molecular landscape and diagnostic technologies. Heliyon 2024; 10:e29909. [PMID: 38707469 PMCID: PMC11068538 DOI: 10.1016/j.heliyon.2024.e29909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/07/2024] Open
Abstract
According to information from the World Health Organization, the world has experienced about 430 million cases of COVID-19, a world-wide health crisis caused by the SARS-CoV-2 virus. This outbreak, originating from China in 2019, has led to nearly 6 million deaths worldwide. As the number of confirmed infections continues to rise, the need for cutting-edge techniques that can detect SARS-CoV-2 infections early and accurately has become more critical. To address this, the Federal Drug Administration (FDA) has issued emergency use authorizations (EUAs) for a wide range of diagnostic tools. These include tests based on detecting nucleic acids and antigen-antibody reactions. The quantitative real-time reverse transcription PCR (qRT-PCR) assay stands out as the gold standard for early virus detection. However, despite its accuracy, qRT-PCR has limitations, such as complex testing protocols and a risk of false negatives, which drive the continuous improvement in nucleic acid and serological testing approaches. The emergence of highly contagious variants of the coronavirus, such as Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529), has increased the need for tests that can specifically identify these mutations. This article explores both nucleic acid-based and antigen-antibody serological assays, assessing the performance of recently approved FDA tests and those documented in scientific research, especially in identifying new coronavirus strains.
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Affiliation(s)
- Nuha Almulla
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Raya Soltane
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Ahlam Alasiri
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Abdou Kamal Allayeh
- Virology Lab 176, Environment and Climate Change Institute, National Research Centre, Giza, 12622, Egypt
| | - Taha Alqadi
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Fatma Alshehri
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Ahlam Hamad Alrokban
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Sameh S. Zaghlool
- Department of Pharmacology and Toxicology, College of Pharmacy, Almaaqal University, 61014, Al-Maaqal, Basra, Iraq
| | - Abdallah Z. Zayan
- Department of Pharmaceutics, Collage of Pharmacy, Almaaqal University, 61014, Basrah, Iraq
| | - Karam F. Abdalla
- Department of Pharmaceutics, Collage of Pharmacy, Almaaqal University, 61014, Basrah, Iraq
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Collage of Pharmacy, Almaaqal University, 61014, Basrah, Iraq
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Muzembo BA, Kitahara K, Ohno A, Khatiwada J, Dutta S, Miyoshi SI. Rapid diagnostic tests and loop-mediated isothermal amplification method for the detection of Shigella species: A systematic review and meta-analysis. J Infect Public Health 2024; 17:1065-1078. [PMID: 38705059 DOI: 10.1016/j.jiph.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024] Open
Abstract
We meta-analyzed the diagnostic accuracy of rapid diagnostic tests (dipsticks) and loop-mediated isothermal amplification (LAMP) method to detect Shigella species. We searched MEDLINE, Embase, Web of Science and Google Scholar from inception to 2023 for studies reporting on the performance of Shigella dipstick and LAMP tests compared with culture or polymerase chain reaction (PCR). Our search identified 2618 studies, of which fourteen met the inclusion criteria for the systematic review. Ten studies covering 4056 tests (from twelve countries) were included in the meta-analysis. The overall pooled sensitivity and specificity were 98% (95% CI: 94-100) and 97% (95% CI: 92-99), respectively. Pooled sensitivity and specificity of dipsticks were 95% and 98%, respectively. In contrast, LAMP showed higher pooled sensitivity (100%) and diagnostic odds ratio (431752), but similar specificity (97%). LAMP and dipstick tests exhibited promising performance, suggesting that they could be useful for assisting in the diagnosis of shigellosis.
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Affiliation(s)
- Basilua Andre Muzembo
- Research Institute of Nursing Care for People and Community, University of Hyogo, Akashi, Japan; Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
| | - Kei Kitahara
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan; Collaborative Research Centre of Okayama University for Infectious Diseases in India at ICMR-NICED, Kolkata, India
| | - Ayumu Ohno
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan; Collaborative Research Centre of Okayama University for Infectious Diseases in India at ICMR-NICED, Kolkata, India
| | | | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shin-Ichi Miyoshi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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Bohórquez JA, Muñoz-Aguilera A, Lanka S, Coronado L, Rosell R, Alberch M, Maddox CW, Ganges L. Development of a new loop-mediated isothermal amplification test for the sensitive, rapid, and economic detection of different genotypes of Classical swine fever virus. Front Cell Infect Microbiol 2024; 14:1372166. [PMID: 38686097 PMCID: PMC11056584 DOI: 10.3389/fcimb.2024.1372166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
Background Classical swine fever virus (CSFV) remains one of the most important pathogens in animal health. Pathogen detection relies on viral RNA extraction followed by RT-qPCR. Novel technologies are required to improve diagnosis at the point of care. Methods A loop-mediated isothermal amplification (LAMP) PCR technique was developed, with primers designed considering all reported CSFV genotypes. The reaction was tested using both fluorometric and colorimetric detection, in comparison to the gold standard technique. Viral strains from three circulating CSFV genotypes were tested, as well as samples from infected animals. Other pathogens were also tested, to determine the LAMP specificity. Besides laboratory RNA extraction methods, a heating method for RNA release, readily available for adaptation to field conditions was evaluated. Results Three primer sets were generated, with one of them showing better performance. This primer set proved capable of maintaining optimal performance at a wide range of amplification temperatures (60°C - 68°C). It was also able to detect CSFV RNA from the three genotypes tested. The assay was highly efficient in detection of samples from animals infected with field strains from two different genotypes, with multiple matrices being detected using both colorimetric and fluorometric methods. The LAMP assay was negative for all the unrelated pathogens tested, including Pestiviruses. The only doubtful result in both fluorometric and colorimetric LAMP was against the novel Pestivirus italiaense, ovine Italy Pestivirus (OVPV), which has proven to have cross-reaction with multiple CSFV diagnostic techniques. However, it is only possible to detect the OVPV in a doubtful result if the viral load is higher than 10000 viral particles. Conclusion The results from the present study show that LAMP could be an important addition to the currently used molecular diagnostic techniques for CSFV. This technique could be used in remote locations, given that it can be adapted for successful use with minimal equipment and minimally invasive samples. The joined use of novel and traditional diagnostic techniques could prove to be a useful alternative to support the CSF control.
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Affiliation(s)
- Jose Alejandro Bohórquez
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Adriana Muñoz-Aguilera
- WOAH Reference Laboratory for Classical Swine Fever, IRTA-CReSA, Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
- Instituto Colombiano Agropecuario (ICA), Bogotá, DC, Colombia
| | - Saraswathi Lanka
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Liani Coronado
- WOAH Reference Laboratory for Classical Swine Fever, IRTA-CReSA, Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
| | - Rosa Rosell
- WOAH Reference Laboratory for Classical Swine Fever, IRTA-CReSA, Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
- Departament d’Acció Climàtica, Alimentació i Agenda Rural, Generalitat de Catalunya, Barcelona, Spain
| | - Mònica Alberch
- WOAH Reference Laboratory for Classical Swine Fever, IRTA-CReSA, Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
| | - Carol W. Maddox
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Llilianne Ganges
- WOAH Reference Laboratory for Classical Swine Fever, IRTA-CReSA, Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
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Bari T, Al Mamun MA, Toet H, Rathinasamy V, Larkins JA, Beddoe T, Spithill TW, Piedrafita D, Greenhill AR. Evaluation of LAMP for Fasciola hepatica detection from faecal samples of experimentally and naturally infected cattle. Vet Parasitol 2024; 327:110132. [PMID: 38280252 DOI: 10.1016/j.vetpar.2024.110132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 01/29/2024]
Abstract
Fasciola hepatica causes liver fluke disease in production animals and humans worldwide. Faecal egg counts (FEC) are the most common diagnostic tool for the diagnosis of liver fluke disease. However, FEC has low sensitivity and is often unreliable for the detection of patent infection. In this study, loop-mediated isothermal amplification (LAMP) was optimised and evaluated for the detection of Fasciola hepatica infection, with the aim of increased sensitivity and making it suitable for on-farm application. LAMP was initially conducted under laboratory conditions, optimised to enable visual detection using calcein dye. DNA extraction based on bead-beating was developed to enable on-farm application. LAMP results were compared to FEC and polymerase chain reaction (PCR). Under laboratory conditions, LAMP was conducted using two incubation methods: a conventional PCR thermocycler and a field-deployable LAMP instrument. When compared to a 'rigorous' FEC protocol consisting of multiple counts using a comparatively large volume of faeces and with infection confirmed post-mortem, LAMP was highly sensitive and specific (using silica membrane DNA extraction sensitivity 88 %, specificity 100 %; using sieving and beat-beating DNA extraction sensitivity 98.9 %, specificity 100 %). When applied on-farm, LAMP was compared to conventional FEC, which suggested high sensitivity but low specificity (sensitivity 97 %, specificity 37.5 %). However, further analysis, comparing field LAMP results to laboratory PCR, suggested that the low specificity was likely the outcome of the inability of conventional FEC to detect all true F. hepatica positive samples. Based on the high sensitivity and specificity of LAMP compared to a 'rigorous' FEC protocol and its ability to be used in field settings, the study demonstrates the potential of LAMP for diagnosing F. hepatica infection in agriculture.
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Affiliation(s)
- Tanjina Bari
- Institute of Innovation, Science and Sustainability (IISS), Federation University, Australia
| | - Md Abdullah Al Mamun
- Faculty of Medicine, Nursing and Health Sciences, Monash University, VIC, Australia; Department of Parasitology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Hayley Toet
- Department of Animal, Plant and Soil Science, Centre for AgriBioscience, La Trobe University, Bundoora, Australia
| | - Vignesh Rathinasamy
- Department of Animal, Plant and Soil Science, Centre for AgriBioscience, La Trobe University, Bundoora, Australia; Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - Jo-Ann Larkins
- Institute of Innovation, Science and Sustainability (IISS), Federation University, Australia
| | - Travis Beddoe
- Department of Animal, Plant and Soil Science, Centre for AgriBioscience, La Trobe University, Bundoora, Australia
| | - Terry W Spithill
- Department of Animal, Plant and Soil Science, Centre for AgriBioscience, La Trobe University, Bundoora, Australia
| | - David Piedrafita
- Institute of Innovation, Science and Sustainability (IISS), Federation University, Australia
| | - Andrew R Greenhill
- Institute of Innovation, Science and Sustainability (IISS), Federation University, Australia; Department of Animal, Plant and Soil Science, Centre for AgriBioscience, La Trobe University, Bundoora, Australia.
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Pirolo M, Menezes M, Poulsen M, Søndergaard V, Damborg P, Poirier AC, La Ragione R, Schjærff M, Guardabassi L. A LAMP point-of-care test to guide antimicrobial choice for treatment of Staphylococcus pseudintermedius pyoderma in dogs. Vet J 2024; 304:106105. [PMID: 38547963 DOI: 10.1016/j.tvjl.2024.106105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 04/16/2024]
Abstract
Staphylococcus pseudintermedius is the most common cause of pyoderma in dogs. We validated a point-of-care (PoC) test based on colorimetric loop-mediated isothermal amplification (LAMP) for rapid S. pseudintermedius identification and susceptibility testing for first line antimicrobials for systemic treatment of canine pyoderma, i.e., lincosamides, first generation cephalosporins and amoxicillin clavulanate. Newly designed LAMP primers targeting clinically relevant resistance genes were combined with a previously validated set of primers targeting spsL for species identification. After laboratory validation on 110 clinical isolates, we assessed the performance of the test on 101 clinical specimens using routine culture and susceptibility testing as a reference standard. The average hands-on and turnaround times for the PoC test were 30 and 90 min, respectively. The assay showed sensitivity and specificity near 100% for both species identification and susceptibility testing when performed on bacterial cultures or clinical specimens in the laboratory. However, the PoC test yielded less accurate results when performed on-site by clinical staff (92% sensitivity and 64% specificity for species identification, 67% sensitivity and 96% specificity for β-lactam susceptibility, and 83% sensitivity and 71% specificity for lincosamide susceptibility). These results indicate that the PoC test should be adapted to a user-friendly technology to facilitate performance and interpretation of results by clinical staff. If properly developed, the test would allow veterinarians to gain rapid information on antimicrobial choice, limiting the risk of treatment failure and facilitating adherence to antimicrobial use guidelines in small animal veterinary dermatology.
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Affiliation(s)
- M Pirolo
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C 1870, Denmark
| | - M Menezes
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C 1870, Denmark
| | - M Poulsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C 1870, Denmark
| | - V Søndergaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C 1870, Denmark
| | - P Damborg
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C 1870, Denmark
| | - A C Poirier
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, UK
| | - R La Ragione
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, UK; Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford GU2 7XH, UK
| | - M Schjærff
- Department of Veterinary Clinical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - L Guardabassi
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C 1870, Denmark.
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Peirano G, Castellanos LR, Matsumura Y, Chaffee R, Castañeda-Mogollón D, Pillai DR, Pitout JDD. Clinical validation of loop-mediated isothermal amplification for the detection of Escherichia coli sequence type complex 131. J Clin Microbiol 2024; 62:e0168723. [PMID: 38385692 PMCID: PMC10935629 DOI: 10.1128/jcm.01687-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/02/2024] [Indexed: 02/23/2024] Open
Abstract
The dissemination of Escherichia coli multidrug-resistant (MDR) STc131 is related to its persistence in the human gastrointestinal tract as efficient gut colonizers. Infection and prevention measures are the cornerstones for preventing STc131 spread. Oral decolonization therapies that target ST131 are being developed. There are no rapid methods available to identify STc131 in human specimens. A loop-mediated isothermal amplification (LAMP) assay (named LAMP-ST131) was developed for the detection of STc131 on well-characterized E. coli isolates and then compared to culture and PCR for urines and stool swabs. With E. coli isolates (n = 720), LAMP-ST131 had a sensitivity (sens) of 100% [95% confidence interval (C.I.) = 98.1-100%)] and a specificity (spec) of 98.9% (95% C.I. = 97.5-99.5%). On urines (n = 550), LAMP-ST131 had a sens of 97.6% (95% C.I. = 89.68-94.33%) and a spec of 92.3% (95% C.I. = 87.68-99.88%), while on stool swabs (n = 278), LAMP-ST131 had a sens of 100% (95% C.I. = 88.7-100%) and a spec of 83.9% (95% C.I. = 78.8-87.9%). LAMP-ST131 detected 10 (urines) and 100 (stool swabs) gene copies/μL. LAMP-ST131 accurately identified STc131 within E. coli isolates and human specimens. The implementation of LAMP-ST131 will aid genomic surveys, enable the rapid implementation of effective infection prevention measures, and identify patients suitable for ST131 decolonization therapies. Such approaches will curb the spread of STc131 and decrease incidence rates of global MDR E. coli infections. IMPORTANCE We developed an accurate non-culture-based loop-mediated isothermal amplification (LAMP) methodology for the detection of (sequence type) STc131 among Escherichia coli isolates and human specimens. The use of LAMP-ST131 for global genomic surveillance studies and to identify patients that are suitable for ST131 decolonization therapies will be important for decreasing multidrug-resistant E. coli infections across the globe.
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Affiliation(s)
- Gisele Peirano
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Precision Laboratories, Calgary, Alberta, Canada
| | | | | | - Ryan Chaffee
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | - Dylan R. Pillai
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Johann D. D. Pitout
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Precision Laboratories, Calgary, Alberta, Canada
- University of Pretoria, Pretoria, Gauteng, South Africa
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Chen Y, Zhu Y, Peng C, Wang X, Wu J, Chen H, Xu J. A Point-of-Care Nucleic Acid Quantification Method by Counting Light Spots Formed by LAMP Amplicons on a Paper Membrane. Biosensors (Basel) 2024; 14:139. [PMID: 38534246 DOI: 10.3390/bios14030139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024]
Abstract
Nucleic acid quantification, allowing us to accurately know the copy number of target nucleic acids, is significant for diagnosis, food safety, agricultural production, and environmental protection. However, current digital quantification methods require expensive instruments or complicated microfluidic chips, making it difficult to popularize in the point-of-care detection. Paper is an inexpensive and readily available material. In this study, we propose a simple and cost-effective paper membrane-based digital loop-mediated isothermal amplification (LAMP) method for nucleic acid quantification. In the presence of DNA fluorescence dyes, the high background signals will cover up the amplicons-formed bright spots. To reduce the background fluorescence signals, a quencher-fluorophore duplex was introduced in LAMP primers to replace non-specific fluorescence dyes. After that, the amplicons-formed spots on the paper membrane can be observed; thus, the target DNA can be quantified by counting the spots. Take Vibrio parahaemolyticus DNA detection as an instance, a good linear relationship is obtained between the light spots and the copy numbers of DNA. The paper membrane-based digital LAMP detection can detect 100 copies target DNA per reaction within 30 min. Overall, the proposed nucleic acid quantification method has the advantages of a simple workflow, short sample-in and answer-out time, low cost, and high signal-to-noise, which is promising for application in resourced limited areas.
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Affiliation(s)
- Yanju Chen
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Yuanyuan Zhu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Cheng Peng
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaofu Wang
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Huan Chen
- Hangzhou Digital-Micro Biotech Co., Ltd., Hangzhou 311215, China
| | - Junfeng Xu
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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9
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Dong M, Kshirsagar A, Politza AJ, Guan W. High Fidelity Machine-Learning-Assisted False Positive Discrimination in Loop-Mediated Isothermal Amplification Using Nanopore-Based Sizing and Counting. ACS Nano 2024; 18:7170-7179. [PMID: 38393338 DOI: 10.1021/acsnano.3c12053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Loop-mediated isothermal amplification (LAMP) is a rapid, sensitive, and cost-effective method for developing point-of-care nucleic acid testing due to its isothermal nature. Yet, LAMP can suffer from the issue of false positives, which can compromise the specificity of the results. LAMP false positives typically arise due to contamination, nonspecific amplification, and nonspecific signal reporting (intercalating dyes, colorimetric, turbidity, etc.). While dye-labeled primers or probes have been introduced for multiplexed detection and enhanced specificity in LAMP assays, they carry the risk of reaction inhibition. This inhibition can result from the labeled primers with fluorophores or quenchers and probes that do not fully dissociate during reaction. This work demonstrated a nanopore-based system for probe-free LAMP readouts by employing amplicon sizing and counting, analogous to an electronic version of gel electrophoresis. We first developed a model to explore LAMP kinetics and verified distinct patterns between true and false positives via gel electrophoresis. Subsequently, we implemented nanopore sized counting and calibrated the event charge deficit (ECD) values and frequencies to ensure a fair analysis of amplicon profiles. This sized counting method, integrated with machine learning, achieved 91.67% accuracy for false positive discrimination, enhancing LAMP's reliability for nucleic acid detection.
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Affiliation(s)
- Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Aneesh Kshirsagar
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Anthony J Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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10
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Moerman A, De Waele JJ, Boelens J. An overview of point-of-care testing for infections in critically ill patients. Expert Rev Mol Diagn 2024; 24:193-200. [PMID: 38414348 DOI: 10.1080/14737159.2024.2322146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/19/2024] [Indexed: 02/29/2024]
Abstract
INTRODUCTION Molecular diagnostic systems for point-of-care (POC) testing are nowadays routinely used and are part of many labs. Although often intended for bedside use outside of the microbiology lab, there is still room for expansion. AREAS COVERED This review discusses the two techniques that are currently the most widespread, real-time polymerase-chain reaction (RT-PCR) and loop-mediated isothermal amplification (LAMP). An overview is provided of the various manufacturers and products as well as the evidence and current use in clinical practice. The article further sheds light on some newer techniques, such as CRISPR-based diagnostics and lab-on-a-chip, which are still in development. EXPERT OPINION With many new platforms and techniques still in the pipeline and their potential currently not yet fully exploited, we expect the use of molecular POC testing to increase in the years to come. However, even when used in hospital - in lab, the main advantages of the tests being fast and easy to perform already provide significant benefits in terms of patient outcome.
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Affiliation(s)
- Alena Moerman
- Department of Medical microbiology, Ghent University Hospital, Gent, Belgium
| | - Jan J De Waele
- Department of Critical Care Medicine, Ghent University Hospital, Gent, Belgium
| | - Jerina Boelens
- Department of Medical microbiology, Ghent University Hospital, Gent, Belgium
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11
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Beard JW, Hunt SL, Evans A, Goenner C, Miller BL. Mimicking an in cellulo environment for enzyme-free paper-based nucleic acid tests at the point of care. bioRxiv 2024:2024.02.27.582375. [PMID: 38464301 PMCID: PMC10925243 DOI: 10.1101/2024.02.27.582375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Point of care (PoC) nucleic acid amplification tests (NAATs) are a cornerstone of public health, providing the earliest and most accurate diagnostic method for many communicable diseases, such as HIV, in the same location the patient receives treatment. Communicable diseases disproportionately impact low-resource communities where NAATs are often unobtainable due to the resource intensive enzymes that drive the tests. Enzyme-free nucleic acid detection methods, such as hybridization chain reaction (HCR), use DNA secondary structures for self-driven amplification schemes producing large DNA nanostructures and capable of single molecule detection in cellulo. These thermodynamically driven DNA-based tests have struggled to penetrate the PoC diagnostic field due to their inadequate limits of detection or complex workflows. Here we present a proof-of-concept NAAT that combines HCR-based amplification of a target nucleic acid sequence with paper-based nucleic acid filtration and enrichment capable of detecting sub pM levels of synthetic DNA. We reconstruct the favorable hybridization conditions of an in cellulo reaction in vitro by incubating HCR in an evaporating, microvolume environment containing poly(ethylene glycol) as a crowding agent. We demonstrate that the kinetics and thermodynamics of DNA-DNA and DNA-RNA hybridization is enhanced by the dynamic evaporating environment and inclusion of crowding agents, bringing HCR closer to meeting PoC NAAT needs.
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Affiliation(s)
- Jeffrey W. Beard
- Department of Dermatology, University of Rochester, Rochester, NY 14627, USA
| | - Samuel L. Hunt
- Department of Dermatology, University of Rochester, Rochester, NY 14627, USA
| | - Alexander Evans
- Department of Biomedical Engineering, University of Rochester, Rochester, NY 14627, USA
| | - Coleman Goenner
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14627, USA
| | - Benjamin L. Miller
- Department of Dermatology, University of Rochester, Rochester, NY 14627, USA
- Department of Biomedical Engineering, University of Rochester, Rochester, NY 14627, USA
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14627, USA
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12
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Jankelow A, Chen CL, Cowell TW, Espinosa de Los Monteros J, Bian Z, Kindratenko V, Koprowski K, Darsi S, Han HS, Valera E, Bashir R. Multiplexed electrical detection of whole viruses from plasma in a microfluidic platform. Analyst 2024; 149:1190-1201. [PMID: 38213181 DOI: 10.1039/d3an01510f] [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: 01/13/2024]
Abstract
The advancement of point-of-care diagnostics is crucial to improving patient outcomes, especially in areas with low access to hospitals or specialized laboratories. In particular, rapid, sensitive, and multiplexed detection of disease biomarkers has great potential to achieve accurate diagnosis and inform high quality care for patients. Our Coulter counting and immunocapture based detection system has previously shown its broad applicability in the detection of cells, proteins, and nucleic acids. This paper expands the capability of the platform by demonstrating multiplexed detection of whole-virus particles using electrically distinguishable hydrogel beads by demonstrating the capability of our platform to achieve simultaneous detection at clinically relevant concentrations of hepatitis A virus (>2 × 103 IU mL-1) and human parvovirus B19 virus like particles (>106 IU mL-1) from plasma samples. The expanded versatility of the differential electrical counting platform allows for more robust and diverse testing capabilities.
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Affiliation(s)
- Aaron Jankelow
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Nick Holonyak Jr Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Biomedical Research Center, Carle Foundation Hospital, Urbana, Illinois, USA
| | - Chih-Lin Chen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Thomas W Cowell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Javier Espinosa de Los Monteros
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Biomedical Research Center, Carle Foundation Hospital, Urbana, Illinois, USA
| | - Zheng Bian
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Nick Holonyak Jr Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Victoria Kindratenko
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Nick Holonyak Jr Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Katherine Koprowski
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Nick Holonyak Jr Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sriya Darsi
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Nick Holonyak Jr Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hee-Sun Han
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Enrique Valera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Nick Holonyak Jr Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Biomedical Research Center, Carle Foundation Hospital, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Nick Holonyak Jr Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Biomedical Research Center, Carle Foundation Hospital, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biomedical and Translation Science, Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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Silva LDC, Costa LHA, Dos Santos ICDO, de Curcio JS, Barbosa AMDF, Anunciação CE, Silveira-Lacerda EDP. Advancing Chikungunya Diagnosis: A Cost-Effective and Rapid Visual employing Loop-mediated isothermal reaction. Diagn Microbiol Infect Dis 2024; 108:116111. [PMID: 38016385 DOI: 10.1016/j.diagmicrobio.2023.116111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/24/2023] [Accepted: 10/14/2023] [Indexed: 11/30/2023]
Abstract
The diagnosis of Chikungunya (CHIKV), along with the simultaneous monitoring of virus circulation in the population or vectors, is essential for global health. Although effective diagnostic methods for CHIKV, such as RT-qPCR, exist, their utilization is constrained by high costs. With the aim of contributing to the field of diagnostics, we have developed a diagnostic assay using isothermal amplification technology with visually interpretable results. This test can detect the virus within a maximum timeframe of 30 minutes. The detection limit of RT-LAMP CHIKV was found to be 66 copies of RNA molecules (Ct ≅ 31.28), and no cross-reactivity with other arboviruses was observed. During test validation, our assay demonstrated a sensitivity of 80.43%, specificity of 100%, and an overall accuracy of 88.89%. By utilizing more cost-effective reagents and equipment compared to RT-qPCR, this test holds the potential for broader application and enhanced accessibility, particularly in point-of-care settings.
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Affiliation(s)
- Lívia do Carmo Silva
- Center for the Study and Research of (Re)Emerging Agents (NUPEREME), Sentinel Unit and International and Travel Medicine Reference Center (USCREMIVI)/, IPTSP/ICB, Federal University of Goiás, Brazil.
| | - Luiz Henrique Alves Costa
- Center for the Study and Research of (Re)Emerging Agents (NUPEREME), Sentinel Unit and International and Travel Medicine Reference Center (USCREMIVI)/, IPTSP/ICB, Federal University of Goiás, Brazil
| | - Isabela Cristina de Oliveira Dos Santos
- Center for the Study and Research of (Re)Emerging Agents (NUPEREME), Sentinel Unit and International and Travel Medicine Reference Center (USCREMIVI)/, IPTSP/ICB, Federal University of Goiás, Brazil
| | - Juliana Santana de Curcio
- Center for the Study and Research of (Re)Emerging Agents (NUPEREME), Sentinel Unit and International and Travel Medicine Reference Center (USCREMIVI)/, IPTSP/ICB, Federal University of Goiás, Brazil
| | - Amanda Munik de Freitas Barbosa
- Center for the Study and Research of (Re)Emerging Agents (NUPEREME), Sentinel Unit and International and Travel Medicine Reference Center (USCREMIVI)/, IPTSP/ICB, Federal University of Goiás, Brazil
| | - Carlos Eduardo Anunciação
- Center for the Study and Research of (Re)Emerging Agents (NUPEREME), Sentinel Unit and International and Travel Medicine Reference Center (USCREMIVI)/, IPTSP/ICB, Federal University of Goiás, Brazil
| | - Elisângela de Paula Silveira-Lacerda
- Center for the Study and Research of (Re)Emerging Agents (NUPEREME), Sentinel Unit and International and Travel Medicine Reference Center (USCREMIVI)/, IPTSP/ICB, Federal University of Goiás, Brazil.
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Martín Ramírez A, Barón Argos L, Lanza Suárez M, Carmona Rubio C, Pérez-Ayala A, Hisam SR, Rubio JM. Malaria diagnosis using a combined system of a simple and fast extraction method with a lyophilised Dual-LAMP assay in a non-endemic setting. Pathog Glob Health 2024; 118:80-90. [PMID: 37415348 PMCID: PMC10769111 DOI: 10.1080/20477724.2023.2232595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023] Open
Abstract
Malaria is a parasitic disease distributed in tropical areas but with a high number of imported cases in non-endemic countries. The most specific and sensitive malaria diagnostic methods are PCR and LAMP. However, both require specific equipment, extraction procedures and a cold chain. This study aims to solve some limitations of LAMP method with the optimization and validation of six LAMP assays, genus and species-specific, using an easy and fast extraction method, the incorporation of a reaction control assay, two ways (Dual) of result reading and reagent lyophilization. The Dual-LAMP assays were validated against the Nested-Multiplex Malaria PCR. A conventional column and saline extraction methods, and the use of lyophilized reaction tubes were also assessed. A new reaction control Dual-LAMP-RC assay was designed. Dual-LAMP-Pspp assay showed no cross-reactivity with other parasites, repeatability and reproducibility of 100%, a significant correlation between parasite concentration and time to amplification and a LoD of 1.22 parasites/µl and 5.82 parasites/µl using column and saline extraction methods, respectively. Sensitivity and specificity of the six Dual-LAMP assays reach values of 100% or close to this, being lower for the Dual-LAMP-Pm. The Dual-LAMP-RC assay worked as expected. Lyophilized Dual-LAMP results were concordant with the reference method. Dual-LAMP malaria assays with the addition of a new reaction control LAMP assay and the use of a fast and easy saline extraction method, provided low limit of detection, no cross-reactivity, and good sensitivity and specificity. Furthermore, the reagent lyophilization and the dual result reading allow their use in most settings.
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Affiliation(s)
- Alexandra Martín Ramírez
- Malaria & Parasitic Emerging Diseases Laboratory. National Microbiology Center, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Lourdes Barón Argos
- Malaria & Parasitic Emerging Diseases Laboratory. National Microbiology Center, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Marta Lanza Suárez
- Malaria & Parasitic Emerging Diseases Laboratory. National Microbiology Center, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Claudia Carmona Rubio
- Malaria & Parasitic Emerging Diseases Laboratory. National Microbiology Center, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Ana Pérez-Ayala
- Department of Clinical Microbiology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Shamilah R. Hisam
- Parasitology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institute of Health, Setia Alam, Selangor, Malaysia
| | - José M. Rubio
- Malaria & Parasitic Emerging Diseases Laboratory. National Microbiology Center, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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15
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Chen Y, Zhu Y, Wang X, Peng C, Wang R, Wang T, Che Y, Wu J, Junfeng Xu. Gravity-driven and rotation-controlled microfluidic chip for point-of-care nucleic acid detection in the fully closed environment. Talanta 2024; 267:125258. [PMID: 37801929 DOI: 10.1016/j.talanta.2023.125258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/08/2023]
Abstract
Point-of-care nucleic acid detection is essential for diagnosis and food safety, especially in resource-limited areas. This study reports a gravity-driven and rotation-controlled (GR) chip-coupled lateral flow-based assay (LFA) for point-of-care nucleic acid detection. The sample solution is added to the inlet of the GR chip and flows into the loop-medicated isothermal amplification (LAMP) chamber by the action of gravity. After the LAMP reaction, the GR chip is manually rotated to allow the amplified solution to flow into the LFA chamber for result readout. The GR chip integrates the LAMP reaction and LFA in a fully closed environment, avoiding the aerosol contamination problem. The GR chip's simple and ingenious structure simplifies the fabrication and reduces its cost, making it possible for point-of-care and even home self-testing.
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Affiliation(s)
- Yanju Chen
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China
| | - Yuanyuan Zhu
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China
| | - Xiaofu Wang
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Cheng Peng
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Rui Wang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Pudong Hospital, Fudan University, Shanghai, 200438, China.
| | - Tingzhang Wang
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China
| | - Yang Che
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China.
| | - Junfeng Xu
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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Ma R, Li C, Gao A, Jiang N, Feng X, Li J, Hu W. Evidence-practice gap analysis in the role of tick in brucellosis transmission: a scoping review. Infect Dis Poverty 2024; 13:3. [PMID: 38191468 PMCID: PMC10773131 DOI: 10.1186/s40249-023-01170-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 12/20/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Brucellosis is a zoonotic affliction instigated by bacteria belonging to the genus Brucella and is characterized by a diverse range of pervasiveness, multiple transmission routes, and serious hazards. It is imperative to amalgamate the current knowledge and identify gaps pertaining to the role of ticks in brucellosis transmission. METHODS We systematically searched China National Knowledge Infrastructure (CNKI), WanFang, Google Scholar, and PubMed on the topic published until April 23, 2022. The procedure was performed in accordance with the Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) guidelines. The selected articles were categorized across three major topic areas, and the potential data was extracted to describe evidence-practice gaps by two reviewers. RESULTS The search identified 83 eligible studies for the final analyses. The results highlighted the potential capacity of ticks in brucellosis transmission as evidenced by the detection of Brucella in 16 different tick species. The pooled overall prevalence of Brucella in ticks was 33.87% (range: 0.00-87.80%). The review also revealed the capability of Brucella to circulate in parasitic ticks' different developmental stages, thus posing a potential threat to animal and human health. Empirical evidence from in vitro rodent infection experiments has revealed that ticks possess the capability to transmit Brucella to uninfected animals (range: 45.00-80.00%). Moreover, significant epidemiological associations have been found between the occurrence of brucellosis in animals and tick control in rangelands, which further suggests that ticks may serve as potential vectors for brucellosis transmission in ruminants. Notably, a mere three cases of human brucellosis resulting from potential tick bites were identified in search of global clinical case reports from 1963 to 2019. CONCLUSIONS It is imperative to improve the techniques used to identify Brucella in ticks, particularly by developing a novel, efficient, precise approach that can be applied in a field setting. Furthermore, due to the lack of adequate evidence of tick-borne brucellosis, it is essential to integrate various disciplines, including experimental animal science, epidemiology, molecular genetics, and others, to better understand the efficacy of tick-borne brucellosis. By amalgamating multiple disciplines, we can enhance our comprehension and proficiency in tackling tick-borne brucellosis.
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Affiliation(s)
- Rui Ma
- School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Chunfu Li
- School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ai Gao
- School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Na Jiang
- School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Xinyu Feng
- School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 20025, China.
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 20025, China.
| | - Jian Li
- School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
- Basic Medical College, Guangxi University of Chinese Medical, Nanning, 530005, Guangxi, China.
| | - Wei Hu
- School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
- Basic Medical College, Guangxi University of Chinese Medical, Nanning, 530005, Guangxi, China.
- Department of Infectious Diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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17
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Wang R, Mao X, Xu J, Yao P, Jiang J, Li Q, Wang F. Engineering of the LAMP-CRISPR/Cas12b platform for Chlamydia psittaci detection. J Med Microbiol 2023; 72. [PMID: 38054656 DOI: 10.1099/jmm.0.001781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023] Open
Abstract
Introduction. Chlamydia psittaci (C. psittaci) is a zoonotic infection, that causes psittacosis (parrot fever) in humans, leading to severe clinical manifestations, including severe pneumonia, adult respiratory distress syndrome, and, in rare cases, death.Gap Statement. Rapid, sensitive and specific detection of C. psittaci facilitates timely diagnosis and treatment of patients.Aim. This study aimed to engineer the LAMP-CRISPR/Cas12b platform for C. psittaci detection.Methodology. The loop-mediated isothermal amplification (LAMP) technique and clustered regularly interspaced short palindromic repeats-CRISPR associated protein 12b (CRISPR-Cas12b) assay were combined to establish two-step and one-tube LAMP-CRISPR/Cas12b reaction systems, respectively, for rapidly detecting C. psittaci.Results. The two-step and one-tube LAMP-CRISPR/Cas12b assay could complete detection within 1 h. No cross-reactivity was observed from non-C. psittaci templates with specific LAMP amplification primers and single-guide RNA (sgRNA) targeting the highly conserved short fragment CPSIT_0429 gene of C. psittaci. The detection limits of the two-step and one-tube LAMP-CRISPR/Cas12b reaction were 102 aM and 103 aM, respectively. The results were consistent with qPCR for nucleic acid detection in 160 clinical samples, including 80 suspected C. psittaci samples, kept in the laboratory.Conclusions. The LAMP-CRISPR/Cas12b assay developed in this study provides a sensitive and specific method for rapidly detecting C. psittaci and offers technical support for its rapid diagnosis.
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Affiliation(s)
- Rong Wang
- School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China
| | - Xujian Mao
- Pathogen Inspection Center, Changzhou Center for Disease Prevention and Control, Changzhou, Jiangsu 213022, PR China
| | - Jian Xu
- Pathogen Inspection Center, Changzhou Center for Disease Prevention and Control, Changzhou, Jiangsu 213022, PR China
| | - Ping Yao
- Pathogen Inspection Center, Changzhou Center for Disease Prevention and Control, Changzhou, Jiangsu 213022, PR China
| | - Jingyi Jiang
- Pathogen Inspection Center, Changzhou Center for Disease Prevention and Control, Changzhou, Jiangsu 213022, PR China
| | - Qiong Li
- Pathogen Inspection Center, Changzhou Center for Disease Prevention and Control, Changzhou, Jiangsu 213022, PR China
| | - Fengming Wang
- School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China
- Pathogen Inspection Center, Changzhou Center for Disease Prevention and Control, Changzhou, Jiangsu 213022, PR China
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18
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Phillips EA, Silverman AD, Joneja A, Liu M, Brown C, Carlson P, Coticchia C, Shytle K, Larsen A, Goyal N, Cai V, Huang J, Hickey JE, Ryan E, Acheampong J, Ramesh P, Collins JJ, Blake WJ. Detection of viral RNAs at ambient temperature via reporter proteins produced through the target-splinted ligation of DNA probes. Nat Biomed Eng 2023; 7:1571-1582. [PMID: 37142844 PMCID: PMC10727988 DOI: 10.1038/s41551-023-01028-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 03/25/2023] [Indexed: 05/06/2023]
Abstract
Nucleic acid assays are not typically deployable in point-of-care settings because they require costly and sophisticated equipment for the control of the reaction temperature and for the detection of the signal. Here we report an instrument-free assay for the accurate and multiplexed detection of nucleic acids at ambient temperature. The assay, which we named INSPECTR (for internal splint-pairing expression-cassette translation reaction), leverages the target-specific splinted ligation of DNA probes to generate expression cassettes that can be flexibly designed for the cell-free synthesis of reporter proteins, with enzymatic reporters allowing for a linear detection range spanning four orders of magnitude and peptide reporters (which can be mapped to unique targets) enabling highly multiplexed visual detection. We used INSPECTR to detect a panel of five respiratory viral targets in a single reaction via a lateral-flow readout and ~4,000 copies of viral RNA via additional ambient-temperature rolling circle amplification of the expression cassette. Leveraging synthetic biology to simplify workflows for nucleic acid diagnostics may facilitate their broader applicability at the point of care.
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Affiliation(s)
| | | | | | | | - Carl Brown
- Sherlock Biosciences, Watertown, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | | | | | | | | | | | | | | | | | - Emily Ryan
- Sherlock Biosciences, Watertown, MA, USA
| | | | | | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Abdul Latif Jameel Clinic for Machine Learning in Health, Massachusetts Institute of Technology, Cambridge, MA, USA
- College of Arts and Sciences, Harvard University, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - William J Blake
- Sherlock Biosciences, Watertown, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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19
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Yin W, Zhuang J, Li J, Xia L, Hu K, Yin J, Mu Y. Digital Recombinase Polymerase Amplification, Digital Loop-Mediated Isothermal Amplification, and Digital CRISPR-Cas Assisted Assay: Current Status, Challenges, and Perspectives. Small 2023; 19:e2303398. [PMID: 37612816 DOI: 10.1002/smll.202303398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/29/2023] [Indexed: 08/25/2023]
Abstract
Digital nucleic acid detection based on microfluidics technology can quantify the initial amount of nucleic acid in the sample with low equipment requirements and simple operations, which can be widely used in clinical and in vitro diagnosis. Recently, isothermal amplification technologies such as recombinase polymerase amplification (RPA), loop-mediated isothermal amplification (LAMP), and clustered regularly interspaced short palindromic repeats-CRISPR associated proteins (CRISPR-Cas) assisted technologies have become a hot spot of attention and state-of-the-art digital nucleic acid chips have provided a powerful tool for these technologies. Herein, isothermal amplification technologies including RPA, LAMP, and CRISPR-Cas assisted methods, based on digital nucleic acid microfluidics chips recently, have been reviewed. Moreover, the challenges of digital isothermal amplification and possible strategies to address them are discussed. Finally, future directions of digital isothermal amplification technology, such as microfluidic chip and device manufacturing, multiplex detection, and one-pot detection, are outlined.
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Affiliation(s)
- Weihong Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Jianjian Zhuang
- Department of Clinical Pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Cancer Center, Zhejiang University School of Medicine, Hangzhou, 310006, P. R. China
| | - Jiale Li
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Liping Xia
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Kai Hu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Juxin Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
- School of information and Electrical Engineering, Hangzhou City University, Hangzhou, 310015, P. R. China
| | - Ying Mu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
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20
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Chua YJ, Sim SPC, Shridharan M, Seow Y. Simultaneous and rapid colorimetric detection of distinct miRNAs using Split-LAMP. Front Bioeng Biotechnol 2023; 11:1271297. [PMID: 38026864 PMCID: PMC10652396 DOI: 10.3389/fbioe.2023.1271297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Aberrant microRNA (miRNA) expressions are often discovered in many life threatening diseases such as cancer. In particular, recent studies show combinations of miRNA levels have greater diagnostic accuracy as opposed to single miRNA levels. For point-of-care applications, rapid and sensitive isothermal amplification with loop-mediated isothermal amplification (LAMP) has gained significant interest. Method: We developed a cost-effective point-of-care testing (POCT) device for multiple miRNAs that can integrate miRNA signals into a single output. Results and Discussion: We demonstrate that the loop primers for LAMP can be broken and be used for miRNA detection. This split-LAMP approach provides a logic AND-gate output for two distinct miRNA inputs. We then show that this is potentially useable in point-of-care testing using pH-sensitive dye to give a rapid, colorimetric endpoint readout within 30 min. This novel logic gate approach can potentially be extended to multiple miRNAs such that there can be a powerful diagnostic concept for multiple short RNAs in a point-of-care rapid test.
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Affiliation(s)
- Yi Jing Chua
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Steven Poh Chuen Sim
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Medha Shridharan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- NUS High School of Mathematics and Science, Clementi, Singapore
| | - Yiqi Seow
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
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21
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Ghimire B, Avin FA, Waliullah S, Ali E, Baysal-Gurel F. Real-Time and Rapid Detection of Phytopythium vexans Using Loop-Mediated Isothermal Amplification Assay. Plant Dis 2023; 107:3394-3402. [PMID: 37018213 DOI: 10.1094/pdis-08-22-1944-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Phytopythium vexans (de Bary) Abad, de Cock, Bala, Robideau, A. M. Lodhi & Levesque is an important waterborne and soil-inhabiting oomycete pathogen causing root and crown rot of various plants including certain woody ornamentals, fruit, and forest trees. Early and accurate detection of Phytopythium in the nursery production system is critical, as this pathogen is quickly transported to neighboring healthy plants through the irrigation system. Conventional methods for the detection of this pathogen are tedious, frequently inconclusive, and costly. Hence, a specific, sensitive, and rapid molecular diagnostic method is required to overcome the limitations of traditional identification. In the current study, loop-mediated isothermal amplification (LAMP) for DNA amplification was developed for the identification of P. vexans. It was evaluated using real-time and colorimetric assays. Several sets of LAMP primers were designed and screened, but PVLSU2 was found to be specific to P. vexans as it did not amplify other closely related oomycetes, fungi, and bacteria. Moreover, the developed assays were sensitive enough to amplify DNA up to 102 fg per reaction. The real-time LAMP assay was more sensitive than traditional PCR and culture-based methods to detect infected plant samples. In addition, both LAMP assays detected as few as 100 zoospores suspended in 100 ml water. These LAMP assays are anticipated to save time in P. vexans detection by disease diagnostic laboratories and research institutions and enable early preparedness in the event of disease outbreaks.
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Affiliation(s)
- Bhawana Ghimire
- Otis L. Floyd Nursery Research Center, Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, McMinnville, TN
| | - Farhat A Avin
- Otis L. Floyd Nursery Research Center, Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, McMinnville, TN
| | - Sumyya Waliullah
- Department of Plant Pathology, College of Agricultural and Environmental Sciences, University of Georgia, Tifton, GA
| | - Emran Ali
- Department of Food and Agriculture, College of Life Sciences and Agriculture, University of New Hampshire, Durham, NH
| | - Fulya Baysal-Gurel
- Otis L. Floyd Nursery Research Center, Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, McMinnville, TN
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22
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Liu CW, Tsutsui H. Sample-to-answer sensing technologies for nucleic acid preparation and detection in the field. SLAS Technol 2023; 28:302-323. [PMID: 37302751 DOI: 10.1016/j.slast.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/16/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
Efficient sample preparation and accurate disease diagnosis under field conditions are of great importance for the early intervention of diseases in humans, animals, and plants. However, in-field preparation of high-quality nucleic acids from various specimens for downstream analyses, such as amplification and sequencing, is challenging. Thus, developing and adapting sample lysis and nucleic acid extraction protocols suitable for portable formats have drawn significant attention. Similarly, various nucleic acid amplification techniques and detection methods have also been explored. Combining these functions in an integrated platform has resulted in emergent sample-to-answer sensing systems that allow effective disease detection and analyses outside a laboratory. Such devices have a vast potential to improve healthcare in resource-limited settings, low-cost and distributed surveillance of diseases in food and agriculture industries, environmental monitoring, and defense against biological warfare and terrorism. This paper reviews recent advances in portable sample preparation technologies and facile detection methods that have been / or could be adopted into novel sample-to-answer devices. In addition, recent developments and challenges of commercial kits and devices targeting on-site diagnosis of various plant diseases are discussed.
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Affiliation(s)
- Chia-Wei Liu
- Department of Mechanical Engineering, University of California, Riverside, CA 92521, USA
| | - Hideaki Tsutsui
- Department of Mechanical Engineering, University of California, Riverside, CA 92521, USA; Department of Bioengineering, University of California, Riverside, CA 92521, USA.
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23
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Borah Slater K, Ahmad M, Poirier A, Stott A, Siedler BS, Brownsword M, Mehat J, Urbaniec J, Locker N, Zhao Y, La Ragione R, Silva SRP, McFadden J. Development of a loop-mediated isothermal amplification (LAMP)-based electrochemical test for rapid detection of SARS-CoV-2. iScience 2023; 26:107570. [PMID: 37664622 PMCID: PMC10470312 DOI: 10.1016/j.isci.2023.107570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/10/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
Rapid, reliable, sensitive, portable, and accurate diagnostics are required to control disease outbreaks such as COVID-19 that pose an immense burden on human health and the global economy. Here we developed a loop-mediated isothermal amplification (LAMP)-based electrochemical test for the detection of SARS-CoV-2 that causes COVID-19. The test is based on the oxidation-reduction reaction between pyrophosphates (generated from positive LAMP reaction) and molybdate that is detected by cyclic voltammetry using inexpensive and disposable carbon screen printed electrodes. Our test showed higher sensitivity (detecting as low as 5.29 RNA copies/μL) compared to the conventional fluorescent reverse transcriptase (RT)-LAMP. We validated our tests using human serum and saliva spiked with SARS-CoV-2 RNA and clinical (saliva and nasal-pharyngeal) swab samples demonstrating 100% specificity and 93.33% sensitivity. Our assay provides a rapid, specific, and sensitive test with an electrochemical readout in less than 45 min that could be adapted for point-of-care settings.
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Affiliation(s)
- Khushboo Borah Slater
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Muhammad Ahmad
- Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, UK
| | - Aurore Poirier
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
| | - Ash Stott
- Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, UK
| | - Bianca Sica Siedler
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Matthew Brownsword
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Jai Mehat
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Joanna Urbaniec
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Nicolas Locker
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Yunlong Zhao
- Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, UK
| | - Roberto La Ragione
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
| | - S. Ravi P. Silva
- Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, UK
| | - Johnjoe McFadden
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
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24
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Mytzka N, Arbaciauskaite S, Sandetskaya N, Mattern K, Kuhlmeier D. A fully integrated duplex RT-LAMP device for the detection of viral infections. Biomed Microdevices 2023; 25:36. [PMID: 37682413 PMCID: PMC10491696 DOI: 10.1007/s10544-023-00676-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2023] [Indexed: 09/09/2023]
Abstract
Respiratory viruses can cause epidemics or pandemics, which are worldwide outbreaks of disease. The severity of these events varies depending on the virus, its characteristics, along with environmental factors. The frequency of epidemics and pandemics caused by respiratory viruses is difficult to predict, but the potential severity of such events underlines the importance of continued monitoring, research, and preparation for emerging infectious diseases. To help improve pandemic preparedness, we created a fully integrated duplex reverse transcription loop-mediated isothermal amplification (RT-LAMP) device targeting two respiratory viruses, influenza A/X-31 virus and bovine coronavirus, as a replacement for SARS-CoV-2. This device can be adapted to any other respiratory virus. In this study, we showed and evaluated a prototype of a microfluidic system, and showed that duplex RT-LAMP can detect and distinguish between the two viruses, with LoDs of 2,000 copies/ml for bovine coronavirus and 200 copies/ml for influenza A/X-31 virus.
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Affiliation(s)
- Nicolas Mytzka
- MicroDiagnostics Unit, Fraunhofer Institute for Cell Therapy and Immunology, 04103, Leipzig, Germany
| | - Skaiste Arbaciauskaite
- MicroDiagnostics Unit, Fraunhofer Institute for Cell Therapy and Immunology, 04103, Leipzig, Germany.
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany.
| | - Natalia Sandetskaya
- MicroDiagnostics Unit, Fraunhofer Institute for Cell Therapy and Immunology, 04103, Leipzig, Germany
| | - Kai Mattern
- MicroDiagnostics Unit, Fraunhofer Institute for Cell Therapy and Immunology, 04103, Leipzig, Germany
| | - Dirk Kuhlmeier
- MicroDiagnostics Unit, Fraunhofer Institute for Cell Therapy and Immunology, 04103, Leipzig, Germany
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25
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Suarez GD, Bayer S, Tang YYK, Suarez DA, Cheung PPH, Nagl S. Rapid microfluidics prototyping through variotherm desktop injection molding for multiplex diagnostics. Lab Chip 2023; 23:3850-3861. [PMID: 37534874 DOI: 10.1039/d3lc00391d] [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] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
In this work, we demonstrate an inexpensive method of prototyping microfluidics using a desktop injection molding machine. A centrifugal microfluidic device with a novel central filling mechanism was developed to demonstrate the technique. We overcame the limitations of desktop machines in replicating microfluidic features by variotherm heating and cooling the mold between 50 °C and 110 °C within two minutes. Variotherm heating enabled good replication of microfeatures, with a coefficient of variation averaging only 3.6% attained for the measured widths of 100 μm wide molded channels. Using this methodology, we produced functional polystyrene centrifugal microfluidic chips, capable of aliquoting fluids into 5.0 μL reaction chambers with 97.5% accuracy. We performed allele-specific loop-mediated isothermal amplification (AS-LAMP) reactions for genotyping CYP2C19 alleles on these chips. Readouts were generated using optical pH sensors integrated onto chips, by drop-casting sensor precursor solutions into reaction chambers before final chip assembly. Positive reactions could be discerned by decreases in pH sensor fluorescence, thresholded against negative control reactions lacking the primers for nucleic acid amplification and with time-to-results averaging 38 minutes. Variotherm desktop injection molding can enable researchers to prototype microfluidic devices more cost-effectively, in an iterative fashion, due to reduced costs of smaller, in-house molds. Designs prototyped this way can be directly translated to mass production, enhancing their commercialization potential and positive impacts.
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Affiliation(s)
- Gianmarco D Suarez
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Steevanson Bayer
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Yuki Yu Kiu Tang
- Quommni Technologies Limited, Tsuen Wan, New Territories, Hong Kong
| | | | - Peter Pak-Hang Cheung
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
| | - Stefan Nagl
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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26
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Khanthaphixay B, Wu L, Yoon JY. Microparticle-Based Detection of Viruses. Biosensors (Basel) 2023; 13:820. [PMID: 37622906 PMCID: PMC10452130 DOI: 10.3390/bios13080820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/04/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023]
Abstract
Surveillance of viral pathogens in both point-of-care and clinical settings is imperative to preventing the widespread propagation of disease-undetected viral outbreaks can pose dire health risks on a large scale. Thus, portable, accessible, and reliable biosensors are necessary for proactive measures. Polymeric microparticles have recently gained popularity for their size, surface area, and versatility, which make them ideal biosensing tools. This review cataloged recent investigations on polymeric microparticle-based detection platforms across eight virus families. These microparticles were used as labels for detection (often with fluorescent microparticles) and for capturing viruses for isolation or purification (often with magnetic microparticles). We also categorized all methods by the characteristics, materials, conjugated receptors, and size of microparticles. Current approaches were compared, addressing strengths and weaknesses in the context of virus detection. In-depth analyses were conducted for each virus family, categorizing whether the polymeric microparticles were used as labels, for capturing, or both. We also summarized the types of receptors conjugated to polymeric microparticles for each virus family.
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Affiliation(s)
| | | | - Jeong-Yeol Yoon
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 75721, USA; (B.K.); (L.W.)
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27
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Liu Y, Kumblathan T, Tao J, Xu J, Feng W, Xiao H, Hu J, Huang CV, Wu Y, Zhang H, Li XF, Le XC. Recent advances in RNA sample preparation techniques for the detection of SARS-CoV-2 in saliva and gargle. Trends Analyt Chem 2023; 165:117107. [PMID: 37317683 PMCID: PMC10204347 DOI: 10.1016/j.trac.2023.117107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023]
Abstract
Molecular detection of SARS-CoV-2 in gargle and saliva complements the standard analysis of nasopharyngeal swabs (NPS) specimens. Although gargle and saliva specimens can be readily obtained non-invasively, appropriate collection and processing of gargle and saliva specimens are critical to the accuracy and sensitivity of the overall analytical method. This review highlights challenges and recent advances in the treatment of gargle and saliva samples for subsequent analysis using reverse transcription polymerase chain reaction (RT-PCR) and isothermal amplification techniques. Important considerations include appropriate collection of gargle and saliva samples, on-site inactivation of viruses in the sample, preservation of viral RNA, extraction and concentration of viral RNA, removal of substances that inhibit nucleic acid amplification reactions, and the compatibility of sample treatment protocols with the subsequent nucleic acid amplification and detection techniques. The principles and approaches discussed in this review are applicable to molecular detection of other microbial pathogens.
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Affiliation(s)
- Yanming Liu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Teresa Kumblathan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jeffrey Tao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jingyang Xu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Wei Feng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Huyan Xiao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jianyu Hu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Camille V Huang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yiping Wu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
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28
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Shukla JL, Husain AA, Bhan S, Singh LR, Kashyap RS. Diagnostic utility of LAMP PCR targeting bcsp-31 gene for human brucellosis infection. Indian J Med Microbiol 2023; 44:100354. [PMID: 37356844 DOI: 10.1016/j.ijmmb.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/27/2022] [Accepted: 01/21/2023] [Indexed: 06/27/2023]
Abstract
PURPOSE Human brucellosis is a neglected zoonotic disease of significant public health concern. Molecular diagnosis of brucella remains challenging in low resource settings, due to the high infrastructure and cost involved. Loop-mediated isothermal amplification (LAMP) is a rapid point of care polymerase chain reaction (PCR) with the utility of on-field molecular diagnosis and offers a convenient alternative to conventional PCR. In the present study, we developed and evaluated the diagnostic utility of in house LAMP PCR targeting the Brucella genus-specific bcsp-31 gene in patients having febrile illness. MATERIALS AND METHODS The analytical sensitivity and specificity of bcsp-31 LAMP PCR was first evaluated using brucella (n = 8) and non-brucella cultures (n = 5), along with spiked clinical samples. The overall diagnostic utility of developed LAMP PCR was then further evaluated in 393 human samples suspected of brucellosis. RESULTS The developed LAMP PCR could detect as low as 8 fg of DNA by visual detection within 35min. We report sensitivity and specificity of the developed LAMP PCR as 90.91% and 99.37%.The accuracy of the developed test assay was found to be 98.60%. In clinical samples, LAMP gave positivity of 20% with the concordance of 89% with conventional PCR. CONCLUSION To conclude, a rapid, efficacious, sensitive LAMP PCR targeting the bcsp 31 gene was developed. The existing LAMP PCR can be used as a point of care screening test in various low resource endemic setting in lieu of conventional PCR for estimation of prevalence data, diagnosis and treatment of brucellosis.
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Affiliation(s)
- Jayshree L Shukla
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), 88/2, Bajaj Nagar, Nagpur, Maharashtra, India
| | - Aliabbas A Husain
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), 88/2, Bajaj Nagar, Nagpur, Maharashtra, India
| | - Surya Bhan
- Deptartment of Biochemistry, North-Eastern Hill University (NEHU), Shillong, India
| | - Lokendra R Singh
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), 88/2, Bajaj Nagar, Nagpur, Maharashtra, India
| | - Rajpal S Kashyap
- Research Center, Dr. G.M. Taori Central India Institute of Medical Sciences (CIIMS), 88/2, Bajaj Nagar, Nagpur, Maharashtra, India.
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Sokolov P, Samokhvalov P, Sukhanova A, Nabiev I. Biosensors Based on Inorganic Composite Fluorescent Hydrogels. Nanomaterials (Basel) 2023; 13:nano13111748. [PMID: 37299650 DOI: 10.3390/nano13111748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]
Abstract
Fluorescent hydrogels are promising candidate materials for portable biosensors to be used in point-of-care diagnosis because (1) they have a greater capacity for binding organic molecules than immunochromatographic test systems, determined by the immobilization of affinity labels within the three-dimensional hydrogel structure; (2) fluorescent detection is more sensitive than the colorimetric detection of gold nanoparticles or stained latex microparticles; (3) the properties of the gel matrix can be finely tuned for better compatibility and detection of different analytes; and (4) hydrogel biosensors can be made to be reusable and suitable for studying dynamic processes in real time. Water-soluble fluorescent nanocrystals are widely used for in vitro and in vivo biological imaging due to their unique optical properties, and hydrogels based on these allow the preservation of these properties in bulk composite macrostructures. Here we review the techniques for obtaining analyte-sensitive fluorescent hydrogels based on nanocrystals, the main methods used for detecting the fluorescent signal changes, and the approaches to the formation of inorganic fluorescent hydrogels via sol-gel phase transition using surface ligands of the nanocrystals.
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Affiliation(s)
- Pavel Sokolov
- Life Improvement by Future Technologies (LIFT) Center, Skolkovo, 143025 Moscow, Russia
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115522 Moscow, Russia
| | - Pavel Samokhvalov
- Life Improvement by Future Technologies (LIFT) Center, Skolkovo, 143025 Moscow, Russia
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115522 Moscow, Russia
| | - Alyona Sukhanova
- Laboratoire de Recherche en Nanosciences, LRN-EA4682, Université de Reims Champagne-Ardenne, 51100 Reims, France
| | - Igor Nabiev
- Life Improvement by Future Technologies (LIFT) Center, Skolkovo, 143025 Moscow, Russia
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115522 Moscow, Russia
- Laboratoire de Recherche en Nanosciences, LRN-EA4682, Université de Reims Champagne-Ardenne, 51100 Reims, France
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Coelho BJ, Neto JP, Sieira B, Moura AT, Fortunato E, Martins R, Baptista PV, Igreja R, Águas H. Hybrid Digital-Droplet Microfluidic Chip for Applications in Droplet Digital Nucleic Acid Amplification: Design, Fabrication and Characterization. Sensors (Basel) 2023; 23:4927. [PMID: 37430841 DOI: 10.3390/s23104927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/05/2023] [Accepted: 05/17/2023] [Indexed: 07/12/2023]
Abstract
Microfluidic-based platforms have become a hallmark for chemical and biological assays, empowering micro- and nano-reaction vessels. The fusion of microfluidic technologies (digital microfluidics, continuous-flow microfluidics, and droplet microfluidics, just to name a few) presents great potential for overcoming the inherent limitations of each approach, while also elevating their respective strengths. This work exploits the combination of digital microfluidics (DMF) and droplet microfluidics (DrMF) on a single substrate, where DMF enables droplet mixing and further acts as a controlled liquid supplier for a high-throughput nano-liter droplet generator. Droplet generation is performed at a flow-focusing region, operating on dual pressure: negative pressure applied to the aqueous phase and positive pressure applied to the oil phase. We evaluate the droplets produced with our hybrid DMF-DrMF devices in terms of droplet volume, speed, and production frequency and further compare them with standalone DrMF devices. Both types of devices enable customizable droplet production (various volumes and circulation speeds), yet hybrid DMF-DrMF devices yield more controlled droplet production while achieving throughputs that are similar to standalone DrMF devices. These hybrid devices enable the production of up to four droplets per second, which reach a maximum circulation speed close to 1540 µm/s and volumes as low as 0.5 nL.
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Affiliation(s)
- Beatriz J Coelho
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
- UCIBIO, I4HB, Department of Life Sciences, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Joana P Neto
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| | - Bárbara Sieira
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| | - André T Moura
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| | - Elvira Fortunato
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| | - Rodrigo Martins
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| | - Pedro V Baptista
- UCIBIO, I4HB, Department of Life Sciences, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Rui Igreja
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| | - Hugo Águas
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
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31
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Park SY, Chae DS, Lee JS, Cho BK, Lee NY. Point-of-Care Testing of the MTF1 Osteoarthritis Biomarker Using Phenolphthalein-Soaked Swabs. Biosensors (Basel) 2023; 13:bios13050535. [PMID: 37232895 DOI: 10.3390/bios13050535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
Osteoarthritis (OA) is the most common joint disease, which accompanies pain and inconvenience in daily life owing to degradation of cartilage and adjacent tissues. In this study, we propose a simple point-of-care testing (POCT) kit for the detection of the MTF1 OA biomarker to achieve on-site clinical diagnosis of OA. The kit contains an FTA card for patient sample treatments, a sample tube for loop-mediated isothermal amplification (LAMP), and a phenolphthalein-soaked swab for naked eye detection. The MTF1 gene was isolated from synovial fluids using an FTA card and amplified using the LAMP method at 65 °C for 35 min. A test part of the phenolphthalein-soaked swab was decolorized in the presence of the MTF1 gene due to the pH change after the LAMP, but the color remained pink in the absence of the MTF1 gene. The control part of the swab served as a reference color in relation to the test part. When real-time LAMP (RT-LAMP), gel electrophoresis, and colorimetric detection of the MTF1 gene were performed, the limit of detection (LOD) was confirmed at 10 fg/μL, and the overall processes were completed in 1 h. The detection of an OA biomarker in the form of POCT was reported for the first time in this study. The introduced method is expected to serve as a POCT platform directly applicable by clinicians for easy and rapid identification of OA.
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Affiliation(s)
- So Yeon Park
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
| | - Dong-Sik Chae
- Department of Orthopedic Surgery, College of Medicine, Catholic Kwandong University, Incheon 21431, Republic of Korea
| | - Jae Sun Lee
- Chief Researcher, Healthcontents, Co., Ltd., Cheongju 28119, Republic of Korea
| | - Byung-Ki Cho
- Department of Orthopaedic Surgery, College of Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
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Venbrux M, Crauwels S, Rediers H. Current and emerging trends in techniques for plant pathogen detection. Front Plant Sci 2023; 14:1120968. [PMID: 37223788 PMCID: PMC10200959 DOI: 10.3389/fpls.2023.1120968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/21/2023] [Indexed: 05/25/2023]
Abstract
Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.
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Affiliation(s)
- Marc Venbrux
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
| | - Sam Crauwels
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
| | - Hans Rediers
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
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de Olazarra AS, Wang SX. Advances in point-of-care genetic testing for personalized medicine applications. Biomicrofluidics 2023; 17:031501. [PMID: 37159750 PMCID: PMC10163839 DOI: 10.1063/5.0143311] [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] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Breakthroughs within the fields of genomics and bioinformatics have enabled the identification of numerous genetic biomarkers that reflect an individual's disease susceptibility, disease progression, and therapy responsiveness. The personalized medicine paradigm capitalizes on these breakthroughs by utilizing an individual's genetic profile to guide treatment selection, dosing, and preventative care. However, integration of personalized medicine into routine clinical practice has been limited-in part-by a dearth of widely deployable, timely, and cost-effective genetic analysis tools. Fortunately, the last several decades have been characterized by tremendous progress with respect to the development of molecular point-of-care tests (POCTs). Advances in microfluidic technologies, accompanied by improvements and innovations in amplification methods, have opened new doors to health monitoring at the point-of-care. While many of these technologies were developed with rapid infectious disease diagnostics in mind, they are well-suited for deployment as genetic testing platforms for personalized medicine applications. In the coming years, we expect that these innovations in molecular POCT technology will play a critical role in enabling widespread adoption of personalized medicine methods. In this work, we review the current and emerging generations of point-of-care molecular testing platforms and assess their applicability toward accelerating the personalized medicine paradigm.
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Affiliation(s)
- A. S. de Olazarra
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - S. X. Wang
- Author to whom correspondence should be addressed:
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Febrer-Sendra B, Fernández-Soto P, García-Bernalt Diego J, Crego-Vicente B, Negredo A, Muñor-Bellido JL, Belhassen-García M, Sánchez-Seco MP, Muro A. A Novel RT-LAMP for the Detection of Different Genotypes of Crimean–Congo Haemorrhagic Fever Virus in Patients from Spain. Int J Mol Sci 2023; 24:ijms24076411. [PMID: 37047384 PMCID: PMC10094476 DOI: 10.3390/ijms24076411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
Crimean–Congo haemorrhagic fever (CCHF) is a potentially lethal tick-borne viral disease with a wide distribution. In Spain, 12 human cases of CCHF have been confirmed, with four deaths. The diagnosis of CCHF is hampered by the nonspecific symptoms, the high genetic diversity of CCHFV, and the biosafety requirements to manage the virus. RT-qPCR and serological tests are used for diagnosis with limitations. Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) could be an effective alternative in the diagnosis of the disease. However, none of the few RT-LAMP assays developed to date has detected different CCHFV genotypes. Here, we designed a RT-LAMP using a degenerate primer set to compensate for the variability of the CCHFV target sequence. RT-LAMP was performed in colorimetric and real-time tests on RT-qPCR-confirmed CCHF patient samples notified in Spain in 2020 and 2021. Urine from an inpatient was analysed by RT-LAMP for the first time and compared with RT-qPCR. The amplicons obtained by RT-qPCR were sequenced and African III and European V genotypes were identified. RT-LAMP amplified both genotypes and was more sensitive than RT-qPCR in urine samples. We have developed a novel, rapid, specific, and sensitive RT-LAMP test that allows the detection of different CCHFV genotypes in clinical samples. This pan-CCHFV RT-LAMP detected viral RNA for the first time in urine samples. It can be easily performed as a single-tube isothermal colorimetric method on a portable platform in real time and without the need for expensive equipment, thus bringing molecular diagnostics closer to rural or resource-poor areas, where CCHF usually occurs.
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35
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Gauthier NPG, Chorlton SD, Krajden M, Manges AR. Agnostic Sequencing for Detection of Viral Pathogens. Clin Microbiol Rev 2023; 36:e0011922. [PMID: 36847515 PMCID: PMC10035330 DOI: 10.1128/cmr.00119-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
The advent of next-generation sequencing (NGS) technologies has expanded our ability to detect and analyze microbial genomes and has yielded novel molecular approaches for infectious disease diagnostics. While several targeted multiplex PCR and NGS-based assays have been widely used in public health settings in recent years, these targeted approaches are limited in that they still rely on a priori knowledge of a pathogen's genome, and an untargeted or unknown pathogen will not be detected. Recent public health crises have emphasized the need to prepare for a wide and rapid deployment of an agnostic diagnostic assay at the start of an outbreak to ensure an effective response to emerging viral pathogens. Metagenomic techniques can nonspecifically sequence all detectable nucleic acids in a sample and therefore do not rely on prior knowledge of a pathogen's genome. While this technology has been reviewed for bacterial diagnostics and adopted in research settings for the detection and characterization of viruses, viral metagenomics has yet to be widely deployed as a diagnostic tool in clinical laboratories. In this review, we highlight recent improvements to the performance of metagenomic viral sequencing, the current applications of metagenomic sequencing in clinical laboratories, as well as the challenges that impede the widespread adoption of this technology.
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Affiliation(s)
- Nick P. G. Gauthier
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Mel Krajden
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Amee R. Manges
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
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Boora S, Khan A, Sharma V, Kaushik S, Mehta PK, Singh S, Kaushik S. RT-LAMP is a potential future molecular diagnostic tool for influenza A virus. Future Virol 2023. [DOI: 10.2217/fvl-2022-0136] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Aim: Influenza A virus (IAV) causes serious illness and is responsible for significant morbidity and mortality. To diagnose IAV infection in its early stages, a quick, sensitive, precise detection method is needed for effective clinical management. Materials & methods: In-house hydroxylnaphthol blue (HNB)-based RT-LAMP assay for early detection of IAV using the HA gene was compared with RT-PCR/multiplex-RT-PCR. Results: For the reference strains of IAV, (H1N1 (A/Texas/50/2012) and H3N2 (A/Malaysia/2089302/2009)) RT-LAMP and RT-PCR/M-RT-PCR exhibited a limit of detection (LOD) of 10 and 100 fg/ml, respectively. Conclusion: HNB-based RT-LAMP is a rapid, sensitive, cost-effective diagnostic tool, and could be a point-of-care test for IAV patients during outbreaks.
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Affiliation(s)
- Sanjit Boora
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Anish Khan
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Vikrant Sharma
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
- Department of Virology, Postgraduate Institute of Medical Education & Research (PGIMER), Chandigarh, 160012, India
| | - Sulochana Kaushik
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Promod K Mehta
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Sandeep Singh
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Samander Kaushik
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
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He F, Li T, Wang H, Du P, Wang W, Tan T, Liu Y, Wang S, Ma Y, Wang Y, Hu P, Abd El-Aty AM. Glucometer-based biosensor for the determination of ractopamine in animal-derived foods using rolling circle amplification. Mikrochim Acta 2023; 190:121. [PMID: 36890258 DOI: 10.1007/s00604-023-05715-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/21/2023] [Indexed: 03/10/2023]
Abstract
Screening for persistent organic pollutants (POPs) in food is a complex and challenging process, as POPs can be present in very low levels and can be difficult to detect. Herein, we developed an ultrasensitive biosensor based on a rolling circle amplification (RCA) platform using a glucometer to determine POP. The biosensor was constructed using gold nanoparticle probes modified with antibodies and dozens of primers, magnetic microparticle probes conjugated with haptens, and targets. After competition, RCA reactions are triggered, numerous RCA products hybridize with the ssDNA-invertase, and the target is successfully transformed into glucose. Using ractopamine as a model analyte, this strategy obtained a linear detection range of 0.038-5.00 ng mL-1 and a detection limit of 0.0158 ng mL-1, which was preliminarily verified by screening in real samples. Compared with conventional immunoassays, this biosensor utilizes the high efficiency of RCA and the portable properties of a glucometer, which effectively improves the sensitivity and simplifies the procedures using magnetic separation technology. Moreover, it has been successfully applied to ractopamine determination in animal-derived foods, revealing its potential as a promising tool for POP screening.
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Affiliation(s)
- Feng He
- Institute of Food & Nutrition Science and Technology, Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- School of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Tengfei Li
- School of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Haijie Wang
- Institute of Food & Nutrition Science and Technology, Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Pengfei Du
- Institute of Food & Nutrition Science and Technology, Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| | - Weiting Wang
- Institute of Food & Nutrition Science and Technology, Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| | - Tianyu Tan
- School of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Yaobo Liu
- Institute of Food & Nutrition Science and Technology, Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Shoujing Wang
- Institute of Food & Nutrition Science and Technology, Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Yanli Ma
- Institute of Food & Nutrition Science and Technology, Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Yuanshang Wang
- Institute of Food & Nutrition Science and Technology, Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Peng Hu
- Institute of Food & Nutrition Science and Technology, Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - A M Abd El-Aty
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353, China
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
- Department of Medical Pharmacology, Medical Faculty, Ataturk University, 25240, Erzurum, Turkey
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Szobi A, Buranovská K, Vojtaššáková N, Lovíšek D, Özbaşak HÖ, Szeibeczederová S, Kapustian L, Hudáčová Z, Kováčová V, Drobná D, Putaj P, Bírová S, Čirková I, Čarnecký M, Kilián P, Jurkáček P, Čabanová V, Boršová K, Sláviková M, Vaňová V, Klempa B, Čekan P, Paul ED. Vivid COVID-19 LAMP is an ultrasensitive, quadruplexed test using LNA-modified primers and a zinc ion and 5-Br-PAPS colorimetric detection system. Commun Biol 2023; 6:233. [PMID: 36864129 PMCID: PMC9979146 DOI: 10.1038/s42003-023-04612-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023] Open
Abstract
Sensitive and rapid point-of-care assays have been crucial in the global response to SARS-CoV-2. Loop-mediated isothermal amplification (LAMP) has emerged as an important diagnostic tool given its simplicity and minimal equipment requirements, although limitations exist regarding sensitivity and the methods used to detect reaction products. We describe the development of Vivid COVID-19 LAMP, which leverages a metallochromic detection system utilizing zinc ions and a zinc sensor, 5-Br-PAPS, to circumvent the limitations of classic detection systems dependent on pH indicators or magnesium chelators. We make important strides in improving RT-LAMP sensitivity by establishing principles for using LNA-modified LAMP primers, multiplexing, and conducting extensive optimizations of reaction parameters. To enable point-of-care testing, we introduce a rapid sample inactivation procedure without RNA extraction that is compatible with self-collected, non-invasive gargle samples. Our quadruplexed assay (targeting E, N, ORF1a, and RdRP) reliably detects 1 RNA copy/µl of sample (=8 copies/reaction) from extracted RNA and 2 RNA copies/µl of sample (=16 copies/reaction) directly from gargle samples, making it one of the most sensitive RT-LAMP tests and even comparable to RT-qPCR. Additionally, we demonstrate a self-contained, mobile version of our assay in a variety of high-throughput field testing scenarios on nearly 9,000 crude gargle samples. Vivid COVID-19 LAMP can be an important asset for the endemic phase of COVID-19 as well as preparing for future pandemics.
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Affiliation(s)
- Adrián Szobi
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Katarína Buranovská
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Nina Vojtaššáková
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Daniel Lovíšek
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Halil Önder Özbaşak
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Sandra Szeibeczederová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Liudmyla Kapustian
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Zuzana Hudáčová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
- Stanford University, 730 Escondido Rd., Stanford, CA, 94305, USA
| | - Viera Kováčová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
- University of Cologne, Institute for Biological Physics, Zülpicher Str. 77, 50937, Köln, Germany
| | - Diana Drobná
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Piotr Putaj
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Stanislava Bírová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Ivana Čirková
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Martin Čarnecký
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Peter Kilián
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Peter Jurkáček
- AstonITM s.r.o., Račianska 153, 831 54, Bratislava, Slovakia
| | - Viktória Čabanová
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
| | - Kristína Boršová
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
| | - Monika Sláviková
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
| | - Veronika Vaňová
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Boris Klempa
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Pavol Čekan
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia.
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA.
| | - Evan D Paul
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia.
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA.
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Luethy PM. Point-of-Care Testing for the Diagnosis of Fungal Infections. Clin Lab Med 2023; 43:209-220. [PMID: 37169443 DOI: 10.1016/j.cll.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Invasive fungal infections are increasing worldwide due to factors such as climate change and immunomodulating therapies. Unfortunately, the detection of these infections is limited due to the low sensitivity and long periods required for laboratory testing. Point-of-care testing could lead to more rapid diagnosis of these often devasting infections. However, there are currently no true point-of-care tests on the market for the detection of fungi. In this article, the current state of fungal antigen and molecular testing is reviewed, with commentary on the potential for development and use in the point-of-care setting.
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Ondraskova K, Sebuyoya R, Moranova L, Holcakova J, Vonka P, Hrstka R, Bartosik M. Electrochemical biosensors for analysis of DNA point mutations in cancer research. Anal Bioanal Chem 2023; 415:1065-85. [PMID: 36289102 DOI: 10.1007/s00216-022-04388-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 02/07/2023]
Abstract
Cancer is a genetic disease induced by mutations in DNA, in particular point mutations in important driver genes that lead to protein malfunctioning and ultimately to tumorigenesis. Screening for the most common DNA point mutations, especially in such genes as TP53, BRCA1 and BRCA2, EGFR, KRAS, or BRAF, is crucial to determine predisposition risk for cancer or to predict response to therapy. In this review, we briefly depict how these genes are involved in cancer, followed by a description of the most common techniques routinely applied for their analysis, including high-throughput next-generation sequencing technology and less expensive low-throughput options, such as real-time PCR, restriction fragment length polymorphism, or high resolution melting analysis. We then introduce benefits of electrochemical biosensors as interesting alternatives to the standard methods in terms of cost, speed, and simplicity. We describe most common strategies involved in electrochemical biosensing of point mutations, relying mostly on PCR or isothermal amplification techniques, and critically discuss major challenges and obstacles that, until now, prevented their more widespread application in clinical settings.
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41
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Marangoni JM, Ng KKS, Emadi A. Strategies for the Voltammetric Detection of Loop-Mediated Isothermal Amplification. Micromachines (Basel) 2023; 14:472. [PMID: 36838172 PMCID: PMC9960872 DOI: 10.3390/mi14020472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is rapidly developing into an important tool for the point-of-use detection of pathogens for both clinical and environmental samples, largely due to its sensitivity, rapidity, and adaptability to portable devices. Many methods are used to monitor LAMP, but not all are amenable to point-of-use applications. Common methods such as fluorescence often require bulky equipment, whereas colorimetric and turbidimetric methods can lack sensitivity. Electrochemical biosensors are becoming increasingly important for these applications due to their potential for low cost, high sensitivity, and capacity for miniaturization into integrated devices. This review provides an overview of the use of voltammetric sensors for monitoring LAMP, with a specific focus on how electroactive species are used to interface between the biochemical products of the LAMP reaction and the voltammetric sensor. Various strategies for the voltammetric detection of DNA amplicons as well as pyrophosphate and protons released during LAMP are presented, ranging from direct DNA binding by electroactive species to the creative use of pyrophosphate-detecting aptamers and pH-sensitive oligonucleotide structures. Hurdles for adapting these devices to point-of-use applications are also discussed.
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Affiliation(s)
- Jesse M. Marangoni
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Kenneth K. S. Ng
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Arezoo Emadi
- Department of Electrical and Computer Engineering, University of Windsor, Windsor, ON N9B 3P4, Canada
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Rahman MM, Nam H, Choi N, Kim J. Development of Molecular-Based Species Identification and Optimization of Reaction Conditions for Molecular Diagnosis of Three Major Asian Planthoppers (Hemiptera: Delphacidae). Insects 2023; 14:124. [PMID: 36835693 PMCID: PMC9962309 DOI: 10.3390/insects14020124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Asian planthoppers (Hemiptera: Delphacidae) that include brown planthoppers (BPH, Nilaparvata lugens, Stål), white-backed planthoppers (WBPH, Sogatella furcifera, Horváth), and small brown planthoppers (SBPH, Laodelphax striatellus, Fallén) are the primary sucking-type pests of rice. These three insects share morphological and sequence similarities. As insecticide resistance patterns and control strategies vary according to species, the accurate discrimination of these species is important. Here, we developed six species-specific primers based on partial mitochondrial genome sequences. The primers were successfully used in multiplex PCR, loop-mediated isothermal amplification (LAMP) assays, and conventional PCR. Here, we used genomic DNA obtained using the DNA-releasing technique (tissue samples were incubated at 95 °C for 5 min with 30 μL nuclease-free water, and the supernatant was used). We showed that multiplex PCR could analyze the density of each species following a mass collection in the field; the LAMP assay can diagnose the species within 40 min; conventional PCR can be widely applied to a large number of field samples, as well as individuals or mass collections. In conclusion, these results demonstrate the potential of the species-specific primers and DNA-releasing technique for accurate multiplex PCR and LAMP assays, which may assist the intensive field monitoring of integrated management of these species.
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Affiliation(s)
- Md-Mafizur Rahman
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia 7003, Bangladesh
| | - Hwayeun Nam
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
- Incheon International Airport Regional Office, Animal and Plant Quarantine Agency, Incheon 22382, Republic of Korea
| | - Nakjung Choi
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Juil Kim
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
- Program of Applied Biology, Division of Bio-Resource Sciences, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Republic of Korea
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Rubio-Monterde A, Quesada-González D, Merkoçi A. Toward Integrated Molecular Lateral Flow Diagnostic Tests Using Advanced Micro- and Nanotechnology. Anal Chem 2023; 95:468-489. [PMID: 36413136 DOI: 10.1021/acs.analchem.2c04529] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Ana Rubio-Monterde
- Paperdrop Diagnostics S.L., MRB, Campus UAB, 08193 Bellaterra, Spain.,Nanobioelectronics and Biosensors Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, 08193 Barcelona, Spain
| | | | - Arben Merkoçi
- Paperdrop Diagnostics S.L., MRB, Campus UAB, 08193 Bellaterra, Spain.,Nanobioelectronics and Biosensors Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, 08193 Barcelona, Spain.,The Barcelona Institute of Science and Technology (BIST), Campus UAB, 08036 Bellaterra, Barcelona Spain.,ICREA, Institució Catalana de Recerca i Estudis Avançats, Pg. Lluis Companys 23, 08010 Barcelona, Spain
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Choi G, Moehling TJ, Meagher RJ. Advances in RT-LAMP for COVID-19 testing and diagnosis. Expert Rev Mol Diagn 2023; 23:9-28. [PMID: 36695788 DOI: 10.1080/14737159.2023.2169071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
INTRODUCTION The SARS-CoV-2 pandemic, and the subsequent limitations on standard diagnostics, has vastly expanded the user base of Reverse Transcription Loop-mediated isothermal Amplification (RT-LAMP) in fundamental research and development. RT-LAMP has also penetrated commercial markets, with emergency use authorizations for clinical diagnosis. AREAS COVERED This review discusses the role of RT-LAMP within the context of other technologies like RT-qPCR and rapid antigen tests, progress in sample preparation strategies to enable simplified workflow for RT-LAMP directly from clinical specimens, new challenges with primer and assay design for the evolving pandemic, prominent detection modalities including colorimetric and CRISPR-mediated methods, and translational research and commercial development of RT-LAMP for clinical applications. EXPERT OPINION RT-LAMP occupies a middle ground between RT-qPCR and rapid antigen tests. The simplicity approaches that of rapid antigen tests, making it suitable for point-of-care use, but the sensitivity nears that of RT-qPCR. RT-LAMP still lags RT-qPCR in fundamental understanding of the mechanism, and the interplay between sample preparation and assay performance. Industry is now beginning to address issues around scalability and usability, which could finally enable LAMP and RT-LAMP to find future widespread application as a diagnostic for other conditions, including other pathogens with pandemic potential.
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Affiliation(s)
- Gihoon Choi
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Taylor J Moehling
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Robert J Meagher
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
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Ngamsom B, Iles A, Kamita M, Kimani R, Wakaba P, Rodriguez-Mateos P, Mungai M, Dyer CE, Walter C, Gitaka J, Pamme N. A sample-to-answer COVID-19 diagnostic device based on immiscible filtration and CRISPR-Cas12a-assisted detection. Talanta Open 2022; 6:100166. [PMID: 36406953 PMCID: PMC9640297 DOI: 10.1016/j.talo.2022.100166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/02/2022] [Accepted: 11/02/2022] [Indexed: 11/11/2022] Open
Abstract
In response to the ongoing coronavirus disease 2019 (COVID-19) pandemic and disparities of vaccination coverage in low-and middle-income countries, it is vital to adopt a widespread testing and screening programme, combined with contact tracing, to monitor and effectively control the infection dispersion in areas where medical resources are limited. This work presents a lab-on-a-chip device, namely 'IFAST-LAMP-CRISPR', as an affordable, rapid and high-precision molecular diagnostic means for detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The herein proposed 'sample-to-answer' platform integrates RNA extraction, amplification and molecular detection with lateral flow readout in one device. The microscale dimensions of the device containing immiscible liquids, coupled with the use of silica paramagnetic beads and guanidine hydrochloride, streamline sample preparation (including RNA extraction, concentration and purification) in 15 min with minimal hands-on steps. The pre-amplification in combination with CRISPR-Cas12a detection assays targeting the nucleoprotein (N) gene achieved visual identification of ≥ 470 copies mL-1 genomic SARS-CoV-2 samples in 45 min. On-chip assays showed the ability to isolate and detect SARS-CoV-2 RNA from 100 genome copies mL-1 of replication-deficient viral particles in 1 h. This simple, affordable and integrated platform demonstrated a visual, faster, and yet specificity- and sensitivity-comparable alternative to the costly gold-standard reverse transcription-polymerase chain reaction (RT-PCR) assay, requiring only a simple heating source. Initial testing illustrates the platform viability both on nasopharyngeal swab and saliva samples collected using the easily accessible Swan-brand cigarette filter, providing a complete workflow for COVID-19 diagnostics in low-resource settings.
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Affiliation(s)
- Bongkot Ngamsom
- School of Natural Sciences, University of Hull, Hull HU6 7RX, UK
| | - Alexander Iles
- School of Natural Sciences, University of Hull, Hull HU6 7RX, UK,Department of Materials and Environmental Chemistry, Stockholm University, SE 106 91, Sweden
| | - Moses Kamita
- Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya
| | - Racheal Kimani
- Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya
| | - Patrick Wakaba
- Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya
| | - Pablo Rodriguez-Mateos
- Department of Materials and Environmental Chemistry, Stockholm University, SE 106 91, Sweden
| | - Mary Mungai
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Charlotte E. Dyer
- Centre for Biomedicine, Hull-York Medical School, University of Hull, Hull HU6 7RX, UK
| | - Cheryl Walter
- Centre for Biomedicine, Hull-York Medical School, University of Hull, Hull HU6 7RX, UK
| | - Jesse Gitaka
- Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya,Corresponding author at: Stockholm University, Sweden
| | - Nicole Pamme
- School of Natural Sciences, University of Hull, Hull HU6 7RX, UK,Department of Materials and Environmental Chemistry, Stockholm University, SE 106 91, Sweden,Corresponding author at: Stockholm University, Sweden
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Abstract
Integrated clustered regularly interspaced short palindromic repeat (CRISPR)-loop-mediated amplification (LAMP) technology is of great importance in CRISPR-based diagnostic systems, which urgently needs to be developed to improve diagnostic accuracy. A labor-free, contamination-free, and fully automated droplet manipulation platform for the CRISPR-LAMP technology has not been developed before. Herein, we propose a fully automated CRISPR-LAMP platform, which can precisely manipulate the CRISPR-LAMP droplet and perform combined reactions with high sensitivity and specificity. SARS-CoV-2 Spike T478K, D614G, P681R, and P681H mutations, typical point mutations of B.1.617.2 (Delta) and Omicron variants, are monitored with this platform with a detection limit of 102 copies/μL. Allele discrimination between the mutants and wild type is significant with the designed one/two-mismatch CRISPR RNA (crRNA) at a limit of 102 copies/μL. Chemically synthesized and modified crRNAs greatly increase the CRISPR-LAMP signal, which advance the wide application. Combined with the previously developed RdRp CRISPR-LAMP assay, clinical results showed that Spike T478K and P681H can discriminate the mutant type form the wild type with 70% (49.66-85.50%, 95% confidence interval) and 78% (57.27-90.62%, 95% confidence interval) sensitivity, respectively, and 100% specificity (51.68-100%, 95% confidence interval), and the RdRp target can detect SARS-CoV-2 strains with 85% sensitivity (65.39-95.14%, 95% confidence interval) and 100% specificity (51.68-100%, 95% confidence interval). We believe that this automatic digital microfluid (DMF) system can advance the integrated CRISPR-LAMP technology with higher stability, sensitivity, and practicability, also for other CRISPR-associated diagnostic platforms.
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Affiliation(s)
- Tong Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Wang Zhao
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Xi Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Xinlian Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Jinhui Zhu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center (Shanghai Customs Port Clinic), 2090 Jinqiao Road, Shanghai 200433, P. R. China
| | - Chuanyong Wu
- Shanghai Hengxin BioTechnology, 1688 North Guo Quan Road, Bldg A8, Rm 801, Shanghai 200438, P. R. China
| | - Zhengan Tian
- Shanghai International Travel Healthcare Center (Shanghai Customs Port Clinic), 2090 Jinqiao Road, Shanghai 200433, P. R. China
| | - Guodong Sui
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, P. R. China
- Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CICAEET), Nanjing University of Information Science & Technology, Nanjing 210044, P. R. China
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Akarapipad P, Bertelson E, Pessell A, Wang TH, Hsieh K. Emerging Multiplex Nucleic Acid Diagnostic Tests for Combating COVID-19. Biosensors (Basel) 2022; 12:bios12110978. [PMID: 36354487 PMCID: PMC9688249 DOI: 10.3390/bios12110978] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 05/29/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has drawn attention to the need for fast and accurate diagnostic testing. Concerns from emerging SARS-CoV-2 variants and other circulating respiratory viral pathogens further underscore the importance of expanding diagnostic testing to multiplex detection, as single-plex diagnostic testing may fail to detect emerging variants and other viruses, while sequencing can be too slow and too expensive as a diagnostic tool. As a result, there have been significant advances in multiplex nucleic-acid-based virus diagnostic testing, creating a need for a timely review. This review first introduces frequent nucleic acid targets for multiplex virus diagnostic tests, then proceeds to a comprehensive and up-to-date overview of multiplex assays that incorporate various detection reactions and readout modalities. The performances, advantages, and disadvantages of these assays are discussed, followed by highlights of platforms that are amenable for point-of-care use. Finally, this review points out the remaining technical challenges and shares perspectives on future research and development. By examining the state of the art and synthesizing existing development in multiplex nucleic acid diagnostic tests, this review can provide a useful resource for facilitating future research and ultimately combating COVID-19.
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Affiliation(s)
- Patarajarin Akarapipad
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Elizabeth Bertelson
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alexander Pessell
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Alvarez-serna BE, Ramírez-chavarría RG, Castillo-villanueva E, Carrillo-reyes J, Ramírez-zamora RM, Buitrón G, Alvarez-icaza L. Label-free and portable field-effect sensor for monitoring RT-LAMP products to detect SARS-CoV-2 in wastewater. Talanta 2022. [DOI: 10.1016/j.talanta.2022.124060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The COVID-19 pandemic caused by the coronavirus SARS-CoV-2 has proven the need for developing reliable and affordable technologies to detect pathogens. Particularly, the detecting the genome in wastewater could be an indicator of the transmission rate to alert on new outbreaks. However, wastewater-based epidemiology remains a technological challenge to develop affordable technologies for sensing pathogens. In this work, we introduce a label-free and portable field-effect transistor (FET)-based sensor to detect N and ORF1ab genes of the SARS-CoV-2 genome. Our sensor integrates the reverse transcription loop-mediated isothermal amplification (RT-LAMP) reaction as a cost-effective molecular detection exhibiting high specificity. The detection relies upon pH changes, due to the RT-LAMP reaction products, which are detected through a simple, but effective, extended-gate FET sensor (EGFET). We evaluate the proposed device by measuring real wastewater samples to detect the presence of SARS-CoV-2 genome, achieving a limit of detection of 0.31 × 10−3 ng/μL for end-point measurement. Moreover, we find the ability of the sensor to perform real-time-like analysis, showing that the RT-LAMP reaction provides a good response after 15 min for concentrations as low as 0.37 ng/μL. Hence, we show that our EGFET sensor offers a powerful tool to detect the presence of the SARS-CoV-2 genome with a naked-eye method, in a straightforward way than the conventional molecular methods for wastewater analysis.
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49
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Lee S, Oh S. Lateral flow biosensor based on LAMP-CRISPR/Cas12a for sensitive and visualized detection of Salmonella spp. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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50
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Xu X, Jia Y, Li R, Wen Y, Liang Y, Lao G, Liu X, Zhou W, Liu H, Xie J, Wang X, Xu W, Sun Q. Rapid and simultaneous detection of multiple pathogens in the lower reproductive tract during pregnancy based on loop-mediated isothermal amplification-microfluidic chip. BMC Microbiol 2022; 22:260. [PMID: 36309654 PMCID: PMC9616700 DOI: 10.1186/s12866-022-02657-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/26/2022] [Indexed: 11/30/2022] Open
Abstract
Background Female reproductive tract infection (RTI) is the common source of varied diseases, especially as an important risk factor for pregnancy outcomes, therefore the rapid, accurate and simultaneous detection of multiple pathogens is in urgent need for assisting the diagnosis and treatment of RTI in pregnant women. Streptococcus agalactiae (S. agalactiae), Enterococcus faecalis (E. faecalis), Gardnerella vaginalis (G. vaginalis), Candida albicans (C. albicans) and Chlamydia trachomatis (C. trachomatis) are five main pathogens in lower genital tract with high risk, serious consequences and clinical demands. The combination of loop-mediated isothermal amplification (LAMP) and microfluidic technology was used to develop the LAMP-microfluidic chip for rapid, simple, sensitive and simultaneous detection of the five target pathogens above. Results Standard strains and clinical isolates were used for the establishment of the novel LAMP method in tube and LAMP-microfluidic chip, followed by the chip detection on 103 clinical samples and PCR verification partially. The sensitivities of LAMP of S. agalactiae, E. faecalis, G. vaginalis, and C. albicans in tube were 22.0, 76.0, 13.2, 1.11 CFU/μL, respectively, and C. trachomatis was 41.3 copies/μL; on LAMP-microfluidic chip they were 260, 154, 3.9 and 7.53 CFU/μL, respectively, and C. trachomatis was 120 copies/μL. The positive coincidence rates of clinical stains in tube and on chip experiments were 100%. Compared with the classic culture method performed in hospitals, the positive coincidence rate of the 103 clinical samples detected by LAMP-microfluidic chip were 100%. For the six inconsistent ones, including four G. vaginalis and two C. albicans positive samples tested by LAMP-microfluidic chip and verified by PCR were negative by culturing method in hospitals, indicating the lack of efficient detection by the classic culturing method. Conclusion Our study suggested that the LAMP-microfluidic chips could simultaneously, efficiently, and accurately detect multiple main pathogens, including S. agalactiae, E. faecalis, G. vaginalis, C. albicans and C. trachomatis, in clinical samples of female RTI to give a great clinical value. Accordingly, this novel method has the potential to provide a valuable reference for female RTI screening and early diagnosis during pregnancy. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02657-0.
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